Title	Year	Journal	Affiliation	Abstract	Gene
Cloning of a cDNA encoding an importin-alpha and down-regulation of the gene by light in rice leaves	1998	Gene	Central Research Institute of Electric Power Industry, Chiba, Japan.	The import of nuclear proteins into nuclei begins with recognition of nuclear localization signal-harboring proteins and binding to a nuclear pore targeting complex. A cDNA for an importin-alpha protein, a subunit of the complex, was isolated from rice plants. The amino acid sequence deduced from the nucleotide sequence of the cDNA exhibited a high homology to those of importin-alpha proteins from many organisms such as Arabidopsis thaliana, Saccharomyces cerevisiae, human, mouse, Xenopus laevis and Drosophila melanogaster. Down-regulation of the transcription by light was shown in the leaves of light- and dark-grown seedlings by RNA blot analysis. The down-regulation was specific to leaves, whereas no light effect was observed in root tissues or calli, in which higher levels of the transcript were detected.	alpha1a
Molecular cloning of a novel importin alpha homologue from rice, by which constitutive photomorphogenic 1 (COP1) nuclear localization signal (NLS)-protein is preferentially nuclear imported	2001	J Biol Chem	National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan. cjjiang@abr.affrc.go.jp	Nuclear import of proteins that contain classical nuclear localization signals (NLS) is initiated by importin alpha, a protein that recognizes and binds to the NLS in the cytoplasm. In this paper, we have cloned a cDNA for a novel importin alpha homologue from rice which is in addition to our previously isolated rice importin alpha1a and alpha2, and we have named it rice importin alpha1b. In vitro binding and nuclear import assays using recombinant importin alpha1b protein demonstrate that rice importin alpha1b functions as a component of the NLS-receptor in plant cells. Analysis of the transcript levels for all three rice importin alpha genes revealed that the genes were not only differentially expressed but that they also responded to dark-adaptation in green leaves. Furthermore, we also show that the COP1 protein bears a bipartite-type NLS and its nuclear import is mediated preferentially by the rice importin alpha1b. These data suggest that each of the different rice importin alpha proteins carry distinct groups of nuclear proteins, such that multiple isoforms of importin alpha contribute to the regulation of plant nuclear protein transport.	alpha1a,alpha1b,alpha2
Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice	2008	Plant J	State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research, Beijing 100101, China.	Pre-harvest sprouting (PHS) or vivipary in cereals is an important agronomic trait that results in significant economic loss. A considerable number of mutations that cause PHS have been identified in several species. However, relatively few viviparous mutants in rice (Oryza sativa L.) have been reported. To explore the mechanism of PHS in rice, we carried out an extensive genetic screening and identified 12 PHS mutants (phs). Based on their phenotypes, these phs mutants were classified into three groups. Here we characterize in detail one of these groups, which contains mutations in genes encoding major enzymes of the carotenoid biosynthesis pathway, including phytoene desaturase (OsPDS), zeta-carotene desaturase (OsZDS), carotenoid isomerase (OsCRTISO) and lycopene beta-cyclase (beta-OsLCY), which are essential for the biosynthesis of carotenoid precursors of ABA. As expected, the amount of ABA was reduced in all four phs mutants compared with that in the wild type. Chlorophyll fluorescence analysis revealed the occurrence of photoinhibition in the photosystem and decreased capacity for eliminating excess energy by thermal dissipation. The greatly increased activities of reactive oxygen species (ROS) scavenging enzymes, and reduced photosystem (PS) II core proteins CP43, CP47 and D1 in leaves of the Oscrtiso/phs3-1mutant and OsLCY RNAi transgenic rice indicated that photo-oxidative damage occurred in PS II, consistent with the accumulation of ROS in these plants. These results suggest that the impairment of carotenoid biosynthesis causes photo-oxidation and ABA-deficiency phenotypes, of which the latter is a major factor controlling the PHS trait in rice.	beta-OsLCY,OsPDS,OsZDS,OsCRTISO|ZEBRA2
A pair of orthologs of a leucine-rich repeat receptor kinase-like disease resistance gene family regulates rice response to raised temperature	2011	BMC Plant Biol	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	BACKGROUND: Rice Xa3/Xa26 disease-resistance gene encodes a leucine-rich repeat (LRR) receptor kinase-type protein against Xanthomonas oryzae pv. oryzae (Xoo) and belongs to a multigene family. However, the functions of most genes in this family are unknown. RESULTS: Here we report that two orthologs of this family, the NRKe from rice variety Nipponbare and 9RKe from variety 93-11 at the RKe locus, have similar functions although they encode different proteins. This pair of orthologs could not mediate resistance to Xoo, but they were transcriptionally induced by raised temperature. Transcriptional activation of NRKe or 9RKe resulted in the formation of temperature-sensitive lesion mimics, which were spots of dead cells associated with accumulation of superoxides, in different organs of the transgenic plants. These plants were more sensitive to high temperature shock than wild-type controls. Transgenic plants carrying a chimeric protein consisting of the LRR domain of NRKe and the kinase domain of Xa3/Xa26 developed the same lesion mimics as the NRKe-transgenic plants, whereas transgenic plants carrying another chimeric protein consisting of the LRR domain of Xa3/Xa26 and the kinase domain of NRKe were free of lesion mimic. All the transgenic plants carrying a chimeric protein were susceptible to Xoo. CONCLUSION: These results suggest that the RKe locus is involved in rice response to raised temperature. The LRR domain of RKe protein appears to be important to sense increased temperature. The RKe-involved temperature-related pathway and Xa3/Xa26-mediated disease-resistance pathway may partially overlap.	RKe,Xa26|Xa3
The ATP-binding cassette transporter OsABCG15 is required for anther development and pollen fertility in rice	2013	J Integr Plant Biol	State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.	Plant male reproductive development is a complex biological process, but the underlying mechanism is not well understood. Here, we characterized a rice (Oryza sativa L.) male sterile mutant. Based on map-based cloning and sequence analysis, we identified a 1,459-bp deletion in an adenosine triphosphate (ATP)-binding cassette (ABC) transporter gene, OsABCG15, causing abnormal anthers and male sterility. Therefore, we named this mutant osabcg15. Expression analysis showed that OsABCG15 is expressed specifically in developmental anthers from stage 8 (meiosis II stage) to stage 10 (late microspore stage). Two genes CYP704B2 and WDA1, involved in the biosynthesis of very-long-chain fatty acids for the establishment of the anther cuticle and pollen exine, were downregulated in osabcg15 mutant, suggesting that OsABCG15 may play a key function in the processes related to sporopollenin biosynthesis or sporopollenin transfer from tapetal cells to anther locules. Consistently, histological analysis showed that osabcg15 mutants developed obvious abnormality in postmeiotic tapetum degeneration, leading to rapid degredation of young microspores. The results suggest that OsABCG15 plays a critical role in exine formation and pollen development, similar to the homologous gene of AtABCG26 in Arabidopsis. This work is helpful to understand the regulatory network in rice anther development.	OsABCG15,CYP704B2,WDA1
ABCG15 encodes an ABC transporter protein, and is essential for post-meiotic anther and pollen exine development in rice	2013	Plant Cell Physiol	Rice Research Institute of Sichuan Agricultural University, Chengdu Wenjiang, Sichuan, 611130, PR China.	In flowering plants, anther and pollen development is critical for male reproductive success. The anther cuticle and pollen exine play an essential role, and in many cereals, such as rice, orbicules/ubisch bodies are also thought to be important for pollen development. The formation of the anther cuticle, exine and orbicules is associated with the biosynthesis and transport of wax, cutin and sporopollenin components. Recently, progress has been made in understanding the biosynthesis of sporopollenin and cutin components in Arabidopsis and rice, but less is known about the mechanisms by which they are transported to the sites of deposition. Here, we report that the rice ATP-binding cassette (ABC) transporter, ABCG15, is essential for post-meiotic anther and pollen development, and is proposed to play a role in the transport of rice anther cuticle and sporopollenin precursors. ABCG15 is highly expressed in the tapetum at the young microspore stage, and the abcg15 mutant exhibits small, white anthers lacking mature pollen, lipidic cuticle, orbicules and pollen exine. Gas chromatography-mass spectrometry (GC-MS) analysis of the abcg15 anther cuticle revealed significant reductions in a number of wax components and aliphatic cutin monomers. The expression level of genes involved in lipid metabolism in the abcg15 mutant was significantly different from their levels in the wild type, possibly due to perturbations in the homeostasis of anther lipid metabolism. Our study provides new insights for understanding the molecular mechanism of the formation of the anther cuticle, orbicules and pollen wall, as well as the machinery for lipid metabolism in rice anthers.	OsABCG15
Overexpression of ACL1 (abaxially curled leaf 1) increased Bulliform cells and induced Abaxial curling of leaf blades in rice	2010	Mol Plant	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	Understanding the genetic mechanism underlying rice leaf-shape development is crucial for optimizing rice configuration and achieving high yields; however, little is known about leaf abaxial curling. We isolated a rice transferred DNA (T-DNA) insertion mutant, BY240, which exhibited an abaxial leaf curling phenotype that co-segregated with the inserted T-DNA. The T-DNA was inserted in the promoter of a novel gene, ACL1 (Abaxially Curled Leaf 1), and led to overexpression of this gene in BY240. Overexpression of ACL1 in wild-type rice also resulted in abaxial leaf curling. ACL1 encodes a protein of 116 amino acids with no known conserved functional domains. Overexpression of ACL2, the only homolog of ACL1 in rice, also induced abaxial leaf curling. RT-PCR analysis revealed high expressions of ACLs in leaf sheaths and leaf blades, suggesting a role for these genes in leaf development. In situ hybridization revealed non-tissue-specific expression of the ACLs in the shoot apical meristem, leaf primordium, and young leaf. Histological analysis showed increased number and exaggeration of bulliform cells and expansion of epidermal cells in the leaves of BY240, which caused developmental discoordination of the abaxial and adaxial sides, resulting in abaxially curled leaves. These results revealed an important mechanism in rice leaf development and provided the genetic basis for agricultural improvement.	ACL1,ACL2
A Point Mutation of Adh1 Gene is Involved in the Repression of Coleoptile Elongation under Submergence in Rice	2006	Breeding Science	Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo	In higher plants, alcoholic fermentation is required to supply NAD+ to the glycolytic pathway, which is responsible for ATP synthesis under anaerobic conditions. Matsumura et al. (1995) previously isolated the reduced adh activity (rad) mutant in rice, in which elongation of the coleoptile is repressed under submergence. However, the rad gene had not been characterized. In the present study, we observed that, in the coleoptile, the Adh1 mRNA levels were comparable between the rad mutant and the wild type cultivar Kinmaze, while the amount of ADH1 protein was much lower in the rad mutant than in the wild type. Sequencing showed that G106 of the Adh1 gene of Kinmaze was replaced with A in the rad mutant, resulting in an E36K substitution in the deduced amino acid sequence. A genotyping experiment using F2 plants from a cross of the rad mutant with the indica cultivar Kasalath indicated that the point mutation was involved in the repression of coleoptile elongation. Furthermore, since the reduced ADH activity appeared to cause an ATP deficiency, elongation of the coleoptile was repressed in the submerged rad mutant.	Adh1
Molecular characterization of cDNA encoding for adenylate kinase of rice (Oryza sativa L.)	1992	Plant J	Institute of Applied Microbiology, University of Tokyo, Japan.	Two types of genes (Adk-a, and Adk-b) encoding for adenylate kinase (AK, EC 2.7.4.3.) were isolated from the cDNA library constructed from poly(A)+ RNA of rice (Oryza sativa L.). Two cDNAs were heterogeneous at 5' and 3' ends of non-coding sequences and had possible polyadenylation signals. One of the genes, Adk-a, had 1154 bp sequences encoding 241 amino acid residues, while the other type, Adk-b, contained 1085 bp sequences encoding for 243 amino acid residues. Homology between Adk-a and Adk-b was 73.7% in nucleotide sequences, and 90.8% in amino acid level. Two genes showed about 53% homology to bovine mitochondrial adenylate kinase (AK2) at nucleotide and amino acid levels. Concerning the codon usage of rice AK genes, T was abundant at the third position of a codon in the reading frames. In order to examine the enzyme activity of the protein encoded by the rice cDNA, Adk-a was cloned into an expression vector, pUC119, which was introduced into Escherichia coli strain CV2, a temperature-sensitive mutant of adenylate kinase. We found that the transformant carrying the rice Adk-a gene in the sense orientation recovered cell growth at non-permissive high temperature (42 degrees C) and expressed enzyme activities higher than the untransformed CV2 and the transformant possessing Adk-a cDNA in the antisense orientation. These observations suggest that rice Adk-a codes a biologically active enzyme. Furthermore, sucrose was found to regulate the transcription of AK genes in rice cell cultures. Organ related accumulation of mRNA in whole plants was also found.	Adk-a,Adk-b
The ANTHER INDEHISCENCE1 gene encoding a single MYB domain protein is involved in anther development in rice	2004	Plant Physiol	CSIRO Plant Industry, Canberra, Australian Capital Territories 2601, Australia.	Using a two-element iAc/Ds transposon-tagging system, we identified a rice (Oryza sativa L. cv Nipponbare) recessive mutant, anther indehiscence1 (aid1), showing partial to complete spikelet sterility. Spikelets of the aid1 mutant could be classified into three types based on the viability of pollen grains and the extent of anther dehiscence. Type 1 spikelets (approximately 25%) were sterile due to a failure in accumulation of starch in pollen grains. Type 2 spikelets (approximately 55%) had viable pollen grains, but anthers failed to dehisce and/or synchronize with anthesis due to failure in septum degradation and stomium breakage, resulting in sterility. Type 3 spikelets (approximately 20%) had normal fertility. In addition, aid1 mutant plants had fewer tillers and flowered 10 to 15 d later than the wild type. The Ds insertion responsible for the aid1 mutation was mapped within the coding region of the AID1 gene on chromosome 6, which is predicted to encode a novel protein of 426 amino acids with a single MYB domain. The MYB domain of AID1 is closely related to that of the telomere-binding proteins of human, mouse, and Arabidopsis, and of single MYB domain transcriptional regulators in plants such as PcMYB1 and ZmIBP1. AID1 was expressed in both the leaves and panicles of wild-type plants, but not in mutant plants.	AID1
Cloning and characterization of AKR4C14, a rice aldo-keto reductase, from Thai Jasmine rice	2012	Protein J	Department of Biochemistry, Faculty of Science, Kasetsart University, Pahonyothin Rd, Bangkok, 10903, Thailand.	Aldo-keto reductase (AKR) is an enzyme superfamily whose members are involved in the metabolism of aldehydes/ketones. The AKR4 subfamily C (AKR4C) is a group of aldo-keto reductases that are found in plants. Some AKR4C(s) in dicot plants are capable of metabolizing reactive aldehydes whereas, such activities have not been reported for AKR4C(s) from monocot species. In this study, we have screened Indica rice genome for genes with significant homology to dicot AKR4C(s) and identified a cluster of putative AKR4C(s) located on the Indica rice chromosome I. The genes including OsI_04426, OsI_04428 and OsI_04429 were successfully cloned and sequenced by qRT-PCR from leaves of Thai Jasmine rice (KDML105). OsI_04428, later named AKR4C14, was chosen for further studies because it shares highest homology to the dicot AKR4C(s). The bacterially expressed recombinant protein of AKR4C14 was successfully produced as a MBP fusion protein and his-tagged protein. The recombinant AKR4C14 were capable of metabolizing sugars and reactive aldehydes i.e. methylglyoxal, a toxic by-product of the glycolysis pathway, glutaraldehyde, and trans-2-hexenal, a natural reactive 2-alkenal. AKR4C14 was highly expressed in green tissues, i.e. leaf sheets and stems, whereas flowers and roots had a significantly lower level of expression. These findings indicated that monocot AKR4C(s) can metabolize reactive aldehydes like the dicot AKR4C(s) and possibly play a role in detoxification mechanism of reactive aldehydes.	AKR4C14|OsI_04428,OsAKR1|OsI_04426,OsI_04429
A novel endosperm transfer cell-containing region-specific gene and its promoter in rice	2011	Plant Mol Biol	Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, Japan.	The endosperm of cereal grains is an important resource for both food and feed. It contains three major types of tissue: starchy endosperm, the aleurone layer, and transfer cells. To improve grain quality and quantity using molecular methods, control of transgene expression directed by distinct temporal and spatial promoter activity is necessary. To identify aleurone layer-specific and/or transfer cell-specific promoters in rice, microarray analyses were performed, comparing the aleurone layer containing transfer cells and the other reproductive and vegetative tissues. After confirmation by RT-PCR analysis, we identified two putative aleurone layer and/or transfer cell-specific genes, AL1 and AL2. The promoter regions of these genes and beta-glucuronidase (GUS) fusion constructs were stably transformed into rice. The GUS expression patterns indicated that the AL1 promoter was active exclusively in the dorsal aleurone layer adjacent to the main vascular bundle. In rice, transfer cells are differentiated in this region. Therefore, the promoter of the AL1 gene exhibits transfer cell-containing region-specific activity. The AL1 gene encodes a putative anthranilate N-hydroxycinnamoyl/benzoyltransferase. The promoter of this gene will be useful for enhancing uptake of nutrients from the mother cells and protecting filial seeds from pathogen attack.	AL1
Molecular characterization of a gene for alanine aminotransferase from rice (Oryza sativa)	1999	Plant Mol Biol	Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, Ibaraki, Japan.	A cDNA clone encoding alanine aminotransferase (AlaAT) has isolated from randomly sequenced clones derived from a cDNA library of maturing rice seeds by comparison to previously identified genes. The deduced amino acid sequence was 88% and 91% homologous to those of the enzymes from barley and broomcorn millet (Panicum miliaceum), respectively. Using this cDNA as a probe, we isolated and sequenced the corresponding genomic clone. Comparison of the sequences of the cDNA and the genomic gene revealed that the coding region of the gene was interrupted by 14 introns 66 to 1547 bp long. Northern and western blotting analyses showed that the gene was expressed at high levels in developing seeds. When the 5'-flanking region between -930 and +85 from the site of initiation of transcription was fused to a reporter gene for beta-glucuronidase (GUS) and then introduced into the rice genome, histochemical staining revealed strong GUS activity in the inner endosperm tissue of developing seeds and weak activity in root tips. Similar tissue-specific expression was also detected by in situ hybridization. These results suggest that AlaAT is involved in nitrogen metabolism during the maturation of rice seed.	AlaAT
Genetic analysis of rice grain quality	1999	TAG Theoretical and Applied Genetics	Institute of Genetics, Chinese Academy of Sciences, Beijing 100101, China	The inheritance of grain quality is more complicated than that of other agronomic traits in cereals due to epistasis, maternal and cytoplasmic effects, and the triploid nature of endosperm. In the present study, an established rice DH population derived from anther culture of an indica/japonica hybrid was used for genetic analysis of rice grain quality. A total of five parameters, amylose content (AC), alkali-spreading score (ASS), gel consistency (GC), percentage of grain with a white core (PGWC) and the square of the white core (SWC), were estimated for the DH lines and the parent varieties. For each parent, the value of each parameter was relatively stable in three locations, Beijing, Hangzhou and Chengdu, while the differences between the parents were significant for all five parameters. AC showed a bimodal distribution, and the distribution of ASS was skewed toward the value of JX17, while the other three parameters displayed continuous distributions among the DH lines with partially transgressive segregations. For AC, a minor and a major gene were found on chromosomes 5 and 6 respectively. The major gene, which should be an allele of wx, explained 91.9% of the total variation. For GC, two QTLs were identified on chromosomes 2 and 7 respectively. For ASS, a minor and a major gene were both located on chromosome 6. The major gene should be the same locus as the alkali degeneration gene (alk). Genetic linkage between alk and wx was found in QTL mapping. For PGWC, two QTLs were located on chromosomes 8 and 12. Only a minor QTL was found for SWC on chromosome 3. The results and the molecular markers presented here may be useful in rice breeding for grain quality improvement.	ALK|SSIIa
OsbZIP58, a basic leucine zipper transcription factor, regulates starch biosynthesis in rice endosperm	2013	J Exp Bot	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, PR China.	Starch composition and the amount in endosperm, both of which contribute dramatically to seed yield, cooking quality, and taste in cereals, are determined by a series of complex biochemical reactions. However, the mechanism regulating starch biosynthesis in cereal seeds is not well understood. This study showed that OsbZIP58, a bZIP transcription factor, is a key transcriptional regulator controlling starch synthesis in rice endosperm. OsbZIP58 was expressed mainly in endosperm during active starch synthesis. osbzip58 null mutants displayed abnormal seed morphology with altered starch accumulation in the white belly region and decreased amounts of total starch and amylose. Moreover, osbzip58 had a higher proportion of short chains and a lower proportion of intermediate chains of amylopectin. Furthermore, OsbZIP58 was shown to bind directly to the promoters of six starch-synthesizing genes, OsAGPL3, Wx, OsSSIIa, SBE1, OsBEIIb, and ISA2, and to regulate their expression. These findings indicate that OsbZIP58 functions as a key regulator of starch synthesis in rice seeds and provide new insights into seed quality control.	ALK|SSIIa,OsBEIIb,OsISA2,RISBZ1|OsbZIP58,BEI|SBE1,Wx
Double repression of soluble starch synthase genes SSIIa and SSIIIa in rice (Oryza sativa L.) uncovers interactive effects on the physicochemical properties of starch	2011	Genome	Institute of Crop Science and the National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing 100081, China.	Soluble starch synthases (SSs) are major enzymes involved in starch biosynthesis in developing rice (Oryza sativa L.) endosperm. Despite extensive studies of SSs in various plant species including rice, the functional modes of action among multiple SS genes are still not clear. Here, we generated transgenic RNA interference (RNAi) repressed lines for seven of the eight members of the rice SS gene family and studied their effects on starch synthesis and grain formation. Consistent with their expression domains, RNAi repression of genes that encode isozymes SSI, SSIIa, and SSIIIa had strong effects on grain development, whereas no obvious phenotypic changes were observed in transgenic plants with the other SS genes being RNAi repressed, indicating functional redundancies among the genes. To study the potential functional interactions of SS genes, we generated SSIIa/SSIIIa double repression lines whose kernels displayed a chalky kernel appearance and had increased amylose levels, increased pasting temperatures, and decreased viscosities. The double mutation also reduced short (degree of polymerization (DP) 5-6) and long (DP 12-23) amylopectin chain contents in the grain and increased the medium long types (DP 7-11). The nonadditive nature of the double mutation line suggests that SSIIa and SSIIIa interact with each other during starch synthesis. Such interaction may be physical via starch phophorylase as indicated by our pair-wise yeast two-hybrid assays on major starch synthesis enzymes. Collectively, the data showed that SSIIa and SSIIIa play distinctive, but partially overlapping, roles during rice grain starch synthesis. The possibility of extensive redundancy or complementarity among SS isozymes is discussed.	ALK|SSIIa,OsSSIIIa|Flo5
Compensation and interaction between RISBZ1 and RPBF during grain filling in rice	2009	Plant J	Transgenic Crop Research and Development Centre, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.	The rice (Oryza sativa L.) basic leucine Zipper factor RISBZ1 and rice prolamin box binding factor (RPBF) are transcriptional activators of rice seed storage protein (SSP) genes in vivo. To ascertain the functions of these trans-activators in seed development, knock-down (KD) transgenic rice plants were generated in which the accumulation of RISBZ1 and RPBF was reduced in an endosperm-specific manner by co-suppression (KD-RISBZ1 and KD-RPBF). The accumulation of most SSPs changed little between individual KD mutants and wild-type plants, whereas a double KD mutant (KD-RISBZ1/KD-RPBF) resulted in a significant reduction of most SSP gene expression and accumulation. The reduction of both trans-activators also caused a greater reduction in seed starch accumulation than individual KD mutants. Storage lipids were accumulated at reduced levels in KD-RISBZ1 and KD-RISBZ1/KD-RPBF seeds. KD-RPBF and KD-RISBZ1/KD-RPBF seeds exhibited multi-layered aleurone cells. Gene expression of DEFECTIVE KERNEL1 (OsDEK1), CRINKLY4 (OsCR4) and SUPERNUMERARY ALEURONE LAYER 1 (OsSAL1) rice homologues was decreased in the KD mutants, suggesting that these genes are regulated by RISBZ1 and RPBF. These phenotypes suggest that combinatorial interactions between RISBZ1 and RPBF play an essential role during grain filling. The functional redundancy and compensation between RISBZ1 and RPBF possibly account for weak effects on the SSP levels in single KD mutants, and help maintain various processes during seed development in rice. Physical interaction between RISBZ1 and RPBF may ensure that these processes are carried out properly.	ALK|SSIIa,GluA,GluD,OsAPL2|osagpl2-3,OsAPS2|OsAGPS2b,OsCR4,ADL1|OsDEK1,RAG1,OsSAL1|RHL,RISBZ1|OsbZIP58,RPBF|OsDof3
Association between nonsynonymous mutations of starch synthase IIa and starch quality in rice (Oryza sativa)	2011	New Phytol	Department of Biology, Washington University of St. Louis, Missouri, 63130, USA Present address: Institute of Bioscience and Biotechnology Research, University of Maryland, College Park, Maryland, 20742, USA. guoqinyu@umd.edu	Starch quality is one of the most important agronomic traits in Asian rice, Oryza sativa. Starch synthase IIa (SsIIa) is a major candidate gene for starch quality variation. Within SsIIa, three nonsynonymous mutations in exon 8 have been shown to affect enzyme activity when expressed in Escherichia coli. To search for the variation in SsIIa that is responsible for starch quality variation in rice, we sequenced the SsIIa exon 8 region and measured starch quality as starch disintegration in alkali for 289 accessions of cultivated rice and 57 accessions of its wild ancestor, Oryza rufipogon. A general linear model and nested clade analysis were used to identify the associations between the three nonsynonymous single nucleotide polymorphisms (SNPs) and starch quality. Among the three nonsynonymous SNPs, we found strong evidence of association at one nucleotide site ('SNP 3'), corresponding to a Leu/Phe replacement at codon 781. A second SNP, corresponding to a Val/Met replacement at codon 737, could potentially show an association with increased sample sizes. Variation in SsIIa enzyme activity is associated with the cohesiveness of rice grains when cooked, and our findings are consistent with selection for more cohesive grains during the domestication of tropical japonica rice.	ALK|SSIIa
ALK, the key gene for gelatinization temperature, is a modifier gene for gel consistency in rice	2011	J Integr Plant Biol	State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science, Hangzhou 310006, China.	Gelatinization temperature (GT) is an important parameter in evaluating the cooking and eating quality of rice. Indeed, the phenotype, biochemistry and inheritance of GT have been widely studied in recent times. Previous map-based cloning revealed that GT was controlled by ALK gene, which encodes a putative soluble starch synthase II-3. Complementation vector and RNAi vector were constructed and transformed into Nipponbare mediated by Agrobacterium. Phenotypic and molecular analyses of transgenic lines provided direct evidence for ALK as a key gene for GT. Meanwhile, amylose content, gel consistency and pasting properties were also affected in transgenic lines. Two of four nonsynonymous single nucleotide polymorphisms in coding sequence of ALK were identified as essential for GT. Based on the single nucleotide polymorphisms (SNPs), two new sets of SNP markers combined with one cleaved amplified polymorphic sequence marker were developed for application in rice quality breeding.	ALK|SSIIa
SNP in starch biosynthesis genes associated with nutritional and functional properties of rice	2012	Sci Rep	Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia.	Starch is a major component of human diets. The relative contribution of variation in the genes of starch biosynthesis to the nutritional and functional properties of the rice was evaluated in a rice breeding population. Sequencing 18 genes involved in starch synthesis in a population of 233 rice breeding lines discovered 66 functional SNPs in exonic regions. Five genes, AGPS2b, Isoamylase1, SPHOL, SSIIb and SSIVb showed no polymorphism. Association analysis found 31 of the SNP were associated with differences in pasting and cooking quality properties of the rice lines. Two genes appear to be the major loci controlling traits under human selection in rice, GBSSI (waxy gene) and SSIIa. GBSSI influenced amylose content and retrogradation. Other genes contributing to retrogradation were GPT1, SSI, BEI and SSIIIa. SSIIa explained much of the variation in cooking characteristics. Other genes had relatively small effects.	ALK|SSIIa
Conservation and implications of eukaryote transcriptional regulatory regions across multiple species	2008	BMC Genomics	School of Mathematical Sciences, Peking University, Beijing 100871, PR China	Background. Increasing evidence shows that whole genomes of eukaryotes are almost entirely transcribed into both protein coding genes and an enormous number of non-protein-coding RNAs (ncRNAs). Therefore, revealing the underlying regulatory mechanisms of transcripts becomes imperative. However, for a complete understanding of transcriptional regulatory mechanisms, we need to identify the regions in which they are found. We will call these transcriptional regulation regions, or TRRs, which can be considered functional regions containing a cluster of regulatory elements that cooperatively recruit transcriptional factors for binding and then regulating the expression of transcripts. Results. We constructed a hierarchical stochastic language (HSL) model for the identification of core TRRs in yeast based on regulatory cooperation among TRR elements. The HSL model trained based on yeast achieved comparable accuracy in predicting TRRs in other species, e.g., fruit fly, human, and rice, thus demonstrating the conservation of TRRs across species. The HSL model was also used to identify the TRRs of genes, such as p53 or OsALYL1, as well as microRNAs. In addition, the ENCODE regions were examined by HSL, and TRRs were found to pervasively locate in the genomes. Conclusion. Our findings indicate that 1) the HSL model can be used to accurately predict core TRRs of transcripts across species and 2) identified core TRRs by HSL are proper candidates for the further scrutiny of specific regulatory elements and mechanisms. Meanwhile, the regulatory activity taking place in the abundant numbers of ncRNAs might account for the ubiquitous presence of TRRs across the genome. In addition, we also found that the TRRs of protein coding genes and ncRNAs are similar in structure, with the latter being more conserved than the former.	OsALYL1
An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice	2013	Plant Cell	National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.	Long awns are important for seed dispersal in wild rice (Oryza rufipogon), but are absent in cultivated rice (Oryza sativa). The genetic mechanism involved in loss-of-awn in cultivated rice remains unknown. We report here the molecular cloning of a major quantitative trait locus, An-1, which regulates long awn formation in O. rufipogon. An-1 encodes a basic helix-loop-helix protein, which regulates cell division. The nearly-isogenic line (NIL-An-1) carrying a wild allele An-1 in the genetic background of the awnless indica Guangluai4 produces long awns and longer grains, but significantly fewer grains per panicle compared with Guangluai4. Transgenic studies confirmed that An-1 positively regulates awn elongation, but negatively regulates grain number per panicle. Genetic variations in the An-1 locus were found to be associated with awn loss in cultivated rice. Population genetic analysis of wild and cultivated rice showed a significant reduction in nucleotide diversity of the An-1 locus in rice cultivars, suggesting that the An-1 locus was a major target for artificial selection. Thus, we propose that awn loss was favored and strongly selected by humans, as genetic variations at the An-1 locus that cause awn loss would increase grain numbers and subsequently improve grain yield in cultivated rice.	An-1
Retrograde regulation of nuclear gene expression in CW-CMS of rice	2007	Plant Mol Biol	Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan.	The CW-cytoplasmic male sterility (CMS) line has the cytoplasm of Oryza rufipogon Griff, and mature pollen is morphologically normal under an optical microscope but lacks the ability to germinate; restorer gene Rf17 has been identified as restoring this ability. The difference between nuclear gene expression in mature anthers was compared for the CW-CMS line, [cms-CW] rf17rf17, and a maintainer line with normal cytoplasm of Oryza sativa L., [normal] rf17rf17. Using a 22-k rice oligoarray we detected 58 genes that were up-regulated more than threefold in the CW-CMS line. Expression in other organs was further investigated for 20 genes using RT-PCR. Five genes, including genes for alternative oxidase, were found to be preferentially expressed in [cms-CW] rf17rf17 but not in [normal] rf17rf17 or [cms-CW] Rf17Rf17. Such [cms-CW] rf17rf17-specific gene expression was only observed in mature anthers but not in leaves, stems, or roots, indicating the presence of anther-specific mitochondrial retrograde regulation of nuclear gene expression, and that Rf17 has a role in restoring the ectopic gene expression. We also used a proteomic approach to discover the retrograde regulated proteins and identified six proteins that were accumulated differently. These results reveal organ-specific induced mitochondrial retrograde pathways affecting nuclear gene expression possibly related to CMS.	OsAOX1c|AOX1c
Unravelling mitochondrial retrograde regulation in the abiotic stress induction of rice ALTERNATIVE OXIDASE 1 genes	2013	Plant Cell Environ	Institute of Rice Research, Anhui Academy of Agricultural Science, Hefei 230031, China.	Mitochondrial retrograde regulation (MRR) is the transduction of mitochondrial signals to mediate nuclear gene expression. It is not clear whether MRR is a common regulation mechanism in plant abiotic stress response. In this study, we analysed the early abiotic stress response of the rice OsAOX1 genes, and the induction of OsAOX1a and OsAOX1b (OsAOX1a/b) was selected as a working model for the stress-induced MRR studies. We found that the induction mediated by the superoxide ion (O2.(-) )-generating chemical methyl viologen was stronger than that of hydrogen peroxide (H2 O2 ). The addition of reactive oxygen species (ROS) scavengers demonstrated that the stress induction was reduced by eliminating O2.(-) . Furthermore, the stress induction did not rely on chloroplast- or cytosol-derived O2.(-) . Next, we generated transgenic plants overexpressing the superoxide dismutase (SOD) gene at different subcellular locations. The results suggest that only the mitochondrial SOD, OsMSD, attenuated the stress induction of OsAOX1a/b specifically. Therefore, our findings demonstrate that abiotic stress initiates the MRR on OsAOX1a/b and that mitochondrial O2.(-) is involved in the process.	OsAOX1c|AOX1c,AOX1a|OsAOX1a,OsAOX1b,OsMSD
AOX1c, a novel rice gene for alternative oxidase; comparison with rice AOX1a and AOX1b	2002	Genes Genet Syst	Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Japan.	A novel gene for alternative oxidase (AOX) was isolated from rice (Oryza sativa L.) and characterized. The deduced amino acid sequence of the novel AOX gene contains features that are conserved among other AOXs. This AOX gene was designated AOX1c based on a phylogenetic analysis of the AOX genes. Northern hybridization analyses revealed that AOX1c and AOX1a/AOX1b transcripts accumulated differently in various rice organs and rice seedlings under low temperature conditions. AOX1c mRNA was mainly present in young leaves under constant light, mature leaves and panicles after heading, but it was not detected in young etiolated leaves and young roots of seedlings or young panicles. On the other hand, the mRNAs of the rice AOX1a and AOX1b genes were mainly present in young roots and mature leaves. Under low temperature conditions, the steady-state mRNA levels of the rice AOX1a and AOX1b genes clearly increased with time but the rice AOX1c gene was apparently not responsive to low temperature. The rice AOX gene family and differences in their regulation are discussed.	OsAOX1c|AOX1c
The Magnaporthe oryzae effector AvrPiz-t targets the RING E3 ubiquitin ligase APIP6 to suppress pathogen-associated molecular pattern-triggered immunity in rice	2012	Plant Cell	Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA.	Although the functions of a few effector proteins produced by bacterial and oomycete plant pathogens have been elucidated in recent years, information for the vast majority of pathogen effectors is still lacking, particularly for those of plant-pathogenic fungi. Here, we show that the avirulence effector AvrPiz-t from the rice blast fungus Magnaporthe oryzae preferentially accumulates in the specialized structure called the biotrophic interfacial complex and is then translocated into rice (Oryza sativa) cells. Ectopic expression of AvrPiz-t in transgenic rice suppresses the flg22- and chitin-induced generation of reactive oxygen species (ROS) and enhances susceptibility to M. oryzae, indicating that AvrPiz-t functions to suppress pathogen-associated molecular pattern (PAMP)-triggered immunity in rice. Interaction assays show that AvrPiz-t suppresses the ubiquitin ligase activity of the rice RING E3 ubiquitin ligase APIP6 and that, in return, APIP6 ubiquitinates AvrPiz-t in vitro. Interestingly, agroinfection assays reveal that AvrPiz-t and AvrPiz-t Interacting Protein 6 (APIP6) are both degraded when coexpressed in Nicotiana benthamiana. Silencing of APIP6 in transgenic rice leads to a significant reduction of flg22-induced ROS generation, suppression of defense-related gene expression, and enhanced susceptibility of rice plants to M. oryzae. Taken together, our results reveal a mechanism in which a fungal effector targets the host ubiquitin proteasome system for the suppression of PAMP-triggered immunity in plants.	APIP6
ARAG1, an ABA-responsive DREB gene, plays a role in seed germination and drought tolerance of rice	2010	Ann Bot	Research Center for Molecular & Developmental Biology, Key Laboratory of Photosynthesis & Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	BACKGROUND AND AIMS: DREB proteins are involved mainly in plant responses to abiotic stresses such as cold, drought or high salinity as well as ABA signalling. However, the function of most rice DREB genes and the underlying molecular mechanisms controlling these responses remains elusive. In this study, ARAG1, a rice DREB gene, was functionally analysed. METHODS: Antisense and over-expression constructs of ARAG1 were introduced into rice by an Agrobacterium-mediated method. RT-PCR and western blot were used to detect ARAG1 accumulation in transgenics. PEG and ABA were used to test their response to abiotic stresses. KEY RESULTS: ARAG1 was expressed in inflorescences, roots, immature embryos and germinating seeds, but not in coleoptiles, leaves or mature embryos. Drought stress and ABA treatment increased transcript levels of the gene rapidly. ARAG1 knockdown line was hypersensitive to ABA application during seed germination and seedling growth. However, the line over-expressing ARAG1 behaved similarly to wild type in these circumstances. Knockdown of ARAG1 weakened tolerance of the transgenic seedlings to drought stress, while over-expression of it increased the tolerance slightly. In addition, activity of alpha-amylases was enhanced in germinating seeds of the knockdown and over-expression lines. CONCLUSIONS: These results indicate that ARAG1 was involved in the ABA signalling and stress responsive pathways.	ARAG1
'Evidence of an auxin signal pathway, microRNA167-ARF8-GH3, and its response to exogenous auxin in cultured rice cells'	2006	Nucleic Acids Res	Department of Biological Science and the Basic Science Research Institute, Sungkyunkwan University, Suwon, Korea 440-746.	MicroRNA167 (miR167) was shown to cleave auxin responsive factor 8 (ARF8) mRNA in cultured rice cells. MiR167 level was found to be controlled by the presence of auxin in the growth medium. When cells grew in auxin-free medium, miR167 level decreased, resulting in an increase in the level of ARF8 mRNA. Cells growing in the normal growth medium containing auxin showed a reversed trend. It was also shown that expression of OsGH3-2, an rice IAA-conjugating enzyme, was positively regulated by ARF8. Delivery of synthesized miR167 into cells led to decrease of both ARF8 mRNA and OsGH3-2 mRNA. This study provides an evidence in which the exogeneous auxin signal is transduced to OsGH3-2 through miR167 and ARF8 in sequence. This proposed auxin signal transduction pathway, auxin-miR167-ARF8-OsGH3-2, could be, in conjunction with the other microRNA-mediated auxin signals, an important one for responding to exogeneous auxin and for determining the cellular free auxin level which guides appropriate auxin responses.	ARF8,OsGH3-2
Identification of a cis-acting element of ART1, a C2H2-type zinc-finger transcription factor for aluminum tolerance in rice	2011	Plant Physiol	Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.	Rice (Oryza sativa) is one of the most aluminum (Al)-tolerant species among small-grain cereals. Recent identification of a transcription factor AL RESISTANCE TRANSCRIPTION FACTOR1 (ART1) revealed that this high Al tolerance in rice is achieved by multiple genes involved in detoxification of Al at different cellular levels. ART1 is a C2H2-type zinc-finger transcription factor and regulates the expression of 31 genes in the downstream. In this study, we attempted to identify a cis-acting element of ART1. We used the promoter region of SENSITIVE TO AL RHIZOTOXICITY1, an Al tolerance gene in the downstream of ART1. With the help of gel-shift assay, we were able to identify the cis-acting element as GGN(T/g/a/C)V(C/A/g)S(C/G). This element was found in the promoter region of 29 genes among 31 ART1-regulated genes. To confirm this cis-acting element in vivo, we transiently introduced this element one or five times tandemly repeated sequence with 35S minimal promoter and green fluorescent protein reporter together with or without ART1 gene in the tobacco (Nicotiana tabacum) mesophyll protoplasts. The results showed that the expression of green fluorescent protein reporter responded to ART1 expression. Furthermore, the expression increased with repetition of the cis-acting element. Our results indicate that the five nucleotides identified are the target DNA-binding sequence of ART1.	ART1
An Al-inducible MATE gene is involved in external detoxification of Al in rice	2011	Plant J	Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.	A number of plant species, including rice, secretes citrate from roots in response to Al stress. Here we characterized the functions of a gene, OsFRDL4 (Os01g0919100) that belongs to the multidrug and toxic compound extrusion (MATE) family in rice (Oryza sativa). Heterologous expression in Xenopus oocyte showed that the OsFRDL4 protein was able to transport citrate and was activated by Al. The expression level of the OsFRDL4 gene in roots was very low in the absence of Al, but was greatly enhanced by Al after short exposure. Furthermore, the OsFRDL4 expression was regulated by ART1, a C2H2-type zinc finger transcription factor for Al tolerance. Transient expression of OsFRDL4 in onion epidermal cells showed that it localized to the plasma membrane. Immunostaining showed that OsFRDL4 was localized in all cells in the root tip. These expression patterns and cell specificity of localization of OsFRDL4 are different from other MATE members identified previously. Knockout of OsFRDL4 resulted in decreased Al tolerance and decreased citrate secretion compared with the wild-type rice, but did not affect citrate concentration in the xylem sap. Furthermore, there is a positive correlation between OsFRDL4 expression level and the amount of citrate secretion in rice cultivars that are differing in Al tolerance. Taken together, our results show that OsFRDL4 is an Al-induced citrate transporter localized at the plasma membrane of rice root cells and is one of the components of high Al tolerance in rice.	ART1,OsFRDL4
A zinc finger transcription factor ART1 regulates multiple genes implicated in aluminum tolerance in rice	2009	Plant Cell	Research Institute for Bioresources, Okayama University, Kurashiki 710-0046, Japan.	Aluminum (Al) toxicity is the major limiting factor of crop production on acid soils, but some plant species have evolved ways of detoxifying Al. Here, we report a C2H2-type zinc finger transcription factor ART1 (for Al resistance transcription factor 1), which specifically regulates the expression of genes related to Al tolerance in rice (Oryza sativa). ART1 is constitutively expressed in the root, and the expression level is not affected by Al treatment. ART1 is localized in the nucleus of all root cells. A yeast one-hybrid assay showed that ART1 has a transcriptional activation potential and interacts with the promoter region of STAR1, an important factor in rice Al tolerance. Microarray analysis revealed 31 downstream transcripts regulated by ART1, including STAR1 and 2 and a couple of homologs of Al tolerance genes in other plants. Some of these genes were implicated in both internal and external detoxification of Al at different cellular levels. Our findings shed light on comprehensively understanding how plants detoxify aluminum to survive in an acidic environment.	ART1,STAR1,STAR2
Plasma membrane-localized transporter for aluminum in rice	2010	Proc Natl Acad Sci U S A	Institute for Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan.	Aluminum (Al) is the most abundant metal in the Earth's crust, but its trivalent ionic form is highly toxic to all organisms at low concentrations. How Al enters cells has not been elucidated in any organisms. Herein, we report a transporter, Nrat1 (Nramp aluminum transporter 1), specific for trivalent Al ion in rice. Nrat1 belongs to the Nramp (natural resistance-associated macrophage protein) family, but shares a low similarity with other Nramp members. When expressed in yeast, Nrat1 transports trivalent Al ion, but not other divalent ions, such as manganese, iron, and cadmium, or the Al-citrate complex. Nrat1 is localized at the plasma membranes of all cells of root tips except epidermal cells. Knockout of Nrat1 resulted in decreased Al uptake, increased Al binding to cell wall, and enhanced Al sensitivity, but did not affect the tolerance to other metals. Expression of Nrat1 is up-regulated by Al in the roots and regulated by a C2H2 zinc finger transcription factor (ART1). We therefore concluded that Nrat1 is a plasma membrane-localized transporter for trivalent Al, which is required for a prior step of final Al detoxification through sequestration of Al into vacuoles.	ART1,Nrat1
Disruption of the rice plastid ribosomal protein s20 leads to chloroplast developmental defects and seedling lethality	2013	G3 (Bethesda)	Development Center of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234.	Plastid ribosomal proteins (PRPs) are essential for ribosome biogenesis, plastid protein biosynthesis, chloroplast differentiation, and early chloroplast development. This study identifies the first rice PRP mutant, asl1 (albino seedling lethality1), which exhibits an albino lethal phenotype at the seedling stage. This albino phenotype was associated with altered chlorophyll (Chl) content and chloroplast development. Map-based cloning revealed that ASL1 encodes PRP S20 (PRPS20), which localizes to the chloroplast. ASL1 showed tissue-specific expression, as it was highly expressed in plumule and young seedlings but expressed at much lower levels in other tissues. In addition, ASL1 expression was regulated by light. The transcript levels of nuclear genes for Chl biosynthesis and chloroplast development were strongly affected in asl1 mutants; transcripts of some plastid genes for photosynthesis were undetectable. Our findings indicate that nuclear-encoded PRPS20 plays an important role in chloroplast development in rice.	ASL1
Mutation of the rice ASL2 gene encoding plastid ribosomal protein L21 causes chloroplast developmental defects and seedling death	2014	Plant Biol (Stuttg)	Development Center of Plant Germplasm Resources, College of Life and Environment Sciences, Shanghai Normal University, Shanghai, China.	The plastid ribosome proteins (PRPs) play important roles in plastid protein biosynthesis, chloroplast differentiation and early chloroplast development. However, the specialised functions of individual protein components of the chloroplast ribosome in rice (Oryza sativa) remain unresolved. In this paper, we identified a novel rice PRP mutant named asl2 (Albino seedling lethality 2) exhibiting an albino, seedling death phenotype. In asl2 mutants, the alteration of leaf colour was associated with chlorophyll (Chl) content and abnormal chloroplast development. Through map-based cloning and complementation, the mutated ASL2 gene was isolated and found to encode the chloroplast 50S ribosome protein L21 (RPL21c), a component of the chloroplast ribosome large subunit, which was localised in chloroplasts. ASL2 was expressed at a higher level in the plumule and leaves, implying its tissue-specific expression. Additionally, the expression of ASL2 was regulated by light. The transcript levels of the majority of genes for Chl biosynthesis, photosynthesis and chloroplast development were strongly affected in asl2 mutants. Collectively, the absence of functional ASL2 caused chloroplast developmental defects and seedling death. This report establishes the important role of RPL21c in chloroplast development in rice.	ASL2
Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives	2010	Theor Appl Genet	CIRAD, UMR Developpement et Amelioration des Plantes, TA-A 96/03, 34398, Montpellier, France. rphilippe@clermont.inra.fr	Asr (ABA, stress, ripening) genes represent a small gene family potentially involved in drought tolerance in several plant species. To analyze their interest for rice breeding for water-limited environments, this gene family was characterized further. Genomic organization of the gene family reveals six members located on four different chromosomes and with the same exon-intron structure. The maintenance of six members of the Asr gene family, which are the result of combination between tandem duplication and whole genome duplication, and their differential regulation under water stress, involves probably some sub-functionalization. The polymorphism of four members was studied in a worldwide collection of 204 accessions of Oryza sativa L. and 14 accessions of wild relatives (O. rufipogon and O. nivara). The nucleotide diversity of the Asr genes was globally low, but contrasted for the different genes, leading to different shapes of haplotype networks. Statistical tests for neutrality were used and compared to their distribution in a set of 111 reference genes spread across the genome, derived from another published study. Asr3 diversity exhibited a pattern concordant with a balancing selection at the species level and with a directional selection in the tropical japonica sub-group. This study provides a thorough description of the organization of the Asr family, and the nucleotide and haplotype diversity of four Asr in Oryza sativa species. Asr3 stood out as the best potential candidate. The polymorphism detected here represents a first step towards an association study between genetic polymorphisms of this gene family and variation in drought tolerance traits.	Asr1,Asr2,Asr4,Asr6,ASR5|OsAsr1,Asr3|OsASR3
Involvement of ASR genes in aluminium tolerance mechanisms in rice	2013	Plant Cell Environ	Programa de Pos-Graduacao em Genetica e Biologia Molecular Programa de Pos-Graduacao em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil.	Among cereal crops, rice is considered the most tolerant to aluminium (Al). However, variability among rice genotypes leads to remarkable differences in the degree of Al tolerance for distinct cultivars. A number of studies have demonstrated that rice plants achieve Al tolerance through an unknown mechanism that is independent of root tip Al exclusion. We have analysed expression changes of the rice ASR gene family as a function of Al treatment. The gene ASR5 was differentially regulated in the Al-tolerant rice ssp. Japonica cv. Nipponbare. However, ASR5 expression did not respond to Al exposure in Indica cv. Taim rice roots, which are highly Al sensitive. Transgenic plants carrying RNAi constructs that targeted the ASR genes were obtained, and increased Al susceptibility was observed in T1 plants. Embryogenic calli of transgenic rice carrying an ASR5-green fluorescent protein fusion revealed that ASR5 was localized in both the nucleus and cytoplasm. Using a proteomic approach to compare non-transformed and ASR-RNAi plants, a total of 41 proteins with contrasting expression patterns were identified. We suggest that the ASR5 protein acts as a transcription factor to regulate the expression of different genes that collectively protect rice cells from Al-induced stress responses.	Asr1,Asr2,Asr4,Asr6,ASR5|OsAsr1
Expression of salt-induced 2-Cys peroxiredoxin from Oryza sativa increases stress tolerance and fermentation capacity in genetically engineered yeast Saccharomyces cerevisiae	2013	Appl Microbiol Biotechnol	Advanced Bio-resource Research Center, Department of Biology, College of Natural Sciences, Kyungpook National University, #1370 Sankyuk-dong, Buk-gu, Daegu 702-701, Republic of Korea. 92kis@hanmail.net	Peroxiredoxins (Prxs), also termed thioredoxin peroxidases (TPXs), are a family of thiol-specific antioxidant enzymes that are critically involved in cell defense and protect cells from oxidative damage. In this study, a putative chloroplastic 2-Cys thioredoxin peroxidase (OsTPX) was identified by proteome analysis from leaf tissue samples of rice (Oryza sativa) seedlings exposed to 0.1 M NaCl for 3 days. To investigate the relationship between the OsTPX gene and the stress response, OsTPX was cloned into the yeast expression vector p426GPD under the control of the glyceraldehyde-3-phosphate dehydrogenase (GPD1) promoter, and the construct was transformed into Saccharomyces cerevisiae cells. OsTPX expression was confirmed by semi-quantitative reverse transcription-polymerase chain reaction and western blot analyses. OsTPX contained two highly conserved cysteine residues (Cys114 and Cys236) and an active site region (FTFVCPT), and it is structurally very similar to human 2-Cys Prx. Heterologous OsTPX expression increased the ability of the transgenic yeast cells to adapt and recover from reactive oxygen species (ROS)-induced oxidative stresses, such as a reduction of cellular hydroperoxide levels in the presence of hydrogen peroxide and menadione, by improving redox homeostasis. OsTPX expression also conferred enhanced tolerance to tert-butylhydroperoxide, heat shock, and high ethanol concentrations. Furthermore, high OsTPX expression improved the fermentation capacity of the yeast during glucose-based batch fermentation at a high temperature (40 degrees C) and at the general cultivation temperature (30 degrees C). The alcohol yield in OsTPX-expressing transgenic yeast increased by approximately 29 % (0.14 g g(-1)) and 21 % (0.12 g g(-1)) during fermentation at 40 and 30 degrees C, respectively, compared to the wild-type yeast. Accordingly, OsTPX-expressing transgenic yeast showed prolonged cell survival during the environmental stresses produced during fermentation. These results suggest that heterologous OsTPX expression increases acquired tolerance to ROS-induced oxidative stress by improving cellular redox homeostasis and improves fermentation capacity due to improved cell survival during fermentation, especially at a high temperature.	BAS1|OsTPX
A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes	2011	Plant Methods	State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P, R, China. wanghb@mail.sysu.edu.cn.	BACKGROUND: Plant protoplasts, a proven physiological and versatile cell system, are widely used in high-throughput analysis and functional characterization of genes. Green protoplasts have been successfully used in investigations of plant signal transduction pathways related to hormones, metabolites and environmental challenges. In rice, protoplasts are commonly prepared from suspension cultured cells or etiolated seedlings, but only a few studies have explored the use of protoplasts from rice green tissue. RESULTS: Here, we report a simplified method for isolating protoplasts from normally cultivated young rice green tissue without the need for unnecessary chemicals and a vacuum device. Transfections of the generated protoplasts with plasmids of a wide range of sizes (4.5-13 kb) and co-transfections with multiple plasmids achieved impressively high efficiencies and allowed evaluations by 1) protein immunoblotting analysis, 2) subcellular localization assays, and 3) protein-protein interaction analysis by bimolecular fluorescence complementation (BiFC) and firefly luciferase complementation (FLC). Importantly, the rice green tissue protoplasts were photosynthetically active and sensitive to the retrograde plastid signaling inducer norflurazon (NF). Transient expression of the GFP-tagged light-related transcription factor OsGLK1 markedly upregulated transcript levels of the endogeneous photosynthetic genes OsLhcb1, OsLhcp, GADPH and RbcS, which were reduced to some extent by NF treatment in the rice green tissue protoplasts. CONCLUSIONS: We show here a simplified and highly efficient transient gene expression system using photosynthetically active rice green tissue protoplasts and its broad applications in protein immunoblot, localization and protein-protein interaction assays. These rice green tissue protoplasts will be particularly useful in studies of light/chloroplast-related processes.	BAS1|OsTPX,GADPH,CAB2R
The GA octodinucleotide repeat binding factor BBR participates in the transcriptional regulation of the homeobox geneBkn3	2003	The Plant Journal	Max-Planck-Institut für Züchtungsforschung, Department of Plant Breeding and Yield Physiology, Carl-von-Linné-Weg 10, 50829 Köln, Germany.	In the dominant mutant Hooded (K), the barley gene BKn3 is overexpressed as a result of a duplication of 305 bp in intron IV. When fused to a cauliflower mosaic virus 35S minimal promoter, the 305 bp element activates gene expression in tobacco, as does a 655 bp BKn3 promoter sequence. Both DNA fragments contain a (GA)8 repeat (GA/TC)8. A one-hybrid screen using the 305 bp element as the DNA target led to the cloning of the barley b recombinant (BBR) protein, which binds specifically to the (GA/TC)8 repeat. BBR is nuclear targeted and is a characterized nuclear localization signal (NLS) sequence, a DNA-binding domain extended up to 90 aa at the C-terminus and a putative N-terminal activation domain. The corresponding gene has no introns and is ubiquitously expressed in barley tissues. In co-transfection experiments, BBR activates (GA/TC)8-containing promoters, and its overexpression in tobacco leads to a pronounced leaf shape modification. BBR has properties of a GAGA-binding factor, but the corresponding gene has no sequence homology to Trl and Psq of Drosophila, which encode functionally analogous proteins. In Arabidopsis, (GA/TC)8 repeats occur particularly within 1500 bp upstream of gene start codons included in some homeodomain genes of different classes. The data presented suggest that expression of the barley BKn3 is regulated, at least in part, by the binding of the transcription factor BBR to GA/TC repeats.	BBR
Rice Brittle culm 6 encodes a dominant-negative form of CesA protein that perturbs cellulose synthesis in secondary cell walls	2011	J Exp Bot	Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan.	The brittle culm (bc) mutants of Gramineae plants having brittle skeletal structures are valuable materials for studying secondary cell walls. In contrast to other recessive bc mutants, rice Bc6 is a semi-dominant bc mutant with easily breakable plant bodies. In this study, the Bc6 gene was cloned by positional cloning. Bc6 encodes a cellulose synthase catalytic subunit, OsCesA9, and has a missense mutation in its highly conserved region. In culms of the Bc6 mutant, the proportion of cellulose was reduced by 38%, while that of hemicellulose was increased by 34%. Introduction of the semi-dominant Bc6 mutant gene into wild-type rice significantly reduced the percentage of cellulose, causing brittle phenotypes. Transmission electron microscopy analysis revealed that Bc6 mutation reduced the cell wall thickness of sclerenchymal cells in culms. In rice expressing a reporter construct, BC6 promoter activity was detected in the culms, nodes, and flowers, and was localized primarily in xylem tissues. This expression pattern was highly similar to that of BC1, which encodes a COBRA-like protein involved in cellulose synthesis in secondary cell walls in rice. These results indicate that BC6 is a secondary cell wall-specific CesA that plays an important role in proper deposition of cellulose in the secondary cell walls.	BC1,Bc6|OsCesA9
BRITTLE CULM1, Which Encodes a COBRA-Like Protein, Affects the Mechanical Properties of Rice Plants	2003	The Plant Cell Online	Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Plant mechanical strength is an important agronomic trait. To understand the molecular mechanism that controls the plant mechanical strength of crops, we characterized the classic rice mutant brittle culm1 (bc1) and isolated BC1 using a map-based cloning approach. BC1, which encodes a COBRA-like protein, is expressed mainly in developing sclerenchyma cells and in vascular bundles of rice. In these types of cells, mutations in BC1 cause not only a reduction in cell wall thickness and cellulose content but also an increase in lignin level, suggesting that BC1, a gene that controls the mechanical strength of monocots, plays an important role in the biosynthesis of the cell walls of mechanical tissues.	BC1
The carbohydrate-binding module (CBM)-like sequence is crucial for rice CWA1/BC1 function in proper assembly of secondary cell wall materials	2010	Plant Signal Behav	Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan	We recently reported that the cwa1 mutation disturbed the deposition and assembly of secondary cell wall materials in the cortical fiber of rice internodes. Genetic analysis revealed that cwa1 is allelic to bc1, which encodes glycosylphosphatidylinositol (GPI)-anchored COBRA-like protein with the highest homology to Arabidopsis COBRA-like 4 (COBL4) and maize Brittle Stalk 2 (Bk2). Our results suggested that CWA1/BC1 plays a role in assembling secondary cell wall materials at appropriate sites, enabling synthesis of highly ordered secondary cell wall structure with solid and flexible internodes in rice. The N-terminal amino acid sequence of CWA1/BC1, as well as its orthologs (COBL4, Bk2) and other BC1-like proteins in rice, shows weak similarity to a family II carbohydrate-binding module (CBM2) of several bacterial cellulases. To investigate the importance of the CBM-like sequence of CWA1/BC1 in the assembly of secondary cell wall materials, Trp residues in the CBM-like sequence, which is important for carbohydrate binding, were substituted for Val residues and introduced into the cwa1 mutant. CWA1/BC1 with the mutated sequence did not complement the abnormal secondary cell walls seen in the cwa1 mutant, indicating that the CBM-like sequence is essential for the proper function of CWA1/BC1, including assembly of secondary cell wall materials.	BC1
Isolation of a novel cell wall architecture mutant of rice with defective Arabidopsis COBL4 ortholog BC1 required for regulated deposition of secondary cell wall components	2010	Planta	Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Japan. 	The plant secondary cell wall is a highly ordered structure composed of various polysaccharides, phenolic components and proteins. Its coordinated regulation of a number of complex metabolic pathways and assembly has not been resolved. To understand the molecular mechanisms that regulate secondary cell wall synthesis, we isolated a novel rice mutant, cell wall architecture1 (cwa1), that exhibits an irregular thickening pattern in the secondary cell wall of sclerenchyma, as well as culm brittleness and reduced cellulose content in mature internodes. Light and transmission electron microscopy revealed that the cwa1 mutant plant has regions of local aggregation in the secondary cell walls of the cortical fibers in its internodes, showing uneven thickness. Ultraviolet microscopic observation indicated that localization of cell wall phenolic components was perturbed and that these components abundantly deposited at the aggregated cell wall regions in sclerenchyma. Therefore, regulation of deposition and assembly of secondary cell wall materials, i.e. phenolic components, appear to be disturbed by mutation of the cwa1 gene. Genetic analysis showed that cwa1 is allelic to brittle culm1 (bc1), which encodes the glycosylphosphatidylinositol-anchored COBRA-like protein specifically in plants. BC1 is known as a regulator that controls the culm mechanical strength and cellulose content in the secondary cell walls of sclerenchyma, but the precise function of BC1 has not been resolved. Our results suggest that CWA1/BC1 has an essential role in assembling cell wall constituents at their appropriate sites, thereby enabling synthesis of solid and flexible internodes in rice.	BC1
BC10, a DUF266-containing and Golgi-located type II membrane protein, is required for cell-wall biosynthesis in rice (Oryza sativa L.)	2009	Plant J	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Glycosyltransferases (GTs) are one of the largest enzyme groups required for the synthesis of complex wall polysaccharides and glycoproteins in plants. However, due to the limited number of related mutants that have observable phenotypes, the biological function(s) of most GTs in cell-wall biosynthesis and assembly have remained elusive. We report here the isolation and in-depth characterization of a brittle rice mutant, brittle culm 10 (bc10). bc10 plants show pleiotropic phenotypes, including brittleness of the plant body and retarded growth. The BC10 gene was cloned through a map-based approach, and encodes a Golgi-located type II membrane protein that contains a domain designated as 'domain of unknown function 266' (DUF266) and represents a multiple gene family in rice. BC10 has low sequence similarity with the domain to a core 2 beta-1,6-N-acetylglucosaminyltransferase (C2GnT), and its in vitro enzymatic activity suggests that it functions as a glycosyltransferase. Monosaccharide analysis of total and fractioned wall residues revealed that bc10 showed impaired cellulose biosynthesis. Immunolocalization and isolation of arabinogalactan proteins (AGPs) in the wild-type and bc10 showed that the level of AGPs in the mutant is significantly affected. BC10 is mainly expressed in the developing sclerenchyma and vascular bundle cells, and its deficiency causes a reduction in the levels of cellulose and AGPs, leading to inferior mechanical properties.	BC10
Brittle Culm 12, a dual-targeting kinesin-4 protein, controls cell-cycle progression and wall properties in rice	2010	Plant J	State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.	Kinesins are encoded by a large gene family involved in many basic processes of plant development. However, the number of functionally identified kinesins in rice is very limited. Here, we report the functional characterization of Brittle Culm12 (BC12), a gene encoding a kinesin-4 protein. bc12 mutants display dwarfism resulting from a significant reduction in cell number and brittleness due to an alteration in cellulose microfibril orientation and wall composition. BC12 is expressed mainly in tissues undergoing cell division and secondary wall thickening. In vitro biochemical analyses verified BC12 as an authentic motor protein. This protein was present in both the nucleus and cytoplasm and associated with microtubule arrays during cell division. Mitotic microtubule array comparison, flow cytometric analysis and expression assays of cyclin-dependent kinase (CDK) complexes in root-tip cells showed that cell-cycle progression is affected in bc12 mutants. BC12 is very probably regulated by CDKA;3 based on yeast two-hybrid and microarray data. Therefore, BC12 functions as a dual-targeting kinesin protein and is implicated in cell-cycle progression, cellulose microfibril deposition and wall composition in the monocot plant rice.	BC12
Mutation of rice BC12/GDD1, which encodes a kinesin-like protein that binds to a GA biosynthesis gene promoter, leads to dwarfism with impaired cell elongation	2011	Plant Cell	Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	The kinesins are a family of microtubule-based motor proteins that move directionally along microtubules and are involved in many crucial cellular processes, including cell elongation in plants. Less is known about kinesins directly regulating gene transcription to affect cellular physiological processes. Here, we describe a rice (Oryza sativa) mutant, gibberellin-deficient dwarf1 (gdd1), that has a phenotype of greatly reduced length of root, stems, spikes, and seeds. This reduced length is due to decreased cell elongation and can be rescued by exogenous gibberellic acid (GA(3)) treatment. GDD1 was cloned by a map-based approach, was expressed constitutively, and was found to encode the kinesin-like protein BRITTLE CULM12 (BC12). Microtubule cosedimentation assays revealed that BC12/GDD1 bound to microtubules in an ATP-dependent manner. Whole-genome microarray analysis revealed the expression of ent-kaurene oxidase (KO2), which encodes an enzyme involved in GA biosynthesis, was downregulated in gdd1. Electrophoretic mobility shift and chromatin immunoprecipitation assays revealed that GDD1 bound to the element ACCAACTTGAA in the KO2 promoter. In addition, GDD1 was shown to have transactivation activity. The level of endogenous GAs was reduced in gdd1, and the reorganization of cortical microtubules was altered. Therefore, BC12/GDD1, a kinesin-like protein with transcription regulation activity, mediates cell elongation by regulating the GA biosynthesis pathway in rice.	BC12,D35|OsKOS3|OsKO2
Brittle culm15 encodes a membrane-associated chitinase-like protein required for cellulose biosynthesis in rice	2012	Plant Physiol	Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Plant chitinases, a class of glycosyl hydrolases, participate in various aspects of normal plant growth and development, including cell wall metabolism and disease resistance. The rice (Oryza sativa) genome encodes 37 putative chitinases and chitinase-like proteins. However, none of them has been characterized at the genetic level. In this study, we report the isolation of a brittle culm mutant, bc15, and the map-based cloning of the BC15/OsCTL1 (for chitinase-like1) gene affected in the mutant. The gene encodes the rice chitinase-like protein BC15/OsCTL1. Mutation of BC15/OsCTL1 causes reduced cellulose content and mechanical strength without obvious alterations in plant growth. Bioinformatic analyses indicated that BC15/OsCTL1 is a class II chitinase-like protein that is devoid of both an amino-terminal cysteine-rich domain and the chitinase activity motif H-E-T-T but possesses an amino-terminal transmembrane domain. Biochemical assays demonstrated that BC15/OsCTL1 is a Golgi-localized type II membrane protein that lacks classical chitinase activity. Quantitative real-time polymerase chain reaction and beta-glucuronidase activity analyses indicated that BC15/OsCTL1 is ubiquitously expressed. Investigation of the global expression profile of wild-type and bc15 plants, using Illumina RNA sequencing, further suggested a possible mechanism by which BC15/OsCTL1 mediates cellulose biosynthesis and cell wall remodeling. Our findings provide genetic evidence of a role for plant chitinases in cellulose biosynthesis in rice, which appears to differ from their roles as revealed by analysis of Arabidopsis (Arabidopsis thaliana).	bc15|OsCTL1
Rice BRITTLE CULM 3 (BC3) encodes a classical dynamin OsDRP2B essential for proper secondary cell wall synthesis	2010	Planta	Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.	"Brittle culm" mutants found in Gramineae crops are suitable materials to study the mechanism of secondary cell wall formation. Through positional cloning, we have identified a gene responsible for the brittle culm phenotype in rice, brittle culm 3 (bc3). BC3 encodes a member of the classical dynamin protein family, a family known to function widely in membrane dynamics. The bc3 mutation resulted in reductions of 28-36% in cellulose contents in culms, leaves, and roots, while other cell wall components remained unaffected. Reductions of cell wall thickness and birefringence were observed in both fiber (sclerenchyma) and parenchymal cells, together with blurring of the wall's layered structures. From promoter-GUS analyses, it was suggested that BC3 expression is directly correlated with active secondary cell wall synthesis. These results suggest that BC3 is tightly involved in the synthesis of cellulose and is essential for proper secondary cell wall construction.	BC3|OsDRP2B
The rice dynamin-related protein DRP2B mediates membrane trafficking, and thereby plays a critical role in secondary cell wall cellulose biosynthesis	2010	Plant J	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Membrane trafficking between the plasma membrane (PM) and intracellular compartments is an important process that regulates the deposition and metabolism of cell wall polysaccharides. Dynamin-related proteins (DRPs), which function in membrane tubulation and vesiculation are closely associated with cell wall biogenesis. However, the molecular mechanisms by which DRPs participate in cell wall formation are poorly understood. Here, we report the functional characterization of Brittle Culm3 (BC3), a gene encoding OsDRP2B. Consistent with the expression of BC3 in mechanical tissues, the bc3 mutation reduces mechanical strength, which results from decreased cellulose content and altered secondary wall structure. OsDRP2B, one of three members of the DRP2 subfamily in rice (Oryza sativa L.), was identified as an authentic membrane-associated dynamin via in vitro biochemical analyses. Subcellular localization of fluorescence-tagged OsDRP2B and several compartment markers in protoplast cells showed that this protein not only lies at the PM and the clathrin-mediated vesicles, but also is targeted to the trans-Golgi network (TGN). An FM4-64 uptake assay in transgenic plants that express green fluorescent protein-tagged OsDRP2B verified its involvement in an endocytic pathway. BC3 mutation and overexpression altered the abundance of cellulose synthase catalytic subunit 4 (OsCESA4) in the PM and in the endomembrane systems. All of these findings lead us to conclude that OsDRP2B participates in the endocytic pathway, probably as well as in post-Golgi membrane trafficking. Mutation of OsDRP2B disturbs the membrane trafficking that is essential for normal cellulose biosynthesis of the secondary cell wall, thereby leading to inferior mechanical properties in rice plants.	BC3|OsDRP2B,OsCesA4|Bc7|bc11
Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides	2006	Plant Mol Biol	College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, Zhejiang, China.	Development of hybrid rice has greatly contributed to increased yields during the past three decades. Two bentazon-lethal mutants 8077S and Norin8m are being utilized in developing new hybrid rice systems. When the male sterile lines are developed in such a mutant background, the problem of F1 seed contamination by self-seeds from the sterile lines can be solved by spraying bentazon at seedling stage. We first determined the sensitivity of the mutant plants to bentazon. Both mutants showed symptoms to bentazon starting from 100 mg/l, which was about 60-fold, lower than the sensitivity threshold of their wild-type controls. In addition, both mutants were sensitive to sulfonylurea-type herbicides. The locus for the mutant phenotype is bel for 8077S and bsl for Norin8m. Tests showed that the two loci are allelic to each other. The two genes were cloned by map-based cloning. Interestingly, both mutant alleles had a single-base deletion, which was confirmed by PCR-RFLP. The two loci are renamed bel ( a ) (for bel) and bel ( b ) (for bsl). The wild-type Bel gene encodes a novel cytochrome P450 monooxgenase, named CYP81A6. Analysis of the mutant protein sequence also revealed the reason for bel ( a ) being slightly tolerant than bel ( b ). Introduction of the wild-type Bel gene rescued the bentazon- and sulfonylurea-sensitive phenotype of bel ( a ) mutant. On the other hand, expression of antisense Bel in W6154S induced a mutant phenotype. Based on these results we conclude that the novel cytochrome P450 monooxygenase CYP81A6 encoded by Bel confers resistance to two different classes of herbicides.	bel|CYP81A6|bsl
A novel rice cytochrome P450 gene, CYP72A31, confers tolerance to acetolactate synthase-inhibiting herbicides in rice and Arabidopsis	2014	Plant Physiol	Agrogenomics Research Center, National Institute of Agrobiological Sciences	Target-site and non-target-site herbicide tolerance are caused by the prevention of herbicide binding to the target enzyme and the reduction to a non-lethal dose of herbicide reaching the target enzyme, respectively. There is little information on the molecular mechanisms involved in non-target-site herbicide tolerance, although it poses the greater threat in the evolution of herbicide-resistant weeds and could potentially be useful for the production of herbicide-tolerant crops because it is often involved in tolerance to multi-herbicides. Bispyribac sodium (BS) is a herbicide that inhibits the activity of acetolactate synthase (ALS). Rice of the indica variety show BS tolerance while japonica rice varieties are BS sensitive. Map-based cloning and complementation tests revealed that a novel cytochrome P450 monooxygenase, CYP72A31, is involved in BS tolerance. Interestingly, BS tolerance was correlated with CYP72A31 mRNA levels in transgenic plants of rice and Arabidopsis. Moreover, Arabidopsis overexpressing CYP72A31 showed tolerance to bensulfuron-methyl (BSM), which belongs to a different class of ALS-inhibiting herbicides, suggesting that CYP72A31 can metabolize BS and BSM to a compound with reduced phytotoxicity. On the other hand, we showed that the cytochrome P450 monooxygenase CYP81A6, which has been reported to confer BSM tolerance, is barely involved, if at all, in BS tolerance, suggesting that the CYP72A31 enzyme has different herbicide specificities compared to CYP81A6. Thus, the CYP72A31 gene is a potentially useful genetic resource in the field of weed control, herbicide development, and molecular breeding in broad range of crop species.	bel|CYP81A6|bsl,CYP72A31
Suppression of a NAC-like transcription factor gene improves boron-toxicity tolerance in rice	2011	Plant Physiol	Laboratory of Plant Nutrition, Division of Applied Life Sciences, Graduate School of Agriculture, Kyoto University, Kyoto 606-8502, Japan.	We identified a gene responsible for tolerance to boron (B) toxicity in rice (Oryza sativa), named BORON EXCESS TOLERANT1. Using recombinant inbred lines derived from the B-toxicity-sensitive indica-ecotype cultivar IR36 and the tolerant japonica-ecotype cultivar Nekken 1, the region responsible for tolerance to B toxicity was narrowed to 49 kb on chromosome 4. Eight genes are annotated in this region. The DNA sequence in this region was compared between the B-toxicity-sensitive japonica cultivar Wataribune and the B-toxicity-tolerant japonica cultivar Nipponbare by eco-TILLING analysis and revealed a one-base insertion mutation in the open reading frame sequence of the gene Os04g0477300. The gene encodes a NAC (NAM, ATAF, and CUC)-like transcription factor and the function of the transcript is abolished in B-toxicity-tolerant cultivars. Transgenic plants in which the expression of Os04g0477300 is abolished by RNA interference gain tolerance to B toxicity.	BET1
Genetic control of a transition from black to straw-white seed hull in rice domestication	2011	Plant Physiol	National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China.	The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter. A 22-bp deletion within exon 3 of the bh4 variant disrupted the Bh4 function, leading to the straw-white hull in cultivated rice. Transgenic study indicated that Bh4 could restore the black pigment on hulls in cv Guangluai 4 and Kasalath. Bh4 sequence alignment of all taxa with the outgroup Oryza barthii showed that the wild rice maintained comparable levels of nucleotide diversity that were about 70 times higher than those in the cultivated rice. The results from the maximum likelihood Hudson-Kreitman-Aguade test suggested that the significant reduction in nucleotide diversity in rice cultivars could be caused by artificial selection. We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication.	Bh4
The role of Bh4 in parallel evolution of hull colour in domesticated and weedy rice	2013	J Evol Biol	Department of Biology, Washington University, St. Louis, MO, USA.	The two independent domestication events in the genus Oryza that led to African and Asian rice offer an extremely useful system for studying the genetic basis of parallel evolution. This system is also characterized by parallel de-domestication events, with two genetically distinct weedy rice biotypes in the US derived from the Asian domesticate. One important trait that has been altered by rice domestication and de-domestication is hull colour. The wild progenitors of the two cultivated rice species have predominantly black-coloured hulls, as does one of the two U.S. weed biotypes; both cultivated species and one of the US weedy biotypes are characterized by straw-coloured hulls. Using Black hull 4 (Bh4) as a hull colour candidate gene, we examined DNA sequence variation at this locus to study the parallel evolution of hull colour variation in the domesticated and weedy rice system. We find that independent Bh4-coding mutations have arisen in African and Asian rice that are correlated with the straw hull phenotype, suggesting that the same gene is responsible for parallel trait evolution. For the U.S. weeds, Bh4 haplotype sequences support current hypotheses on the phylogenetic relationship between the two biotypes and domesticated Asian rice; straw hull weeds are most similar to indica crops, and black hull weeds are most similar to aus crops. Tests for selection indicate that Asian crops and straw hull weeds deviate from neutrality at this gene, suggesting possible selection on Bh4 during both rice domestication and de-domestication.	Bh4
Analysis of transcriptional and upstream regulatory sequence activity of two environmental stress-inducible genes, NBS-Str1 and BLEC-Str8, of rice	2012	Transgenic Res	Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi, 110021, India.	Two abiotic stress-inducible upstream regulatory sequences (URSs) from rice have been identified and functionally characterized in rice. NBS-Str1 and BLEC-Str8 genes have been identified, by analysing the transcriptome data of cold, salt and desiccation stress-treated 7-day-old rice (Oryza sativa L. var. IR64) seedling, to be preferentially responsive to desiccation and salt stress, respectively. NBS-Str1 and BLEC-Str8 genes code for putative NBS (nucleotide binding site)-LRR (leucine rich repeat) and beta-lectin domain protein, respectively. NBS-Str1 URS is induced in root tissue, preferentially in vascular bundle, during 3 and 24 h of desiccation stress condition in transgenic 7-day-old rice seedling. In mature transgenic plants, this URS shows induction in root and shoot tissue under desiccation stress as well as under prolonged (1 and 2 day) salt stress. BLEC-Str8 URS shows basal activity under un-stressed condition, however, it is inducible under salt stress condition in both root and leaf tissues in young seedling and mature plants. Activity of BLEC-Str8 URS has been found to be vascular tissue preferential, however, under salt stress condition its activity is also found in the mesophyll tissue. NBS-Str1 and BLEC-Str8 URSs are inducible by heavy metal, copper and manganese. Interestingly, both the URSs have been found to be non responsive to ABA treatment, implying them to be part of ABA-independent abiotic stress response pathway. These URSs could prove useful for expressing a transgene in a stress responsive manner for development of stress tolerant transgenic systems.	BLEC-Str8
Identification and mapping of two brown planthopper resistance genes in rice	2001	TAG Theoretical and Applied Genetics	College of Life Sciences, Wuhan University, Wuhan 430072, China, CN	The brown planthopper (BPH) is one of the most serious insect pests of rice. In this study, we conducted a molecular marker-based genetic analysis of the BPH resistance of ’B5’, a highly resistant line that derived its resistant genes from the wild rice Oryza officinalis. Insect resistance was evaluated using 250 F3 families from a cross between ’B5’ and ’Minghui 63’, based on which the resistance of each F2 plant was inferred. Two bulks were made by mixing, respectively, DNA samples from highly resistant plants and highly susceptible plants selected from the F2 population. The bulks were surveyed for restriction fragment length polymorphism using probes representing all 12 chromosomes at regular intervals. The survey revealed two genomic regions on chromosome 3 and chromosome 4 respectively that contained genes for BPH resistance. The existence of the two loci were further assessed by QTL (quantitative trait locus) analysis, which resolved these two loci to a 14.3-cM interval on chromosome 3 and a 0.4-cM interval on chromosome 4. Comparison of the chromosomal locations and reactions to BPH biotypes indicated that these two genes are different from at least nine of the ten previously identified BPH resistance genes. Both of the genes had large effects on BPH resistance and the two loci acted essentially independent of each other in determining t he resistance. These two genes may be a useful BPH resistance resource for rice breeding programs.	Bph14
Identification and characterization of Bph14, a gene conferring resistance to brown planthopper in rice	2009	Proc Natl Acad Sci U S A	Key Laboratory of Ministry of Education for Plant Development Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China.	Planthoppers are highly destructive pests in crop production worldwide. Brown planthopper (BPH) causes the most serious damage of the rice crop globally among all rice pests. Growing resistant varieties is the most effective and environment-friendly strategy for protecting the crop from BPH. More than 19 BPH-resistance genes have been reported and used to various extents in rice breeding and production. In this study, we cloned Bph14, a gene conferring resistance to BPH at seedling and maturity stages of the rice plant, using a map-base cloning approach. We show that Bph14 encodes a coiled-coil, nucleotide-binding, and leucine-rich repeat (CC-NB-LRR) protein. Sequence comparison indicates that Bph14 carries a unique LRR domain that might function in recognition of the BPH insect invasion and activating the defense response. Bph14 is predominantly expressed in vascular bundles, the site of BPH feeding. Expression of Bph14 activates the salicylic acid signaling pathway and induces callose deposition in phloem cells and trypsin inhibitor production after planthopper infestation, thus reducing the feeding, growth rate, and longevity of the BPH insects. Our work provides insights into the molecular mechanisms of rice defense against insects and facilitates the development of resistant varieties to control this devastating insect.	Bph14
The Bphi008a gene interacts with the ethylene pathway and transcriptionally regulates MAPK genes in the response of rice to brown planthopper feeding	2011	Plant Physiol	State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, People's Republic of China.	We examined ways in which the Brown planthopper induced008a (Bphi008a; AY256682) gene of rice (Oryza sativa) enhances the plant's resistance to a specialist herbivore, the brown planthopper (BPH; Nilaparvata lugens). Measurement of the expression levels of ethylene synthases and of ethylene emissions showed that BPH feeding rapidly initiated the ethylene signaling pathway and up-regulated Bphi008a transcript levels after 6 to 96 h of feeding. In contrast, blocking ethylene transduction (using 1-methylcyclopropene) reduced Bphi008a transcript levels in wild-type plants fed upon by BPH. In vitro kinase assays showed that Bphi008a can be phosphorylated by rice Mitogen-activated Protein Kinase5 (OsMPK5), and yeast two-hybrid assays demonstrated that the carboxyl-terminal proline-rich region of Bphi008a interacts directly with this kinase. Furthermore, bimolecular fluorescence complementation assays showed that this interaction occurs in the nucleus. Subsequently, we found that Bphi008a up-regulation and down-regulation were accompanied by different changes in transcription levels of OsMPK5, OsMPK12, OsMPK13, and OsMPK17 in transgenic plants. Immunoblot analysis also showed that the OsMPK5 protein level increased in overexpressing plants and decreased in RNA interference plants after BPH feeding. In transgenic lines, changes in the expression levels of several enzymes that are important components of the defenses against the BPH were also observed. Finally, yeast two-hybrid screening results showed that Bphi008a is able to interact with a b-ZIP transcription factor (OsbZIP60) and a RNA polymerase polypeptide (SDRP).	Bphi008a,OsACO3,OsACO5|OsACO6,OsACO7,OsACS2,OsACS4,OS-ACS5|OsACS5,OsACS6,OsbZIP60,OsWJUMK1|OsMPK12|OsBWMK1,OsMPK13|OsBIMK2,OsMPK17,OsMSRMK2|OsMAP1|OsMPK5|OsMAPK2|OsMAPK5|OsBIMK1,SDRP
The Rice brassinosteroid-deficient dwarf2 mutant, defective in the rice homolog of Arabidopsis DIMINUTO/DWARF1, is rescued by the endogenously accumulated alternative bioactive brassinosteroid, dolichosterone	2005	Plant Cell	BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan.	We have identified a rice (Oryza sativa) brassinosteroid (BR)-deficient mutant, BR-deficient dwarf2 (brd2). The brd2 locus contains a single base deletion in the coding region of Dim/dwf1, a homolog of Arabidopsis thaliana DIMINUTO/DWARF1 (DIM/DWF1). Introduction of the wild-type Dim/dwf1 gene into brd2 restored the normal phenotype. Overproduction and repression of Dim/dwf1 resulted in contrasting phenotypes, with repressors mimicking the brd2 phenotype and overproducers having large stature with increased numbers of flowers and seeds. Although brd2 contains low levels of common 6-oxo-type BRs, the severity of the brd2 phenotype is much milder than brd1 mutants and most similar to d2 and d11, which show a semidwarf phenotype at the young seedling stage. Quantitative analysis suggested that in brd2, the 24-methylene BR biosynthesis pathway is activated and the uncommon BR, dolichosterone (DS), is produced. DS enhances the rice lamina joint bending angle, rescues the brd1 dwarf phenotype, and inhibits root elongation, indicating that DS is a bioactive BR in rice. Based on these observations, we discuss an alternative BR biosynthetic pathway that produces DS when Dim/dwf1 is defective.	brd2|DIM|DWF1
BRK1, a Bub1-related kinase, is essential for generating proper tension between homologous kinetochores at metaphase I of rice meiosis	2012	Plant Cell	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Bub1 (for budding uninhibited by benzimidazole 1), one of the main spindle checkpoint kinases, acts as a kinetochore scaffold for assembling other checkpoint proteins. Here, we identify a plant Bub1-related kinase 1 (BRK1) in rice (Oryza sativa). The brk1 mutants are sterile due to the precocious separation of sister chromatids at the onset of anaphase I. The centromeric recruitment of SHUGOSHIN1 and phosphorylation of histone H2A at Thr-134 (H2A-pT134) depend on BRK1. Although the homologs can faithfully separate from each other at the end of meiosis I, the uncorrected merotelic attachment of paired sister kinetochores at the early stage of metaphase I in brk1 reduces the tension across homologous kinetochores, causes the metaphase I spindle to be aberrantly shaped, and subsequently affects the synchronicity of homolog separation at the onset of anaphase I. In addition, the phosphorylation of inner centromeric histone H3 at Ser-10 (H3-pS10) during diakinesis depends on BRK1. Therefore, we speculate that BRK1 may be required for normal localization of Aurora kinase before the onset of metaphase I, which is responsible for correcting the merotelic attachment.	BRK1
BEAK LIKE SPIKELET1 is Required for Lateral Development of Lemma and Palea in Rice	2012	Plant Molecular Biology Reporter	National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China	Lemma and palea are unique floral structures found only in Poaceae, and are responsible for protecting the inner floral organs and kernels from environmental stresses. However, the mechanism underlying specification of their morphology remains unclear. In this study, we characterized a rice mutant, beak like spikelet1 (bls1), which specifically affects development of the lemma and palea. In bls1 mutant, floral-organ identity and floral-organ patterning are normal, and the defects occur at the stage of the lemma and palea expansion, whereas the other aspects of floral architecture and form are not affected. We isolated BLS1 by positional cloning and found that it encodes a protein with a conserved domain of unknown function. BLS1 is expressed strongly in young inflorescence, specifically the young lemmas and paleas of spikelets. Subcellular localization analysis showed that BLS1 is localized in the nucleus. Expression of the AP1-like and SEP-like floral homeotic genes were not changed in the bls1 mutant. Our study suggested that BLS1 is required for lateral development of the lemma and palea and does not function at stages of floral-organ initiation and patterning.	BLS1|BSG1
Beak-shaped grain 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice	2013	Sci China Life Sci	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	Grain shape and size both determine grain weight and therefore crop yield. However, the molecular mechanisms controlling grain shape and size are still largely unknown. Here, we isolated a rice mutant, beak-shaped grain1 (bsg1), which produced beak-shaped grains of decreased width, thickness and weight with a loosely interlocked lemma and palea that were unable to close tightly. Starch granules were also irregularly packaged in the bsg1 grains. Consistent with the lemma and palea shapes, the outer parenchyma cell layers of these bsg1 tissues developed fewer cells with decreased size. Map-based cloning revealed that BSG1 encoded a DUF640 domain protein, TRIANGULAR HULL 1, of unknown function. Quantitative PCR and GUS fusion reporter assays showed that BSG1 was expressed mainly in the young panicle and elongating stem. The BSG1 mutation affected the expression of genes potentially involved in the cell cycle and GW2, an important regulator of grain size in rice. Our results suggest that BSG1 determines grain shape and size probably by modifying cell division and expansion in the grain hull.	BLS1|BSG1,GW2
Screening for resistance against Pseudomonas syringae in rice-FOX Arabidopsis lines identified a putative receptor-like cytoplasmic kinase gene that confers resistance to major bacterial and fungal pathogens in Arabidopsis and rice	2011	Plant Biotechnol J	National Institute of Agrobiological Sciences, Tsukuba, Japan RIKEN, Plant Science Center, Yokohama, Japan.	Approximately 20,000 of the rice-FOX Arabidopsis transgenic lines, which overexpress 13,000 rice full-length cDNAs at random in Arabidopsis, were screened for bacterial disease resistance by dip inoculation with Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). The identities of the overexpressed genes were determined in 72 lines that showed consistent resistance after three independent screens. Pst DC3000 resistance was verified for 19 genes by characterizing other independent Arabidopsis lines for the same genes in the original rice-FOX hunting population or obtained by reintroducing the genes into ecotype Columbia by floral dip transformation. Thirteen lines of these 72 selections were also resistant to the fungal pathogen Colletotrichum higginsianum. Eight genes that conferred resistance to Pst DC3000 in Arabidopsis have been introduced into rice for overexpression, and transformants were evaluated for resistance to the rice bacterial pathogen, Xanthomonas oryzae pv. oryzae. One of the transgenic rice lines was highly resistant to Xanthomonas oryzae pv. oryzae. Interestingly, this line also showed remarkably high resistance to Magnaporthe grisea, the fungal pathogen causing rice blast, which is the most devastating rice disease in many countries. The causal rice gene, encoding a putative receptor-like cytoplasmic kinase, was therefore designated as BROAD-SPECTRUM RESISTANCE 1. Our results demonstrate the utility of the rice-FOX Arabidopsis lines as a tool for the identification of genes involved in plant defence and suggest the presence of a defence mechanism common between monocots and dicots.	BSR1
Expression profiling of starch metabolism-related plastidic translocator genes in rice	2006	Planta	CREST, Japan Science and Technology Corporation, Omiya, Saitama, Japan.	The genes encoding the major putative rice plastidic translocators involved in the carbon flow related to starch metabolism were identified by exhaustive database searches. The genes identified were two for the triose phosphate/phosphate translocator (TPT), five for the glucose 6-phosphate/phosphate translocator (GPT) including putatively non-functional ones, four for the phosphoenolpyruvate/phosphate translocator (PPT), three for the putative ADP-glucose translocator (or Brittle-1 protein, BT1), two for the plastidic nucleotide transport protein (NTT), and one each for the plastidic glucose translocator (pGlcT) and the maltose translocator (MT). The expression patterns of the genes in various photosynthetic and non-photosynthetic organs were examined by quantitative real-time PCR. OsBT1-1 was specifically expressed in the seed and its transcript level tremendously increased at the onset of vigorous starch production in the endosperm, suggesting that the ADP-glucose synthesized in the cytosol is a major precursor for starch biosynthesis in the endosperm amyloplast. In contrast, all of the genes for OsTPT, OsPPT, and OsNTT were mainly expressed in source tissues, suggesting that their proteins play essential roles in the regulation of carbohydrate metabolism in chloroplasts. Substantial expression of the four OsGPT genes and the OspGlcT gene in both source and sink organs suggests that the transport of glucose phosphate and glucose is physiologically important in both photosynthetic and non-photosynthetic tissues. The present study shows that comprehensive analysis of expression patterns of the plastidic translocator genes is a valuable tool for the elucidation of the functions of the translocators in the regulation of starch metabolism in rice.	OsBT1-1,OsMT,OsPGLCT,OsBT1-2,OsBT1-3,OsGPT2-3
H3K36 methylation is critical for brassinosteroid-regulated plant growth and development in rice	2012	Plant J	State Key Laboratory of Genetic Engineering, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200433, China.	Methylation of histone lysine residues plays an essential role in epigenetic regulation of gene expression in eukaryotes. Enzymes involved in establishment of the repressive H3K9 and H3K27 methylation marks have been previously characterized, but the deposition and function of H3K4 and H3K36 methylation remain uncharacterized in rice. Here, we report that rice SDG725 encodes a H3K36 methyltransferase, and its down-regulation causes wide-ranging defects, including dwarfism, shortened internodes, erect leaves and small seeds. These defects resemble the phenotypes previously described for some brassinosteroid-knockdown mutants. Consistently, transcriptome analyses revealed that SDG725 depletion results in down-regulation by more than two-fold of over 1000 genes, including D11, BRI1 and BU1, which are known to be involved in brassinosteroid biosynthesis or signaling pathways. Chromatin immunoprecipitation analyses showed that levels of H3K36me2/3 are reduced in chromatin at some regions of these brassinosteroid-related genes in SDG725 knockdown plants, and that SDG725 protein is able to directly bind to these target genes. Taken together, our data indicate that SDG725-mediated H3K36 methylation modulates brassinosteroid-related gene expression, playing an important role in rice plant growth and development.	BU1,D11|CYP724B1,D61|OsBRI1,SDG725
BRASSINOSTEROID UPREGULATED1, encoding a helix-loop-helix protein, is a novel gene involved in brassinosteroid signaling and controls bending of the lamina joint in rice	2009	Plant Physiol	Disease Resistance Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.	Brassinosteroids (BRs) are involved in many developmental processes and regulate many subsets of downstream genes throughout the plant kingdom. However, little is known about the BR signal transduction and response network in monocots. To identify novel BR-related genes in rice (Oryza sativa), we monitored the transcriptomic response of the brassinosteroid deficient1 (brd1) mutant, with a defective BR biosynthetic gene, to brassinolide treatment. Here, we describe a novel BR-induced rice gene BRASSINOSTEROID UPREGULATED1 (BU1), encoding a helix-loop-helix protein. Rice plants overexpressing BU1 (BU1:OX) showed enhanced bending of the lamina joint, increased grain size, and resistance to brassinazole, an inhibitor of BR biosynthesis. In contrast to BU1:OX, RNAi plants designed to repress both BU1 and its homologs displayed erect leaves. In addition, compared to the wild type, the induction of BU1 by exogenous brassinolide did not require de novo protein synthesis and it was weaker in a BR receptor mutant OsbriI (Oryza sativa brassinosteroid insensitive1, d61) and a rice G protein alpha subunit (RGA1) mutant d1. These results indicate that BU1 protein is a positive regulator of BR response: it controls bending of the lamina joint in rice and it is a novel primary response gene that participates in two BR signaling pathways through OsBRI1 and RGA1. Furthermore, expression analyses showed that BU1 is expressed in several organs including lamina joint, phloem, and epithelial cells in embryos. These results indicate that BU1 may participate in some other unknown processes modulated by BR in rice.	BU1,D1|RGA1,D61|OsBRI1
Loss-of-function of a rice brassinosteroid biosynthetic enzyme, C-6 oxidase, prevents the organized arrangement and polar elongation of cells in the leaves and stem	2002	The Plant Journal	BioScience Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan	Molecular genetic and physiological studies on brassinosteroid (BR)-related mutants of dicot plants have revealed that BRs play important roles in normal plant growth and development. However, little is known about the function of BR in monocots (grasses), except for the phenotypic analysis of a rice mutant partially insensitive to BR signaling. To investigate the function of BR in monocots, we identified and characterized BR-deficient mutants of rice, BR-deficient dwarf1 (brd1). The brd1 mutants showed a range of abnormalities in organ development and growth, the most striking of which were defects in the elongation of the stem and leaves. Light microscopic observations revealed that this abnormality was primarily owing to a failure in the organization and polar elongation of the leaf and stem cells. The accumulation profile of BR compounds in the brd1 mutants suggested that these plants may be deficient in the activity of BR C-6 oxidase. Therefore, we cloned a rice gene, OsDWARF, which has a high sequence similarity to the tomato C-6 oxidase gene, DWARF. Introduction of the wild-type OsDWARF gene into brd1 rescued the abnormal phenotype of the mutants. The OsDWARF gene was expressed at a low level in all of the examined tissues, with preferential expression in the leaf sheath, and the expression was negatively regulated by brassinolide treatment. On the basis of these findings, we discuss the biological function of BRs in rice plants.	OsDWARF
Isolation and characterization of a rice dwarf mutant with a defect in brassinosteroid biosynthesis	2002	Plant Physiol	Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan. morimasa@nias.affrc.go.jp	We have isolated a new recessive dwarf mutant of rice (Oryza sativa L. cv Nipponbare). Under normal growth conditions, the mutant has very short leaf sheaths; has short, curled, and frizzled leaf blades; has few tillers; and is sterile. Longitudinal sections of the leaf sheaths revealed that the cell length along the longitudinal axis is reduced, which explains the short leaf sheaths. Transverse sections of the leaf blades revealed enlargement of the motor cells along the dorsal-ventral axis, which explains the curled and frizzled leaf blades. In addition, the number of crown roots was smaller and the growth of branch roots was weaker than those in the wild-type plant. Because exogenously supplied brassinolide considerably restored the normal phenotypes, we designated the mutant brassinosteroid-dependent 1 (brd1). Further, under darkness, brd1 showed constitutive photomorphogenesis. Quantitative analyses of endogenous sterols and brassinosteroids (BRs) indicated that BR-6-oxidase, a BR biosynthesis enzyme, would be defective. In fact, a 0.2-kb deletion was detected in the genomic region of OsBR6ox (a rice BR-6-oxidase gene) in the brd1 mutant. These results indicate that BRs are involved in many morphological and physiological processes in rice, including the elongation and unrolling of leaves, development of tillers, skotomorphogenesis, root differentiation, and reproductive growth, and that the defect of BR-6-oxidase caused the brd1 phenotype.	OsDWARF
A CCCH-type zinc finger nucleic acid-binding protein quantitatively confers resistance against rice bacterial blight disease	2012	Plant Physiol	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.	Bacterial blight is a devastating disease of rice (Oryza sativa) caused by Xanthomonas oryzae pv oryzae (Xoo). Zinc finger proteins harboring the motif with three conserved cysteine residues and one histidine residue (CCCH) belong to a large family. Although at least 67 CCCH-type zinc finger protein genes have been identified in the rice genome, their functions are poorly understood. Here, we report that one of the rice CCCH-type zinc finger proteins, C3H12, containing five typical CX(8)-CX(5)-CX(3)-H zinc finger motifs, is involved in the rice-Xoo interaction. Activation of C3H12 partially enhanced resistance to Xoo, accompanied by the accumulation of jasmonic acid (JA) and induced expression of JA signaling genes in rice. In contrast, knockout or suppression of C3H12 resulted in partially increased susceptibility to Xoo, accompanied by decreased levels of JA and expression of JA signaling genes in rice. C3H12 colocalized with a minor disease resistance quantitative trait locus to Xoo, and the enhanced resistance of randomly chosen plants in the quantitative trait locus mapping population correlated with an increased expression level of C3H12. The C3H12 protein localized in the nucleus and possessed nucleic acid-binding activity in vitro. These results suggest that C3H12, as a nucleic acid-binding protein, positively and quantitatively regulates rice resistance to Xoo and that its function is likely associated with the JA-dependent pathway.	C3H12
The arbuscular mycorrhizal symbiosis promotes the systemic induction of regulatory defence-related genes in rice leaves and confers resistance to pathogen infection	2012	Mol Plant Pathol	Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Parc de Recerca UAB, Edifici CRAG, Campus UAB, Bellaterra (Cerdanyola del Valles), 08193, Barcelona, Spain.	Arbuscular mycorrhizal (AM) symbioses are mutualistic associations between soil fungi and most vascular plants. Their association benefits the host plant by improving nutrition, mainly phosphorus nutrition, and by providing increased capability to cope with adverse conditions. In this study, we investigated the transcriptional changes triggered in rice leaves as a result of AM symbiosis, focusing on the relevance of the plant defence response. We showed that root colonization by the AM fungus Glomus intraradices is accompanied by the systemic induction of genes that play a regulatory role in the host defence response, such as OsNPR1, OsAP2, OsEREBP and OsJAmyb. Genes involved in signal transduction processes (OsDUF26 and OsMPK6) and genes that function in calcium-mediated signalling processes (OsCBP, OsCaM and OsCML4) are also up-regulated in leaves of mycorrhizal rice plants in the absence of pathogen infection. In addition, the mycorrhizal rice plants exhibit a stronger induction of defence marker genes [i.e. pathogenesis-related (PR) genes] in their leaves in response to infection by the blast fungus Magnaporthe oryzae. Evidence indicates that mycorrhizal rice plants show enhanced resistance to the rice blast fungus. Overall, these results suggest that the protective effect of the AM symbiosis in rice plants relies on both the systemic activation of defence regulatory genes in the absence of pathogen challenge and the priming for stronger expression of defence effector genes during pathogen infection. The possible mechanisms involved in the mycorrhiza-induced resistance to M. oryzae infection are discussed.	OsCaM,OsCBP,OsDUF26
Collapsed abnormal pollen1 gene encoding the Arabinokinase-like protein is involved in pollen development in rice	2013	Plant Physiol	Department of Biological Production, Faculty of Bioresource Sciences, Akita Prefectural University, Akita 010-0195, Japan. uken@akita-pu.ac.jp	We isolated a pollen-defective mutant, collapsed abnormal pollen1 (cap1), from Tos17 insertional mutant lines of rice (Oryza sativa). The cap1 heterozygous plant produced equal numbers of normal and collapsed abnormal grains. The abnormal pollen grains lacked almost all cytoplasmic materials, nuclei, and intine cell walls and did not germinate. Genetic analysis of crosses revealed that the cap1 mutation did not affect female reproduction or vegetative growth. CAP1 encodes a protein consisting of 996 amino acids that showed high similarity to Arabidopsis (Arabidopsis thaliana) l-arabinokinase, which catalyzes the conversion of l-arabinose to l-arabinose 1-phosphate. A wild-type genomic DNA segment containing CAP1 restored mutants to normal pollen grains. During rice pollen development, CAP1 was preferentially expressed in anthers at the bicellular pollen stage, and the effects of the cap1 mutation were mainly detected at this stage. Based on the metabolic pathway of l-arabinose, cap1 pollen phenotype may have been caused by toxic accumulation of l-arabinose or by inhibition of cell wall metabolism due to the lack of UDP-l-arabinose derived from l-arabinose 1-phosphate. The expression pattern of CAP1 was very similar to that of another Arabidopsis homolog that showed 71% amino acid identity with CAP1. Our results suggested that CAP1 and related genes are critical for pollen development in both monocotyledonous and dicotyledonous plants.	CAP1,OsARA1
Isolation and characterization of cDNA clones encoding cdc2 homologues from Oryza sativa: a functional homologue and cognate variants	1992	Mol Gen Genet	National Institute of Agrobiological Resources, Ibaraki, Japan.	Using probes obtained by PCR amplification, we have isolated two cognate rice cDNAs (cdc2Os-1 and cdc2Os-2) encoding structural homologues of the cdc2+/CDC28 (cdc2) protein kinase from a cDNA library prepared from cultured rice cells. Comparison of the deduced amino acid sequences of cdc2Os-1 and cdc2Os-2 showed that they are 83% identical. They are 62% identical to CDC28 of Saccharomyces cerevisiae and much more similar to the yeast and mammalian p34cdc2 kinases than to rice R2, a cdc2-related kinase isolated previously by screening the same rice cDNA library with a different oligonucleotide probe. Southern blot analysis indicated that the three rice clones (cdc2Os-1, cdc2Os-2 and R2) are derived from distinct genes and are each found in a single copy per rice haploid genome. RNA blot analysis revealed that these genes are expressed in proliferating rice cells and in young rice seedlings. cdc2Os-1 could complement a temperature-sensitive yeast mutant of cdc28. However, despite the similarity in structure, both cdc2Os-2 and R2 were unable to complement the same mutant. Thus, the present results demonstrate the presence of structurally related, but functionally distinct cognates of the cdc2 cell cycle kinase in rice.	cdc2Os-1,cdc2Os-2,R2
Differential expression of genes for cyclin-dependent protein kinases in rice plants	1999	Plant Physiol	Institute of Molecular and Cellular Biosciences, University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-0032, Japan. mumeda@imcbns.iam.u-tokyo.ac.jp	Cyclin-dependent protein kinases (CDKs) play key roles in regulating the eukaryotic cell cycle. We have analyzed the expression of four rice (Oryza sativa) CDK genes, cdc2Os1, cdc2Os2, cdc2Os3, and R2, by in situ hybridization of sections of root apices. Transcripts of cdc2Os1, cdc2Os2, and R2 were detected uniformly in the dividing region of the root apex. cdc2Os1 and cdc2Os2 were also expressed in differentiated cells such as those in the sclerenchyma, pericycle, and parenchyma of the central cylinder. By contrast, signals corresponding to transcripts of cdc2Os3 were distributed only in patches in the dividing region. Counterstaining of sections with 4', 6-diamidino-2-phenylindole and double-target in situ hybridization with a probe for histone H4 transcripts revealed that cdc2Os3 transcripts were abundant from the G2 to the M phase, but were less abundant or absent during the S phase. The levels of the Cdc2Os3 protein and its associated histone H1-kinase activity were reduced by treatment of cultured cells with hydroxyurea, which blocks cycling cells at the onset of the S phase. Our results suggest that domains other than the conserved amino acid sequence (the PSTAIRE motif) have important roles in the function of non-PSTAIRE CDKs in distinct cell-cycle phases.	cdc2Os-1,cdc2Os-2,CDKB2;1|cdc2Os3,R2
A rice homolog of Cdk7/MO15 phosphorylates both cyclin-dependent protein kinases and the carboxy-terminal domain of RNA polymerase II	1998	The Plant Journal	Institute of Molecular and Cellular Biosciences, University of Tokyo, Japan.	The activation of cyclin-dependent protein kinases (CDKs) requires phosphorylation of a threonine residue within the T-loop by a CDK-activating kinase (CAK). The R2 protein of rice is very similar to CAKs of animals and fission yeast at the amino acid level but phosphorylation by R2 has not yet been demonstrated. When R2 was overexpressed in a CAK-deficient mutant of budding yeast, it suppressed the temperature sensitivity of the mutation. Immunoprecipitates of rice proteins with the anti-R2 antibody phosphorylated human CDK2, one of the rice CDKs (Cdc2Os1), and the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II of Arabidopsis. Mutational analysis indicated that R2 phosphorylated the threonine residue within the T-loop of CDK2 and Cdc2Os1. R2 was found mainly in two protein complexes which had molecular masses of 190 kDa and 70 kDa, respectively, whilst the CDK- and CTD-kinase activities associated with R2 were identified in a complex of 105 kDa. These results indicate that R2 is closely related to CAKs of animals and fission yeast in terms of its phosphorylation activity and, moreover, that this CAK of rice is distinct from a CAK of the dicotyledonous plant Arabidopsis.	cdc2Os-1,R2
Isolation and characterization of a rice cDNA encoding B1-type cyclin-dependent kinase	2006	Plant Biotechnology	Institute of Molecular and Cellular Biosciences, The University of Tokyo	Cyclin-dependent kinases (CDKs) are central players that control the cell cycle. In plants, A- and B-type CDKs are directly involved in cell cycle regulation. B-type CDK (CDKB) is unique to plants; however, only limited information on this kinase has been accumulated thus far. In the present study, we identified a rice cDNA encoding CDKB1;1 and studied its expression in suspension-cultured cells and plant tissues. We found that this enzyme was expressed in actively dividing cells in suspension cultures and was downregulated by the depletion of sucrose from the medium. In plants, the CDKB1;1 transcripts were highly expressed in the shoot and root apical meristems, but not in mature plant organs. These results suggested that CDKB1 is mainly involved in mitotic cell division during plant development.	CDKB1;1
CDKB2 is involved in mitosis and DNA damage response in rice	2012	Plant J	Plant Genome Engineering Research Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan.	DNA damage checkpoints delay mitotic cell-cycle progression in response to DNA stress, stalling the cell cycle to allow time for repair. CDKB is a plant-specific cyclin-dependent kinase (CDK) that is required for the G(2)/M transition of the cell cycle. In Arabidopsis, DNA damage leads the degradation of CDKB2, and the subsequent G(2) arrest gives cells time to repair damaged DNA. G(2) arrest also triggers transition from the mitotic cycle to endoreduplication, leading to the presence of polyploid cells in many tissues. In contrast, in rice (Oryza sativa), polyploid cells are found only in the endosperm. It was unclear whether endoreduplication contributes to alleviating DNA damage in rice (Oryza sativa). Here, we show that DNA damage neither down-regulates Orysa;CDKB2;1 nor induces endoreduplication in rice. Furthermore, we found increased levels of Orysa;CDKB2;1 protein upon DNA damage. These results suggest that CDKB2 functions differently in Arabidopsis and rice in response to DNA damage. Arabidopsis may adopt endoreduplication as a survival strategy under genotoxic stress conditions, but rice may enhance DNA repair capacity upon genotoxic stress. In addition, polyploid cells due to endomitosis were present in CDKB2;1 knockdown rice, suggesting an important role for Orysa;CDKB2;1 during mitosis.	CDKB2;1|cdc2Os3
An OsCEBiP/OsCERK1-OsRacGEF1-OsRac1 module is an essential early component of chitin-induced rice immunity	2013	Cell Host Microbe	Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.	OsCEBiP, a chitin-binding protein, and OsCERK1, a receptor-like kinase, are plasma membrane (PM) proteins that form a receptor complex essential for fungal chitin-driven immune responses in rice. The signaling events immediately following chitin perception are unclear. Investigating the spatiotemporal regulation of the rice small GTPase OsRac1, we find that chitin induces rapid activation of OsRac1 at the PM. Searching for OsRac1 interactors, we identified OsRacGEF1 as a guanine nucleotide exchange factor for OsRac1. OsRacGEF1 interacts with OsCERK1 and is activated when its C-terminal S549 is phosphorylated by the cytoplasmic domain of OsCERK1 in response to chitin. Activated OsRacGEF1 is required for chitin-driven immune responses and resistance to rice blast fungus infection. Further, a protein complex including OsCERK1 and OsRacGEF1 is transported from the endoplasmic reticulum to the PM. Collectively, our results suggest that OsCEBiP, OsCERK1, OsRacGEF1, and OsRac1 function as key components of a "defensome" critically engaged early during chitin-induced immunity.	CEBiP
Plant cells recognize chitin fragments for defense signaling through a plasma membrane receptor	2006	Proc Natl Acad Sci U S A	Department of Biochemistry, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan. kaku@isc.meiji.ac.jp	Chitin is a major component of fungal cell walls and serves as a molecular pattern for the recognition of potential pathogens in the innate immune systems of both plants and animals. In plants, chitin oligosaccharides have been known to induce various defense responses in a wide range of plant cells including both monocots and dicots. To clarify the molecular machinery involved in the perception and transduction of chitin oligosaccharide elicitor, a high-affinity binding protein for this elicitor was isolated from the plasma membrane of suspension-cultured rice cells. Characterization of the purified protein, CEBiP, as well as the cloning of the corresponding gene revealed that CEBiP is actually a glycoprotein consisting of 328 amino acid residues and glycan chains. CEBiP was predicted to have a short membrane spanning domain at the C terminus. Knockdown of CEBiP gene by RNA interference resulted in the suppression of the elicitor-induced oxidative burst as well as the gene responses, showing that CEBiP plays a key role in the perception and transduction of chitin oligosaccharide elicitor in the rice cells. Structural analysis of CEBiP also indicated the presence of two LysM motifs in the extracellular portion of CEBiP. As the LysM motif has been known to exist in the putative Nod-factor receptor kinases involved in the symbiotic signaling between leguminous plants and rhizobial bacteria, the result indicates the involvement of partially homologous plasma membrane proteins both in defense and symbiotic signaling in plant cells.	CEBiP
Perception of the chitin oligosaccharides contributes to disease resistance to blast fungus Magnaporthe oryzae in rice	2010	Plant J	Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.	Chitin is a component of fungal cell walls, and its fragments act as elicitors in many plants. The plasma membrane glycoprotein CEBiP, which possesses LysM domains, is a receptor for the chitin elicitor (CE) in rice. Here, we report that the perception of CE by CEBiP contributes to disease resistance against the rice blast fungus, Magnaporthe oryzae, and that enhanced responses to CE by engineering CEBiP increase disease tolerance. Knockdown of CEBiP expression allowed increased spread of the infection hyphae. To enhance defense responses to CE, we constructed chimeric genes composed of CEBiP and Xa21, which mediate resistance to rice bacterial leaf blight. The expression of either CRXa1 or CRXa3, each of which contains the whole extracellular portion of CEBiP, the whole intracellular domain of XA21, and the transmembrane domain from either CEBiP or XA21, induced cell death accompanied by an increased production of reactive oxygen and nitrogen species after treatment with CE. Rice plants expressing the chimeric receptor exhibited necrotic lesions in response to CE and became more resistant to M. oryzae. Deletion of the first LysM domain in CRXA1 abolished these cellular responses. These results suggest that CEs are produced and recognized through the LysM domain of CEBiP during the interaction between rice and M. oryzae and imply that engineering pattern recognition receptors represents a new strategy for crop protection against fungal diseases.	CEBiP
OsLYP4 and OsLYP6 play critical roles in rice defense signal transduction	2013	Plant Signal Behav	State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources; School of Life Sciences; Sun Yat-sen University; P.R. China.	Plant innate immunity relies on successful detection of trespassing pathogens through recognizing their microbe-associated molecular patterns (MAMPs) by pattern recognition receptors (PRRs) at the cell surface. We recently reported two rice lysin motif (LysM)-containing proteins, OsLYP4 and OsLYP6, as dual functional PRRs sensing bacterial peptidoglycan (PGN) and fungal chitin. Here we further demonstrated the important roles of OsLYP4 and OsLYP6 in rice defense signaling, as silencing of either LYP impaired the defense marker gene activation induced by either bacterial pathogen Xanthomonas oryzaecola or fungal pathogen Magnaporthe oryzae. Moreover, we found that OsLYP4 and OsLYP6 could form homo- and hetero-dimers, and could interact with CEBiP, suggesting an unexpected complexity of chitin perception in rice.	CEBiP,LYP4|OsLYP4,LYP6|OsLYP6
Effector-mediated suppression of chitin-triggered immunity by magnaporthe oryzae is necessary for rice blast disease	2012	Plant Cell	School of Biosciences, University of Exeter, Geoffrey Pope Building, Exeter EX4 4QD, United Kingdom.	Plants use pattern recognition receptors to defend themselves from microbial pathogens. These receptors recognize pathogen-associated molecular patterns (PAMPs) and activate signaling pathways that lead to immunity. In rice (Oryza sativa), the chitin elicitor binding protein (CEBiP) recognizes chitin oligosaccharides released from the cell walls of fungal pathogens. Here, we show that the rice blast fungus Magnaporthe oryzae overcomes this first line of plant defense by secreting an effector protein, Secreted LysM Protein1 (Slp1), during invasion of new rice cells. We demonstrate that Slp1 accumulates at the interface between the fungal cell wall and the rice plasma membrane, can bind to chitin, and is able to suppress chitin-induced plant immune responses, including generation of reactive oxygen species and plant defense gene expression. Furthermore, we show that Slp1 competes with CEBiP for binding of chitin oligosaccharides. Slp1 is required by M. oryzae for full virulence and exerts a significant effect on tissue invasion and disease lesion expansion. By contrast, gene silencing of CEBiP in rice allows M. oryzae to cause rice blast disease in the absence of Slp1. We propose that Slp1 sequesters chitin oligosaccharides to prevent PAMP-triggered immunity in rice, thereby facilitating rapid spread of the fungus within host tissue.	CEBiP
CERK1, a LysM receptor kinase, is essential for chitin elicitor signaling in Arabidopsis	2007	Proc Natl Acad Sci U S A	Department of Life Sciences, Faculty of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan.	Chitin is a major component of fungal cell walls and serves as a microbe-associated molecular pattern (MAMP) for the detection of various potential pathogens in innate immune systems of both plants and animals. We recently showed that chitin elicitor-binding protein (CEBiP), plasma membrane glycoprotein with LysM motifs, functions as a cell surface receptor for chitin elicitor in rice. The predicted structure of CEBiP does not contain any intracellular domains, suggesting that an additional component(s) is required for signaling through the plasma membrane into the cytoplasm. Here, we identified a receptor-like kinase, designated CERK1, which is essential for chitin elicitor signaling in Arabidopsis. The KO mutants for CERK1 completely lost the ability to respond to the chitin elicitor, including MAPK activation, reactive oxygen species generation, and gene expression. Disease resistance of the KO mutant against an incompatible fungus, Alternaria brassicicola, was partly impaired. Complementation with the WT CERK1 gene showed cerk1 mutations were responsible for the mutant phenotypes. CERK1 is a plasma membrane protein containing three LysM motifs in the extracellular domain and an intracellular Ser/Thr kinase domain with autophosphorylation/myelin basic protein kinase activity, suggesting that CERK1 plays a critical role in fungal MAMP perception in plants.	CEBiP
Two LysM receptor molecules, CEBiP and OsCERK1, cooperatively regulate chitin elicitor signaling in rice	2010	Plant J	Department of Life Sciences, Faculty of Agriculture, Meiji University, Kawasaki, Kanagawa, Japan.	Chitin is a major molecular pattern for various fungi, and its fragments, chitin oligosaccharides, are known to induce various defense responses in plant cells. A plasma membrane glycoprotein, CEBiP (chitin elicitor binding protein) and a receptor kinase, CERK1 (chitin elicitor receptor kinase) (also known as LysM-RLK1), were identified as critical components for chitin signaling in rice and Arabidopsis, respectively. However, it is not known whether each plant species requires both of these two types of molecules for chitin signaling, nor the relationships between these molecules in membrane signaling. We report here that rice cells require a LysM receptor-like kinase, OsCERK1, in addition to CEBiP, for chitin signaling. Knockdown of OsCERK1 resulted in marked suppression of the defense responses induced by chitin oligosaccharides, indicating that OsCERK1 is essential for chitin signaling in rice. The results of a yeast two-hybrid assay indicated that both CEBiP and OsCERK1 have the potential to form hetero- or homo-oligomers. Immunoprecipitation using a membrane preparation from rice cells treated with chitin oligosaccharides suggested the ligand-induced formation of a receptor complex containing both CEBiP and OsCERK1. Blue native PAGE and chemical cross-linking experiments also suggested that a major portion of CEBiP exists as homo-oligomers even in the absence of chitin oligosaccharides.	CEBiP,OsCERK1
Functional characterization of CEBiP and CERK1 homologs in arabidopsis and rice reveals the presence of different chitin receptor systems in plants	2012	Plant Cell Physiol	Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa, 214-8571 Japan.	Chitin is a representative microbe-associated molecular pattern (MAMP) molecule for various fungi and induces immune responses in many plant species. It has been clarified that the chitin signaling in rice requires a receptor kinase OsCERK1 and a receptor-like protein (Os)CEBiP, which specifically binds chitin oligosaccharides. On the other hand, Arabidopsis requires a receptor kinase (At)CERK1 for chitin signaling but it is not clear whether the plant also requires a CEBiP-like molecule for chitin perception/signaling. To clarify the similarity/difference of the chitin receptor in these two model plants, we first characterized CEBiP homologs in Arabidopsis. Only one of three CEBiP homologs, AtCEBiP (LYM2), showed a high-affinity binding for chitin oligosaccharides similar to rice CEBiP. AtCEBiP also represented the major chitin-binding protein in the Arabidopsis membrane. However, the single/triple knockout (KO) mutants of Arabidopsis CEBiP homologs and the overexpressor of AtCEBiP showed chitin-induced defense responses similar to wild-type Arabidopsis, indicating that AtCEBiP is biochemically functional as a chitin-binding protein but does not contribute to signaling. Studies of the chitin binding properties of the ectodomains of At/OsCERK1 and the chimeric receptors consisting of ecto/cytosolic domains of these molecules indicated that AtCERK1 is sufficient for chitin perception by itself.	CEBiP
CFL1, a WW domain protein, regulates cuticle development by modulating the function of HDG1, a class IV homeodomain transcription factor, in rice and Arabidopsis	2011	Plant Cell	State Key Laboratory for Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, People's Republic of China.	Plants have a chemically heterogeneous lipophilic layer, the cuticle, which protects them from biotic and abiotic stresses. The mechanisms that regulate cuticle development are poorly understood. We identified a rice (Oryza sativa) dominant curly leaf mutant, curly flag leaf1 (cfl1), and cloned CFL1, which encodes a WW domain protein. We overexpressed both rice and Arabidopsis CFL1 in Arabidopsis thaliana; these transgenic plants showed severely impaired cuticle development, similar to that in cfl1 rice. Reduced expression of At CFL1 resulted in reinforcement of cuticle structure. At CFL1 was predominantly expressed in specialized epidermal cells and in regions where dehiscence and abscission occur. Biochemical evidence showed that At CFL1 interacts with HDG1, a class IV homeodomain-leucine zipper transcription factor. Suppression of HDG1 function resulted in similar defective cuticle phenotypes in wild-type Arabidopsis but much alleviated phenotypes in At cfl1-1 mutants. The expression of two cuticle development-associated genes, BDG and FDH, was downregulated in At CFL1 overexpressor and HDG1 suppression plants. HDG1 binds to the cis-element L1 box, which exists in the regulatory regions of BDG and FDH. Our results suggest that rice and Arabidopsis CFL1 negatively regulate cuticle development by affecting the function of HDG1, which regulates the downstream genes BDG and FDH.	CFL1
CHIMERIC FLORAL ORGANS1, encoding a monocot-specific MADS box protein, regulates floral organ identity in rice	2012	Plant Physiol	Rice Research Institute , Southwest University, Chongqing 400715, China.	The control of floral organ identity by homeotic MADS box genes is well established in eudicots. However, grasses have highly specialized outer floral organs, and the identities of the genes that regulate the highly specialized outer floral organs of grasses remain unclear. In this study, we characterized a MIKC-type MADS box gene, CHIMERIC FLORAL ORGANS (CFO1), which plays a key role in the regulation of floral organ identity in rice (Oryza sativa). The cfo1 mutant displayed defective marginal regions of the palea, chimeric floral organs, and ectopic floral organs. Map-based cloning demonstrated that CFO1 encoded the OsMADS32 protein. Phylogenetic analysis revealed that CFO1/OsMADS32 belonged to a monocot-specific clade in the MIKC-type MADS box gene family. The expression domains of CFO1 were mainly restricted to the marginal region of the palea and inner floral organs. The floral organ identity gene DROOPING LEAF (DL) was expressed ectopically in all defective organs of cfo1 flowers. Double mutant analysis revealed that loss of DL function mitigated some of the defects of floral organs in cfo1 flowers. We propose that the CFO1 gene plays a pivotal role in maintaining floral organ identity through negative regulation of DL expression.	CFO1|OsMADS32,DL
Rice cytokinin GATA transcription Factor1 regulates chloroplast development and plant architecture	2013	Plant Physiol	Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1.	Chloroplast biogenesis has been well documented in higher plants, yet the complex methods used to regulate chloroplast activity under fluctuating environmental conditions are not well understood. In rice (Oryza sativa), the CYTOKININ-RESPONSIVE GATA TRANSCRIPTION FACTOR1 (Cga1) shows increased expression following light, nitrogen, and cytokinin treatments, while darkness and gibberellin reduce expression. Strong overexpression of Cga1 produces dark green, semidwarf plants with reduced tillering, whereas RNA interference knockdown results in reduced chlorophyll and increased tillering. Coexpression, microarray, and real-time expression analyses demonstrate a correlation between Cga1 expression and the expression of important nucleus-encoded, chloroplast-localized genes. Constitutive Cga1 overexpression increases both chloroplast biogenesis and starch production but also results in delayed senescence and reduced grain filling. Growing the transgenic lines under different nitrogen regimes indicates potential agricultural applications for Cga1, including manipulation of biomass, chlorophyll/chloroplast content, and harvest index. These results indicate a conserved mechanism by which Cga1 regulates chloroplast development in higher plants.	Cga1
Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice	2014	Nature Genetics	National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China.	Grain chalkiness is a highly undesirable quality trait in the marketing and consumption of rice grain. However, the molecular basis of this trait is poorly understood. Here we show that a major quantitative trait locus (QTL), Chalk5, influences grain chalkiness, which also affects head rice yield and many other quality traits. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase (V-PPase) with inorganic pyrophosphate (PPi) hydrolysis and H+-translocation activity. Elevated expression of Chalk5 increases the chalkiness of the endosperm, putatively by disturbing the pH homeostasis of the endomembrane trafficking system in developing seeds, which affects the biogenesis of protein bodies and is coupled with a great increase in small vesicle-like structures, thus forming air spaces among endosperm storage substances and resulting in chalky grain. Our results indicate that two consensus nucleotide polymorphisms in the Chalk5 promoter in rice varieties might partly account for the differences in Chalk5 mRNA levels that contribute to natural variation in grain chalkiness.	Chalk5
Combined expression of chitinase and beta-1,3-glucanase genes in indica rice (Oryza sativa L.) enhances resistance against Rhizoctonia solani	2008	Plant Science	Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar, Madurai 625021, Tamil Nadu, India	Agrobacterium-mediated transformation of rice was done using the binary vector pNSP3, harbouring the rice chitinase (chi11) gene under maize ubiquitin promoter and the tobacco beta-1,3-glucanase gene under CaMV 35S promoter in the same T-DNA. Four of the six T0 plants had single copies of complete T-DNAs, while the other two had complex integration patterns. Three of the four single-copy lines showed a 3:1 segregation ratio in the T1 generation. Northern and western blot analyses of T1 plants revealed constitutive expression of chitinase and beta-1,3-glucanase genes. Homozygous T2 plants of the single-copy lines CG20, CG27 and CG53 showed 62-, 9.6- and 11-fold higher chitinase activity over the control plants. beta-1,3-Glucanase activity was 1.1- to 2.5-fold higher in the transgenic plants. Bioassay of homozygous T2 plants of the three single-copy transgenic lines against Rhizoctonia solani revealed a 60% reduction in sheath blight Disease Index in the first week. The Disease Index increased from 61.8 in the first week to 90.6 in the third week in control plants, while it remained low (26.8–34.2) in the transgenic T3 plants in the corresponding period, reflecting the persistence of sheath blight resistance for a longer period.	chi11
Mendel's green cotyledon gene encodes a positive regulator of the chlorophyll-degrading pathway	2007	Proc Natl Acad Sci U S A	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.	Mutants that retain greenness of leaves during senescence are known as "stay-green" mutants. The most famous stay-green mutant is Mendel's green cotyledon pea, one of the mutants used in determining the law of genetics. Pea plants homozygous for this recessive mutation (known as i at present) retain greenness of the cotyledon during seed maturation and of leaves during senescence. We found tight linkage between the I locus and stay-green gene originally found in rice, SGR. Molecular analysis of three i alleles including one with no SGR expression confirmed that the I gene encodes SGR in pea. Functional analysis of sgr mutants in pea and rice further revealed that leaf functionality is lowered despite a high chlorophyll a (Chl a) and chlorophyll b (Chl b) content in the late stage of senescence, suggesting that SGR is primarily involved in Chl degradation. Consistent with this observation, a wide range of Chl-protein complexes, but not the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) large subunit, were shown to be more stable in sgr than wild-type plants. The expression of OsCHL and NYC1, which encode the first enzymes in the degrading pathways of Chl a and Chl b, respectively, was not affected by sgr in rice. The results suggest that SGR might be involved in activation of the Chl-degrading pathway during leaf senescence through translational or posttranslational regulation of Chl-degrading enzymes.	OsCHL
Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development	2006	Plant Mol Biol	Department of Plant Science, Seoul National University, Seoul, 151-921, Republic of Korea.	Photosynthetic organisms exhibit a green color due to the accumulation of chlorophyll pigments in chloroplasts. Mg-protoporphyrin IX chelatase (Mg-chelatase) comprises three subunits (ChlH, ChlD and ChlI) and catalyzes the insertion of Mg(2+) into protoporphyrin IX, the last common intermediate precursor in both chlorophyll and heme biosyntheses, to produce Mg-protoporphyrin IX (MgProto). Chlorophyll deficiency in higher plants results in chlorina (yellowish-green) phenotype. To date, 10 chlorina (chl) mutants have been isolated in rice, but the corresponding genes have not yet been identified. Rice Chl1 and Chl9 genes were mapped to chromosome 3 and isolated by map-based cloning. A missense mutation occurred in a highly conserved amino acid of ChlD in the chl1 mutant and ChlI in the chl9 mutant. Ultrastructural analyses have revealed that the grana are poorly stacked, resulting in the underdevelopment of chloroplasts. In the seedlings fed with aminolevulinate-dipyridyl in darkness, MgProto levels in the chl1 and chl9 mutants decreased up to 25% and 31% of that in wild-type, respectively, indicating that the Mg-chelatase activity is significantly reduced, causing the eventual decrease in chlorophyll synthesis. Furthermore, Northern blot analysis indicated that the nuclear genes encoding the three subunits of Mg-chelatase and LhcpII in chl1 mutant are expressed about 2-fold higher than those in WT, but are not altered in the chl9 mutant. This result indicates that the ChlD subunit participates in negative feedback regulation of plastid-to-nucleus in the expression of nuclear genes encoding chloroplast proteins, but not the ChlI subunit.	Chl1|OsChlD,Chl9|OsChlI
CHD3 protein recognizes and regulates methylated histone H3 lysines 4 and 27 over a subset of targets in the rice genome	2012	Proc Natl Acad Sci U S A	National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.	Histone lysine methylation is an important component of the epigenetic system demarcating transcriptionally active and inactive chromatin domains. It is of primary importance in understanding how different histone lysine methylation marks and a specific combination of them are read and interpreted by chromatin proteins to regulate gene expression. In this paper, we report that the rice CHD3 protein CHR729 that was required for many aspects of plant development can interact with dimethylated histone H3 lysine 4 (H3K4me2, a mark associated with moderately expressed or repressed genes) and with trimethylated histone H3 lysine 27 (H3K27me3, a mark associated with repressed genes), respectively, through the chromodomains and the plant homeodomain (PHD) finger of the protein. A mutation or down-regulation of the gene provoked a decrease of H3K27me3 and H3K4me3 (a mark associated with active genes). Genome-wide analysis revealed that H3K27me3 and H3K4me3, respectively, were lost from about 56 and 23% of marked loci, which correspond mostly to under-expressed or repressed genes. In the mutant, a higher-than-expected proportion of down-regulated genes lost H3K4me3, among which many encode DNA-binding transcription factors. These results suggest that the rice CHD3 protein is a bifunctional chromatin regulator able to recognize and modulate H3K4 and H3K27 methylation over repressed or tissue-specific genes, which may be associated with regulation of a gene transcription program of plant development.	CHR729|OsCHD3
Enhanced resistance to blast (Magnaporthe grisea) in transgenic Japonica rice by constitutive expression of rice chitinase	1999	Theor Appl Genet	National Institute of Agrobiological Resources, 2-1-2,Kannondai , Tsukuba, 305-8602, Japan, JP.	Rice blast is the most devastating plant disease in Japan. Our goal is to create new rice varieties which show enhanced resistance against blast, regardless of the race of blast. By an Agrobacterium-mediated transformation method, we reintroduced a rice class-I chitinase gene, Cht-2 or Cht-3, under the control of the enhanced CaMV 35S promoter and a hygromycin phosphotransferase gene, as a selection marker into the Japonica rice varieties Nipponbare and Koshihikari, which have retained the best popularity over a long period in Japan. In regenerated plants (R(0)), the Cht-2 product was found to accumulate intracellularly whereas the Cht-3 product was found to be targeted extracellularly. The transgenic rice plants which constitutively expressed either chitinase gene showed significantly higher resistance against the rice blast pathogen Magnaporthe grisea races 007.0 and 333. Both high-level expression of the chitinase and blast-resistance were stably inherited by the next generation in several lines.	Cht-2,Cht-3
Identification and characterization of two new members of the GRAS gene family in rice responsive to N-acetylchitooligosaccharide elicitor	2003	Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression	State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Zi Jin Harbor Campus, Yu Hang Tang Road 388, Hangzhou 310058, China	None	CIGR1,CIGR2,SLR1|OsGAI
A rice virescent-yellow leaf mutant reveals new insights into the role and assembly of plastid caseinolytic protease in higher plants	2013	Plant Physiol	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, People's Republic of China.	The plastidic caseinolytic protease (Clp) of higher plants is an evolutionarily conserved protein degradation apparatus composed of a proteolytic core complex (the P and R rings) and a set of accessory proteins (ClpT, ClpC, and ClpS). The role and molecular composition of Clps in higher plants has just begun to be unraveled, mostly from studies with the model dicotyledonous plant Arabidopsis (Arabidopsis thaliana). In this work, we isolated a virescent yellow leaf (vyl) mutant in rice (Oryza sativa), which produces chlorotic leaves throughout the entire growth period. The young chlorotic leaves turn green in later developmental stages, accompanied by alterations in chlorophyll accumulation, chloroplast ultrastructure, and the expression of chloroplast development- and photosynthesis-related genes. Positional cloning revealed that the VYL gene encodes a protein homologous to the Arabidopsis ClpP6 subunit and that it is targeted to the chloroplast. VYL expression is constitutive in most tissues examined but most abundant in leaf sections containing chloroplasts in early stages of development. The mutation in vyl causes premature termination of the predicted gene product and loss of the conserved catalytic triad (serine-histidine-aspartate) and the polypeptide-binding site of VYL. Using a tandem affinity purification approach and mass spectrometry analysis, we identified OsClpP4 as a VYL-associated protein in vivo. In addition, yeast two-hybrid assays demonstrated that VYL directly interacts with OsClpP3 and OsClpP4. Furthermore, we found that OsClpP3 directly interacts with OsClpT, that OsClpP4 directly interacts with OsClpP5 and OsClpT, and that both OsClpP4 and OsClpT can homodimerize. Together, our data provide new insights into the function, assembly, and regulation of Clps in higher plants.	OsClpP3,CLPP4,OsClpP5,VYL,CLPR4,v-ATP-E
COE1, an LRR-RLK responsible for commissural vein pattern formation in rice	2010	Plant J	Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan.	Summary Leaf veins have a complex network pattern. Formation of this vein pattern has been widely studied as a model of tissue pattern formation in plants. To understand the molecular mechanism governing the vascular patterning process, we isolated the rice mutant, commissural vein excessive1 (coe1). The coe1 mutants had short commissural vein (CV) intervals and produced clustered CVs. Application of 1-N-naphthylphthalamic acid and brefeldin A decreased CV intervals, and application of 1-naphthaleneacetic acid increased CV intervals in wild-type rice; however, coe1 mutants were insensitive to these chemicals. COE1 encodes a leucine-rich repeat receptor-like kinase, whose amino acid sequence is similar to that of brassinosteroid-insensitive 1-associated receptor kinase 1 (BAK1), and which is localized at the plasma membrane. Because of the sequence similarity of COE1 to BAK1, we also examined the involvement of brassinosteroids in CV formation. Brassinolide, an active brassinosteroid, decreased the CV intervals of wild-type rice, and brassinazole, an inhibitor of brassinosteroid biosynthesis, increased the CV intervals of wild-type rice, but coe1 mutants showed insensitivity to these chemicals. These results suggest that auxin and brassinosteroids regulate CV intervals in opposite directions, and COE1 may regulate CV intervals downstream of auxin and brassinosteroid signals.	COE1,OsBISERK1|OsSERK1|OsBAK1
OsCAD2 is the major CAD gene responsible for monolignol biosynthesis in rice culm	2012	Plant Cell Rep	Bioscience and Biotechnology Center, Nagoya University, Chikusa-ku, Nagoya, Aichi, Japan.	Cinnamyl alcohol dehydrogenase (CAD) catalyzes the last step of monolignol biosynthesis. The rice genome contains 12 CAD-like genes, and whereas the proteins encoded by OsCAD2 and OsCAD7 are known to function in monolignol biosynthesis, the degree to which these enzymes contribute to this process and the involvement of the enzymes encoded by the remaining ten genes is unclear. This paper investigates the role of OsCAD2 and the nine other OsCAD-like proteins in monolignol biosynthesis. Among the OsCAD genes analyzed, OsCAD2, an enzyme belonging to the bona fide CAD phylogenetic group, was the most abundantly expressed gene in the uppermost internode, and was expressed at levels that were more than seven times greater than those of the second most abundantly expressed gene, OsCAD1. Promoter-GUS analysis of OsCAD2 (pCAD::GUS) in the internode, sheath, and roots revealed that GUS expression was strong in tissues that accumulated high levels of lignin. Furthermore, expression always preceded lignin accumulation, showing the tight correlation between OsCAD2 expression and monolignol biosynthesis. Additionally, expression of pCAD::GUS was well synchronized with that of rice caffeic acid 3-O-methyltransferase (OsCOMT::GUS), suggesting that the two enzymes function cooperatively during monolignol biosynthesis. Co-expression network analysis of eight OsCAD genes further revealed that, among the OsCAD genes, expression of OsCAD2 was most tightly associated with the transcription of lignin biosynthesis-related genes. These results suggest that OsCAD2 is largely responsible for monolignol biosynthesis in rice, which is similar to that indicated for the predominant role of other plant bona fide CAD protein to monolignol biosynthesis.	COMT,GH2|OsCAD2
Flavonoid 3'-O-methyltransferase from rice: cDNA cloning, characterization and functional expression	2006	Phytochemistry	Bio/Molecular Informatics Center, Department of Molecular Biotechnology, Konkuk University, 1 Hwayang-dong, Kwangjin-gu, Seoul 143-701, Republic of Korea.	Plant O-methyltransferases (OMTs) are known to be involved in methylation of plant secondary metabolites, especially phenylpropanoid and flavonoid compounds. An OMT, ROMT-9, was cloned and characterized from rice using a reverse transcriptase polymerase chain reaction (RT-PCR). The blast results for ROMT-9 showed a 73% identity with caffeic acid OMTs from maize and Triticum aestivum. ROMT-9 was expressed in Escherichia coli and its recombinant protein was purified using affinity chromatography. It was then tested for its ability to transfer the methyl group of S-adenosyl-l-methionine to the flavonoid substrates, eriodictyol, luteolin, quercetin, and taxifolin, all of which have a 3'-hydroxyl functional group. The reaction products were analyzed using TLC, HPLC, HPLC/MS, and NMR spectroscopy. The NMR analysis showed that ROMT-9 transferred the methyl group specifically to the 3'-hydroxyl group of quercetin, resulting in the formation of its methoxy derivative. Furthermore, ROMT-9 converted flavonoids containing the 3'-hydroxy functional group such as eriodictyol, luteolin, quercetin and taxifolin into the corresponding methoxy derivatives, suggesting that ROMT-9 is an OMT with strict specificity for the 3'-hydroxy group of flavonoids.	COMT
Proteomic analysis of rice defense response induced by probenazole	2008	Phytochemistry	Institute of Plant and Microbial Biology, Academia Sinica, 128, Sec. 2, Academia Road, Taipei 11529, Taiwan.	Here, we report the first proteomic analysis of rice defense response induced by probenazole (PBZ), an agricultural chemical that has been widely used to protect rice plants from rice blast and the bacterial blight pathogen. Two-dimensional gel electrophoresis (2-DE) was utilized to identify a total of 40 protein spots including 9 protein spots that are up-regulated by PBZ and 31 abundant protein spots. A total of 11 unique proteins from these 9 spots were identified by LC-MS/MS, and the majority of them were classified and/or possessed orthologs in defense-related functions. Five protein spots with only one protein species identified in each spot appear to be PBZ-regulated proteins. They are a putative glutathione S-transferase GSTU17, a putative phenylalanine ammonia-lyase (PAL, XP_466843), a putative caffeic acid 3-O-methyltransferase (COMT), a putative NADH-ubiquinone oxidoreductase, and a putative glucose-1-phosphate adenyltransferase. However, the other six protein species identified from the remaining four protein spots could not be conclusively described as PBZ-regulated proteins due to either the co-migration of two protein species in one spot or the presence of one protein species in two spots. Through real-time reverse transcription polymerase chain reaction (RT-PCR), it was determined that PAL (XP_466843) is likely regulated at the protein level, whereas GSTU17 and COMT were regulated at the mRNA level after PBZ application. Interestingly, the mRNA transcripts of two PAL paralogs were found to be up-regulated by PBZ. We propose that PAL, COMT, and GSTU17 are likely to confer PBZ-induced disease resistance via such functions as biosynthesis and transport of flavonoid-type phytoalexin and/or lignin biogenesis.	COMT
Molecular and functional analyses of COPT/Ctr-type copper transporter-like gene family in rice	2011	BMC Plant Biol	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	BACKGROUND: The copper (Cu) transporter (COPT/Ctr) gene family has an important role in the maintenance of Cu homeostasis in different species. The rice COPT-type gene family consists of seven members (COPT1 to COPT7). However, only two, COPT1 and COPT5, have been characterized for their functions in Cu transport. RESULTS: Here we report the molecular and functional characterization of the other five members of the rice COPT gene family (COPT2, COPT3, COPT4, COPT6, and COPT7). All members of the rice COPT family have the conserved features of known COPT/Ctr-type Cu transporter genes. Among the proteins encoded by rice COPTs, COPT2, COPT3, and COPT4 physically interacted with COPT6, respectively, except for the known interaction between COPT1 and COPT5. COPT2, COPT3, or COPT4 cooperating with COPT6 mediated a high-affinity Cu uptake in the yeast Saccharomyces cerevisiae mutant that lacked the functions of ScCtr1 and ScCtr3 for Cu uptake. COPT7 alone could mediate a high-affinity Cu uptake in the yeast mutant. None of the seven COPTs alone or in cooperation could complement the phenotypes of S. cerevisiae mutants that lacked the transporter genes either for iron uptake or for zinc uptake. However, these COPT genes, which showed different tissue-specific expression patterns and Cu level-regulated expression patterns, were also transcriptionally influenced by deficiency of iron, manganese, or zinc. CONCLUSION: These results suggest that COPT2, COPT3, and COPT4 may cooperate with COPT6, respectively, and COPT7 acts alone for Cu transport in different rice tissues. The endogenous concentrations of iron, manganese, or zinc may influence Cu homeostasis by influencing the expression of COPTs in rice.	COPT1,COPT5
Expression profiling and bioinformatic analyses of a novel stress-regulated multispanning transmembrane protein family from cereals and Arabidopsis	2003	Plant Physiol	Departement des Sciences biologiques, Universite du Quebec a Montreal, Case Postale 8888, succursale Centre-ville, Canada H3C 3P8.	Cold acclimation is a multigenic trait that allows hardy plants to develop efficient tolerance mechanisms needed for winter survival. To determine the genetic nature of these mechanisms, several cold-responsive genes of unknown function were identified from cold-acclimated wheat (Triticum aestivum). To identify the putative functions and structural features of these new genes, integrated genomic approaches of data mining, expression profiling, and bioinformatic predictions were used. The analyses revealed that one of these genes is a member of a small family that encodes two distinct groups of multispanning transmembrane proteins. The cold-regulated (COR)413-plasma membrane and COR413-thylakoid membrane groups are potentially targeted to the plasma membrane and thylakoid membrane, respectively. Further sequence analysis of the two groups from different plant species revealed the presence of a highly conserved phosphorylation site and a glycosylphosphatidylinositol-anchoring site at the C-terminal end. No homologous sequences were found in other organisms suggesting that this family is specific to the plant kingdom. Intraspecies and interspecies comparative gene expression profiling shows that the expression of this gene family is correlated with the development of freezing tolerance in cereals and Arabidopsis. In addition, several members of the family are regulated by water stress, light, and abscisic acid. Structure predictions and comparative genome analyses allow us to propose that the cor413 genes encode putative G-protein-coupled receptors.	COR413-TM1|Oscor413-tm1,Oscor413-pm1
Identification of cDNA encoding cytochrome c oxidase subunit 5c (COX5c) from rice. Comparison of its expression with nuclear-encoded and mitochondrial-encoded COX genes	1999	Genes Genet Syst	Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo 	Little is presently known about the nuclear-encoded genes for cytochrome c oxidase (COX) in higher plants. In rice, only the nuclear-encoded COX5b gene has been reported. To understand the relationship between the expression of nuclear-encoded and mitochondrial-encoded COX genes in rice, we first characterized a cDNA encoding one of the other nuclear COX genes, COX5c, which encodes 63 amino acids. The deduced amino acid sequence of COX5c from rice was highly homologous to that from sweet potato. Genomic Southern hybridization indicated that the rice COX5c subunit is encoded by a single copy of the COX5c gene. Furthermore, we compared the expression patterns of the nuclear-encoded COX5c and COX5b genes with the expression pattern of the mitochondrial-encoded COX1 gene among several organs by Northern blot analysis. The results suggested that regulatory systems of expression between the nuclear-encoded and the mitochondrial-encoded COX genes are different among different organs in rice.	COX5c,coxVb|COX5b
Low temperature treatment at the young microspore stage induces protein changes in rice anthers	2006	Molecular & Cellular Proteomics	Research Council Centre of Excellence for Integrative Legume Research, Research School of Biological Sciences, Australian National University, Canberra, Australian Capital Territory 0200, Australia.	Male reproductive development in rice is very sensitive to various forms of environmental stresses including low temperature. A few days of cold treatment (< 20 degrees C) at the young microspore stage induce severe pollen sterility and thus large grain yield reductions. To investigate this phenomenon, anther proteins at the early stages of microspore development, with or without cold treatment at 12 degrees C, were extracted, separated by two-dimensional gel electrophoresis, and compared. The cold-sensitive cultivar Doongara and the relatively cold-tolerant cultivar HSC55 were used. The abundance of 37 anther proteins was changed more than 2-fold after 1, 2, and 4 days of cold treatment in cv. Doongara. Among them, one protein was newly induced, 32 protein spots were up-regulated, and four protein spots were down-regulated. Of these 37 protein spots, we identified two anther-specific proteins (putative lipid transfer protein and Osg6B) and a calreticulin that were down-regulated and a cystine synthase, a beta-6 subunit of the 20 S proteasome, an H protein of the glycine cleavage system, cytochrome c oxidase subunit VB, an osmotin protein homologue, a putative 6-phospho-gluconolactonase, a putative adenylate kinase, a putative cysteine proteinase inhibitor, ribosomal protein S12E, a caffeoyl-CoA O-methyltransferase, and a monodehydroascorbate reductase that were up-regulated. Identification of these proteins is available upon request. Accumulation of these proteins did not vary greatly after cold treatment in panicles of cv. Doongara or in the anthers of the cv. HSC55. The newly induced protein named Oryza sativa cold-induced anther protein (OsCIA) was identified as an unknown protein. The OsCIA protein was detected in panicles, leaves, and seedling tissues under normal growth conditions. Quantitative real time RT-PCR analysis of OsCIA mRNA expression showed no significant change between low temperature-treated and untreated plants. A possible regulatory role for the newly induced protein is proposed.	coxVb|COX5b,OsCIA
Enhanced tolerance to chilling stress in OsMYB3R-2 transgenic rice is mediated by alteration in cell cycle and ectopic expression of stress genes	2009	Plant Physiol	Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	MYB transcription factors play central roles in plant responses to abiotic stresses. How stress affects development is poorly understood. Here, we show that OsMYB3R-2 functions in both stress and developmental processes in rice (Oryza sativa). Transgenic plants overexpressing OsMYB3R-2 exhibited enhanced cold tolerance. Cold treatment greatly induced the expression of OsMYB3R-2, which encodes an active transcription factor. We show that OsMYB3R-2 specifically bound to a mitosis-specific activator cis-element, (T/C)C(T/C)AACGG(T/C)(T/C)A, a conserved sequence that was found in promoters of cyclin genes such as OsCycB1;1 and OsKNOLLE2. In addition, overexpression of OsMYB3R-2 in rice led to higher transcript levels of several G2/M phase-specific genes, including OsCycB1;1, OsCycB2;1, OsCycB2;2, and OsCDC20.1, than those in OsMYB3R-2 antisense lines or wild-type plants in response to cold treatment. Flow cytometry analysis revealed an increased cell mitotic index in overexpressed transgenic lines of OsMYB3R-2 after cold treatment. Furthermore, resistance to cold stress in the transgenic plants overexpressing OsCycB1;1 was also enhanced. The level of cellular free proline was increased in the overexpressed rice lines of OsMYB3R-2 and OsCycB1;1 transgenic plants compared with wild-type plants under the cold treatment. These results suggest that OsMYB3R-2 targets OsCycB1;1 and regulates the progress of the cell cycle during chilling stress. OsCPT1, which may be involved in the dehydration-responsive element-binding factor 1A pathway, showed the same transcription pattern in response to cold as did OsCycB1;1 in transgenic rice. Therefore, a cold resistance mechanism in rice could be mediated by regulating the cell cycle, which is controlled by key genes including OsMYB3R-2.	CPT1,CycB1;1,OsMYB3R-2
The Rice COLEOPTILE PHOTOTROPISM1 gene encoding an ortholog of Arabidopsis NPH3 is required for phototropism of coleoptiles and lateral translocation of auxin	2005	Plant Cell	Botanical Gardens, Graduate School of Science, Osaka City University, Kisaichi, Katano-shi, Osaka 576-0004, Japan.	We isolated a mutant, named coleoptile phototropism1 (cpt1), from gamma-ray-mutagenized japonica-type rice (Oryza sativa). This mutant showed no coleoptile phototropism and severely reduced root phototropism after continuous stimulation. A map-based cloning strategy and transgenic complementation test were applied to demonstrate that a NPH3-like gene deleted in the mutant corresponds to CPT1. Phylogenetic analysis of putative CPT1 homologs of rice and related proteins indicated that CPT1 has an orthologous relationship with Arabidopsis thaliana NPH3. These results, along with those for Arabidopsis, demonstrate that NPH3/CPT1 is a key signal transduction component of higher plant phototropism. In an extended study with the cpt1 mutant, it was found that phototropic differential growth is accompanied by a CPT1-independent inhibition of net growth. Kinetic investigation further indicated that a small phototropism occurs in cpt1 coleoptiles. This response, induced only transiently, was thought to be caused by the CPT1-independent growth inhibition. The 3H-indole-3-acetic acid applied to the coleoptile tip was asymmetrically distributed between the two sides of phototropically responding coleoptiles. However, no asymmetry was induced in cpt1 coleoptiles, indicating that lateral translocation of auxin occurs downstream of CPT1. It is concluded that the CPT1-dependent major phototropism of coleoptiles is achieved by lateral auxin translocation and subsequent growth redistribution.	CPT1
Central region component1, a novel synaptonemal complex component, is essential for meiotic recombination initiation in rice	2013	Plant Cell	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	In meiosis, homologous recombination entails programmed DNA double-strand break (DSB) formation and synaptonemal complex (SC) assembly coupled with the DSB repair. Although SCs display extensive structural conservation among species, their components identified are poorly conserved at the sequence level. Here, we identified a novel SC component, designated central region component1 (CRC1), in rice (Oryza sativa). CRC1 colocalizes with ZEP1, the rice SC transverse filament protein, to the central region of SCs in a mutually dependent fashion. Consistent with this colocalization, CRC1 interacts with ZEP1 in yeast two-hybrid assays. CRC1 is orthologous to Saccharomyces cerevisiae pachytene checkpoint2 (Pch2) and Mus musculus THYROID receptor-interacting protein13 (TRIP13) and may be a conserved SC component. Additionally, we provide evidence that CRC1 is essential for meiotic DSB formation. CRC1 interacts with homologous pairing aberration in rice meiosis1 (PAIR1) in vitro, suggesting that these proteins act as a complex to promote DSB formation. PAIR2, the rice ortholog of budding yeast homolog pairing1, is required for homologous chromosome pairing. We found that CRC1 is also essential for the recruitment of PAIR2 onto meiotic chromosomes. The roles of CRC1 identified here have not been reported for Pch2 or TRIP13.	CRC1,PAIR1,PAIR2,ZEP1
The auxin responsive AP2/ERF transcription factor CROWN ROOTLESS5 is involved in crown root initiation in rice through the induction of OsRR1, a type-A response regulator of cytokinin signaling	2011	Plant J	Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.	Cytokinin is known to have negative effects on de novo auxin-induced root formation. However, the regulatory mechanisms of root initiation by both cytokinin and auxin are poorly understood. In this study, we characterized a rice mutant, termed crown rootless5 (crl5), which produced fewer crown roots and displayed impaired initiation of crown root primordia. The expression of CRL5, which encodes a member of the large AP2/ERF transcription factor family protein, was observed in the stem region where crown root initiation occurs. Exogenous auxin treatment induced CRL5 expression without de novo protein biosynthesis, which also required the degradation of AUX/IAA proteins. A putative auxin response element in the CRL5 promoter region specifically interacted with a rice ARF, demonstrating that CRL5 may be a direct target of an ARF, similar to CRL1/ADVENTITIOUS ROOTLESS1 (ARL1) that also regulates crown root initiation. A crl1 crl5 double mutant displayed an additive phenotype, indicating that these two genes function in different genetic pathways for crown root initiation. In addition, ProACT:CRL5/WT showed a cytokinin-resistant phenotype for crown root initiation, and also up-regulated the expression of two negative regulators of cytokinin signaling, OsRR1 and OsRR2, which were downregulated in crl5. Transgenic plants that over-expressed OsRR1 under the control of the CRL5 promoter in a crl5 mutant background produced a higher number of crown roots than the crl5 plant. Taken together, these results indicate that auxin-induced CRL5 promotes crown root initiation through repression of cytokinin signaling by positively regulating type-A RR, OsRR1.	CRL1|ARL1,Crl5,OsRR1,OsRR2
Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants	2008	Cell Res	State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100094, China.	WRKY transcription factors have many regulatory roles in response to biotic and abiotic stresses. In this study, we isolated a rice WRKY gene (OsWRKY31) that is induced by the rice blast fungus Magnaporthe grisea and auxin. This gene encodes a polypeptide of 211 amino-acid residues and belongs to a subgroup of the rice WRKY gene family that probably originated after the divergence of monocot and dicot plants. OsWRKY31 was found to be localized to the nucleus of onion epidermis cells to transiently express OsWRKY31-eGFP fusion protein. Analysis of OsWRKY31 and its mutants fused with a Gal4 DNA-binding domain indicated that OsWRKY31 has transactivation activity in yeast. Overexpression of the OsWRKY31 gene was found to enhance resistance against infection with M. grisea, and the transgenic lines exhibited reduced lateral root formation and elongation compared with wild-type and RNAi plants. The lines with overexpression showed constitutive expression of many defense-related genes, such as PBZ1 and OsSci2, as well as early auxin-response genes, such as OsIAA4 and OsCrl1 genes. Furthermore, the plants with overexpression were less sensitive to exogenously supplied IBA, NAA and 2,4-D at high concentrations, suggesting that overexpression of the OsWRKY31 gene might alter the auxin response or transport. These results also suggest that OsWRKY31 might be a common component in the signal transduction pathways of the auxin response and the defense response in rice.	CRL1|ARL1,OsIAA4,OsPR10a|PBZ1,OsWRKY31,OsWRKY55|WRKY55a|WRKY55b
Studies on sodium bypass flow in lateral rootless mutants lrt1 and lrt2, and crown rootless mutant crl1 of rice (Oryza sativa L.)	2010	Plant Cell Environ	Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Brighton BN19QG, UK. B.Faiyue@sussex.ac.uk	An apoplastic pathway, the so-called bypass flow, is important for Na+ uptake in rice (Oryza sativa L.) under saline conditions; however, the precise site of entry is not yet known. We report the results of our test of the hypothesis that bypass flow of Na+ in rice occurs at the site where lateral roots emerge from the main roots. We investigated Na+ uptake and bypass flow in lateral rootless mutants (lrt1, lrt2), a crown rootless mutant (crl1), their wild types (Oochikara, Nipponbare and Taichung 65, respectively) and in seedlings of rice cv. IR36. The results showed that shoot Na+ concentration in lrt1, lrt2 and crl1 was lower (by 20-23%) than that of their wild types. In contrast, the bypass flow quantified using trisodium-8-hydroxy-1,3,6-pyrenetrisulphonic acid (PTS) was significantly increased in the mutants, from an average of 1.1% in the wild types to 3.2% in the mutants. Similarly, bypass flow in shoots of IR36 where the number of lateral and crown roots had been reduced through physical and hormonal manipulations was dramatically increased (from 5.6 to 12.5%) as compared to the controls. The results suggest that the path of bypass flow in rice is not at the sites of lateral root emergence.	CRL1|ARL1
ARL1, a LOB-domain protein required for adventitious root formation in rice	2005	Plant J	State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310029, China.	Adventitious roots constitute the bulk of the fibrous root system in cereals. Compared with the current understanding of shoot development, knowledge of the molecular mechanisms of development of the adventitious roots of cereals is limited. We have isolated and characterized a novel gene controlling the initiation of adventitious root primordia in rice (Oryza sativa L.). The gene, designated Adventitious rootless1 (ARL1), encodes a protein with a LATERAL ORGAN BOUNDARIES (LOB) domain. It is expressed in lateral and adventitious root primordia, tiller primordia, vascular tissues, scutellum, and young pedicels. ARL1 is a nuclear protein and can form homodimers. ARL1 is an auxin- and ethylene-responsive gene, and the expression pattern of ARL1 in roots parallels auxin distribution. Our findings suggest that ARL1 is an auxin-responsive factor involved in auxin-mediated cell dedifferentiation, and that it promotes the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder in the stem.	CRL1|ARL1
Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling	2005	Plant Cell	Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.	Although the importance of auxin in root development is well known, the molecular mechanisms involved are still unknown. We characterized a rice (Oryza sativa) mutant defective in crown root formation, crown rootless1 (crl1). The crl1 mutant showed additional auxin-related abnormal phenotypic traits in the roots, such as decreased lateral root number, auxin insensitivity in lateral root formation, and impaired root gravitropism, whereas no abnormal phenotypic traits were observed in aboveground organs. Expression of Crl1, which encodes a member of the plant-specific ASYMMETRIC LEAVES2/LATERAL ORGAN BOUNDARIES protein family, was localized in tissues where crown and lateral roots are initiated and overlapped with beta-glucuronidase staining controlled by the DR5 promoter. Exogenous auxin treatment induced Crl1 expression without de novo protein biosynthesis, and this induction required the degradation of AUXIN/INDOLE-3-ACETIC ACID proteins. Crl1 contains two putative auxin response elements (AuxREs) in its promoter region. The proximal AuxRE specifically interacted with a rice AUXIN RESPONSE FACTOR (ARF) and acted as a cis-motif for Crl1 expression. We conclude that Crl1 encodes a positive regulator for crown and lateral root formation and that its expression is directly regulated by an ARF in the auxin signaling pathway.	CRL1|ARL1
Molecular mechanism of crown root initiation and the different mechanisms between crown root and radicle in rice	2011	Plant Signal Behav	Graduate School of Bioagricultural Sciences, Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, Japan.	Monocot plants produce numerous adventitious (crown) roots. The plant hormone auxin has positive effects on crown root formation, while cytokinin suppresses it. We have demonstrated that auxin-induced CROWN ROOTLESS5 (CRL5) regulates crown root initiation in rice through the induction of OsRR1, a negative regulator of cytokinin signaling. CRL5 overexpressing calli formed adventitious roots, although CRL5 overexpressing plants did not induce ectopic roots, suggesting that CRL5, which promotes de novo root initiation, might function only in de-differentiated cells. A radicle initiated normally in a crl5 mutant, in spite of the defect in crown root initiation, whereas crown roots, but not a radicle, were produced in a radicleless1 (ral1) mutant. A crl5 ral1 double mutant displayed an additive phenotype, showing that the formation of each root is regulated by different genetic mechanisms in rice.	Crl5
Molecular cloning and characterization of calreticulin, a calcium-binding protein involved in the regeneration of rice cultured suspension cells	2000	Eur J Biochem	Department of Molecular Biology, National Institute of Agrobiological Resources, Tsukuba, Japan.	A full-length cDNA clone encoding a phosphoprotein (pp56) involved in the regeneration of rice (Oryza sativa L.)-cultured suspension cells was isolated by screening a rice cultured suspension cell cDNA library. The 1558-bp cDNA sequence contains an ORF encoding an acidic (pI 4.38) protein of 424 amino acids (47.9 kDa), sharing 70-93% and 50-53% homology with other plant and mammalian calreticulins, respectively. Sequence analysis of the cDNA clone revealed several significant conserved motifs, including a calreticulin family repeat motif in the central domain and two calreticulin family motifs in the N-domain, indicating that this gene is a rice calreticulin (CRO1). The CRO1 gene in long-term rice cultured suspension cells shows constitutive expression in both suspension culture and regeneration media. In contrast, expression of the CRO1 gene in short-term rice cultured suspension cells, which possess regeneration potential, is increased dramatically when these cells are transferred to the regeneration medium. After approximately 2 weeks in the regeneration medium, the expression of the CRO1 gene reverts to constitutive levels. These results demonstrate the presence of calreticulin in rice cultured suspension cells and its developmental regulation during the regeneration of rice cultured suspension cells.	CRO1
Cyclic electron flow around photosystem I via chloroplast NAD(P)H dehydrogenase (NDH) complex performs a significant physiological role during photosynthesis and plant growth at low temperature in rice	2011	Plant J	Department of Applied Plant Science, Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 981-8555, Japan. wataru.yamori@biochem.tohoku.ac.jp	The role of NAD(P)H dehydrogenase (NDH)-dependent cyclic electron flow around photosystem I in photosynthetic regulation and plant growth at several temperatures was examined in rice (Oryza sativa) that is defective in CHLORORESPIRATORY REDUCTION 6 (CRR6), which is required for accumulation of sub-complex A of the chloroplast NDH complex (crr6). NdhK was not detected by Western blot analysis in crr6 mutants, resulting in lack of a transient post-illumination increase in chlorophyll fluorescence, and confirming that crr6 mutants lack NDH activity. When plants were grown at 28 or 35 degrees C, all examined photosynthetic parameters, including the CO(2) assimilation rate and the electron transport rate around photosystems I and II, at each growth temperature at light intensities above growth light (i.e. 800 mumol photons m(-2) sec(-1)), were similar between crr6 mutants and control plants. However, when plants were grown at 20 degrees C, all the examined photosynthetic parameters were significantly lower in crr6 mutants than control plants, and this effect on photosynthesis caused a corresponding reduction in plant biomass. The F(v)/F(m) ratio was only slightly lower in crr6 mutants than in control plants after short-term strong light treatment at 20 degrees C. However, after long-term acclimation to the low temperature, impairment of cyclic electron flow suppressed non-photochemical quenching and promoted reduction of the plastoquinone pool in crr6 mutants. Taken together, our experiments show that NDH-dependent cyclic electron flow plays a significant physiological role in rice during photosynthesis and plant growth at low temperature.	CRR6
Calcium-activated (p)ppGpp synthetase in chloroplasts of land plants	2007	J Biol Chem	Cell-Free Science and Technology Research Center, Ehime University, Matsuyama, Japan. tozaway@ccr.ehime-u.ac.jp	The genetic system of chloroplasts, including the machinery for transcription, translation, and DNA replication, exhibits substantial similarity to that of eubacteria. Chloroplasts are also thought to possess a system for generating guanosine 5'-triphosphate ((p)ppGpp), which triggers the stringent response in eubacteria, with genes encoding chloroplastic (p)ppGpp synthetase having been identified. We now describe the identification and characterization of genes (OsCRSH1, OsCRSH2, and OsCRSH3) for a novel type of (p)ppGpp synthetase in rice. The proteins encoded by these genes contain a putative chloroplast transit peptide at the NH(2) terminus, a central RelA-SpoT-like domain, and two EF-hand motifs at the COOH terminus. The recombinant OsCRSH1 protein was imported into chloroplasts in vitro, and genetic complementation analysis revealed that expression of OsCRSH1 suppressed the phenotype of an Escherichia coli mutant deficient in the RelA and SpoT enzymes. Biochemical analysis showed that the OsCRSH proteins possess (p)ppGpp synthetase activity that is dependent both on Ca(2+) and on the EF-hand motifs. A data base search identified a CRSH homolog in the dicotyledon Arabidopsis thaliana, indicating that such genes are conserved among both monocotyledonous and dicotyledonous land plants. CRSH proteins thus likely function as Ca(2+)-activated (p)ppGpp synthetases in plant chloroplasts, implicating both Ca(2+) and (p)ppGpp signaling in regulation of the genetic system of these organelles.	OsCRSH3
Carbon starved anther encodes a MYB domain protein that regulates sugar partitioning required for rice pollen development	2010	Plant Cell	School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	In flowering plants, sink tissues rely on transport of carbohydrates from photosynthetic tissues (sources) for nutrition and energy. However, how sugar partitioning in plants is regulated at the molecular level during development remains unknown. We have isolated and characterized a rice (Oryza sativa) mutant, carbon starved anther (csa), that showed increased sugar contents in leaves and stems and reduced levels of sugars and starch in floral organs. In particular, the csa mutant had reduced levels of carbohydrates in later anthers and was male sterile. The csa mutant had reduced accumulation of (14)C-labeled sugars in anther sink tissue. CSA was isolated by map-based cloning and was shown to encode an R2R3 MYB transcription factor that was expressed preferentially in the anther tapetal cells and in the sugar-transporting vascular tissues. In addition, the expression of MST8, encoding a monosaccharide transporter, was greatly reduced in csa anthers. Furthermore, CSA was found to be associated in vivo and in vitro with the promoter of MST8. Our findings suggest that CSA is a key transcriptional regulator for sugar partitioning in rice during male reproductive development. This study also establishes a molecular model system for further elucidation of the genetic control of carbon partitioning in plants.	CSA,OsMST8
Mutation in CSA creates a new photoperiod-sensitive genic male sterile line applicable for hybrid rice seed production	2013	Proc Natl Acad Sci U S A	State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	Rice is a major staple food worldwide. Making hybrid rice has proved to be an effective strategy to significantly increase grain yield. Current hybrid rice technologies rely on male sterile lines and have been used predominantly in indica cultivars. However, intrinsic problems exist in the implementation of these technologies, such as limited germplasms and unpredictable conversions from sterility to fertility in the field. Here, we describe a photoperiod-controlled male sterile line, carbon starved anther (csa), which contains a mutation in an R2R3 MYB transcription regulator of pollen development. This mutation was introduced into indica and japonica rice, and it rendered male sterility under short-day conditions and male fertility under long-day conditions in both lines. Furthermore, F(1) plants of csa and a restorer line JP69 exhibited heterosis (hybrid vigor), suggesting the feasibility of using this mutation to create hybrid rice. The csa-based photoperiod-sensitive male sterile line allows the establishment of a stable two-line hybrid system, which promises to have a significant impact on agriculture.	CSA
Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice	2012	Plant Physiol	Joint BioEnergy Institute, Emeryville, California 94608, USA.	Mixed-linkage glucan (MLG) is a cell wall polysaccharide containing a backbone of unbranched (1,3)- and (1,4)-linked beta-glucosyl residues. Based on its occurrence in plants and chemical characteristics, MLG has primarily been associated with the regulation of cell wall expansion due to its high and transient accumulation in young, expanding tissues. The Cellulose synthase-like F (CslF) subfamily of glycosyltransferases has previously been implicated in mediating the biosynthesis of this polymer. We confirmed that the rice (Oryza sativa) CslF6 gene mediates the biosynthesis of MLG by overexpressing it in Nicotiana benthamiana. Rice cslf6 knockout mutants show a slight decrease in height and stem diameter but otherwise grew normally during vegetative development. However, cslf6 mutants display a drastic decrease in MLG content (97% reduction in coleoptiles and virtually undetectable in other tissues). Immunodetection with an anti-MLG monoclonal antibody revealed that the coleoptiles and leaves retain trace amounts of MLG only in specific cell types such as sclerenchyma fibers. These results correlate with the absence of endogenous MLG synthase activity in mutant seedlings and 4-week-old sheaths. Mutant cell walls are weaker in mature stems but not seedlings, and more brittle in both stems and seedlings, compared to wild type. Mutants also display lesion mimic phenotypes in leaves, which correlates with enhanced defense-related gene expression and enhanced disease resistance. Taken together, our results underline a weaker role of MLG in cell expansion than previously thought, and highlight a structural role for MLG in nonexpanding, mature stem tissues in rice.	CslF6
Map-based cloning of the rice cold tolerance gene Ctb1	2010	Plant Science	National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1, Toyohira, Sapporo, 062-8555, Japan	Low temperatures during the booting stage reduce rice yields by causing cold-induced male sterility. We previously mapped a quantitative trait locus for cold tolerance, Ctb1, to a 56-kb region containing 7 putative genes. In this study we further mapped Ctb1 to a 17-kb region containing two genes that encode an F-box protein and a ser/thr protein kinase. The F-box protein gene was preferentially expressed in young panicles, while the ser/thr protein kinase gene was expressed in leaves and young panicles. Both genes were cloned from a cold-tolerant variety, Norin-PL8, and introduced into a cold-sensitive variety, Hokkai241, and a cold-sensitive line, BT4-74-8. The cold tolerance of T2 and T3 progenies was assessed by measuring the degree of spikelet fertility in plants treated with cool water irrigation (19 °C, 25 cm) or cool air (12 °C, 4 days). The results indicated that the F-box protein gene confers cold tolerance. Cold tolerance is associated with greater anther length, and the transgenic plants had longer anthers than non-transformed controls. The F-box protein interacts with a subunit of the E3 ubiquitin ligase, Skp1, suggesting that an ubiquitin–proteasome pathway is involved in cold tolerance at the booting stage.	Ctb1
Physical mapping and putative candidate gene identification of a quantitative trait locus Ctb1 for cold tolerance at the booting stage of rice	2004	Theor Appl Genet	National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1, Toyohira, Sapporo, Hokkaido, Japan. kjsaito@affrc.go.jp	Norin-PL8 is a cold-tolerant variety of rice (Oryza sativa L.) that was developed by introgressing chromosomal segments from a cold-tolerant tropical japonica variety, Silewah, into a template japonica variety, Hokkai241. We previously identified two closely linked quantitative trait loci, Ctb1 and Ctb2, for cold tolerance at the booting stage of Norin-PL8 in the long arm of chromosome 4. We report here the physical mapping of Ctb1 and the identification of the candidate genes. A total of 2,008 segregating individuals were screened for recombination in the Ctb1 region by a PCR-based screening, and a series of near-isogenic lines (NILs) were developed from progenies of recombinants. A comparison of the degrees of cold tolerance of the NILs indicated that Ctb1 is located in the 56-kb region covered by a bacterial artificial chromosome clone, OSJNBa0058 K23, that had been sequenced by the International Rice Genome Sequence Project. We found seven open reading frames (ORFs) in the 56-kb region. Two ORFs encoded receptor-like protein kinases that are possibly involved in signal transduction pathways. Proteins that may be associated with a ubiquitin-proteasome pathway were encoded by three ORFs, two of which encoded F-box proteins and one of which encoded a protein with a BAG domain. The other two ORFs encoded a protein with an OTU domain and an unknown protein. We were also able to show that Ctb1 is likely to be associated with anther length, which is one of major factors in cold tolerance at the booting stage.	Ctb1
Identification of two closely linked quantitative trait loci for cold tolerance on chromosome 4 of rice and their association with anther length	2001	TAG Theoretical and Applied Genetics	National Agricultural Research Center for Hokkaido Region, Hitsujigaoka 1, Toyohira, Sapporo, Hokkaido 062-8555, Japan	Norin-PL8 is a cold-tolerant variety of rice (Oryza sativa L.) that was developed by introgressing chromosomal segments from a cold-tolerant javanica variety, Silewah. We previously detected quantitative trait loci (QTLs) for cold tolerance of Norin-PL8 in the introgressions on chromosomes 3 and 4. We provide fine mapping of the QTLs on chromosome 4 and the association between the QTLs and anther length, which has been reported to be a major component of cold tolerance. Interval mapping using a segregating population derived from an advanced backcross progeny indicated that a QTL for cold tolerance is probably located from the center to the proximal end of the introgression. For fine mapping, we developed a set of near-isogenic lines (NILs) from recombinants in the segregating population. Comparison of cold tolerance between the NILs indicated that either the proximal end or the center of the introgression is necessary for cold tolerance. From these results, we concluded that there are at least two QTLs for cold tolerance, tentatively designated as Ctb-1 and Ctb-2, in the introgression on chromosome 4. The map distance between Ctb-1 and Ctb-2 is estimated to be 4.7–17.2 cM. In order to investigate the mechanism underlying cold tolerance by the QTLs, we compared anther lengths of the NILs. The results indicate that both Ctb-1 and Ctb-2 are associated with anther length.	Ctb1
Genome-wide expression analysis of HSP70 family genes in rice and identification of a cytosolic HSP70 gene highly induced under heat stress	2013	Funct Integr Genomics	Department of Plant Molecular Systems Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 446-701, South Korea. khjung2010@khu.ac.kr	The heat shock protein 70 (HSP70) gene family plays a key role in protecting plant cells or tissues from thermal or oxidative stress. Although many studies have elucidated the molecular functions of individual family members, genome-wide analysis of this family is still limited, especially for crop species. Our objective was to integrate various meta-profiling data into the context of a phylogenetic tree, which would enable us to perform fine evaluation of functional dominancy or redundancy within this family. Our data indicated that a loss-of-function mutant of a rice cytosolic HSP70 gene (OsctHSP70-1) did not show a clear defective phenotype in response to high temperature because of the existence of another gene family member that was closely clustered with OsctHSP70-1 and had similar expression patterns. Moreover, the second gene showed much stronger anatomical expression. We indirectly analyzed the function of OsctHSP70-1 by studying GUS activity under the control of the endogenous promoter. We also designed a probable interaction network mediated by OsctHSP70-1 and used co-expression analysis among its components to refine the network, suggesting more probable model to explain the function of OsctHSP70-1.	OsctHSP70-1
Thermodynamic basis for the stabilities of three CutA1s from Pyrococcus horikoshii,Thermus thermophilus, and Oryza sativa, with unusually high denaturation temperatures	2008	Biochemistry	RIKEN SPring-8 Center, Harima Institute, 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan.	In order to elucidate the stabilization mechanism of CutA1 from Pyrococcus horikoshii (PhCutA1) with a denaturation temperature of nearly 150 degrees C, GuHCl denaturation and heat denaturation were examined at neutral and acidic pHs. As a comparison, CutA1 proteins from Thermus thermophilus (TtCutA1) and Oryza sativa (OsCutA1) were also examined, which have lower optimum growth temperatures of 75 and 28 degrees C, respectively, than that (98 degrees C) of P. horikoshii. GuHCl-induced unfolding and refolding curves of the three proteins showed hysteresis effects due to an unusually slow unfolding rate. The midpoints of refolding for PhCutA1, TtCutA1 and OsCutA1 were 5.7 M, 3.3 M, and 2.3 M GuHCl, respectively, at pH 8.0 and 37 degrees C. DSC experiments with TtCutA1 and OsCutA1 showed that the denaturation temperatures were remarkably high, 112.8 and 97.3 degrees C, respectively, at pH 7.0 and that the good heat reversibility was amenable to thermodynamic analyses. At acidic pH, TtCutA1 showed higher stability to both heat and denaturant than PhCutA1. Combined with the data for DSC and denaturant denaturation, the unfolding Gibbs energy of PhCutA1 could be depicted as a function of temperature. It was experimentally revealed that (1) the unusually high stability of PhCutA1 basically originates from a common trimer structure of the three proteins, (2) the stability of PhCutA1 is superior to those of the other two CutA1s over all temperatures above 0 degrees C at neutral pH, due to the decrease in both enthalpy and entropy, and (3) ion pairs of PhCutA1 contribute to the unusually high stability at neutral pH.	OsCutA1
The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice	2010	Planta	College of Life Sciences, Northeast Forestry University, 150040 Harbin, Heilongjiang, China.	The cell cycle is an important process during seed development in plants and its progression is driven by a number of core regulators such as the cyclins. Currently, however, little is known regarding the role of the cyclins in embryo and endosperm development in cereals. In our current study, we show that the knockdown of Orysa;CycB1;1 in rice results in the production of abnormal seeds, which at maturity contain only an enlarged embryo. It was further found that a delayed and abnormal cellularization occurred in the endosperm in these knockdown seeds which eventually became abortive. Moreover, the observed development of the enlarged embryo was also morphologically abnormal and found to be caused by an enlarged cell size rather than an increased cell number. Expression analysis showed that Orysa;CycB1;1 transcripts were localized in the endosperm and embryo. Genome-wide transcriptional profiling further indicated that a large number of genes are responsible for the phenotype of the enlarged embryo. The results of the knockdown of Orysa;CycB1;1 via an endosperm or an embryo-specific promoter also suggest that the enlarged embryo may be correlated to the abortive endosperm. Our results suggest that Orysa;CycB1;1 expression is critical for endosperm formation via the regulation of mitotic division, and that the endosperm plays an important role in maintenance of embryo development in rice.	CycB1;1
The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3	2012	Cell Res	National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	Increased crop yields are required to support rapid population growth worldwide. Grain weight is a key component of rice yield, but the underlying molecular mechanisms that control it remain elusive. Here, we report the cloning and characterization of a new quantitative trait locus (QTL) for the control of rice grain length, weight and yield. This locus, GL3.1, encodes a protein phosphatase kelch (PPKL) family - Ser/Thr phosphatase. GL3.1 is a member of the large grain WY3 variety, which is associated with weaker dephosphorylation activity than the small grain FAZ1 variety. GL3.1-WY3 influences protein phosphorylation in the spikelet to accelerate cell division, thereby resulting in longer grains and higher yields. Further studies have shown that GL3.1 directly dephosphorylates its substrate, Cyclin-T1;3, which has only been rarely studied in plants. The downregulation of Cyclin-T1;3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation. Our findings suggest a new mechanism for the regulation of grain size and yield that is driven through a novel phosphatase-mediated process that affects the phosphorylation of Cyclin-T1;3 during cell cycle progression, and thus provide new insight into the mechanisms underlying crop seed development. We bred a new variety containing the natural GL3.1 allele that demonstrated increased grain yield, which indicates that GL3.1 is a powerful tool for breeding high-yield crops.	Cyclin-T1;3,GL3.1|qGL3-1|qGL3|OsPPKL1
Gibberellin modulates anther development in rice via the transcriptional regulation of GAMYB	2009	Plant Cell	Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.	Gibberellins (GAs) play important roles in regulating reproductive development, especially anther development. Our previous studies revealed that the MYB transcriptional factor GAMYB, an important component of GA signaling in cereal aleurone cells, is also important for anther development. Here, we examined the physiological functions of GA during anther development through phenotypic analyses of rice (Oryza sativa) GA-deficient, GA-insensitive, and gamyb mutants. The mutants exhibited common defects in programmed cell death (PCD) of tapetal cells and formation of exine and Ubisch bodies. Microarray analysis using anther RNAs of these mutants revealed that rice GAMYB is involved in almost all instances of GA-regulated gene expression in anthers. Among the GA-regulated genes, we focused on two lipid metabolic genes, a cytochrome P450 hydroxylase CYP703A3 and beta-ketoacyl reductase, both of which might be involved in providing a substrate for exine and Ubisch body. GAMYB specifically interacted with GAMYB binding motifs in the promoter regions in vitro, and mutation of these motifs in promoter-beta-glucuronidase (GUS) transformants caused reduced GUS expression in anthers. Furthermore, a knockout mutant for CYP703A3 showed gamyb-like defects in exine and Ubisch body formation. Together, these results suggest that GA regulates exine formation and the PCD of tapetal cells and that direct activation of CYP703A3 by GAMYB is key to exine formation.	CYP703A3,OsMYBGA|OsGAMYB,KAR
Cytochrome P450 family member CYP704B2 catalyzes the {omega}-hydroxylation of fatty acids and is required for anther cutin biosynthesis and pollen exine formation in rice	2010	Plant Cell	School of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai 200240, China.	The anther cuticle and microspore exine act as protective barriers for the male gametophyte and pollen grain, but relatively little is known about the mechanisms underlying the biosynthesis of the monomers of which they are composed. We report here the isolation and characterization of a rice (Oryza sativa) male sterile mutant, cyp704B2, which exhibits a swollen sporophytic tapetal layer, aborted pollen grains without detectable exine, and undeveloped anther cuticle. In addition, chemical composition analysis indicated that cutin monomers were hardly detectable in the cyp704B2 anthers. These defects are caused by a mutation in a cytochrome P450 family gene, CYP704B2. The CYP704B2 transcript is specifically detected in the tapetum and the microspore from stage 8 of anther development to stage 10. Heterologous expression of CYP704B2 in yeast demonstrated that CYP704B2 catalyzes the production of omega -hydroxylated fatty acids with 16 and 18 carbon chains. Our results provide insights into the biosynthesis of the two biopolymers sporopollenin and cutin. Specifically, our study indicates that the omega -hydroxylation pathway of fatty acids relying on this ancient CYP704B family, conserved from moss to angiosperms, is essential for the formation of both cuticle and exine during plant male reproductive and spore development.	CYP704B2
CYP714B1 and CYP714B2 encode gibberellin 13-oxidases that reduce gibberellin activity in rice	2013	Proc Natl Acad Sci U S A	RIKEN Plant Science Center, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.	Bioactive gibberellins (GAs) control many aspects of growth and development in plants. GA(1) has been the most frequently found bioactive GA in various tissues of flowering plants, but the enzymes responsible for GA(1) biosynthesis have not been fully elucidated due to the enzymes catalyzing the 13-hydroxylation step not being identified. Because of the lack of mutants defective in this enzyme, biological significance of GA 13-hydroxylation has been unknown. Here, we report that two cytochrome P450 genes, CYP714B1 and CYP714B2, encode GA 13-oxidase in rice. Transgenic Arabidopsis plants that overexpress CYP714B1 or CYP714B2 show semidwarfism. There was a trend that the levels of 13-OH GAs including GA(1) were increased in these transgenic plants. Functional analysis using yeast or insect cells shows that recombinant CYP714B1 and CYP714B2 proteins can convert GA(12) into GA(53) (13-OH GA(12)) in vitro. Moreover, the levels of 13-OH GAs including GA(1) were decreased, whereas those of 13-H GAs including GA(4) (which is more active than GA(1)) were increased, in the rice cyp714b1 cyp714b2 double mutant. These results indicate that CYP714B1 and CYP714B2 play a predominant role in GA 13-hydroxylation in rice. The double mutant plants appear phenotypically normal until heading, but show elongated uppermost internode at the heading stage. Moreover, CYP714B1 and CYP714B2 expression was up-regulated by exogenous application of bioactive GAs. Our results suggest that GA 13-oxidases play a role in fine-tuning plant growth by decreasing GA bioactivity in rice and that they also participate in GA homeostasis.	CYP714B1,CYP714B2
Rice CYP734As function as multisubstrate and multifunctional enzymes in brassinosteroid catabolism	2011	Plant J	Institute for Advanced Research, Nagoya University, Nagoya, Aichi 464-8601, Japan. sakamoto@iar.nagoya-u.ac.jp	Catabolism of brassinosteroids regulates the endogenous level of bioactive brassinosteroids. In Arabidopsis thaliana, bioactive brassinosteroids such as castasterone (CS) and brassinolide (BL) are inactivated mainly by two cytochrome P450 monooxygenases, CYP734A1/BAS1 and CYP72C1/SOB7/CHI2/SHK1; CYP734A1/BAS1 inactivates CS and BL by means of C-26 hydroxylation. Here, we characterized CYP734A orthologs from Oryza sativa (rice). Overexpression of rice CYP734As in transgenic rice gave typical brassinosteroid-deficient phenotypes. These transformants were deficient in both the bioactive CS and its precursors downstream of the C-22 hydroxylation step. Consistent with this result, recombinant rice CYP734As utilized a range of C-22 hydroxylated brassinosteroid intermediates as substrates. In addition, rice CYP734As can catalyze hydroxylation and the second and third oxidations to produce aldehyde and carboxylate groups at C-26 in vitro. These results indicate that rice CYP734As are multifunctional, multisubstrate enzymes that control the endogenous bioactive brassinosteroid content both by direct inactivation of CS and by the suppression of CS biosynthesis by decreasing the levels of brassinosteroid precursors.	CYP734A2,CYP734A4,CYP734A5,CYP734A6
Picking sides: distinct roles for CYP76M6 and CYP76M8 in rice oryzalexin biosynthesis	2013	Biochem J	Department of Biochemistry, Iowa State University, Ames, 50011, USA.	Natural products biosynthesis often requires the action of multiple CYPs (cytochromes P450), whose ability to introduce oxygen, increasing solubility, is critical for imparting biological activity. In previous investigations of rice diterpenoid biosynthesis, we characterized CYPs that catalyse alternative hydroxylation of ent-sandaracopimaradiene, the precursor to the rice oryzalexin antibiotic phytoalexins. In particular, CYP76M5, CYP76M6 and CYP76M8 were all shown to carry out C-7beta hydroxylation, whereas CYP701A8 catalyses C-3alpha hydroxylation, with oxy groups found at both positions in oryzalexins A-D, suggesting that these may act consecutively in oryzalexin biosynthesis. In the present paper, we report that, although CYP701A8 only poorly reacts with 7beta-hydroxy-ent-sandaracopimaradiene, CYP76M6 and CYP76M8 readily react with 3alpha-hydroxy-ent-sandaracopimaradiene. Notably, their activity yields distinct products, resulting from hydroxylation at C-9beta by CYP76M6 or C-7beta by CYP76M8, on different sides of the core tricyclic ring structure. Thus CYP76M6 and CYP76M8 have distinct non-redundant roles in orzyalexin biosynthesis. Moreover, the resulting 3alpha,7beta- and 3alpha,9beta-diols correspond to oryzalexins D and E respectively. Accordingly, the results of the present study complete the functional identification of the biosynthetic pathway underlying the production of these bioactive phytoalexins. In addition, the altered regiochemistry catalysed by CYP76M6 following C-3alpha hydroxylation has some implications for its active-site configuration, offering further molecular insight.	CYP76M6,CYP76M8
CYP76M7 is an ent-cassadiene C11alpha-hydroxylase defining a second multifunctional diterpenoid biosynthetic gene cluster in rice	2009	Plant Cell	Department of Biochemistry, Iowa State University, Ames, Iowa 50011, USA.	Biosynthetic gene clusters are common in microbial organisms, but rare in plants, raising questions regarding the evolutionary forces that drive their assembly in multicellular eukaryotes. Here, we characterize the biochemical function of a rice (Oryza sativa) cytochrome P450 monooxygenase, CYP76M7, which seems to act in the production of antifungal phytocassanes and defines a second diterpenoid biosynthetic gene cluster in rice. This cluster is uniquely multifunctional, containing enzymatic genes involved in the production of two distinct sets of phytoalexins, the antifungal phytocassanes and antibacterial oryzalides/oryzadiones, with the corresponding genes being subject to distinct transcriptional regulation. The lack of uniform coregulation of the genes within this multifunctional cluster suggests that this was not a primary driving force in its assembly. However, the cluster is dedicated to specialized metabolism, as all genes in the cluster are involved in phytoalexin metabolism. We hypothesize that this dedication to specialized metabolism led to the assembly of the corresponding biosynthetic gene cluster. Consistent with this hypothesis, molecular phylogenetic comparison demonstrates that the two rice diterpenoid biosynthetic gene clusters have undergone independent elaboration to their present-day forms, indicating continued evolutionary pressure for coclustering of enzymatic genes encoding components of related biosynthetic pathways.	CYP76M7
Auxin responsiveness of a novel cytochrome p450 in rice coleoptiles	2003	Plant Physiol	Institut fur Biologie II, Schanzlestrasse 1, D-79104 Freiburg, Germany. christian.chaban@uni-freiburg.de	An early auxin-induced gene was isolated from rice (Oryza sativa L. subsp. japonica cv Nihonmasari) coleoptiles by a fluorescent-labeled differential display screen. The full-length gene contains conserved domains characteristic for the cytochrome p450 superfamily. This gene, designated as CYP87A3, was weakly expressed in dark-grown coleoptiles but was up-regulated rapidly and transiently when coleoptile segments were incubated in 5 microm indole-3-acetic acid. This induction by auxin could not be suppressed by cycloheximide. Depletion of segments from endogenous auxin reduced the amount of CYP87A3 transcripts. The CYP87A3 transcript level was rapidly, although transiently, up-regulated in response to light as well. The observed pattern of gene regulation might indicate a role in the suppression of auxin-induced coleoptile growth. The role of CYP87A3 is discussed with respect to auxin signaling in the regulation of coleoptile growth.	CYP87A3
Rice CYP90D2 and CYP90D3 catalyze C-23 hydroxylation of brassinosteroids in vitro	2012	Plant Physiol Biochem	Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa 921 8836, Japan. sakamoto@ishikawa-pu.ac.jp	Brassinosteroids are biosynthesized from campesterol via several cytochrome P450 (P450)-catalyzed oxidative reactions. We report the biochemical characterization of two brassinosteroid-biosynthetic P450s from rice: CYP90D2 and CYP90D3. A rice dwarf mutant, ebisu dwarf (d2), which contains a defective copy of CYP90D2, is known to be a brassinosteroid-deficient mutant, and CYP90D2 has been considered to act as a C-3 dehydrogenase. However, in vitro biochemical assays using baculovirus/insect cell-produced proteins revealed that both CYP90D2 and CYP90D3 catalyze C-23 hydroxylation of various 22-hydroxylated brassinosteroids, but with markedly different catalytic efficiencies. Both enzymes preferentially convert (22S,24R)-22-hydroxyergost-4-en-3-one, (22S,24R)-22-hydroxy-5alpha-ergostan-3-one, and 3-epi-6-deoxocathasterone to the corresponding 23-hydroxylated products, but are less active in the conversion of (22S)-22-hydroxycampesterol and 6-deoxocathasterone, in vitro. Consistently, the levels of 23-hydroxylated products of these intermediates, namely, 6-deoxoteasterone, 3-dehydro-6-deoxoteasterone, and 6-deoxotyphasterol were decreased in d2 mutants. These results indicate that CYP90D2 and CYP90D3 can act as brassinosteroid C-23 hydroxylases in rice.	CYP90D3,D2|CYP90D2
A rice brassinosteroid-deficient mutant, ebisu dwarf (d2), is caused by a loss of function of a new member of cytochrome P450	2003	Plant Cell	BioScience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan.	We characterized a rice dwarf mutant, ebisu dwarf (d2). It showed the pleiotropic abnormal phenotype similar to that of the rice brassinosteroid (BR)-insensitive mutant, d61. The dwarf phenotype of d2 was rescued by exogenous brassinolide treatment. The accumulation profile of BR intermediates in the d2 mutants confirmed that these plants are deficient in late BR biosynthesis. We cloned the D2 gene by map-based cloning. The D2 gene encoded a novel cytochrome P450 classified in CYP90D that is highly similar to the reported BR synthesis enzymes. Introduction of the wild D2 gene into d2-1 rescued the abnormal phenotype of the mutants. In feeding experiments, 3-dehydro-6-deoxoteasterone, 3-dehydroteasterone, and brassinolide effectively caused the lamina joints of the d2 plants to bend, whereas more upstream compounds did not cause bending. Based on these results, we conclude that D2/CYP90D2 catalyzes the steps from 6-deoxoteasterone to 3-dehydro-6-deoxoteasterone and from teasterone to 3-dehydroteasterone in the late BR biosynthesis pathway.	CYP90D3,D2|CYP90D2
CYP93G2 is a flavanone 2-hydroxylase required for C-glycosylflavone biosynthesis in rice	2010	Plant Physiol	School of Biological Sciences, The University of Hong Kong, Hong Kong, China.	C-Glycosylflavones are ubiquitous in the plant kingdom, and many of them have beneficial effects on human health. They are a special group of flavonoid glycosides in which the sugars are C-linked to the flavone skeleton. It has been long presumed that C-glycosylflavones have a different biosynthetic origin from O-glycosylflavonoids. In rice (Oryza sativa), a C-glucosyltransferase (OsCGT) that accepts 2-hydroxyflavanone substrates and a dehydratase activity that selectively converts C-glucosyl-2-hydroxyflavanones to 6C-glucosylflavones were recently described. In this study, we provide in vitro and in planta evidence that the rice P450 CYP93G2 protein encoded by Os06g01250 is a functional flavanone 2-hydroxylase. CYP93G2 is related to the CYP93B subfamily, which consists of dicot flavone synthase II enzymes. In the presence of NADPH, recombinant CYP93G2 converts naringenin and eriodictyol to the corresponding 2-hydroxyflavanones. In addition, CYP93G2 generates 2-hydroxyflavanones, which are modified by O-glycosylation in transgenic Arabidopsis (Arabidopsis thaliana). Coexpression of CYP93G2 and OsCGT in Arabidopsis resulted in the production of C-glucosyl-2-hydroxyflavanones in the dibenzoylmethane tautomeric form. The same structure was reported previously for the in vitro OsCGT reaction products. Thus, CYP93G2 generates 2-hydroxyflavanone substrates from flavanones for C-glucosylation by OsCGT in planta. Furthermore, knocking down Os06g01250 in rice (O. sativa subsp. japonica 'Zhonghua 11') preferentially depleted the accumulation of C-glycosylapigenin, C-glycosylluteolin, and C-glycosylchrysoeriol but did not affect the levels of tricin, which is frequently present as O-glycosides in cereals. Taken together, our work conclusively assigned CYP93G2 as the first enzyme that channels flavanones to C-glycosylflavone biosynthesis in rice.	CYP93G2,OsCGT
Oryza sativa cytochrome P450 family member OsCYP96B4 reduces plant height in a transcript dosage dependent manner	2011	PLoS One	Rice Functional Genomics Group, Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore.	BACKGROUND: Plant cytochromes P450 are involved in a wide range of biosynthetic reactions and play various roles in plant development. However, little is known about the biological functions of the subfamily CYP96 in plants. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report a novel semi-dwarf rice mutant, in which a single copy of transposon dissociator (Ds) was inserted into the gene OsCYP96B4 (Oryza sativa Cytochrome P450 96B4). The mutant exhibits the defects in cell elongation and pollen germination, which can be complemented by the wild type OsCYP96B4 and be rescued by remobilization of the Ds element with the presence of the transposase Activator (Ac). Transgenic plants harboring OsCYP96B4 double-stranded RNA interference construct mimicked the mutant phenotype. The oscyp96b4 mutant phenotype could not be rescued by all the tested phytohormones and it was found that OsCYP96B4 reduced plant height in a transcript dosage dependent manner. Heterologous expression of OsCYP96B4 in Schizosaccharomyces pombe resulted in missegregation and wider cells. Further investigation showed that the mutant exhibited the defects in the metabolism of some lipid molecular species when compared with the wild type. CONCLUSIONS/SIGNIFICANCE: The oscyp96b4 mutant is a novel rice semi-dwarf mutant. Our data suggest that OsCYP96B4 might be involved in lipid metabolism and regulate cell elongation.	OsCYP96B4
The rice semi-dwarf mutant sd37, caused by a mutation in CYP96B4, plays an important role in the fine-tuning of plant growth	2014	PLoS One	State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ; National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, China.	Plant cytochrome P450 has diverse roles in developmental processes and in the response to environmental cues. Here, we characterized the rice (Oryza sativa L ssp. indica cultivar 3037) semi-dwarf mutant sd37, in which the gene CYP96B4 (Cytochrome P450 96B subfamily) was identified and confirmed as the target by map-based cloning and a complementation test. A point mutation in the SRS2 domain of CYP96B4 resulted in a threonine to lysine substitution in the sd37 mutant. Examination of the subcellular localization of the protein revealed that SD37 was ER-localized protein. And SD37 was predominantly expressed in the shoot apical meristem and developing leaf and root maturation zone but not in the root apical meristem. The sd37 leaves, panicles, and seeds were smaller than those of the wild type. Histological analysis further revealed that a decrease in cell number in the mutant, specifically in the shoots, was the main cause of the dwarf phenotype. Microarray analysis demonstrated that the expression of several cell division-related genes was disturbed in the sd37 mutant. In addition, mutation or strongly overexpression of SD37 results in dwarf plants but moderate overexpression increases plant height. These data suggest that CYP96B4 may be an important regulator of plant growth that affects plant height in rice.	OsCYP96B4
Rice carotenoid beta-ring hydroxylase CYP97A4 is involved in lutein biosynthesis	2012	Plant Cell Physiol	National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, PR China.	Lutein is the most abundant plant carotenoid and plays essential roles in photosystem assembly and stabilization, as well as protection against photostress. To date, only a few lutein biosynthesis genes have been identified in crop plants. In this study, the rice Cyt P450 gene CYP97A4 encoding a carotenoid beta-ring hydroxylase was shown to be involved in lutein biosynthesis. The results revealed that CYP97A4 was preferentially expressed in leaf compared with spikelet, sheath, stalk and root, and encoded a protein localized at the subcellular level to the chloroplasts. Compared with the wild type, the three allelic mutants of CYP97A4 displayed lutein reductions of 12-24% with substantially increased alpha-carotene, while Chl a/b levels were unaltered. The increased alpha-carotene in the mutants led to greater sensitivity under high light stress. Similarly, reactive oxygen species (ROS) imaging of leaves treated with intense light showed that the mutants generally accumulated greater levels of ROS compared with wild-type plants, which probably caused detrimental effects to the plant photosystem. In conclusion, this study demonstrated the important role of CYP97A4 in alpha-carotene hydroxylation in rice, and knock-out of the gene reduced lutein and increased alpha-carotene, contributing to sensitivity to intense light.	CYP97A4
OsTGAP1, a bZIP transcription factor, coordinately regulates the inductive production of diterpenoid phytoalexins in rice	2009	J Biol Chem	Biotechnology Research Center, The University of Tokyo, Tokyo 113-8657, Japan.	Production of major diterpenoid phytoalexins, momilactones and phytocassanes, is induced in rice upon recognition of pathogenic invasion as plant defense-related compounds. We recently showed that biosynthetic genes for momilactones are clustered on rice chromosome 4 and co-expressed after elicitation, mimicking pathogen attack. Because genes for most metabolic pathways in plants are not organized in gene clusters, examination of the mechanism(s) regulating the expression of such clustered genes is needed. Here, we report a chitin oligosaccharide elicitor-inducible basic leucine zipper transcription factor, OsTGAP1, which is essential for momilactone biosynthesis and regulates the expression of the five genes in the cluster. The knock-out mutant for OsTGAP1 had almost no expression of the five clustered genes (OsCPS4, OsKSL4, CYP99A2, CYP99A3, and OsMAS) or production of momilactones upon elicitor treatment. Inductive expression of OsKSL7 for phytocassane biosynthesis was also largely affected in the ostgap1 mutant, although phytocassane accumulation still occurred. Conversely, OsTGAP1-overexpressing lines exhibited enhanced expression of the clustered genes and hyperaccumulation of momilactones in response to the elicitor. Furthermore, enhanced expression of OsKSL7 and hyperaccumulation of phytocassanes was also observed. We also found that OsTGAP1 overexpression can influence transcriptional up-regulation of OsDXS3 in the methylerythritol phosphate pathway, eventually leading to inductive production of diterpenoid phytoalexins. These results indicate that OsTGAP1 functions as a key regulator of the coordinated transcription of genes involved in inductive diterpenoid phytoalexin production in rice and mainly exerts an essential role on expression of the clustered genes for momilactone biosynthesis.	CYP99A2,CYP99A3,MAS,OsCPS4|OsCyc1,OsDTS2|OsKSL4|OsKS4,OsTGAP1|OsbZIP37
CYP99A3: functional identification of a diterpene oxidase from the momilactone biosynthetic gene cluster in rice	2011	Plant J	Department of Biochemistry, Biophysics, and Molecular Biology, Iowa State University, Ames, IA 50011, USA.	Rice (Oryza sativa) produces momilactone diterpenoids as both phytoalexins and allelochemicals. Strikingly, the rice genome contains a biosynthetic gene cluster for momilactone production, located on rice chromosome 4, which contains two cytochrome P450 (CYP) mono-oxygenases, CYP99A2 and CYP99A3, with undefined roles; although it has been previously shown that RNA interference double knock-down of this pair of closely related CYPs reduced momilactone accumulation. Here we attempted biochemical characterization of CYP99A2 and CYP99A3, which was ultimately achieved by complete gene recoding, enabling functional recombinant expression in bacteria. With these synthetic gene constructs it was possible to demonstrate that while CYP99A2 does not exhibit significant activity with diterpene substrates, CYP99A3 catalyzes consecutive oxidations of the C19 methyl group of the momilactone precursor syn-pimara-7,15-diene to form, sequentially, syn-pimaradien-19-ol, syn-pimaradien-19-al, and syn-pimaradien-19-oic acid. These are presumably intermediates in momilactone biosynthesis, as a C19 carboxylic acid moiety is required for formation of the core 19,6-gamma-lactone ring structure. We further were able to detect syn-pimaradien-19-oic acid in rice plants, which indicates physiological relevance for the observed activity of CYP99A3. In addition, we found that CYP99A3 also oxidized syn-stemod-13(17)-ene at C19 to produce, sequentially, syn-stemoden-19-ol, syn-stemoden-19-al, and syn-stemoden-19-oic acid, albeit with lower catalytic efficiency than with syn-pimaradiene. Although the CYP99A3 syn-stemodene-derived products were not detected in planta, these results nevertheless provide a hint at the currently unknown metabolic fate of this diterpene in rice. Regardless of any wider role, our results strongly indicate that CYP99A3 acts as a multifunctional diterpene oxidase in momilactone biosynthesis.	CYP99A2,CYP99A3
Distinct roles of protein disulfide isomerase and P5 sulfhydryl oxidoreductases in multiple pathways for oxidation of structurally diverse storage proteins in rice	2011	Plant Cell	Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.	In the rice (Oryza sativa) endosperm, storage proteins are synthesized on the rough endoplasmic reticulum (ER), in which prolamins are sorted to protein bodies (PBs) called type-I PB (PB-I). Protein disulfide isomerase (PDI) family oxidoreductase PDIL2;3, an ortholog of human P5, contains a conserved structural disulfide in the redox-inactive thioredoxin-like (TRX) domain and was efficiently targeted to the surface of PB-I in a redox active site-dependent manner, whereas PDIL1;1, an ortholog of human PDI, was localized in the ER lumen. Complementation analyses using PDIL1;1 knockout esp2 mutant indicated that the a and a' TRX domains of PDIL1;1 exhibited similar redox activities and that PDIL2;3 was unable to perform the PDIL1;1 functions. PDIL2;3 knockdown inhibited the accumulation of Cys-rich 10-kD prolamin (crP10) in the core of PB-I. Conversely, crP10 knockdown dispersed PDIL2;3 into the ER lumen. Glutathione S-transferase-PDIL2;3 formed a stable tetramer when it was expressed in Escherichia coli, and the recombinant PDIL2;3 tetramer facilitated alpha-globulin(C79F) mutant protein to form nonnative intermolecular disulfide bonds in vitro. These results indicate that PDIL2;3 and PDIL1;1 are not functionally redundant in sulfhydryl oxidations of structurally diverse storage proteins and play distinct roles in PB development. We discuss PDIL2;3-dependent and PDIL2;3-independent oxidation pathways that sustain disulfide bonds of crP10 in PB-I.	CysP13|CpP13|PG5a|Prol-06,CysR10|crP10,PDIL2;3,GLB1
The same nuclear proteins bind to the 5?-flanking regions of genes for the rice seed storage protein: 16 kDa albumin, 13 kDa prolamin and type II glutelin	1996	Plant Mol Biol	Department of Applied Biological Sciences, School of Agricultural Sciences, 464-01, Chikusa-ku, Nagoya, Japan	Expression of rice seed storage-protein genes is dramatically regulated over a short period of seed maturation. To characterize the expression mechanism of the rice seed storage protein genes, their expression of major storage protein genes (16 kDa albumin, 13 kDa prolamin and type II glutelin) were compared by RNA blot analysis. Their coordinate expression suggests that the transcriptional regulatory machinery is shared among the glutelin, prolamin and albumin-genes. We isolated two novel genomic genes for prolamins (PG5a and PG5b) and obtained the promoter region of the glutelin gene by PCR. The 5'-flanking regions of these three rice seed storage protein genes were found to contain some similar conserved sequences. Nuclear extract partially purified from maturing rice seeds was used for the gel shift assay of the 5' region of the RA gene. We identified two DNA sequences of RA gene which were recognized by independent DNA-binding proteins. The complexes of these DNA sequences and DNA-binding proteins were inhibited by the fragments containing the 5' regions of the prolamin and glutelin genes, suggesting that these three genes share transcription factors.	CysP13|CpP13|PG5a|Prol-06,PG5b|Prol-08
Cytokinin activity of cis-zeatin and phenotypic alterations induced by overexpression of putative cis-Zeatin-O-glucosyltransferase in rice	2012	Plant Physiol	RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan.	cis-Zeatin (cZ) is generally regarded as a cytokinin with little or no activity, compared with the highly active trans-zeatin (tZ). Although recent studies suggested possible roles for cZ, its physiological significance remains unclear. In our studies with rice (Oryza sativa), cZ inhibited seminal root elongation and up-regulated cytokinin-inducible genes, and its activities were comparable to those of tZ. Tracer experiments showed that exogenously supplied cZ-riboside was mainly converted into cZ derivatives but scarcely into tZ derivatives, indicating that isomerizations of cZ derivatives into tZ derivatives are a minor pathway in rice cytokinin metabolism. We identified three putative cZ-O-glucosyltransferases (cZOGT1, cZOGT2, and cZOGT3) in rice. The cZOGTs preferentially catalyzed O-glucosylation of cZ and cZ-riboside rather than tZ and tZ-riboside in vitro. Transgenic rice lines ectopically overexpressing the cZOGT1 and cZOGT2 genes exhibited short-shoot phenotypes, delay of leaf senescence, and decrease in crown root number, while cZOGT3 overexpressor lines did not show shortened shoots. These results propose that cZ activity has a physiological impact on the growth and development of rice.	cZOGT1,cZOGT2,cZOGT3
Isolation and characterization of a dominant dwarf gene, d-h, in rice	2014	PLoS One	Department of Plant Science, Research Institute of Agriculture and Life Sciences and Plant Genomics and Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul, Korea.	Plant height is an important agronomic trait that affects grain yield. Previously, we reported a novel semi-dominant dwarf mutant, HD1, derived from chemical mutagenesis using N-methyl-N-nitrosourea (MNU) on a japonica rice cultivar, Hwacheong. In this study, we cloned the gene responsible for the dwarf mutant using a map-based approach. Fine mapping revealed that the mutant gene was located on the short arm of chromosome 1 in a 48 kb region. Sequencing of the candidate genes and rapid amplification of cDNA ends-polymerase chain reaction (RACE-PCR) analysis identified the gene, d-h, which encodes a protein of unknown function but whose sequence is conserved in other cereal crops. Real-time (RT)-PCR analysis and promoter activity assays showed that the d-h gene was primarily expressed in the nodes and the panicle. In the HD1 plant, the d-h gene was found to carry a 63-bp deletion in the ORF region that was subsequently confirmed by transgenic experiments to be directly responsible for the gain-of-function phenotype observed in the mutant. Since the mutant plants exhibit a defect in GA response, but not in the GA synthetic pathway, it appears that the d-h gene may be involved in a GA signaling pathway.	D-h
Rice heterotrimeric G-protein alpha subunit (RGA1): in silico analysis of the gene and promoter and its upregulation under abiotic stress	2013	Plant Physiol Biochem	Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.	Heterotrimeric G-protein complexes (Galpha, Gbeta and Ggamma) operate at the apex of diverse signal transduction systems along with their cognate transmembrane G-protein coupled receptors (GPCRs) and appropriate downstream effectors in the plant. Rice Galpha in response to stress has not been well studied. Here, we report the in silico analysis of Galpha subunit from Oryza sativa cv. Indica group Swarna [RGA1(I), accession number HQ634688], its promoter and its transcript upregulation in response to abiotic stresses. Genomic sequence of RGA1(I) contains thirteen exonic and twelve intronic segments. Phylogenetic analysis of RGA1(I) demonstrated high homology with Sorghum and maize and is distantly related to barley and wheat. Promoter sequence analysis of RGA1(I) confirms the presence of stress-related cis-regulatory elements viz. ABA, MeJAE, ARE, GT-1 boxes and LTR suggesting its active and possible independent roles in abiotic stress signalling. Expasy PROSITE database of protein families and domains revealed important motifs, patterns and biologically significant sites in RGA1(I). Three dimensional structure of RGA1(I) protein predicted by I-TASSER server and its stereochemical qualities were validated by PROCHECK and QMEAN server indicating the acceptability of the predicted model. The transcript profiling of RGA1(I) showed upregulation following NaCl, cold and drought stress. Under elevated temperature, its transcript was down regulated. Heavy metal(loid)s stress showed rhythmic and strong upregulation. It showed a rhythmic response in ABA stress. These findings provide a critical evidence for its active role in regulation of abiotic stresses in rice. These findings suggest its possible exploitation in the development of abiotic stress tolerance in crops.	D1|RGA1
Molecular cloning and characterization of RGA1 encoding a G protein alpha subunit from rice (Oryza sativa L. IR-36)	1995	Plant Mol Biol	Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Chinju, Korea.	A cDNA clone, RGA1, was isolated by using a GPA1 cDNA clone of Arabidopsis thaliana G protein alpha subunit as a probe from a rice (Oryza sativa L. IR-36) seedling cDNA library from roots and leaves. Sequence analysis of genomic clone reveals that the RGA1 gene has 14 exons and 13 introns, and encodes a polypeptide of 380 amino acid residues with a calculated molecular weight of 44.5 kDa. The encoded protein exhibits a considerable degree of amino acid sequence similarity to all the other known G protein alpha subunits. A putative TATA sequence (ATATGA), a potential CAAT box sequence (AGCAATAC), and a cis-acting element, CCACGTGG (ABRE), known to be involved in ABA induction are found in the promoter region. The RGA1 protein contains all the consensus regions of G protein alpha subunits except the cysteine residue near the C-terminus for ADP-ribosylation by pertussis toxin. The RGA1 polypeptide expressed in Escherichia coli was, however, ADP-ribosylated by 10 microM [adenylate-32P] NAD and activated cholera toxin. Southern analysis indicates that there are no other genes similar to the RGA1 gene in the rice genome. Northern analysis reveals that the RGA1 mRNA is 1.85 kb long and expressed in vegetative tissues, including leaves and roots, and that its expression is regulated by light.	D1|RGA1
Heterotrimeric G protein alpha subunit is involved in rice brassinosteroid response	2006	Cell Res	Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Nanxincun 20, Xiangshan, Beijing 100093, China.	Heterotrimeric G proteins are known to function as messengers in numerous signal transduction pathways. The null mutation of RGA (rice heterotrimeric G protein alpha subunit), which encodes the alpha subunit of heterotrimeric G protein in rice, causes severe dwarfism and reduced responsiveness to gibberellic acid in rice. However, less is known about heterotrimeric G protein in brassinosteroid (BR) signaling, one of the well-understood phytohormone pathways. In the present study, we used root elongation inhibition assay, lamina inclination assay and coleoptile elongation analysis to demonstrated reduced sensitivity of d1 mutant plants (caused by the null mutation of RGA) to 24-epibrassinolide (24-epiBL), which belongs to brassinosteroids and plays a wide variety of roles in plant growth and development. Moreover, RGA transcript level was decreased in 24-epiBL-treated seedlings in a dose-dependent manner. Our results show that RGA is involved in rice brassinosteroid response, which may be beneficial to elucidate the molecular mechanisms of G protein signaling and provide a novel perspective to understand BR signaling in higher plants.	D1|RGA1
Study of novel d1 alleles, defective mutants of the α subunit of heterotrimeric G-protein in rice	2009	Genes Genet Syst	Department of Bioscience, Fukui Prefectural University	It has been shown that the disruption of the α-subunit gene of heterotorimeric G-proteins (Gα) results in dwarf traits, the erection of leaves and the setting of small seeds in rice. These mutants are called d1. We have studied the expression profiles of the transcripts and translation products of rice Gα in ten alleles of d1 including five additional alleles newly identified. By RT-PCR, the transcripts of the Gα gene were detected in the all d1 alleles. By western blot, the Gα proteins were not detected in the plasma membrane fractions of the d1 alleles with the exception of d1-4. In d1-4, one amino acid change in the GTP-binding box A of the Gα protein was occurred and even in this case the Gα protein was only just detectable in the plasma membrane fraction. Given that the Gα protein did not accumulate in the plasma membrane fraction in d1-8 which has a deletion of just a single amino acid in the Gα protein, it is likely that a proper conformation of the Gα is necessary for accumulation of Gα protein in the plasma membrane. Nine alleles of d1 showed a severer phenotype whilst d1-4 exhibited a mild phenotype with respect to seed size and elongation pattern of internodes. As brassinosteroid signaling was known to be partially impaired in d1s, the sensitivity to 24-epibrassinolide (24-epiBL) was compared among d1 alleles in a T65 genetic background. Only d1-4 showed responses similar to wild type rice. The results show that the d1-4 mutant is a mild allele in terms of the phenotype and mild hyposensitivity to the exogenously applied 24-epiBL.	D1|RGA1
Suppression of the rice heterotrimeric G protein beta-subunit gene, RGB1, causes dwarfism and browning of internodes and lamina joint regions	2011	Plant J	Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka Kenjyojima, Eiheiji-cho, Yoshida-gun, Fukui 910-1195, Japan.	In the present study, we investigated the function of the heterotrimeric G protein beta-subunit (Gbeta) gene (RGB1) in rice. RGB1 knock-down lines were generated in the wild type and d1-5, a mutant deficient for the heterotrimeric G protein alpha-subunit (Galpha) gene (RGA1). Both transgenic lines showed browning of the lamina joint regions and nodes that could be attributed to a reduction of RGB1 function, as the abnormality was not observed in d1-5. The RGB1 knock-down lines generated in d1-5 were shorter, suggesting RGB1 to be a positive regulator of cellular proliferation, in addition to RGA1. The number of sterile seeds also increased in both RGB1 knock-down lines. These results suggest that Gbetagamma and Galpha cooperatively function in cellular proliferation and seed fertility. We discuss the potential predominant role of RGB1 in G protein signaling in rice.	D1|RGA1,RGB1
The U-box E3 ubiquitin ligase TUD1 functions with a heterotrimeric G alpha subunit to regulate Brassinosteroid-mediated growth in rice	2013	PLoS Genet	State Key Laboratory of Molecular Developmental Biology, Chinese Academy of Sciences and National Center for Plant Gene Research, Beijing, China.	Heterotrimeric G proteins are an important group of signaling molecules found in eukaryotes. They function with G-protein-coupled-receptors (GPCRs) to transduce various signals such as steroid hormones in animals. Nevertheless, their functions in plants are not well-defined. Previous studies suggested that the heterotrimeric G protein alpha subunit known as D1/RGA1 in rice is involved in a phytohormone gibberellin-mediated signaling pathway. Evidence also implicates D1 in the action of a second phytohormone Brassinosteroid (BR) and its pathway. However, it is unclear how D1 functions in this pathway, because so far no partner has been identified to act with D1. In this study, we report a D1 genetic interactor Taihu Dwarf1 (TUD1) that encodes a functional U-box E3 ubiquitin ligase. Genetic, phenotypic, and physiological analyses have shown that tud1 is epistatic to d1 and is less sensitive to BR treatment. Histological observations showed that the dwarf phenotype of tud1 is mainly due to decreased cell proliferation and disorganized cell files in aerial organs. Furthermore, we found that D1 directly interacts with TUD1. Taken together, these results demonstrate that D1 and TUD1 act together to mediate a BR-signaling pathway. This supports the idea that a D1-mediated BR signaling pathway occurs in rice to affect plant growth and development.	D1|RGA1,TUD1
Function and expression pattern of the alpha subunit of the heterotrimeric G protein in rice	2010	Plant Cell Physiol	Department of Bioscience, Fukui Prefectural University, 4-1-1 Matsuoka Kenjyojima, Eiheiji-cho, Yoshida-gun, Fukui, 910-1195 Japan.	The d1 mutant, which is deficient for the heterotrimeric G-protein alpha subunit (Galpha) gene of rice, shows dwarfism and sets small round seeds. To determine whether dwarfism in d1 is due to a reduction in cell number or to shortened cell length, the cell number of the leaf sheath, the internode, the root and the lemma was compared between Nipponbare, a wild-type rice and d1-5, a d1 allele derived from Nipponbare. Our results indicate that the cell number was reduced in all organs analyzed in d1-5. In addition, cell enlargement was found in roots and lemma of d1-5, although the organ length in d1-5 was shorter than that of wild-type rice. These results suggest that rice Galpha participates in cell proliferation in rice. Western blot analyses using anti-Galpha antibody and RT-PCR analyses indicate that Galpha is mostly expressed in the developing organs. Galpha promoter activity studies using the GUS reporter gene confirmed that the expression of Galpha was highest in developing organs. We conclude that rice Galpha participates in the regulation of cell number in a developmental stage-dependent manner.	D1|RGA1
Heterotrimeric G protein signaling is required for epidermal cell death in rice	2009	Plant Physiol	Physiologie und Entwicklungsbiologie der Pflanzen, Botanisches Institut, Universitat Kiel, 24118 Kiel, Germany.	In rice (Oryza sativa) adventitious root primordia are formed at the nodes as part of normal development. Upon submergence of rice plants, adventitious roots emerge from the nodes preceded by death of epidermal cells above the root primordia. Cell death is induced by ethylene and mediated by hydrogen peroxide (H(2)O(2)). Pharmacological experiments indicated that epidermal cell death was dependent on signaling through G proteins. Treatment with GTP-gamma-S induced epidermal cell death, whereas GDP-beta-S partially inhibited ethylene-induced cell death. The dwarf1 (d1) mutant of rice has repressed expression of the Galpha subunit RGA1 of heterotrimeric G protein. In d1 plants, cell death in response to ethylene and H(2)O(2) was nearly completely abolished, indicating that signaling through Galpha is essential. Ethylene and H(2)O(2) were previously shown to alter gene expression in epidermal cells that undergo cell death. Transcriptional regulation was not generally affected in the d1 mutant, indicating that altered gene expression is not sufficient to trigger cell death in the absence of Galpha. Analysis of genes encoding proteins related to G protein signaling revealed that four small GTPase genes, two GTPase-activating protein genes, and one GDP dissociation inhibitor gene but not RGA1 were differentially expressed in epidermal cells above adventitious roots, indicating that Galpha activity is regulated posttranscriptionally.	D1|RGA1
Rice gibberellin-insensitive dwarf mutant gene Dwarf1 encodes the alpha-subunit of GTP-binding protein	1999	Proc Natl Acad Sci U S A	Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan.	A rice Dwarf 1 gene was identified by using a map-based cloning strategy. Its recessive mutant allele confers a dwarf phenotype. Linkage analysis revealed that a cDNA encoding the alpha-subunit of GTP-binding protein cosegregated with d1 in 3,185 d1 segregants. Southern hybridization analysis with this cDNA as a probe showed different band patterns in several d1 mutant lines. In at least four independent d1 mutants, no gene transcript was observed by Northern hybridization analysis. Sequencing analysis revealed that an 833-bp deletion had occurred in one of the mutant alleles, which resulted in an inability to express GTP-binding protein. A transgenic d1 mutant with GTP-binding protein gene restored the normal phenotype. We conclude that the rice Dwarf 1 gene encodes GTP-binding protein and that the protein plays an important role in plant growth and development. Because the d1 mutant is classified as gibberellin-insensitive, we suggest that the GTP-binding protein might be associated with gibberellin signal transduction.	D1|RGA1
Rice dwarf mutantd1, which is defective in the a subunit of the heterotrimeric G protein, affects gibberellin signal transduction	2000	Proc Natl Acad Sci U S A	Bioscience Center and Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.	Previously, we reported that the rice dwarf mutant, d1, is defective in the alpha subunit of the heterotrimeric G protein (Galpha). In the present study, gibberellin (GA) signaling in d1 and the role of the Galpha protein in the GA-signaling pathway were investigated. Compared with the wild type, GA induction of alpha-amylase activity in aleurone cells of d1 was greatly reduced. Relative to the wild type, the GA(3)-treated aleurone layer of d1 had lower expression of Ramy1A, which encodes alpha-amylase, and OsGAMYB, which encodes a GA-inducible transcriptional factor, and no increase in expression of Ca(2 +)-ATPase. However, in the presence of high GA concentrations, alpha-amylase induction occurred even in d1. The GA sensitivity of second leaf sheath elongation in d1 was similar to that of the wild type in terms of dose responsiveness, but the response of internode elongation to GA was much lower in d1. Furthermore, Os20ox expression was up-regulated, and the GA content was elevated in the stunted internodes of d1. All these results suggest that d1 affects a part of the GA-signaling pathway, namely the induction of alpha-amylase in the aleurone layer and internode elongation. In addition, a double mutant between d1 and another GA-signaling mutant, slr, revealed that SLR is epistatic to the D1, supporting that the Galpha protein is involved in GA signaling. However, the data also provide evidence for the presence of an alternative GA-signaling pathway that does not involve the Galpha protein. It is proposed that GA signaling via the Galpha protein may be more sensitive than that of the alternative pathway, as indicated by the low GA responsiveness of this Galpha-independent pathway.	D1|RGA1,OsMYBGA|OsGAMYB
A metastable DWARF1 epigenetic mutant affecting plant stature in rice	2009	Proc Natl Acad Sci U S A	Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.	Epigenetic mutations confer heritable changes in gene expression that are not due to changes in the underlying sequence of the DNA. We identified a spontaneous rice mutant, Epi-d1, that shows a metastable dwarf phenotype. The phenotype is mitotically and meiotically inheritable and corresponds to the metastable epigenetic silencing of the DWARF1 (D1) gene. The silenced state is correlated with repressive histone and DNA methylation marks in the D1 promoter region but is not associated with DNA sequence alterations. Compared with other known epigenetic silenced loci in plants such as paramutable maize alleles and silent Arabidopsis genes, the Epi-d1 silencing phenomenon shows a high level of bidirectional metastable mutability. Epigenetic alleles such as Epi-d1 could thus provide for rapid adaptation under selective conditions.	D1|RGA1
Suppression of the heterotrimeric G protein causes abnormal morphology, including dwarfism, in rice	1999	Proc Natl Acad Sci U S A	Department of Bioscience, Fukui Prefectural University, Fukui 910-1195, Japan.	Transgenic rice containing an antisense cDNA for the alpha subunit of rice heterotrimeric G protein produced little or no mRNA for the subunit and exhibited abnormal morphology, including dwarf traits and the setting of small seeds. In normal rice, the mRNA for the alpha subunit was abundant in the internodes and florets, the tissues closely related to abnormality in the dwarf transformants. The position of the alpha-subunit gene was mapped on rice chromosome 5 by mapping with the restriction fragment length polymorphism. The position was closely linked to the locus of a rice dwarf mutant, Daikoku dwarf (d-1), which is known to exhibit abnormal phenotypes similar to those of the transformants that suppressed the endogenous mRNA for the alpha subunit by antisense technology. Analysis of the cDNAs for the alpha subunits of five alleles of Daikoku dwarf (d-1), ID-1, DK22, DKT-1, DKT-2, and CM1361-1, showed that these dwarf mutants had mutated in the coding region of the alpha-subunit gene. These results show that the G protein functions in the formation of normal internodes and seeds in rice.	D1|RGA1
The heterotrimeric G protein alpha subunit acts upstream of the small GTPase Rac in disease resistance of rice	2002	Proc Natl Acad Sci U S A	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan.	We used rice dwarf1 (d1) mutants lacking a single-copy Galpha gene and addressed Galpha's role in disease resistance. d1 mutants exhibited a highly reduced hypersensitive response to infection by an avirulent race of rice blast. Activation of PR gene expression in the leaves of the mutants infected with rice blast was delayed for 24 h relative to the wild type. H(2)O(2) production and PR gene expression induced by sphingolipid elicitors (SE) were strongly suppressed in d1 cell cultures. Expression of the constitutively active OsRac1, a small GTPase Rac of rice, in d1 mutants restored SE-dependent defense signaling and resistance to rice blast. Galpha mRNA was induced by an avirulent race of rice blast and SE application on the leaf. These results indicated the role of Galpha in R gene-mediated disease resistance of rice. We have proposed a model for the defense signaling of rice in which the heterotrimeric G protein functions upstream of the small GTPase OsRac1 in the early steps of signaling.	D1|RGA1,OsRac1
Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice	2006	Nat Biotechnol	Field Production Science Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midoricho, Nishi-Tokyo, Tokyo 188-0002, Japan. orchardist@fm.a.u-tokyo.ac.jp	New cultivars with very erect leaves, which increase light capture for photosynthesis and nitrogen storage for grain filling, may have increased grain yields. Here we show that the erect leaf phenotype of a rice brassinosteroid-deficient mutant, osdwarf4-1, is associated with enhanced grain yields under conditions of dense planting, even without extra fertilizer. Molecular and biochemical studies reveal that two different cytochrome P450s, CYP90B2/OsDWARF4 and CYP724B1/D11, function redundantly in C-22 hydroxylation, the rate-limiting step of brassinosteroid biosynthesis. Therefore, despite the central role of brassinosteroids in plant growth and development, mutation of OsDWARF4 alone causes only limited defects in brassinosteroid biosynthesis and plant morphology. These results suggest that regulated genetic modulation of brassinosteroid biosynthesis can improve crops without the negative environmental effects of fertilizers.	D11|CYP724B1,OsDWARF4|CYP90B2,OsCPD1
A novel cytochrome P450 is implicated in brassinosteroid biosynthesis via the characterization of a rice dwarf mutant, dwarf11, with reduced seed length	2005	Plant Cell	Fukui Prefectural University, Faculty of Bioscience, Kenjyojima, Matsuoka-cho, Yoshida-gun, Fukui 910-1195, Japan.	We have characterized a rice (Oryza sativa) dwarf mutant, dwarf11 (d11), that bears seeds of reduced length. To understand the mechanism by which seed length is regulated, the D11 gene was isolated by a map-based cloning method. The gene was found to encode a novel cytochrome P450 (CYP724B1), which showed homology to enzymes involved in brassinosteroid (BR) biosynthesis. The dwarf phenotype of d11 mutants was restored by the application of the brassinolide (BL). Compared with wild-type plants, the aberrant D11 mRNA accumulated at higher levels in d11 mutants and was dramatically reduced by treatment with BL, implying that the gene is feedback-regulated by BL. Precise determination of the defective step(s) in BR synthesis in d11 mutants proved intractable because of tissue specificity and the complex control of BR accumulation in plants. However, 6-deoxotyphasterol (6-DeoxoTY) and typhasterol (TY), but not any upstream intermediates before these compounds, effectively restored BR response in d11 mutants in a lamina joint bending assay. Multiple lines of evidence together suggest that the D11/CYP724B1 gene plays a role in BR synthesis and may be involved in the supply of 6-DeoxoTY and TY in the BR biosynthesis network in rice.	D11|CYP724B1
RAV-Like1 maintains brassinosteroid homeostasis via the coordinated activation of BRI1 and biosynthetic genes in rice	2010	Plant Cell	Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center, Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.	Temporal and spatial variation in the levels of and sensitivity to hormones are essential for the development of higher organisms. Traditionally, end-product feedback regulation has been considered as the key mechanism for the achievement of cellular homeostasis. Brassinosteroids (BRs) are plant steroid hormones that are perceived by the cell surface receptor kinase Brassinosteroid Insensitive1. Binding of these hormones to the receptor activates BR signaling and eventually suppresses BR synthesis. This report shows that RAVL1 regulates the expression of the BR receptor. Furthermore, RAVL1 is also required for the expression of the BR biosynthetic genes D2, D11, and BRD1 that are subject to BR negative feedback. Activation by RAVL1 was coordinated via E-box cis-elements in the promoters of the receptor and biosynthetic genes. Also, RAVL1 is necessary for the response of these genes to changes in cellular BR homeostasis. Genetic evidence is presented to strengthen the observation that the primary action of RAVL1 mediates the expression of genes involved in BR signaling and biosynthesis. This study thus describes a regulatory circuit modulating the homeostasis of BR in which RAVL1 ensures the basal activity of both the signaling and the biosynthetic pathways.	D11|CYP724B1,D2|CYP90D2,D61|OsBRI1,RAVL1
The multiple contributions of phytochromes to the control of internode elongation in rice	2011	Plant Physiol	Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. iwamas@nias.affrc.go.jp	Although phyAphyBphyC phytochrome-null mutants in rice (Oryza sativa) have morphological changes and exhibit internode elongation, even as seedlings, it is unknown how phytochromes contribute to the control of internode elongation. A gene for 1-aminocyclopropane-1-carboxylate oxidase (ACO1), which is an ethylene biosynthesis gene contributing to internode elongation, was up-regulated in phyAphyBphyC seedlings. ACO1 expression was controlled mainly by phyA and phyB, and a histochemical analysis showed that ACO1 expression was localized to the basal parts of leaf sheaths of phyAphyBphyC seedlings, similar to mature wild-type plants at the heading stage, when internode elongation was greatly promoted. In addition, the transcription levels of several ethylene- or gibberellin (GA)-related genes were changed in phyAphyBphyC mutants, and measurement of the plant hormone levels indicated low ethylene production and bioactive GA levels in the phyAphyBphyC mutants. We demonstrate that ethylene induced internode elongation and ACO1 expression in phyAphyBphyC seedlings but not in the wild type and that the presence of bioactive GAs was necessary for these effects. These findings indicate that phytochromes contribute to multiple steps in the control of internode elongation, such as the expression of the GA biosynthesis gene OsGA3ox2, ACO1 expression, and the onset of internode elongation.	d18|OsGA3ox2,OsACO1,PHYA,PHYB|OsphyB,PHYC
Gibberellin is not a regulator of miR156 in rice juvenile-adult phase change	2012	Rice	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan	Plant hormone gibberellin (GA) promotes juvenile-adult phase change in higher plants. To confirm the functions of GA in rice, I used dwarf mutant d18-dy. d18-dy is a loss-of-function allele of D18, which encodes GA3ox2. d18-dy mutant exhibited long juvenile phase in morphological traits such as the size of the shoot apical meristem (SAM), shape of leaf blades, presence or absence of midribs and node–internode differentiation in stem. In contrast, expression patterns of juvenile-adult phase change markers miR156 and miR172 were similar between wild type and d18-dy. In addition, d18-dy mutation and GA did not affect expression levels of downstream genes of miR156. GA does not function upstream of miR156 in juvenile-adult phase change.	d18|OsGA3ox2
OsDOG, a gibberellin-induced A20/AN1 zinc-finger protein, negatively regulates gibberellin-mediated cell elongation in rice	2011	J Plant Physiol	Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	The A20/AN1 zinc-finger proteins (ZFPs) play pivotal roles in animal immune responses and plant stress responses. From previous gibberellin (GA) microarray data and A20/AN1 ZFP family member association, we chose Oryza sativa dwarf rice with overexpression of gibberellin-induced gene (OsDOG) to examine its function in the GA pathway. OsDOG was induced by gibberellic acid (GA(3)) and repressed by the GA-synthesis inhibitor paclobutrazol. Different transgenic lines with constitutive expression of OsDOG showed dwarf phenotypes due to deficiency of cell elongation. Additional GA(1) and real-time PCR quantitative assay analyses confirmed that the decrease of GA(1) in the overexpression lines resulted from reduced expression of GA3ox2 and enhanced expression of GA2ox1 and GA2ox3. Adding exogenous GA rescued the constitutive expression phenotypes of the transgenic lines. OsDOG has a novel function in regulating GA homeostasis and in negative maintenance of plant cell elongation in rice.	d18|OsGA3ox2,GA2OX3,OsGA2ox1,OsDOG|OsSAP11
The rice YABBY1 gene is involved in the feedback regulation of gibberellin metabolism	2007	Plant Physiol	National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.	Gibberellin (GA) biosynthesis is regulated by feedback control providing a mechanism for GA homeostasis in plants. However, regulatory elements involved in the feedback control are not known. In this report, we show that a rice (Oryza sativa) YABBY1 (YAB1) gene had a similar expression pattern as key rice GA biosynthetic genes GA3ox2 and GA20ox2. Overexpression of YAB1 in transgenic rice resulted in a semidwarf phenotype that could be fully rescued by applied GA. Quantification of the endogenous GA content revealed increases of GA(20) and decreases of GA(1) levels in the overexpression plants, in which the transcripts of the biosynthetic gene GA3ox2 were decreased. Cosuppression of YAB1 in transgenic plants induced expression of GA3ox2. The repression of GA3ox2 could be obtained upon treatment by dexamethasone of transgenic plants expressing a YAB1-glucocorticoid receptor fusion. Importantly, we show that YAB1 bound to a GA-responsive element within the GA3ox2 promoter. In addition, the expression of YAB1 was deregulated in GA biosynthesis and signaling mutants and could be either transiently induced by GA or repressed by a GA inhibitor. Finally, either overexpression or cosuppression of YAB1 impaired GA-mediated repression of GA3ox2. These data together suggest that YAB1 is involved in the feedback regulation of GA biosynthesis in rice.	d18|OsGA3ox2,OsYABBY1|OsYAB1,sd1|GA20ox2
Cloning and functional analysis of two gibberellin 3 beta -hydroxylase genes that are differently expressed during the growth of rice	2001	Proc Natl Acad Sci U S A	Bioscience Center, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.	We have cloned two gibberellin (GA) 3 beta-hydroxylase genes, OsGA3ox1 and OsGA3ox2, from rice by screening a genomic library with a DNA fragment obtained by PCR using degenerate primers. We have used full-scan GC-MS and Kovats retention indices to show function for the two encoded recombinant fusion proteins. Both proteins show 3 beta-hydroxylase activity for the steps GA(20) to GA(1), GA(5) to GA(3), GA(44) to GA(38), and GA(9) to GA(4). In addition, indirect evidence suggests that the OsGA3ox1 protein also has 2,3-desaturase activity, which catalyzes the steps GA(9) to 2,3-dehydro-GA(9) and GA(20) to GA(5) (2,3-dehydro GA(20)), and 2 beta-hydroxylase activity, which catalyzes the steps GA(1) to GA(8) and GA(4) to GA(34). Molecular and linkage analysis maps the OsGA3ox1 gene to the distal end of the short arm of chromosome 5; the OsGA3ox2 gene maps to the distal end of the short arm of chromosome 1 that corresponds to the D18 locus. The association of the OsGA3ox2 gene with the d18 locus is confirmed by sequence and complementation analysis of three d18 alleles. Complementation of the d18-AD allele with the OxGA3ox2 gene results in transgenic plants with a normal phenotype. Although both genes show transient expression, the highest level for OsGA3ox1 is from unopened flower. The highest level for OsGA3ox2 is from elongating leaves.	d18|OsGA3ox2,OsGA3ox1
The rice GERMINATION DEFECTIVE 1, encoding a B3 domain transcriptional repressor, regulates seed germination and seedling development by integrating GA and carbohydrate metabolism	2013	Plant J	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research-Beijing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	It has been shown that seed development is regulated by a network of transcription factors in Arabidopsis including LEC1 (LEAFY COTYLEDON1), L1L (LEC1-like) and the B3 domain factors LEC2, FUS3 (FUSCA3) and ABI3 (ABA-INSENSITIVE3); however, molecular and genetic regulation of seed development in cereals is poorly understood. To understand seed development and seed germination in cereals, a large-scale screen was performed using our T-DNA mutant population, and a mutant germination-defective1 (gd1) was identified. In addition to the severe germination defect, the gd1 mutant also shows a dwarf phenotype and abnormal flower development. Molecular and biochemical analyses revealed that GD1 encodes a B3 domain-containing transcription factor with repression activity. Consistent with the dwarf phenotype of gd1, expression of the gibberelic acid (GA) inactivation gene OsGA2ox3 is increased dramatically, accompanied by reduced expression of GA biosynthetic genes including OsGA20ox1, OsGA20ox2 and OsGA3ox2 in gd1, resulting in a decreased endogenous GA(4) level. Exogenous application of GA not only induced GD1 expression, but also partially rescued the dwarf phenotype of gd1. Furthermore, GD1 binds to the promoter of OsLFL1, a LEC2/FUS3-like gene of rice, via an RY element, leading to significant up-regulation of OsLFL1 and a large subset of seed maturation genes in the gd1 mutant. Plants over-expressing OsLFL1 partly mimic the gd1 mutant. In addition, expression of GD1 was induced under sugar treatment, and the contents of starch and soluble sugar are altered in the gd1 mutant. These data indicate that GD1 participates directly or indirectly in regulating GA and carbohydrate homeostasis, and further regulates rice seed germination and seedling development.	d18|OsGA3ox2,GD1,OsGA20ox1,OsLFL1
Proteomic identification of small, copper-responsive proteins in germinating embryos of Oryza sativa	2009	Ann Bot	College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China.	BACKGROUND AND AIMS: Although copper (Cu) is an essential micronutrient for plants and algae, excess Cu is toxic to most plants and can cause a wide range of deleterious effects. To investigate the response of rice (Oryza sativa) to Cu stress, a proteomic approach was used to analyse Cu stress-induced changes in the expression of low molecular-weight proteins in germinating rice seed embryos. METHODS: Rice seeds were germinated in the presence or absence of 200 microm Cu for 6 d, and embryos, including newly formed shoots and radicles, were isolated. After proteins were extracted from the germinating embryos and separated by two-dimensional PAGE, 16 proteins in the 6- to 25-kDa range were identified using MALDI-TOF mass spectrometry. KEY RESULTS AND CONCLUSIONS: Thirteen of the proteins identified, including metallothionein-like protein, membrane-associated protein-like protein, putative wall-associated protein kinase, pathogenesis-related proteins and the putative small GTP-binding protein Rab2, were up-regulated by Cu stress. Three proteins, a putative small cytochrome P450 (CYP90D2), a putative thioredoxin and a putative GTPase, were down-regulated by Cu stress. As far as is known, this study provides the first proteomic evidence that metallothionein and CYP90D2 are Cu-responsive proteins in plants. These findings may lead to a better understanding of plant molecular responses to toxic metal exposure.	D2|CYP90D2
A comprehensive genetic study reveals a crucial role of CYP90D2/D2 in regulating plant architecture in rice (Oryza sativa)	2013	New Phytol	State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.	Brassinosteroids (BRs) are essential regulators of plant architecture. Understanding how BRs control plant height and leaf angle would facilitate development of new plant type varieties by biotechnology. A number of mutants involved in BR biosynthesis have been isolated but many of them lack detailed genetic analysis. Here, we report the isolation and characterization of a severe dwarf mutant, chromosome segment deleted dwarf 1 (csdd1), which was deficient in BR biosynthesis in rice. We isolated the mutant by screening a tissue culture-derived population, cloned the gene by mapping, and confirmed its function by complementary and RNAi experiments, combined with physiological and chemical analysis. We showed that the severe dwarf phenotype was caused by a complete deletion of a cytochrome P450 gene, CYP90D2/D2, which was further confirmed in two independent T-DNA insertion lines in different genetic backgrounds and by RNA interference. Our chemical analysis suggested that CYP90D2/D2 might catalyze C-3 dehydrogenation step in BR biosynthesis. We have demonstrated that the CYP90D2/D2 gene plays a more important role than previously reported. Allelic mutations of CYP90D2/D2 confer varying degrees of dwarfism and leaf angle, thus providing useful information for molecular breeding in grain crop plants.	D2|CYP90D2
DWARF10, an RMS1/MAX4/DAD1 ortholog, controls lateral bud outgrowth in rice	2007	Plant J	Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo 113-0032, Japan.	Plant architecture is mostly determined by shoot branching patterns. Apical dominance is a well-known control mechanism in the development of branching patterns, but little is known regarding its role in monocots such as rice. Here, we show that the concept of apical dominance can be applied to tiller bud outgrowth of rice. In dwarf10 (d10), an enhanced branching mutant of rice, apical dominance can be observed, but the inhibitory effects of the apical meristem was reduced. D10 is a rice ortholog of MAX4/RMS1/DAD1 that encodes a carotenoid cleavage dioxygenase 8 and is supposed to be involved in the synthesis of an unidentified inhibitor of shoot branching. D10 expression predominantly occurs in vascular cells in most organs. Real-time polymerase chain reaction analysis revealed that accumulation of D10 mRNA is induced by exogenous auxin. Moreover, D10 expression is upregulated in six branching mutants, d3, d10, d14, d17, d27 and high tillering dwarf (htd1). No such effects were found for D3 or HTD1, the MAX2 and MAX3 orthologs, respectively, of rice. These findings imply that D10 transcription might be a critical step in the regulation of the branching inhibitor pathway. In addition, we present observations that suggest that FINE CULM1 (FC1), a rice ortholog of teosinte branched 1 (tb1), possibly works independently of the branching inhibitor pathway.	D27,D3,HTD1|OsCCD7,HTD2|D88|D14,D10|OsCCD8|OsCCD8b,OsTB1|FC1
DWARF27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud outgrowth	2009	Plant Cell	State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Tillering in rice (Oryza sativa) is one of the most important agronomic traits that determine grain yields. Previous studies on rice tillering mutants have shown that the outgrowth of tiller buds in rice is regulated by a carotenoid-derived MAX/RMS/D (more axillary branching) pathway, which may be conserved in higher plants. Strigolactones, a group of terpenoid lactones, have been recently identified as products of the MAX/RMS/D pathway that inhibits axillary bud outgrowth. We report here the molecular genetic characterization of d27, a classic rice mutant exhibiting increased tillers and reduced plant height. D27 encodes a novel iron-containing protein that localizes in chloroplasts and is expressed mainly in vascular cells of shoots and roots. The phenotype of d27 is correlated with enhanced polar auxin transport. The phenotypes of the d27 d10 double mutant are similar to those of d10, a mutant defective in the ortholog of MAX4/RMS1 in rice. In addition, 2'-epi-5-deoxystrigol, an identified strigolactone in root exudates of rice seedlings, was undetectable in d27, and the phenotypes of d27 could be rescued by supplementation with GR24, a synthetic strigolactone analog. Our results demonstrate that D27 is involved in the MAX/RMS/D pathway, in which D27 acts as a new member participating in the biosynthesis of strigolactones.	D27
Strigolactone biosynthesis in Medicago truncatula and rice requires the symbiotic GRAS-type transcription factors NSP1 and NSP2	2011	Plant Cell	Department of Plant Science, Laboratory of Molecular Biology, Wageningen University, 6708 PB Wageningen, The Netherlands.	Legume GRAS (GAI, RGA, SCR)-type transcription factors NODULATION SIGNALING PATHWAY1 (NSP1) and NSP2 are essential for rhizobium Nod factor-induced nodulation. Both proteins are considered to be Nod factor response factors regulating gene expression after symbiotic signaling. However, legume NSP1 and NSP2 can be functionally replaced by nonlegume orthologs, including rice (Oryza sativa) NSP1 and NSP2, indicating that both proteins are functionally conserved in higher plants. Here, we show that NSP1 and NSP2 are indispensable for strigolactone (SL) biosynthesis in the legume Medicago truncatula and in rice. Mutant nsp1 plants do not produce SLs, whereas in M. truncatula, NSP2 is essential for conversion of orobanchol into didehydro-orobanchol, which is the main SL produced by this species. The disturbed SL biosynthesis in nsp1 nsp2 mutant backgrounds correlates with reduced expression of DWARF27, a gene essential for SL biosynthesis. Rice and M. truncatula represent distinct phylogenetic lineages that split approximately 150 million years ago. Therefore, we conclude that regulation of SL biosynthesis by NSP1 and NSP2 is an ancestral function conserved in higher plants. NSP1 and NSP2 are single-copy genes in legumes, which implies that both proteins fulfill dual regulatory functions to control downstream targets after rhizobium-induced signaling as well as SL biosynthesis in nonsymbiotic conditions.	D27,OsNSP1,OsNSP2
The Arabidopsis ortholog of rice DWARF27 acts upstream of MAX1 in the control of plant development by strigolactones	2012	Plant Physiol	Plant Energy Biology , University of Western Australia, Crawley, Western Australia 6009, Australia.	Strigolactones (SLs) are carotenoid-derived plant hormones that regulate shoot branching, secondary growth, root development, and responses to soil phosphate. In Arabidopsis (Arabidopsis thaliana), SL biosynthesis requires the sequential action of two carotenoid cleavage dioxygenases, MORE AXILLARY GROWTH3 (MAX3) and MAX4, followed by a cytochrome P450, MAX1. In rice (Oryza sativa), the plastid-localized protein DWARF27 (OsD27) is also necessary for SL biosynthesis, but the equivalent gene in Arabidopsis has not been identified. Here, we use phylogenetic analysis of D27-like sequences from photosynthetic organisms to identify AtD27, the likely Arabidopsis ortholog of OsD27. Using reverse genetics, we show that AtD27 is required for the inhibition of secondary bud outgrowth and that exogenous application of the synthetic SL GR24 can rescue the increased branching phenotype of an Atd27 mutant. Furthermore, we use grafting to demonstrate that AtD27 operates on a nonmobile precursor upstream of MAX1 in the SL biosynthesis pathway. Consistent with the plastid localization of OsD27, we also show that AtD27 possesses a functional plastid transit peptide. We demonstrate that AtD27 transcripts are subject to both local feedback and auxin-dependent signals, albeit to a lesser extent than MAX3 and MAX4, suggesting that early steps in SL biosynthesis are coregulated at the transcriptional level. By identifying an additional component of the canonical SL biosynthesis pathway in Arabidopsis, we provide a new tool to investigate the regulation of shoot branching and other SL-dependent developmental processes.	D27
Identification and characterization of HTD2: a novel gene negatively regulating tiller bud outgrowth in rice	2009	Planta	State Key Laboratory of Rice Biology, China National Rice Research Institute, 310006 Hangzhou, Zhejiang, China. lwzzju@163.com	Tiller number is highly regulated by controlling the formation of tiller bud and its subsequent outgrowth in response to endogenous and environmental signals. Here, we identified a rice mutant htd2 from one of the 15,000 transgenic rice lines, which is characterized by a high tillering and dwarf phenotype. Phenotypic analysis of the mutant showed that the mutation did not affect formation of tiller bud, but promoted the subsequent outgrowth of tiller bud. To isolate the htd2 gene, a map-based cloning strategy was employed and 17 new insertions-deletions (InDels) markers were developed. A high-resolution physical map of the chromosomal region around the htd2 gene was made using the F(2) and F(3) population. Finally, the gene was mapped in 12.8 kb region between marker HT41 and marker HT52 within the BAC clone OSJNBa0009J13. Cloning and sequencing of the target region from the mutant showed that the T-DNA insertion caused a 463 bp deletion between the promoter and first exon of an esterase/lipase/thioesterase family gene in the 12.8 kb region. Furthermore, transgenic rice with reduced expression level of the gene exhibited an enhanced tillering and dwarf phenotype. Accordingly, the esterase/lipase/thioesterase family gene (TIGR locus Os03g10620) was identified as the HTD2 gene. HTD2 transcripts were expressed mainly in leaf. Loss of function of HTD2 resulted in a significantly increased expression of HTD1, D10 and D3, which were involved in the strigolactone biosynthetic pathway. The results suggest that the HTD2 gene could negatively regulate tiller bud outgrowth by the strigolactone pathway.	D3,HTD1|OsCCD7,HTD2|D88|D14,D10|OsCCD8|OsCCD8b
Rice tillering dwarf mutant dwarf3 has increased leaf longevity during darkness-induced senescence or hydrogen peroxide-induced cell death	2007	Genes Genet Syst	Graduate School of Agricultural and Life Sciences, The University of Tokyo	Senescence or cell death in plant leaves is known to be inducible by darkness or H(2)O(2). When the Arabidopsis gene MAX2/ORE9 is disrupted, leaf senescence or cell death in response to the above stimuli is delayed. Because the rice (Oryza sativa L.) gene DWARF3 (D3) is orthologous to MAX2/ORE9, we wished to know whether disruption of D3 also results in increased longevity in leaves. We found that darkness-induced senescence or H(2)O(2)-induced cell death in the third leaf [as measured by chlorophyll degradation, membrane ion leakage and expression of senescence-associated genes (SAGs)] in a d3 rice mutant was delayed by 1-3 d compared to that in its reference line Shiokari. Moreover, the mRNA levels of D3, HTD1 and D10, which are orthologs of Arabidopsis MAX2/ORE9, MAX3 and MAX4, respectively, increased during cell death. These results suggest that D3 protein in rice, like MAX2/ORE9 in Arabidopsis, is involved in leaf senescence or cell death.	D3,HTD1|OsCCD7,D10|OsCCD8|OsCCD8b
Genetic interaction between 2 tillering genes, reduced culm number 1 (rcn1) and tillering dwarf gene d3, in rice	2007	J Hered	Department of Crop Science Obihiro University of Agriculture and Veterinary Medicine, Nishi Inada-cho, Obihiro, Hokkaido, Japan.	Mutant genes, reduced culm number 1 (rcn1) and bunketsuwaito tillering dwarf (d3), affect tiller number in rice (Oryza sativa L.) in opposite directions. The d3 mutant was reported to increase tiller number and reduce plant stature. Our objective was to compare the phenotype of the d3rcn1 double mutant with each single mutant and parental rice cultivar "Shiokari" and to clarify whether the Rcn1 gene interacted with the D3 gene. We recovered a new rcn1 mutant from Shiokari and developed d3rcn1 double mutant with Shiokari genetic background. A new rcn1 mutant, designated as "S-97-61" exhibited a reduction in tiller number and plant stature to about the same level as the previously reported original rcn1 mutant. Three near-isogenic lines, rcn1 mutant, d3 mutant, and d3rcn1 double mutant, were grown together with the parental Shiokari. The reduction in tillering by the rcn1 mutation was independent of the d3 genotype, and tillering number of d3rcn1 double mutant was between those of the d3 and rcn1 mutants. These results demonstrated that the Rcn1 gene was not involved in the D3-associated pathway in tillering control.	D3,Rcn1
The rice HIGH-TILLERING DWARF1 encoding an ortholog of Arabidopsis MAX3 is required for negative regulation of the outgrowth of axillary buds	2006	Plant J	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Rice tillering is an important agronomic trait for grain production. The HIGH-TILLERING DWARF1 (HTD1) gene encodes an ortholog of Arabidopsis MAX3. Complementation analyses for HTD1 confirm that the defect in HTD1 is responsible for both high-tillering and dwarf phenotypes in the htd1 mutant. The rescue of the Arabidopsis max3 mutant phenotype by the introduction of Pro(35S):HTD1 indicates HTD1 is a carotenoid cleavage dioxygenase that has the same function as MAX3 in synthesis of a carotenoid-derived signal molecule. The HTD1 gene is expressed in both shoot and root tissues. By evaluating Pro(HTD1):GUS expression, we found that the HTD1 gene is mainly expressed in vascular bundle tissues throughout the plant. Auxin induction of HTD1 expression suggests that auxin may regulate rice tillering partly through upregulation of HTD1 gene transcription. Restoration of dwarf phenotype after the removal of axillary buds indicates that the dwarfism of the htd1 mutant may be a consequence of excessive tiller production. In addition, the expression of HTD1, D3 and OsCCD8a in the htd1 and d3 mutants suggests a feedback mechanism may exist for the synthesis and perception of the carotenoid-derived signal in rice. Characterization of MAX genes in Arabidopsis, and identification of their orthologs in pea, petunia and rice indicates the existence of a conserved mechanism for shoot-branching regulation in both monocots and dicots.	D3,HTD1|OsCCD7,D10|OsCCD8|OsCCD8b
DWARF 53 acts as a repressor of strigolactone signalling in rice	2013	Nature	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China	Strigolactones (SLs) are a group of newly identified plant hormones that control plant shoot branching. SL signalling requires the hormone-dependent interaction of DWARF 14 (D14), a probable candidate SL receptor, with DWARF 3 (D3), an F-box component of the Skp-Cullin-F-box (SCF) E3 ubiquitin ligase complex. Here we report the characterization of a dominant SL-insensitive rice (Oryza sativa) mutant dwarf 53 (d53) and the cloning of D53, which encodes a substrate of the SCF(D3) ubiquitination complex and functions as a repressor of SL signalling. Treatments with GR24, a synthetic SL analogue, cause D53 degradation via the proteasome in a manner that requires D14 and the SCF(D3) ubiquitin ligase, whereas the dominant form of D53 is resistant to SL-mediated degradation. Moreover, D53 can interact with transcriptional co-repressors known as TOPLESS-RELATED PROTEINS. Our results suggest a model of SL signalling that involves SL-dependent degradation of the D53 repressor mediated by the D14-D3 complex.	D3,D53,HTD2|D88|D14
D14-SCF(D3)-dependent degradation of D53 regulates strigolactone signalling	2013	Nature	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China [2] National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.	Strigolactones (SLs), a newly discovered class of carotenoid-derived phytohormones, are essential for developmental processes that shape plant architecture and interactions with parasitic weeds and symbiotic arbuscular mycorrhizal fungi. Despite the rapid progress in elucidating the SL biosynthetic pathway, the perception and signalling mechanisms of SL remain poorly understood. Here we show that DWARF 53 (D53) acts as a repressor of SL signalling and that SLs induce its degradation. We find that the rice (Oryza sativa) d53 mutant, which produces an exaggerated number of tillers compared to wild-type plants, is caused by a gain-of-function mutation and is insensitive to exogenous SL treatment. The D53 gene product shares predicted features with the class I Clp ATPase proteins and can form a complex with the alpha/beta hydrolase protein DWARF 14 (D14) and the F-box protein DWARF 3 (D3), two previously identified signalling components potentially responsible for SL perception. We demonstrate that, in a D14- and D3-dependent manner, SLs induce D53 degradation by the proteasome and abrogate its activity in promoting axillary bud outgrowth. Our combined genetic and biochemical data reveal that D53 acts as a repressor of the SL signalling pathway, whose hormone-induced degradation represents a key molecular link between SL perception and responses.	D3,D53,HTD2|D88|D14
Suppression of tiller bud activity in tillering dwarf mutants of rice	2005	Plant Cell Physiol	Graduate School of Agriculture and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657 Japan.	In this study, we analyzed five tillering dwarf mutants that exhibit reduction of plant stature and an increase in tiller numbers. We show that, in the mutants, axillary meristems are normally established but the suppression of tiller bud activity is weakened. The phenotypes of tillering dwarf mutants suggest that they play roles in the control of tiller bud dormancy to suppress bud activity. However, tillering dwarf mutants show the dependence of both node position and planting density on their growth, which implies that the functions of tillering dwarf genes are independent of the developmental and environmental control of bud activity. Map-based cloning of the D3 gene revealed that it encodes an F-box leucine-trich repeat (LRR) protein orthologous to Arabidopsis MAX2/ORE9. This indicates the conservation of mechanisms controlling axillary bud activity between monocots and eudicots. We suggest that tillering dwarf mutants are suitable for the study of bud activity control in rice and believe that future molecular and genetic studies using them may enable significant progress in understanding the control of tillering and shoot branching.	D3
DWARF50 (D50), a rice (Oryza sativa L.) gene encoding inositol polyphosphate 5-phosphatase, is required for proper development of intercalary meristem	2012	Plant Cell Environ	Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan. ikanna@cc.tuat.ac.jp	Rice internodes are vital for supporting high-yield panicles, which are controlled by various factors such as cell division, cell elongation and cell wall biosynthesis. Therefore, formation and regulation of the internode cell-producing intercalary meristem (IM) are important for determining the shape of internodes. To understand the regulation of internode development, we analysed a rice dwarf mutant, dwarf 50 (d50). Previously, we reported that parenchyma cells in the elongated internodes of d50 ectopically deposit cell wall phenolics. In this study, we revealed that D50 encodes putative inositol polyphosphate 5-phosphatase (5PTase), which may be involved in phosphoinositide signalling required for many essential cellular functions, such as cytoskeleton organization, endocytosis and vesicular trafficking in eukaryotes. Analysis of the rice genome revealed 20 putative 5PTases including D50. The d50 mutation induced abnormally oriented cell division, irregular deposition of cell wall pectins and thick actin bundles in the parenchyma cells of the IM, resulting in abnormally organized cell files of the internode parenchyma and dwarf phenotype. Our results suggest that the putative 5PTase, encoded by D50, is essential for IM formation, including the direction of cell division, deposition of cell wall pectins and control of actin organization.	D50
Loss-of-function mutations in the rice homeobox gene OSH15 affect the architecture of internodes resulting in dwarf plants	1999	EMBO J	Nagoya University, BioScience Center, Chikusa, Nagoya 464-8601, USA.	The rice homeobox gene OSH15 (Oryza sativa homeobox) is a member of the knotted1-type homeobox gene family. We report here on the identification and characterization of a loss-of-function mutation in OSH15 from a library of retrotransposon-tagged lines of rice. Based on the phenotype and map position, we have identified three independent deletion alleles of the locus among conventional morphological mutants. All of these recessive mutations, which are considered to be null alleles, exhibit defects in internode elongation. Introduction of a 14 kbp genomic DNA fragment that includes all exons, introns and 5'- and 3'- flanking sequences of OSH15 complemented the defects in internode elongation, confirming that they were caused by the loss-of-function of OSH15. Internodes of the mutants had abnormal-shaped epidermal and hypodermal cells and showed an unusual arrangement of small vascular bundles. These mutations demonstrate a role for OSH15 in the development of rice internodes. This is the first evidence that the knotted1-type homeobox genes have roles other than shoot apical meristem formation and/or maintenance in plant development.	D6|OSH15|Oskn3
Overexpression of rice OSH genes induces ectopic shoots on leaf sheaths of transgenic rice plants	2000	Dev Biol	BioScience Center, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.	Five rice homeobox (OSH) genes were overexpressed under the control of the cauliflower mosaic virus 35S promoter or the rice actin gene promoter in transgenic rice plants. Almost all of the transgenic plants showed abnormal phenotypes, which could be classified into three types according to their severity. Plants with the most severe phenotype formed only green organs, with many shoot apices on their adaxial sides. Plants with an intermediate phenotype formed bladeless leaves with normally developed leaf sheaths. Plants with a mild phenotype formed normal leaf sheaths and blades, but lacked ligules and showed diffusion of the blade-sheath boundary. The leaf structure of this phenotype was similar to that of dominant maize mutants, such as Kn1, Rs1, Lg3, and Lg4. Based on these phenotypes, we suggest that ectopic expression of the rice OSH genes interferes with the development of leaf blades and maintains leaves in less differentiated states. These results are discussed in relation to the leaf maturation schedule hypothesis (M. Freeling et al., 1992, BioEssays 14, 227-236).	D6|OSH15|Oskn3,OSH1|Oskn1,OSH43,OSH6,OSH71|Oskn2
Disruption of KNOX gene suppression in leaf by introducing its cDNA in rice	2008	Plant Science	Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan	KNOX class 1 homeobox genes play a crucial role in formation and/or maintenance of the shoot apical meristem (SAM) in plants, and their SAM-specific expression is essential for normal development of plants. We examined regulation of expression of OSH1, a KNOX gene in rice. A 5′ upstream region of OSH1 had the ability to direct the expression of a reporter gene in leaf in addition to the SAM. Introduction of OSH1 cDNA without a promoter sequence caused ectopic expression of both endogenous OSH1 and introduced OSH1 cDNA itself into the leaf, which resulted in morphological abnormalities in the leaf resembling those of the overexpressors. These results indicate that an extra copy of OSH1 exons with no promoter sequence disrupts suppression of OSH1 in the transgenic leaf. Introduction of cDNAs of two other KNOX genes, OSH15 and OSH71, also showed ectopic expression. These results suggest that the exon sequences of KNOX genes function as one of the major cis-regulatory elements of KNOX gene expression. We present and discuss a possible model which interprets these results.	D6|OSH15|Oskn3,OSH1|Oskn1,OSH71|Oskn2
SUI-family genes encode phosphatidylserine synthases and regulate stem development in rice	2013	Planta	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	In vascular plants, the regulation of stem cell niche determines development of aerial shoot which consists of stems and lateral organs. Intercalary meristem (IM) controls internode elongation in rice and other grasses, however little attention has been paid to the underlying mechanism of stem cell maintenance. Here, we investigated the stem development in rice and showed that the Shortened Uppermost Internode 1 (SUI1) family of genes are pivotal for development of rice stems. We demonstrated that SUI-family genes regulate the development of IM for internode elongation and also the cell expansion of the panicle stem rachis in rice. The SUI-family genes encoded base-exchange types of phosphatidylserine synthases (PSSs), which possessed enzymatic activity in a yeast complementary assay. Overexpression of SUI1 and SUI2 caused outgrowths of internodes during vegetative development, and we showed that expression patterns of Oryza Sativa Homeobox 15 (OSH15) and Histone4 were impaired. Furthermore, genome-wide gene expression analysis revealed that overexpression and RNA knockdown of SUI-family genes affected downstream gene expression related to phospholipid metabolic pathways. Moreover, using Ultra-performance liquid chromatography-quadrupole time of flight-mass spectrometry, we analyzed PS contents in different genetic backgrounds of rice and showed that the quantity of very long chain fatty acids PS is affected by transgene of SUI-family genes. Our study reveals a new mechanism conveyed by the SUI1 pathway and provides evidence to link lipid metabolism with plant stem cell maintenance.	D6|OSH15|Oskn3,OsSUI1,SUI2,SUI3
Isolation and characterization of a rice homebox gene, OSH15	1998	Plant Mol Biol	Nagoya University, BioScience Center, Chikusa, Japan.	In many eukaryotic organisms including plants, homeobox genes are thought to be master regulators that establish the cellular or regional identities and specify the fundamental body plan. We isolated and characterized a cDNA designated OSH15 (Oryza sativa homeobox 15) that encodes a KNOTTED-type homeodomain protein. Transgenic tobacco plants overexpressing the OSH15 cDNA showed a dramatically altered morphological phenotype caused by disturbance of specific aspects of tobacco development, thereby indicating the involvement of OSH15 in plant development. We analyzed the in situ mRNA localization of OSH15 through the whole plant life cycle, comparing the expression pattern with that of another rice homeobox gene, OSH1. In early embryogenesis, both genes were expressed as the same pattern at a region where the shoot apical meristem would develop later. In late embryogenesis, the expression pattern of the two genes became different. Whereas the expression of OSH1 continued within the shoot apical meristem, OSH15 expression within the shoot apical meristem ceased but became observable in a ring shaped pattern at the boundaries of some embryonic organs. This pattern of expression was similar to that observed around vegetative or reproductive shoots, or the floral meristem in mature plants. RNA in situ localization data suggest that OSH15 may play roles in the shoot organization during early embryogenesis and thereafter, OSH15 may be involved in morphogenetic events around the shoot apical meristem.	D6|OSH15|Oskn3,OSH1|Oskn1
Characterization of the KNOX class homeobox genes Oskn2 and Oskn3 identified in a collection of cDNA libraries covering the early stages of rice embryogenesis	1999	Plant Mol Biol	Institute of Molecular Plant Sciences, Leiden University, The Netherlands.	For identification of genes involved in embryogenesis in the model cereal rice, we have constructed a collection of cDNA libraries of well-defined stages of embryo development before, during and after organ differentiation. Here, we focus on the possible role of KNOX (maize Knotted1-like) class homeobox genes in regulation of rice embryogenesis. Three types of KNOX clones were identified in libraries of early zygotic embryos. Two of these, Oskn2 and Oskn3, encode newly described KNOX genes, whereas the third (Oskn1) corresponds to the previously described OSH1 gene. In situ hybridizations showed that during the early stages of embryo development, all three KNOX genes are expressed in the region where the shoot apical meristem (SAM) is organizing, suggesting that these genes are involved in regulating SAM formation. Whereas OSH1 was previously proposed to function also in SAM maintenance, Oskn3 may be involved in patterning organ positions, as its expression was found to mark the boundaries of different embryonic organs following SAM formation. The expression pattern of Oskn2 suggested an additional role in scutellum and epiblast development. Transgenic expression of Oskn2 and Oskn3 in tobacco further supported their involvement in cell fate determination, like previously reported for Knotted1 and OSH1 ectopic expression. Whereas Oskn3 transformants showed the most pronounced phenotypic effects during vegetative development, Oskn2 transformants showed relatively mild alterations in the vegetative phase but a more severely affected flower morphology. The observation that the KNOX genes produce similar though distinct phenotypic reponses in tobacco, indicates that their gene products act on overlapping but different sets of target genes, or that cell-type specific factors determine their precise action.	D6|OSH15|Oskn3,OSH1|Oskn1,OSH71|Oskn2
Developmental regulation and downstream effects of the knox class homeobox genes Oskn2 and Oskn3 from rice	2002	Plant Mol Biol	Institute of Molecular Plant Sciences, Leiden University, Clusius Laboratory, The Netherlands.	Plant homeobox genes of the class 1 knox (knotted1-like) type are involved in the regulation of shoot apical meristem formation and function. Their expression generally occurs either throughout the meristem or specifically at the lateral organ boundaries. Down-regulation in the organ primordia is tightly controlled and misexpression in leaves leads to a perturbed development. Here, the transcriptional control of two rice knox genes, Oskn2 and Oskn3, was addressed, showing that the promoter sequences of both genes mediate the initial down-regulation during lateral organ formation, but are insufficient to keep expression in lateral organs stably off. Therefore, maintenance of the repressed state requires control elements outside the promoter regions. Ectopic expression of Oskn2 or Oskn3 induced similar defects in panicle branching. internode elongation and leaf patterning. However, small differences suggested that their target gene specificities are not completely overlapping. This was supported by the observation that Oskn3 protein but not Oskn2 could interact with two reported recognition sequences of a KNOX protein from barley. Finally, protein-protein interactions may contribute to the functioning of KNOX proteins, as the ability of Oskn3 and Oskn2 to form heterodimers could be demonstrated.	D6|OSH15|Oskn3,OSH71|Oskn2
KNOX homeobox genes are sufficient in maintaining cultured cells in an undifferentiated state in rice	2001	Genesis	Plant Genetics Laboratory, National Institute of Genetics, Shizuoka-ken, Japan.	We produced transgenic rice calli, which constitutively express each of four KNOX family class 1 homeobox genes of rice, OSH1, OSH16, OSH15, and OSH71, and found that constitutive and ectopic expression of such genes inhibits normal regeneration from transformed calli, which showed continuous growth around their shoot-regenerating stages. Transgenic calli transferred onto regeneration medium began to display green spots, a sign of regeneration, but most of the transformants continued to propagate green spots at given stages. In the normal shoot-regeneration process of calli, expression of endogenous OSH1 was restricted in presumptive shoot-regenerating regions of calli and not observed in other areas. This restricted expression pattern should be required for further differentiation of the regenerating shoots. Thus our present results support the proposed function that KNOX family class 1 homeobox genes play a role in the formation and maintenance of the undetermined meristematic state of cells.	D6|OSH15|Oskn3,OSH1|Oskn1,OSH6,OSH71|Oskn2
Regional expression of the rice KN1-type homeobox gene family during embryo, shoot, and flower development	1999	Plant Cell	Nagoya University, BioScience Center, Chikusa, Nagoya 464-8601, Japan.	We report the isolation, sequence, and pattern of gene expression of members of the KNOTTED1 (KN1)-type class 1 homeobox gene family from rice. Phylogenetic analysis and mapping of the rice genome revealed that all of the rice homeobox genes that we have isolated have one or two direct homologs in maize. Of the homeobox genes that we tested, all exhibited expression in a restricted region of the embryo that defines the position at which the shoot apical meristem (SAM) would eventually develop, prior to visible organ formation. Several distinct spatial and temporal expression patterns were observed for the different genes in this region. After shoot formation, the expression patterns of these homeobox genes were variable in the region of the SAM. These results suggest that the rice KN1-type class 1 homeobox genes function cooperatively to establish the SAM before shoot formation and that after shoot formation, their functions differ.	D6|OSH15|Oskn3,OSH1|Oskn1,OSH10,OSH3,OSH43,OSH6,OSH71|Oskn2
Positive autoregulation of a KNOX gene is essential for shoot apical meristem maintenance in rice	2011	Plant Cell	Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka, Japan.	Self-maintenance of the shoot apical meristem (SAM), from which aerial organs are formed throughout the life cycle, is crucial in plant development. Class I Knotted1-like homeobox (KNOX) genes restrict cell differentiation and play an indispensable role in maintaining the SAM. However, the mechanism that positively regulates their expression is unknown. Here, we show that expression of a rice (Oryza sativa) KNOX gene, Oryza sativa homeobox1 (OSH1), is positively regulated by direct autoregulation. Interestingly, loss-of-function mutants of OSH1 lose the SAM just after germination but can be rescued to grow until reproductive development when they are regenerated from callus. Double mutants of osh1 and d6, a loss-of-function mutant of OSH15, fail to establish the SAM both in embryogenesis and regeneration. Expression analyses in these mutants reveal that KNOX gene expression is positively regulated by the phytohormone cytokinin and by KNOX genes themselves. We demonstrate that OSH1 directly binds to five KNOX loci, including OSH1 and OSH15, through evolutionarily conserved cis-elements and that the positive autoregulation of OSH1 is indispensable for its own expression and SAM maintenance. Thus, the maintenance of the indeterminate state mediated by positive autoregulation of a KNOX gene is an indispensable mechanism of self-maintenance of the SAM.	D6|OSH15|Oskn3,OSH1|Oskn1
Functional analysis of the conserved domains of a rice KNOX homeodomain protein, OSH15	2001	Plant Cell	BioScience Center, Nagoya University, Chikusa, Nagoya 464-0814, Japan.	The rice KNOX protein OSH15 consists of four conserved domains: the MEINOX domain, which can be divided into two subdomains (KNOX1 and KNOX2); the GSE domain; the ELK domain; and the homeodomain (HD). To investigate the function of each domain, we generated 10 truncated proteins with deletions in the conserved domains and four proteins with mutations in the conserved amino acids in the HD. Transgenic analysis suggested that KNOX2 and HD are essential for inducing the abnormal phenotype and that the KNOX1 and ELK domains affect phenotype severity. We also found that both KNOX2 and HD are necessary for homodimerization and that only HD is needed for binding of OSH15 to its target sequence. Transactivation studies suggested that both the KNOX1 and ELK domains play a role in suppressing target gene expression. On the basis of these findings, we propose that overproduced OSH15 probably acts as a dimer and may ectopically suppress the expression of target genes that induce abnormal morphology in transgenic plants.	D6|OSH15|Oskn3
OsBLE3, a brassinolide-enhanced gene, is involved in the growth of rice	2006	Phytochemistry	National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba 305-8602, Japan.	Brassinosteroids (BRs) are a group of plant hormones involved in a wide range of plant growth and developmental processes. To investigate the mechanism of BR action in monocots, a brassinolide (BL) upregulated gene designated OsBLE3 was identified, cloned and characterized in rice. It was mainly expressed in roots and leaf sheaths with levels of expression directly dependent on the dose of BL. In situ hybridization detected OsBLE3 mRNA in the shoot apical meristem, organ primordia and vascular tissue. Furthermore, its expression was enhanced by co-treatment with BL and low concentrations of IAA. These results, and the existence of auxin response elements in the 5'-flanking region of the OsBLE3 gene, indicate that OsBLE3 expression is under control of both BR and auxin. The GUS reporter gene driven by a 2277 bp OsBLE3 putative promoter was mainly expressed in vascular tissues, branch root primordia and was responsive to exogenous BL treatment. OsBLE3 transcript levels were greatly reduced in brd1 plants, a BL deficient mutant, compared to the wild type control. In OsBRI1 antisense transgenic rice and OsBLE3, the BR-insensitive mutant expression of OsBLE3 in response to exogenous BL treatment was significantly lower compared to that in control plants transformed with a vacant vector. Reduced OsBLE3 expression and growth retardation was also observed in OsBLE3 antisense transgenic rice plants. Internode cell length of the OsBLE3 antisense transgenic lines was about 70% of that in the vacant vector transformed control lines. These results suggest that OsBLE3 is involved in cell elongation in rice through dual regulation by BL and IAA.	D61|OsBRI1,OsBLE3
Kinase activity of OsBRI1 is essential for brassinosteroids to regulate rice growth and development	2013	Plant Sci	National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China.	Brassinosteroids (BRs) are steroid hormones that participate in multiple biological processes. In this paper, we characterized a classic rice mutant Fn189 (dwarf54, d54) showing semi-dwarf stature and erect leaves. The coleoptile elongation and root growth was less affected in Fn189 than wild-type plant by the exogenous application of eBL, the most active form of BRs. Lamina joint inclination assay and morphological analysis in darkness further showed that Fn189 mutant plant was insensitive to exogenous eBL. Through map-based cloning, Fn189 was found to be a novel allelic mutant of the DWARF 61 (D61) gene, which encodes the putative BRs receptor OsBRI1. A single base mutation caused the I834F substitution in the OsBRI1 kinase domain. Consequently, kinase activity of OsBRI1 was found to decrease dramatically. Taken together, the kinase activity of OsBRI1 is essential for brassinosteroids to regulate normal plant growth and development in rice.	D61|OsBRI1
Small and round seed 5 gene encodes alpha-tubulin regulating seed cell elongation in rice	2012	Rice (N Y)	Faculty of Biotechnology, Fukui Prefectural University, 4-1-1 Kenjojima, Matsuoka, Eiheiji-Town, Fukui 910-1195, Japan.	Seed size is an important trait in determinant of rice seed quality and yield. In this study, we report a novel semi-dominant mutant Small and round seed 5 (Srs5) that encodes alpha-tubulin protein. Lemma cell length was reduced in Srs5 compared with that of the wild-type. Mutants defective in the G-protein alpha subunit (d1-1) and brassinosteroid receptor, BRI1 (d61-2) also exhibited short seed phenotypes, the former due to impaired cell numbers and the latter due to impaired cell length. Seeds of the double mutant of Srs5 and d61-2 were smaller than those of Srs5 or d61-2. Furthermore, SRS5 and BRI1 genes were highly expressed in Srs5 and d61-2 mutants. These data indicate that SRS5 independently regulates cell elongation of the brassinosteroid signal transduction pathway.	D61|OsBRI1,TID1|SRS5
Loss of function of a rice brassinosteroid insensitive1 homolog prevents internode elongation and bending of the lamina joint	2000	Plant Cell	Nagoya University, BioScience Center, Chikusa, Nagoya 464-8601, Japan.	Brassinosteroids (BRs) are plant growth-promoting natural products required for plant growth and development. Physiological studies have demonstrated that exogenous BR, alone or in combination with auxin, enhance bending of the lamina joint of rice. However, little is known about the function of endogenous BR in rice or other grass species. We report here the phenotypical and molecular characterization of a rice dwarf mutant, d61, that is less sensitive to BR compared to the wild type. We cloned a rice gene, OsBRI1, with extensive sequence similarity to that of the Arabidopsis BRI gene, which encodes a putative BR receptor kinase. Linkage analysis showed that the OsBRI1 gene is closely linked to the d61 locus. Single nucleotide substitutions found at different sites of the d61 alleles would give rise to amino acid changes in the corresponding polypeptides. Furthermore, introduction of the entire OsBRI1 coding region, including the 5' and 3' flanking sequences, into d61 plants complemented the mutation to display the wild-type phenotype. Transgenic plants carrying the antisense strand of the OsBRI1 transcript showed similar or even more severe phenotypes than those of the d61 mutants. Our results show that OsBRI1 functions in various growth and developmental processes in rice, including (1) internode elongation, by inducing the formation of the intercalary meristem and the longitudinal elongation of internode cells; (2) bending of the lamina joint; and (3) skotomorphogenesis.	D61|OsBRI1
The role of OsBRI1 and its homologous genes, OsBRL1 and OsBRL3, in rice	2006	Plant Physiol	Bioscience and Biotechnology Center, Nagoya University Chikusa, Nagoya 464-8601, Japan.	Since first identifying two alleles of a rice (Oryza sativa) brassinosteroid (BR)-insensitive mutant, d61, that were also defective in an orthologous gene in Arabidopsis (Arabidopsis thaliana) BRASSINOSTEROID INSENSITIVE1 (BRI1), we have isolated eight additional alleles, including null mutations, of the rice BRI1 gene OsBRI1. The most severe mutant, d61-4, exhibited severe dwarfism and twisted leaves, although pattern formation and differentiation were normal. This severe shoot phenotype was caused mainly by a defect in cell elongation and the disturbance of cell division after the determination of cell fate. In contrast to its severe shoot phenotype, the d61-4 mutant had a mild root phenotype. Concomitantly, the accumulation of castasterone, the active BR in rice, was up to 30-fold greater in the shoots, while only 1.5-fold greater in the roots. The homologous genes for OsBRI1, OsBRL1 and OsBRL3, were highly expressed in roots but weakly expressed in shoots, and their expression was higher in d61-4 than in the wild type. Based on these observations, we conclude that OsBRI1 is not essential for pattern formation or organ initiation, but is involved in organ development through controlling cell division and elongation. In addition, OsBRL1 and OsBRL3 are at least partly involved in BR perception in the roots.	D61|OsBRI1,OsBRL1,OsBRL3
Morphological alteration caused by brassinosteroid insensitivity increases the biomass and grain production of rice	2006	Plant Physiol	Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.	The rice (Oryza sativa) dwarf mutant d61 phenotype is caused by loss of function of a rice BRASSINOSTEROID INSENSITIVE1 ortholog, OsBRI1. We have identified nine d61 alleles, the weakest of which, d61-7, confers agronomically important traits such as semidwarf stature and erect leaves. Because erect-leaf habit is considered to increase light capture for photosynthesis, we compared the biomass and grain production of wild-type and d61-7 rice. The biomass of wild type was 38% higher than that of d61-7 at harvest under conventional planting density because of the dwarfism of d61-7. However, the biomass of d61-7 was 35% higher than that of wild type at high planting density. The grain yield of wild type reached a maximum at middensity, but the yield of d61-7 continued to increase with planting density. These results indicate that d61-7 produces biomass more effectively than wild type, and consequently more effectively assimilates the biomass in reproductive organ development at high planting density. However, the small grain size of d61-7 counters any increase in grain yield, leading to the same grain yield as that of wild type even at high density. We therefore produced transgenic rice with partial suppression of endogenous OsBRI1 expression to obtain the erect-leaf phenotype without grain changes. The estimated grain yield of these transformants was about 30% higher than that of wild type at high density. These results demonstrate the feasibility of generating erect-leaf plants by modifying the expression of the brassinosteroid receptor gene in transgenic rice plants.	D61|OsBRI1
RPL1, a gene involved in epigenetic processes regulates phenotypic plasticity in rice	2012	Mol Plant	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.	Organisms can adjust their phenotype in response to changing environmental conditions. This phenomenon is termed phenotypic plasticity. Despite its ubiquitous occurrence, there has been very little study on the molecular mechanism of phenotypic plasticity. In this study, we isolated a rice (Oryza sativa L.) mutant, rice plasticity 1 (rpl1), that displayed increased environment-dependent phenotypic variations. RPL1 was expressed in all tissues examined. The protein was localized in the nucleus and its distribution in the nucleus overlapped with heterochromatin. The rpl1 mutation led to an increase in DNA methylation on repetitive sequences and a decrease in overall histone acetylation. In addition, the mutation affected responses of the rice plant to phytohormones such as brassinosteroid, gibberellin, and cytokinin. Analysis of the putative rice brassinosteroid receptor OsBRI1, a key hormone signaling gene, indicated that RPL1 may be involved in the regulation of epigenomic modification of the gene. These data suggest that RPL1 regulated phenotypic plasticity likely through its involvement in epigenetic processes affecting responses of the plant to phytohormones.	D61|OsBRI1,RPL1
dad-1, A putative programmed cell death suppressor gene in rice	1997	Plant Cell Physiol	Laboratory of Plant Pathology & Genetic Engineering, College of Agriculture, Okayama University, Japan.	The human dad-1 cDNA homolog was isolated from rice plants. The amino acid sequence of the predicted protein product is well conserved in both animals and plants. This rice dad-1 homolog can rescue the temperature-sensitive dad-1 mutants of hamster cells from apoptotic death, suggesting that the rice dad-1 homolog also functions as a suppressor for programmed cell death.	DAD-1|DAD1
Putrescine differently influences the effect of salt stress on polyamine metabolism and ethylene synthesis in rice cultivars differing in salt resistance	2010	J Exp Bot	Groupe de Recherche en Physiologie vegetale (GRPV), Universite catholique de Louvain, 5 (Bte 13) Place Croix du Sud, Louvain-la-Neuve, Belgium.	Effects of salt stress on polyamine metabolism and ethylene production were examined in two rice (Oryza sativa L.) cultivars [I Kong Pao (IKP), salt sensitive; and Pokkali, salt resistant] grown for 5 d and 12 d in nutrient solution in the presence or absence of putrescine (1 mM) and 0, 50, and 100 mM NaCl. The salt-sensitive (IKP) and salt-resistant (Pokkali) cultivars differ not only in their mean levels of putrescine, but also in the physiological functions assumed by this molecule in stressed tissues. Salt stress increased the proportion of conjugated putrescine in salt-resistant Pokkali and decreased it in the salt-sensitive IKP, suggesting a possible protective function in response to NaCl. Activities of the enzymes ornithine decarboxylase (ODC; EC 4.1.1.17) and arginine decarboxylase (ADC; EC 4.1.1.19) involved in putrescine synthesis were higher in salt-resistant Pokkali than in salt-sensitive IKP. Both enzymes were involved in the response to salt stress. Salt stress also increased diamine oxidase (DAO; 1.4.3.6) and polyamine oxidase (PAO EC 1.5.3.11) activities in the roots of salt-resistant Pokkali and in the shoots of salt-sensitive IKP. Gene expression followed by reverse transcription-PCR suggested that putrescine could have a post-translational impact on genes coding for ADC (ADCa) and ODC (ODCa and ODCb) but could induce a transcriptional activation of genes coding for PAO (PAOb) mainly in the shoot of salt-stressed plants. The salt-resistant cultivar Pokkali produced higher amounts of ethylene than the salt-sensitive cultivar IKP, and exogenous putrescine increased ethylene synthesis in both cultivars, suggesting no direct antagonism between polyamine and ethylene pathways in rice.	DAO,ODCa,ODCb
A role for a dioxygenase in auxin metabolism and reproductive development in rice	2013	Dev Cell	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.	Indole-3-acetic acid (IAA), the natural auxin in plants, regulates many aspects of plant growth and development. Extensive analyses have elucidated the components of auxin biosynthesis, transport, and signaling, but the physiological roles and molecular mechanisms of auxin degradation remain elusive. Here, we demonstrate that the dioxygenase for auxin oxidation (DAO) gene, encoding a putative 2-oxoglutarate-dependent-Fe (II) dioxygenase, is essential for anther dehiscence, pollen fertility, and seed initiation in rice. Rice mutant lines lacking a functional DAO display increased levels of free IAA in anthers and ovaries. Furthermore, exogenous application of IAA or overexpression of the auxin biosynthesis gene OsYUCCA1 phenocopies the dao mutants. We show that recombinant DAO converts the active IAA into biologically inactive 2-oxoindole-3-acetic acid (OxIAA) in vitro. Collectively, these data support a key role of DAO in auxin catabolism and maintenance of auxin homeostasis central to plant reproductive development.	DAO,OsYUCCA1
The rice mutant dwarf bamboo shoot 1: a leaky mutant of the NACK-type kinesin-like gene can initiate organ primordia but not organ development	2005	Plant Cell Physiol	Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi, 464-8601 Japan. sazuka@agr.nagoya-u.ac.jp	That plant dwarfism is caused by hormonal defects related to gibberellin and brassinosteroid has been well documented. Other contributing elements, however, have not been elucidated. Here, we report on one of the most severe dwarf mutants of rice, dwarf bamboo shoot 1 (dbs1). Most mutant plants died within 1 month after sowing, but a few (5.2%) survived and grew. Vacuolation enlarged cells in the leaf primordia and seminal root before abortion, which disrupted the organized cell files in these organs. Relative to the severe defects in shoot and root growth, the overall structure of the dbs1 embryo was almost normal. Similarly, initiation and organogenesis of the leaf primordia at the shoot apical meristem and those of the lateral root primordia at the root elongation zone occurred normally. These observations suggest that DBS1 is involved in the growth and development of organs but not in organ initiation or organogenesis. Positional cloning of DBS1 revealed that it encoded a NACK-type kinesin-like protein (OsNACK), homologous to the essential components of a mitogen-activated protein kinase cascade during plant cytokinesis. A BLAST search indicated that DBS1 was the only gene encoding the OsNACK-type protein in the rice genome, and the dbs1 mutant produced only small amounts of the translatable DBS1 mRNA. Thus, we conclude that the dbs1 mutation causes a severe defect in DBS1 function but does not completely shut it down. We discuss the leaky phenotype of dbs1 under the restricted functioning of OsNACK.	DBS1|OsNACK
DCW11, down-regulated gene 11 in CW-type cytoplasmic male sterile rice, encoding mitochondrial protein phosphatase 2c is related to cytoplasmic male sterility	2008	Plant Cell Physiol	Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan.	Causes of cytoplasmic male sterility (CMS) in plants have been studied for two decades, and mitochondrial chimeric genes have been predicted to induce CMS. However, it is unclear what happens after CMS-associated proteins accumulate in mitochondria. In our previous study of microarray analysis, we found that 140 genes are aberrantly regulated in anthers of CW-type CMS of rice (Oryza sativa L.). In the present study, we investigated DCW11, one of the down-regulated genes in CW-CMS encoding a protein phosphatase 2C (PP2C). DCW11 mRNA was preferentially expressed in anthers, with the highest expression in mature pollen. As predicted by the N-terminal sequence, DCW11 signal peptide-green fluorescent protein (GFP) fusion protein was localized in mitochondria. Knockdown of DCW11 in wild-type rice by RNA interference caused a major loss of seed-set fertility, without visible defect in pollen development. Since this knockdown phenotype resembled that of CW-CMS, we concluded that the down-regulation of DCW11 is correlated with CW-CMS. This idea was supported by the up-regulation of alternative oxidase 1a (AOX1a), which is known to be regulated by mitochondrial retrograde signaling, in DCW11 knockdown lines. Down-regulation of DCW11 and up-regulation of AOX1a were also observed in two other types of rice CMS. Our result indicates that DCW11 could play a role as a mitochondrial signal transduction mediator in pollen germination.	DCW11,AOX1a|OsAOX1a
Cytoplasmic male sterility-related protein kinase, OsNek3, is regulated downstream of mitochondrial protein phosphatase 2C, DCW11	2009	Plant Cell Physiol	Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan.	OsNek3 (Oryza sativa L. NIMA-related kinase) and DCW11 encoding a mitochondrial putative protein phosphatase 2C were found in our previous microarray study as down-regulated genes in the rice CW-CMS line, which lacked pollen germination ability. Further analysis of DCW11 revealed that DCW11 is strongly correlated with CW-CMS occurrence. Here we show the relationship between OsNek3 and DCW11. OsNek3 was preferentially expressed in mature pollen. A knockout mutant with Tos17 inserted into OsNek3 did not show any pollen-defective phenotype. On the other hand, plants overexpressing OsNek3 occasionally produced a peculiar pollen structure in which the outer cell wall of four pollen grains fused together even at the mature pollen stages, which resembled that of quartet mutants in Arabidopsis. OsNek3 was shown to interact with a LIM domain-containing protein, OsPLIM2b, whose expression was strongly specific in mature pollen, suggesting that OsNek3 might play a role in pollen germination. OsNek3 was shown to be down-regulated in DCW11-knockdown lines, whereas osnek3 mutation did not result in DCW11 down-regulation. These results suggest that OsNek3 is downstream of DCW11 in retrograde signaling from the mitochondria to the nucleus and is involved in CW-CMS.	DCW11,OsNek3,OsPLIM2b
Dwarf and deformed flower 1, encoding an F-box protein, is critical for vegetative and floral development in rice (Oryza sativa L.)	2012	Plant J	Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Fujian Agriculture & Forestry University, Fuzhou 350002, China. ylduan863@fjau.edu.cn	Recent studies have shown that F-box proteins constitute a large family in eukaryotes, and play pivotal roles in regulating various developmental processes in plants. However, their functions in monocots are still obscure. In this study, we characterized a recessive mutant dwarf and deformed flower 1-1 (ddf1-1) in Oryza sativa (rice). The mutant is abnormal in both vegetative and reproductive development, with significant size reduction in all organs except the spikelet. DDF1 controls organ size by regulating both cell division and cell expansion. In the ddf1-1 spikelet, the specification of floral organs in whorls 2 and 3 is altered, with most lodicules and stamens being transformed into glume-like organs and pistil-like organs, respectively, but the specification of lemma/palea and pistil in whorls 1 and 4 is not affected. DDF1 encodes an F-box protein anchored in the nucleolus, and is expressed in almost all vegetative and reproductive tissues. Consistent with the mutant floral phenotype, DDF1 positively regulates B-class genes OsMADS4 and OsMADS16, and negatively regulates pistil specification gene DL. In addition, DDF1 also negatively regulates the Arabidopsis LFY ortholog APO2, implying a functional connection between DDF1 and APO2. Collectively, these results revealed that DDF1, as a newly identified F-box gene, is a crucial genetic factor with pleiotropic functions for both vegetative growth and floral organ specification in rice. These findings provide additional insights into the molecular mechanism controlling monocot vegetative and reproductive development.	DDF1,OsMADS16|SPW1,OsMADS4,RFL|APO2
Rice DECUSSATE controls phyllotaxy by affecting the cytokinin signaling pathway	2012	Plant J	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan. RIKEN Plant Science Center, Tsurumi, Yokohama 230-0045, Japan.	Phyllotaxy is defined as a spatial arrangement of leaves on the stem. The mechanism responsible for this extremely regular pattern is one of the most fascinating enigmas in plant biology. In this study, we identified a gene regulating the phyllotactic pattern in rice. Loss-of-function mutants of the DECUSSATE (DEC) gene displayed a phyllotactic conversion from normal distichous to decussate. The dec mutants had an enlarged SAM with enhanced cell division activity. In contrast to the SAM, the size of the root apical meristem (RAM) in dec was reduced, and cell division activity was suppressed. These phenotypes indicate that DEC has opposite functions in SAM and RAM. Map-based cloning revealed that DEC encodes a plant-specific protein containing a glutamine-rich region and a conserved motif. Although its molecular function is unclear, the conserved domain is shared with fungi and animals. Expression analysis showed that several type-A response regulator genes that act in the cytokinin (CK) signaling pathway were downregulated in the dec mutant. In addition, dec seedlings showed a reduced responsiveness to exogenous CK. Our results suggest that DEC is a factor that controls the phyllotactic pattern by affecting the CK signaling in rice. (c) 2012 The Authors. The Plant Journal (c) 2012 Blackwell Publishing Ltd.	DEC
The SMALL AND ROUND SEED1 (SRS1/DEP2) gene is involved in the regulation of seed size in rice	2010	Genes Genet Syst	Department of Bioscience, Fukui Prefectural University	The causal gene of a novel small and round seed mutant 1 (srs1) was identified in rice by map-based cloning and named SMALL AND ROUND SEED 1 (SRS1). The SRS1 gene is identical to the previously identified DENSE AND ERECT PANICLE 2 (DEP2). The SRS1/DEP2 gene encodes a novel protein of 1365 amino acids residues without known functional domains. In the longitudinal direction of the lemma, both cell length and cell number are reduced in srs1-1 compared to the wild type, whereas in the lateral cross section of the lemma, cell length in srs1-1 is greater than that in the wild type, but the cell number in srs1-1 is the same as that in wild type. These results suggest that the small and round seed phenotype of srs1-1 is due to the reduction in both cell length and cell number in the longitudinal direction, and the elongation of the cells in the lateral direction of the lemma. The SRS1 mRNA and proteins are abundant in wild type rice specifically in young organs, namely young leaves, internodes and panicles. Interestingly, the tissues expressing SRS1 are closely related to the tissues that exhibit abnormalities in the srs1 mutants.	DEP2|EP2|SRS1
Rice DENSE AND ERECT PANICLE 2 is essential for determining panicle outgrowth and elongation	2010	Cell Res	National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.	The architecture of the panicle, including grain size and panicle morphology, directly determines grain yield. Panicle erectness, which is selected for achieving ideal plant architecture in the northern part of China, has drawn increasing attention of rice breeders. Here, dense and erect panicle 2 (dep2) mutant, which shows a dense and erect panicle phenotype, was identified. DEP2 encodes a plant-specific protein without any known functional domain. Expression profiling of DEP2 revealed that it is highly expressed in young tissues, with most abundance in young panicles. Morphological and expression analysis indicated that mutation in DEP2 mainly affects the rapid elongation of rachis and primary and secondary branches, but does not impair the initiation or formation of panicle primordia. Further analysis suggests that decrease of panicle length in dep2 is caused by a defect in cell proliferation during the exponential elongation of panicle. Despite a more compact plant type in the dep2 mutant, no significant alteration in grain production was found between wild type and dep2 mutant. Therefore, the study of DEP2 not only strengthens our understanding of the molecular genetic basis of panicle architecture but also has important implications for rice breeding.	DEP2|EP2|SRS1
Erect panicle2 encodes a novel protein that regulates panicle erectness in indica rice	2010	Genetics	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Rice (Oryza sativa L.) inflorescence (panicle) architecture is an important agronomic trait for rice breeding. A number of high-yielding japonica rice strains, characterized by an erect panicle (EP) of their architecture, have been released as commercial varieties in China. But no EP-type indica varieties are released so far. Here, we identified two allelic erect-panicle mutants in indica rice, erect panicle2-1 (ep2-1) and erect panicle2-2 (ep2-2), exhibiting the characteristic erect panicle phenotype. Both mutants were derived from spontaneous mutation. We cloned the EP2 gene by way of a map-based cloning strategy, and a transgenic complementation test rescued the phenotype of ep2-1. Anatomical investigations revealed that the ep2 mutants have more vascular bundles and a thicker stem than that of wild-type plants, explaining the panicle erectness phenotype in ep2 mutants. It was shown that EP2 was specifically expressed in the vascular bundles of internodes by GUS staining and RT-PCR. EP2 encodes a novel plant-specific protein, which localizes to the endoplasmic reticulum with unknown biochemical function. In addition, EP2 also regulates other panicle characteristics, such as panicle length and grain size, but grain number per panicle shows little change, indicating that the mutation of the ep2 gene could be applied in EP-type indica rice breeding.	DEP2|EP2|SRS1
Fine mapping and candidate gene analysis of dense and erect panicle 3, DEP3, which confers high grain yield in rice (Oryza sativa L.)	2011	Theor Appl Genet	Department of Plant Science, Seoul National University, Seoul, 151-921, Korea.	Architecture of the rice inflorescence, which is determined mainly by the morphology, number and length of primary and secondary inflorescence branches, is an important agronomical trait. In the current study, we characterized a novel dense and erect panicle (EP) mutant, dep3, derived from the Oryza sativa ssp. japonica cultivar Hwacheong treated with N-methyl-N-nitrosourea. The panicle of the dep3 mutant remained erect from flowering to full maturation, whereas the panicle of the wild type plant began to droop after flowering. The dep3 mutation also regulated other panicle characteristics, including panicle length, grain shape and grain number per panicle. Anatomical observations revealed that the dep3 mutant had more small vascular bundles and a thicker culm than wild type plants, explaining the EP phenotype. Genetic analysis indicated that the phenotype with the dense and EP was controlled by a single recessive gene, termed dep3. The DEP3 gene was identified as the candidate via a map-based cloning approach and was predicted to encode a patatin-like phospholipase A2 (PLA2) superfamily domain-containing protein. The mutant allele gene carried a 408 bp genomic deletion within LOC_Os06g46350, which included the last 47 bp coding region of the third exon and the first 361 bp of the 3'-untranslated region. Taken together, our results indicated that the patatin-like PLA2 might play a significant role in the formation of vascular bundles, and that the dep3 mutant may provide another EP resource for rice breeding programs.	DEP3
Over-expression in the nucleotide-binding site-leucine rich repeat gene DEPG1 increases susceptibility to bacterial leaf streak disease in transgenic rice plants	2012	Mol Biol Rep	Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361005, People's Republic of China.	Bacterial leaf streak of rice (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is a widely-spread disease in the main rice-producing areas of the world. Investigating the genes that play roles in rice-Xoc interactions helps us to understand the defense signaling pathway in rice. Here we report a differentially expressed protein gene (DEPG1), which regulates susceptibility to BLS. DEPG1 is a nucleotide-binding site (NBS)-leucine rich repeat (LRR) gene, and the deduced protein sequence of DEPG1 has approximately 64% identity with that of the disease resistance gene Pi37. Phylogenetic analysis of DEPG1 and the 18 characterized NBS-LRR genes revealed that DEPG1 is more closely related to Pi37. DEPG1 protein is located to the cytoplasm, which was confirmed by transient expression of DEPG1-GFP (green fluorescent protein) fusion construct in onion epidermal cells. Semi-quantitative PCR assays showed that DEPG1 is widely expressed in rice, and is preferentially expressed in internodes, leaf blades, leaf sheaths and flag leaves. Observation of cross sections of leaves from the transgenic plants with a DEPG1-promoter::glucuronidase (GUS) fusion gene revealed that DEPG1 is also highly expressed in mesophyll tissues where Xoc mainly colonizes. Additionally, Xoc negatively regulates expression of DEPG1 at the early stage of the pathogen infection, and so do the three defense-signal compounds including salicylic acid (SA), methyl jasmonate (MeJA) and 1-aminocyclopropane-1-carboxylic-acid (ACC). Transgenic rice plants overexpressing DEPG1 exhibit enhanced susceptibility to Xoc compared to the wild-type controls. Moreover, enhanced susceptibility to Xoc may be mediated by inhibition of the expression of some SA biosynthesis-related genes and pathogenesis-related genes that may contribute to the disease resistance. Taken together, DEPG1 plays roles in the interactions between rice and BLS pathogen Xoc.	DEPG1
Overexpression of OsKTN80a, a katanin P80 ortholog, caused the repressed cell elongation and stalled cell division mediated by microtubule apparatus defects in primary root in Oryza sativa	2014	J Integr Plant Biol	State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China.	Katanin, a microtubule-severing enzyme, consists of two subunits: the catalytic subunit P60, and the regulatory subunit P80. In several species, P80 functions in meiotic spindle organization, the flagella biogenesis, the neuronal development, and the male gamete production. However, the P80 function in higher plants remains elusive. In this study, we found that there are three katanin P80 orthologs (OsKTN80a, OsKTN80b, and OsKTN80c) in Oryza sativa L. Overexpression of OsKTN80a caused the retarded root growth of rice seedlings. Further investigation indicates that the retained root growth was caused by the repressed cell elongation in the elongation zone and the stalled cytokinesis in the division zone in the root tip. The in vivo examination suggests that OsKTN80a acts as a microtubule stabilizer. We prove that OsKTN80a, possibly associated with OsKTN60, is involved in root growth via regulating the cell elongation and division.	DGL1|OsKTN60,OsKTN80a,OsKTN80b|OsWD40-111,OsKTN80c|OsWD40-26
Analysis of the rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling	2005	Plant Physiol	Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.	Molecular genetic studies of plant dwarf mutants have indicated that gibberellin (GA) and brassinosteroid (BR) are two major factors that determine plant height; dwarf mutants that are caused by other defects are relatively rare, especially in monocot species. Here, we report a rice (Oryza sativa) dwarf mutant, dwarf and gladius leaf 1 (dgl1), which exhibits only minimal response to GA and BR. In addition to the dwarf phenotype, dgl1 produces leaves with abnormally rounded tip regions. Positional cloning of DGL1 revealed that it encodes a 60-kD microtubule-severing katanin-like protein. The protein was found to be important in cell elongation and division, based on the observed cell phenotypes. GA biosynthetic genes are up-regulated in dgl1, but the expression of BR biosynthetic genes is not enhanced. The enhanced expression of GA biosynthetic genes in dgl1 is not caused by inappropriate GA signaling because the expression of these genes was repressed by GA3 treatment, and degradation of the rice DELLA protein SLR1 was triggered by GA3 in this mutant. Instead, aberrant microtubule organization caused by the loss of the microtubule-severing function of DGL1 may result in enhanced expression of GA biosynthetic genes in that enhanced expression was also observed in a BR-deficient mutant with aberrant microtubule organization. These results suggest that the function of DGL1 is important for cell and organ elongation in rice, and aberrant DGL1-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling.	DGL1|OsKTN60,SLR1|OsGAI
DH1, a LOB domain-like protein required for glume formation in rice	2008	Plant Mol Biol	Yangzhou University, Yangzhou, Jiangsu, 225009, People's Republic of China.	T-DNA tagging is a high throughput strategy for identifying and cloning functional genes in plants. In this study, we screened 4416 lab-created T(1) rice T-DNA tagged lines and identified a mutant, designated dh1 (degenerated hull1), with phenotype of degenerated hull and naked pistils and stamens. Approximately 60% florets on the dh1 panicle defected in forming normal palea and lemma. Instead, they formed degenerative velum-like or filamentous organs accompanying with the lack of lodicules, stamens and pistils at different degree. A 361 bp of genomic sequence flanking the T-DNA isolated using TAIL-PCR (Thermal asymmetric interlaced PCR) co-segregated with the mutation phenotype. Results of blastn and gene prediction revealed the T-DNA inserted into the promoter region of a function-predicted gene at 283 bp upstream of its transcription start site (TSS). The predicted gene encoded a LOB (Lateral Organ Boundaries) domain-like protein. RT-PCR analyses indicated the transcription level of target candidate gene, DH1, decreased significantly in dh1 mutant. RNAi aimed at DH1 in wild type plants could partially result in the mutation phenotype of dh1. DH1 could also rescue the mutation phenotype in the complement experiment. The result of transformation by a fused expression vector, pDH1::GFP, revealed that DH1 had the keen spatial and temporal characteristics of expressing at axillary bud, young panicle and floral organs but not at root, leaf, node and culm, and strongly expressing at young tissues but weakly at mature organs. The dh1 presented severer mutation phenotype under relatively longer daylight than under shorter daylight implied that shorter daylight induced the expression of gene(s) redundant to DH1 in function and partially compensated for the loss-of-function. It is the first time to report the LOB-domain gene participating in the development of floral organs in rice.	DH1
Comprehensive expression analysis suggests overlapping and specific roles of rice glutathione S-transferase genes during development and stress responses	2010	BMC Genomics	National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi-110067, India. mjain@nipgr.res.in	BACKGROUND: Glutathione S-transferases (GSTs) are the ubiquitous enzymes that play a key role in cellular detoxification. Although several GSTs have been identified and characterized in various plant species, the knowledge about their role in developmental processes and response to various stimuli is still very limited. In this study, we report genome-wide identification, characterization and comprehensive expression analysis of members of GST gene family in crop plant rice, to reveal their function(s). RESULTS: A systematic analysis revealed the presence of at least 79 GST genes in the rice genome. Phylogenetic analysis grouped GST proteins into seven classes. Sequence analysis together with the organization of putative motifs indicated the potential diverse functions of GST gene family members in rice. The tandem gene duplications have contributed a major role in expansion of this gene family. Microarray data analysis revealed tissue-/organ- and developmental stage-specific expression patterns of several rice GST genes. At least 31 GST genes showed response to plant hormones auxin and cytokinin. Furthermore, expression analysis showed the differential expression of quite a large number of GST genes during various abiotic stress (20), arsenate stress (32) and biotic stress (48) conditions. Many of the GST genes were commonly regulated by developmental processes, hormones, abiotic and biotic stresses. CONCLUSION: The transcript profiling suggests overlapping and specific role(s) of GSTs during various stages of development in rice. Further, the study provides evidence for the role of GSTs in mediating crosstalk between various stress and hormone response pathways and represents a very useful resource for functional analysis of selected members of this family in rice.	DHAR1|OsDHAR1,OsDHAR2,OsGSTT1,OsTCHQD1
Molecular cloning and characterization of a rice dehydroascorbate reductase	2000	FEBS Lett	Department of Biology, Faculty of Science, Shizuoka University, Shizuoka, Japan.	Plant dehydroascorbate reductase (DHAR), which re-reduces oxidized ascorbate to maintain an appropriate level of ascorbate, is very important, but no gene or cDNA for plant DHAR has been cloned yet. Here, we describe a cDNA for a rice glutathione-dependent DHAR (designated DHAR1). A recombinant Dhar1p produced in Escherichia coli was functional. The expression sequence tag database suggests that Dhar1p homologs exist in various plants. Furthermore, the rice Dhar1p has a low similarity to rat DHAR, although the rice enzyme has a considerably higher specific activity than the mammalian one. The mRNA level of DHAR1, the protein level of Dhar1p and the DHAR activity in rice seedlings were elevated by high temperature, suggesting the protection role of DHAR at high temperature.	DHAR1|OsDHAR1
Genetic interaction of OsMADS3, DROOPING LEAF, and OsMADS13 in specifying rice floral organ identities and meristem determinacy	2011	Plant Physiol	School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	Grass plants develop unique floral patterns that determine grain production. However, the molecular mechanism underlying the specification of floral organ identities and meristem determinacy, including the interaction among floral homeotic genes, remains largely unknown in grasses. Here, we report the interactions of rice (Oryza sativa) floral homeotic genes, OsMADS3 (a C-class gene), OsMADS13 (a D-class gene), and DROOPING LEAF (DL), in specifying floral organ identities and floral meristem determinacy. The interaction among these genes was revealed through the analysis of double mutants. osmads13-3 osmads3-4 displayed a loss of floral meristem determinacy and generated abundant carpelloid structures containing severe defective ovules in the flower center, which were not detectable in the single mutant. In addition, in situ hybridization and yeast two-hybrid analyses revealed that OsMADS13 and OsMADS3 did not regulate each other's transcription or interact at the protein level. This indicates that OsMADS3 plays a synergistic role with OsMADS13 in both ovule development and floral meristem termination. Strikingly, osmads3-4 dl-sup6 displayed a severe loss of floral meristem determinacy and produced supernumerary whorls of lodicule-like organs at the forth whorl, suggesting that OsMADS3 and DL synergistically terminate the floral meristem. Furthermore, the defects of osmads13-3 dl-sup6 flowers appeared identical to those of dl-sup6, and the OsMADS13 expression was undetectable in dl-sup6 flowers. These observations suggest that DL and OsMADS13 may function in the same pathway specifying the identity of carpel/ovule and floral meristem. Collectively, we propose a model to illustrate the role of OsMADS3, DL, and OsMADS13 in the specification of flower organ identity and meristem determinacy in rice.	DL,OsMADS13,OSMADS3
SUPERWOMAN1 and DROOPING LEAF genes control floral organ identity in rice	2003	Development	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.	We analyzed recessive mutants of two homeotic genes in rice, SUPERWOMAN1 (SPW1) and DROOPING LEAF (DL). The homeotic mutation spw1 transforms stamens and lodicules into carpels and palea-like organs, respectively. Two spw1 alleles, spw1-1 and spw1-2, show the same floral phenotype and did not affect vegetative development. We show that SPW1 is a rice APETALA3 homolog, OsMADS16. In contrast, two strong alleles of the dl locus, drooping leaf-superman1 (dl-sup1) and drooping leaf-superman2 (dl-sup2), cause the complete transformation of the gynoecium into stamens. In these strong mutants, many ectopic stamens are formed in the region where the gynoecium is produced in the wild-type flower and they are arranged in a non-whorled, alternate pattern. The intermediate allele dl-1 (T65), results in an increase in the number of stamens and stigmas, and carpels occasionally show staminoid characteristics. In the weakest mutant, dl-2, most of the flowers are normal. All four dl alleles cause midrib-less drooping leaves. The flower of the double mutant, spw1 dl-sup, produces incompletely differentiated organs indefinitely after palea-like organs are produced in the position where lodicules are formed in the wild-type flower. These incompletely differentiated organs are neither stamens nor carpels, but have partial floral identity. Based on genetic and molecular results, we postulate a model of stamen and carpel specification in rice, with DL as a novel gene controlling carpel identity and acting mutually and antagonistically to the class B gene, SPW1.	DL,OsMADS16|SPW1
Temporal and spatial regulation of DROOPING LEAF gene expression that promotes midrib formation in rice	2011	Plant J	Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-8654, Japan.	Genes involved in the differentiation and development of tissues and organs are temporally and spatially regulated in plant development. The DROOPING LEAF (DL) gene, a member of the YABBY gene family, promotes midrib formation in the leaf and carpel specification in the flower. Consistent with these functions, DL is initially expressed in the central region of the leaf primordia (presumptive midrib) and in the presumptive carpel primordia in the meristem. To understand the regulatory mechanism underlying DL expression, we tried to identify cis-regulatory regions required for temporal and spatial expression of this gene. We found that the cis region responsible for the presumptive midrib-specific expression in the leaf primordia is located in intron 2. Next, we confined the region to a sequence of about 200bp, which corresponds to a conserved non-coding sequence (CNS) identified by phylogenetic footprinting. In addition, a sequence termed DG1, incorporating a 5' upstream region of about 7.4kb, and introns 1 and 2, was shown to be sufficient to induce DL in the presumptive midrib, and to suppress it in other regions in the leaf primordia. By contrast, the regulatory region required for carpel-specific expression was not included in the DG1 sequence. We modified Oryza sativa (rice) plant architecture by expressing an activated version of DL (DL-VP16) in a precise manner using the DG1 sequence: the resulting transgenic plant produced a midrib in the distal region of the leaf blade, where there is no midrib in wild type, and formed more upright leaves compared with the wild type.	DL
The YABBY gene DROOPING LEAF regulates carpel specification and midrib development in Oryza sativa	2004	Plant Cell	Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.	In this article, we report that carpel specification in the Oryza sativa (rice) flower is regulated by the floral homeotic gene DROOPING LEAF (DL) that is distinct from the well-known ABC genes. Severe loss-of-function mutations of DL cause complete homeotic transformation of carpels into stamens. Molecular cloning reveals that DL is a member of the YABBY gene family and is closely related to the CRABS CLAW (CRC) gene of Arabidopsis thaliana. DL is expressed in the presumptive region (carpel anlagen), where carpel primordia would initiate, and in carpel primordia. These results suggest that carpel specification is regulated by DL in rice flower development. Whereas CRC plays only a partial role in carpel identity, DL may have been recruited to have the more essential function of specifying carpels during the evolution of rice. We also show that DL interacts antagonistically with class B genes and controls floral meristem determinacy. In addition, severe and weak dl alleles fail to form a midrib in the leaf. The phenotypic analysis of dl mutants, together with analyses of the spatial expression patterns and ectopic expression of DL, demonstrate that DL regulates midrib formation by promoting cell proliferation in the central region of the rice leaf.	DL
Rice MADS6 interacts with the floral homeotic genes SUPERWOMAN1, MADS3, MADS58, MADS13, and DROOPING LEAF in specifying floral organ identities and meristem fate	2011	Plant Cell	Institute of Plant Science, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	AGAMOUS-LIKE6 (AGL6) genes play essential roles in flower development, but whether and how they work with floral organ identity genes remain less understood. Here, we describe interactions of the rice (Oryza sativa) AGL6 gene MADS6 with other rice floral homeotic genes in flower development. Genetic analyses revealed that MADS6 specifies the identity of the three inner whorls and floral meristem determinacy redundantly with SUPERWOMAN1/MADS16 (B-gene) or MADS3 (C-gene). MADS6 was shown to define carpel/ovule development and floral determinacy by interacting with MADS13 (D-gene) and control the palea and floral meristem identities together with the YABBY gene DROOPING LEAF. Expression analyses revealed that the transcript levels of six B-, C-, and E-class genes were reduced in mads6-1 at the early flower developmental stage, suggesting that MADS6 is a key regulator of early flower development. Moreover, MADS6 can directly bind to a putative regulatory motif on MADS58 (C-gene), and mads6-1 mads58 displayed phenotypes similar to that of mads6-1. These results suggest that MADS6 is a key player in specifying flower development via interacting with other floral homeotic genes in rice, thus providing new insights into the mechanism by which flower development is controlled.	DL,OsMADS13,OsMADS16|SPW1,OSMADS3,OSMADS58,OsMADS6|MFO1
A transposon, Ping, is integrated into intron 4 of the DROOPING LEAF gene of rice, weakly reducing its expression and causing a mild drooping leaf phenotype	2008	Plant Cell Physiol	Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657 Japan.	The YABBY gene DROOPING LEAF (DL) regulates midrib formation in the leaves and carpel specification in the flowers of rice (Oryza sativa L). We found a new dl allele (dl-5) that caused a mild phenotype in the descendants of a mutable line, IM294. In plants homozygous for this allele, midrib structures were formed but their sizes were reduced. Molecular analysis revealed that a transposon, Ping, was inserted in the fourth intron of DL. Together with mPing and Pong, Ping is a member of a transposon family that was first identified as a group of active transposable elements in rice. Our finding of the Ping insertion in the DL gene is a first indication that Ping is active in planta, and that it can be transposed and integrated in a new locus. Ping seems to be still active because it was excised from intron 4 of DL at a relatively high frequency in rice calli. Real-time PCR analysis and in situ hybridization indicated that DL transcript levels were reduced in dl-5 without alterations in the spatial expression pattern of the DL gene. The reduction of DL expression may be due to inefficient splicing of the large intron caused by Ping insertion. By comparing the expression levels of DL and leaf phenotypes in the dl mutants with different severities, we confirmed our previous hypothesis that DL promotes cell proliferation in the central region of leaf primordia, and that this cell proliferation is critical for midrib formation in the mature leaves.	DL
The DROOPING LEAF and OsETTIN2 genes promote awn development in rice	2014	Plant J	Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Bunkyo-ku, Tokyo, 113-8657, Japan.	The awn is a long needle-like appendage that, in some grass species, is formed on the lemma that encloses floral organs together with the palea. In rice, most wild species and most strains of Oryza sativa ssp. indica generate an awn, whereas most strains of O. sativa ssp. japonica do not. In japonica, the long-awn characteristic appears to have been lost during domestication and breeding programs. Here, we found that the genes DROOPING LEAF (DL) and OsETTIN2 (OsETT2) are involved in awn development in the awned indica strain Kasalath. Genetic analyses and RNA-silencing experiments indicate that DL and OsETT2 act independently in awn formation, and that either gene alone is not sufficient for awn development. Scanning electron microscopy revealed that the top region of the lemma (a putative awn primordium) is larger in an awned floret than in an awnless floret. OsETT2 is expressed in the awn primordium in the awned indica floret, but not in the awnless japonica floret except in the provascular bundle. DL is expressed underneath the primordium at similar levels in both indica and japonica florets, suggesting non-cell-autonomous action. We hypothesize that loss of expression of OsETT2 in the awn primordium is probably associated with the failure of awn formation in japonica strains.	DL,OsETT2|OsETTIN2
Identification and localisation of the rice nicotianamine aminotransferase gene OsNAAT1 expression suggests the site of phytosiderophore synthesis in rice	2008	Plant Mol Biol	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Rice plants (Oryza sativa L.) take up iron using iron-chelating compounds known as mugineic acid family phytosiderophores (MAs). In the biosynthetic pathway of MAs, nicotianamine aminotransferase (NAAT) catalyses the key step from nicotianamine to the 3''-keto form. In the present study, we identified six rice NAAT genes (OsNAAT1-6) by screening a cDNA library made from Fe-deficient rice roots and by searching databases. Among the NAAT homologues, OsNAAT1 belongs to a subgroup containing barley functional NAAT (HvNAAT-A and HvNAAT-B) as well as a maize homologue cloned by cDNA library screening (ZmNAAT1). Northern blot and RT-PCR analysis showed that OsNAAT1, but not OsNAAT2-6, was strongly up-regulated by Fe deficiency, both in roots and shoots. The OsNAAT1 protein had NAAT enzyme activity in vitro, confirming that the OsNAAT1 gene encodes functional NAAT. Promoter-GUS analysis revealed that OsNAAT1 was expressed in companion and pericycle cells adjacent to the protoxylem of Fe-sufficient roots. In addition, expression was induced in all cells of Fe-deficient roots, with particularly strong GUS activity evident in the companion and pericycle cells. OsNAAT1 expression was also observed in the companion cells of Fe-sufficient shoots, and was clearly induced in all the cells of Fe-deficient leaves. These expression patterns highly resemble those of OsNAS1, OsNAS2 and OsDMAS1, the genes responsible for MAs biosynthesis for Fe acquisition. These findings strongly suggest that rice synthesizes MAs in whole Fe-deficient roots to acquire Fe from the rhizosphere, and also in phloem cells to maintain metal homeostasis facilitated by MAs-mediated long-distance transport.	OsDMAS1,OsNAAT1,OsNAAT2,OsNAAT3,OsNAAT4,OsNAAT5,OsNAAT6
Cloning and characterization of deoxymugineic acid synthase genes from graminaceous plants	2006	J Biol Chem	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657.	Graminaceous plants have evolved a unique mechanism to acquire iron through the secretion of a family of small molecules, called mugineic acid family phytosiderophores (MAs). All MAs are synthesized from l-Met, sharing the same pathway from l-Met to 2'-deoxymugineic acid (DMA). DMA is synthesized through the reduction of a 3''-keto intermediate by deoxymugineic acid synthase (DMAS). We have isolated DMAS genes from rice (OsDMAS1), barley (HvDMAS1), wheat (TaD-MAS1), and maize (ZmDMAS1). Their nucleotide sequences indicate that OsDMAS1 encodes a predicted polypeptide of 318 amino acids, whereas the other three orthologs all encode predicted polypeptides of 314 amino acids and are highly homologous (82-97.5%) to each other. The DMAS proteins belong to the aldo-keto reductase superfamily 4 (AKR4) but do not fall within the existing subfamilies of AKR4 and appear to constitute a new subfamily within the AKR4 group. All of the proteins showed DMA synthesis activity in vitro. Their enzymatic activities were highest at pH 8-9, consistent with the hypothesis that DMA is synthesized in subcellular vesicles. Northern blot analysis revealed that the expression of each of the above DMAS genes is up-regulated under iron-deficient conditions in root tissue, and that of the genes OsDMAS1 and TaDMAS1 is up-regulated in shoot tissue. OsDMAS1 promoter-GUS analysis in iron-sufficient roots showed that its expression is restricted to cells participating in long distance transport and that it is highly up-regulated in the entire root under iron-deficient conditions. In shoot tissue, OsDMAS1 promoter drove expression in vascular bundles specifically under iron-deficient conditions.	OsDMAS1
A receptor-like protein RMC is involved in regulation of iron acquisition in rice	2013	J Exp Bot	State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China.	Iron (Fe) is one of the essential mineral elements for plant growth and development. Acquisition of Fe by plants is mediated by a complex network involving Fe mobilization, uptake by root cells, and transport within plants. Here, we evaluated the role of a previously clarified gene encoding a receptor-like protein from rice, OsRMC, in the regulation of Fe acquisition by comparing Fe concentration, biomass, and expression patterns of genes associated with Fe mobilization and transport in wild-type (WT) rice with those in OsRMC overexpression and RNA interference (RNAi) knockdown transgenic rice plants. Expression of OsRMC was upregulated in both shoots and roots upon exposure of WT to Fe-deficient medium. Expression levels of OsRMC were positively correlated with Fe concentration in rice plants under both Fe-sufficient and Fe-deficient conditions such that overexpression and RNAi lines had higher and lower Fe concentration in both roots and shoots than WT plants, respectively. Moreover, overexpression of OsRMC conferred greater accumulation of Fe in mature seeds under Fe-sufficient conditions. OsRMC may also play a role in regulation of Fe deficiency-induced changes in root growth, as evidenced by greater and smaller root systems of OsRMC overexpression lines and RNAi lines than WT under Fe-deficient conditions, respectively. Several Fe deficiency-responsive genes including OsDMAS1, OsNAS1, OsNAS2, OsNAAT1, OsIRT1, OsYSL15, and OsIRO2 were up- and downregulated in OsRMC-overexpressing and RNAi plants compared with WT rice plants. These novel findings highlight an important role of OsRMC played in mediation of Fe acquisition and root growth in rice, particularly under Fe-deficient conditions.	OsDMAS1,OsIRO2,OsIRT1,OsNAAT1,OsNAS1,OsNAS2,OsRMC|OsRLK,OsYSL15
Expression of iron-acquisition-related genes in iron-deficient rice is co-ordinately induced by partially conserved iron-deficiency-responsive elements	2005	J Exp Bot	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Rice plants (Oryza sativa L.) utilize the iron chelators known as mugineic acid family phytosiderophores (MAs) to acquire iron from the rhizosphere. Synthesis of MAs and uptake of MA-chelated iron are strongly induced under conditions of iron deficiency. Microarray analysis was used to characterize the expression profile of rice in response to iron deficiency at the genomic level. mRNA extracted from iron-deficient or iron-sufficient rice roots or leaves was hybridized to a rice array containing 8987 cDNA clones. An induction ratio of greater than 2.0 in roots was observed for 57 genes, many of which are involved in iron-uptake mechanisms, including every identified or predicted step in the methionine cycle and the biosynthesis of MAs from methionine. Northern analysis confirmed that the expression of genes encoding every step in the methionine cycle is thoroughly induced by iron deficiency in roots, and almost thoroughly induced in leaves. A promoter search revealed that the iron-deficiency-induced genes related to iron uptake possessed sequences homologous to the iron-deficiency-responsive cis-acting elements IDE1 and IDE2 in their promoter regions, at a higher rate than that showing no induction under Fe deficiency. These results suggest that rice genes involved in iron acquisition are co-ordinately regulated by conserved mechanisms in response to iron deficiency, in which IDE-mediated regulation plays a significant role.	OsDMAS1,FDH,OsAPT1|APRT,OsDEP,OsRPI|RPI
The expression of iron homeostasis-related genes during rice germination	2007	Plant Mol Biol	Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.	To characterize Fe homeostasis during the early stages of seed germination, a microarray analysis was performed. mRNAs extracted from fully mature seeds or seeds harvested 1-3 days after sowing were hybridized to a rice microarray containing approximately 22,000 cDNA oligo probes. Many Fe deficiency-inducible genes were strongly expressed throughout early seed germination. These results suggest that the demand for Fe is extremely high during germination. Under Fe-deficient conditions, rice produces and secretes a metal-cation chelator called deoxymugineic acid (DMA) to acquire Fe from the soil. In addition, DMA and its intermediate nicotianamine (NA) are thought to be involved in long distance Fe transport in rice. Using promoter-beta-glucuronidase (GUS) analysis, we investigated the expression patterns during seed germination of the Fe deficiency-inducible genes OsNAS1, OsNAS2, OsNAS3, OsNAAT1, and OsDMAS1, which encode enzymes that participate in the biosynthesis of DMA, and the transporter genes OsYSL2 and OsIRT1, which are involved in Fe transport. All of these genes were expressed in germinating seeds prior to protrusion of the radicle. These results suggest that DMA and NA are produced and involved in Fe transport during germination.	OsDMAS1
Identification of OsbHLH133 as a regulator of iron distribution between roots and shoots in Oryza sativa	2013	Plant Cell Environ	State Key Laboratory of Plant Physiology and Biochemistry Joint Research Laboratory in Genomics and Nutriomics, College of Life Sciences, Zhejiang University, Hangzhou, China.	Iron (Fe) is an essential micronutrient element for plant growth. Regulation of Fe-deficiency signalling networks is one of the many functions reported for basic helix-loop-helix (bHLH) transcription factors in plants. In the present study, OsbHLH133 was found to be induced by Fe-deficiency conditions in Oryza sativa. Insertional inactivation of OsbHLH133 (bhlh133) resulted in growth retardation, with enhanced Fe concentration seen in shoots, and reduced Fe concentration in roots. Overexpression of OsbHLH133 had the opposite effect, that is resulted in an enhanced Fe concentration in roots and reduced Fe concentration in shoots and also in xylem sap. Microarray analysis showed that some of the genes encoding Fe-related functions were up-regulated under Fe-sufficient conditions, in bhlh133 mutant plants compared to wild-type plants. Significant differential expression of a number of signalling pathways, including calcium signalling, was also seen in bhlh133 plants compared to wild-type plants, independent of Fe conditions.	OsDMAS1,OsENA1,OsAPT1|APRT,OsbHLH133,TOM1|OsZIFL4,OsDEP,OsRPI|RPI
Deoxymugineic acid increases Zn translocation in Zn-deficient rice plants	2008	Plant Mol Biol	Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Deoxymugineic acid (DMA) is a member of the mugineic acid family phytosiderophores (MAs), which are natural metal chelators produced by graminaceous plants. Rice secretes DMA in response to Fe deficiency to take up Fe in the form of Fe(III)-MAs complex. In contrast with barley, the roots of which secrete MAs in response to Zn deficiency, the amount of DMA secreted by rice roots was slightly decreased under conditions of low Zn supply. There was a concomitant increase in endogenous DMA in rice shoots, suggesting that DMA plays a role in the translocation of Zn within Zn-deficient rice plants. The expression of OsNAS1 and OsNAS2 was not increased in Zn-deficient roots but that of OsNAS3 was increased in Zn-deficient roots and shoots. The expression of OsNAAT1 was also increased in Zn-deficient roots and dramatically increased in shoots; correspondingly, HPLC analysis was unable to detect nicotianamine in Zn-deficient shoots. The expression of OsDMAS1 was increased in Zn-deficient shoots. Analyses using the positron-emitting tracer imaging system (PETIS) showed that Zn-deficient rice roots absorbed less (62)Zn-DMA than (62)Zn(2+). Importantly, supply of (62)Zn-DMA rather than (62)Zn(2+) increased the translocation of (62)Zn into the leaves of Zn-deficient plants. This was especially evident in the discrimination center (DC). These results suggest that DMA in Zn-deficient rice plants has an important role in the distribution of Zn within the plant rather than in the absorption of Zn from the soil.	OsDMAS1
Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice	2011	BMC Plant Biol	Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi-110021, India.	BACKGROUND: In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed in many plant species at progressive stages of development by using microarray and sequence-by synthesis-technologies to identify genes that regulate anther development. Here we report a comprehensive analysis of rice anther transcriptomes at four distinct stages, focusing on identifying regulatory components that contribute to male meiosis and germline development. Further, these transcriptomes have been compared with the transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. RESULTS: Transcriptome profiling of four stages of anther development in rice including pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA) revealed about 22,000 genes expressing in at least one of the anther developmental stages, with the highest number in MA (18,090) and the lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes specifically expressed in anther stages. From this sub-set, 453 genes were specific to TPA, while 78 and 184 genes were expressed specifically in MA and SCP, respectively. The expression pattern of selected genes has been validated using real time PCR and in situ hybridizations. Gene ontology and pathway analysis of stage-specific genes revealed that those encoding transcription factors and components of protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. CONCLUSIONS: Not only have we provided the transcriptome constituents of four landmark stages of anther development in rice but we have also identified genes that express exclusively in these stages. It is likely that many of these candidates may therefore contribute to specific aspects of anther and/or male gametophyte development in rice. In addition, the gene sets that have been produced will assist the plant reproductive community in building a deeper understanding of underlying regulatory networks and in selecting gene candidates for functional validation.	DMC1A|DMC1
Filament formation and robust strand exchange activities of the rice DMC1A and DMC1B proteins	2008	Nucleic Acids Res	Consolidated Research Institute for Advanced Science and Medical Care, Waseda University, 513 Wasedatsurumaki-cho, Shinjuku-ku, Tokyo 162-0041, Japan.	The DMC1 protein, a meiosis-specific DNA recombinase, catalyzes strand exchange between homologous chromosomes. In rice, two Dmc1 genes, Dmc1A and Dmc1B, have been reported. Although the Oryza sativa DMC1A protein has been partially characterized, however the biochemical properties of the DMC1B protein have not been defined. In the present study, we expressed the Oryza sativa DMC1A and DMC1B proteins in bacteria and purified them. The purified DMC1A and DMC1B proteins formed helical filaments along single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), and promoted robust strand exchange between ssDNA and dsDNA over five thousand base pairs in the presence of RPA, as a co-factor. The DMC1A and DMC1B proteins also promoted strand exchange in the absence of RPA with long DNA substrates containing several thousand base pairs. In contrast, the human DMC1 protein strictly required RPA to promote strand exchange with these long DNA substrates. The strand-exchange activity of the Oryza sativa DMC1A protein was much higher than that of the DMC1B protein. Consistently, the DNA-binding activity of the DMC1A protein was higher than that of the DMC1B protein. These biochemical differences between the DMC1A and DMC1B proteins may provide important insight into their functional differences during meiosis in rice.	DMC1A|DMC1
A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice	2011	Proc Natl Acad Sci U S A	Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA.	DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counteract transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons. Here we report the functional characterization of the DNA glycosylase/lyase DNG701 in rice. DNG701 encodes a large (1,812 amino acid residues) DNA glycosylase domain protein. Recombinant DNG701 protein showed 5-meC DNA glycosylase and lyase activities in vitro. Knockout or knockdown of DNG701 in rice plants led to DNA hypermethylation and reduced expression of the retrotransposon Tos17. Tos17 showed less transposition in calli derived from dng701 knockout mutant seeds compared with that in wild-type calli. Overexpression of DNG701 in both rice calli and transgenic plants substantially reduced DNA methylation levels of Tos17 and enhanced its expression. The overexpression also led to more frequent transposition of Tos17 in calli. Our results demonstrate that rice DNG701 is a 5-meC DNA glycosylase/lyase responsible for the demethylation of Tos17 and this DNA demethylase plays a critical role in promoting Tos17 transposition in rice calli.	DNG701
A leucine-rich repeat receptor-like kinase gene is involved in the specification of outer cell layers in rice roots	2012	Plant J	Institute of Plant Science and Resources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan.	Root outer cell layers of Oryza sativa (rice), which comprise the epidermis, exodermis and sclerenchyma, play an important role in protecting the roots from various stresses in soil, but the molecular mechanisms for the specification of these cell layers are poorly understood. In this work, we report on defective in outer cell layer specification 1 (Docs1), which is involved in the specification of outer cell layers in rice roots. Docs1 was isolated by map-based cloning using a mutant (c68) defective in the outer cell layers of primary roots. It encodes a leucine-rich repeat receptor-like kinase (LRR RLK). Docs1 mRNA was expressed in all tissues including roots, leaf blades and sheaths, and flowers. Immunostaining with an anti-Docs1 antibody showed that Docs1 was localized at the epidermis and exodermis, depending on the root region. Furthermore, Docs1 showed polar localization at the distal side. Subcellular examination showed that Docs1 was localized to the plasma membrane. Comparison of genome-wide transcriptional profiles between the wild-type and the knock-out mutant roots using microarray analysis showed that 61 and 41 genes were up- and downregulated in the mutant, including genes encoding putative transcription factors and genes potentially involved in cell wall metabolism. These results suggest that Docs1 might directly or indirectly regulate multiple genes involved in the proper development of root outer cell layers in rice.	Docs1
An AT-hook gene is required for palea formation and floral organ number control in rice	2011	Dev Biol	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences.	Grasses have highly specialized flowers and their outer floral organ identity remains unclear. In this study, we identified and characterized rice mutants that specifically disrupted the development of palea, one of the outer whorl floral organs. The depressed palea1 (dp1) mutants show a primary defect in the main structure of palea, implying that palea is a fusion between the main structure and marginal tissues on both sides. The sterile lemma at the palea side is occasionally elongated in dp1 mutants. In addition, we found a floral organ number increase in dp1 mutants at low penetration. Both the sterile lemma elongation and the floral organ number increase phenotype are enhanced by the mutation of an independent gene SMALL DEGENERATIVE PALEA1 (SDP1), whose single mutation causes reduced palea size. E function and presumable A function floral homeotic genes were found suppressed in the dp1-2 mutant. We identified the DP1 gene by map-based cloning and found it encodes a nuclear-localized AT-hook DNA binding protein, suggesting a grass-specific role of chromatin architecture modification in flower development. The DP1 enhancer SDP1 was also positional cloned, and was found identical to the recently reported RETARDED PALEA1 (REP1) gene encoding a TCP family transcription factor. We further found that SDP1/REP1 is downstreamly regulated by DP1.	DP1,REP1
Rice pollen hybrid incompatibility caused by reciprocal gene loss of duplicated genes	2010	Proc Natl Acad Sci U S A	Plant Genetics Laboratory, Genetic Strains Research Center, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.	Genetic incompatibility is a barrier contributing to species isolation and is caused by genetic interactions. We made a whole genome survey of two-way interacting loci acting within the gametophyte or zygote using independence tests of marker segregations in an F(2) population from an intersubspecific cross between O. sativa subspecies indica and japonica. We detected only one reproducible interaction, and identified paralogous hybrid incompatibility genes, DOPPELGANGER1 (DPL1) and DOPPELGANGER2 (DPL2), by positional cloning. Independent disruptions of DPL1 and DPL2 occurred in indica and japonica, respectively. DPLs encode highly conserved, plant-specific small proteins ( approximately 10 kDa) and are highly expressed in mature anther. Pollen carrying two defective DPL alleles became nonfunctional and did not germinate, suggesting an essential role for DPLs in pollen germination. Although rice has many duplicated genes resulting from ancient whole genome duplication, the origin of this gene duplication was in recent small-scale gene duplication, occurring after Oryza-Brachypodium differentiation. Comparative analyses suggested the geographic and phylogenetic distribution of these two defective alleles, showing that loss-of-function mutations of DPL1 genes emerged multiple times in indica and its wild ancestor, O. rufipogon, and that the DPL2 gene defect is specific to japonica cultivars.	DPL1,DPL2
Defective pollen wall is required for anther and microspore development in rice and encodes a fatty acyl carrier protein reductase	2011	Plant Cell	Institute of Plant Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	Aliphatic alcohols naturally exist in many organisms as important cellular components; however, their roles in extracellular polymer biosynthesis are poorly defined. We report here the isolation and characterization of a rice (Oryza sativa) male-sterile mutant, defective pollen wall (dpw), which displays defective anther development and degenerated pollen grains with an irregular exine. Chemical analysis revealed that dpw anthers had a dramatic reduction in cutin monomers and an altered composition of cuticular wax, as well as soluble fatty acids and alcohols. Using map-based cloning, we identified the DPW gene, which is expressed in both tapetal cells and microspores during anther development. Biochemical analysis of the recombinant DPW enzyme shows that it is a novel fatty acid reductase that produces 1-hexadecanol and exhibits >270-fold higher specificity for palmiltoyl-acyl carrier protein than for C16:0 CoA substrates. DPW was predominantly targeted to plastids mediated by its N-terminal transit peptide. Moreover, we demonstrate that the monocot DPW from rice complements the dicot Arabidopsis thaliana male sterile2 (ms2) mutant and is the probable ortholog of MS2. These data suggest that DPWs participate in a conserved step in primary fatty alcohol synthesis for anther cuticle and pollen sporopollenin biosynthesis in monocots and dicots.	DPW
Dro1, a major QTL involved in deep rooting of rice under upland field conditions	2011	J Exp Bot	National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan. yuga@affrc.go.jp	Developing a deep root system is an important strategy for avoiding drought stress in rice. Using the 'basket' method, the ratio of deep rooting (RDR; the proportion of total roots that elongated through the basket bottom) was calculated to evaluate deep rooting. A new major quantitative trait locus (QTL) controlling RDR was detected on chromosome 9 by using 117 recombinant inbred lines (RILs) derived from a cross between the lowland cultivar IR64, with shallow rooting, and the upland cultivar Kinandang Patong (KP), with deep rooting. This QTL explained 66.6% of the total phenotypic variance in RDR in the RILs. A BC(2)F(3) line homozygous for the KP allele of the QTL had an RDR of 40.4%, compared with 2.6% for the homozygous IR64 allele. Fine mapping of this QTL was undertaken using eight BC(2)F(3) recombinant lines. The RDR QTL Dro1 (Deeper rooting 1) was mapped between the markers RM24393 and RM7424, which delimit a 608.4 kb interval in the reference cultivar Nipponbare. To clarify the influence of Dro1 in an upland field, the root distribution in different soil layers was quantified by means of core sampling. A line homozygous for the KP allele of Dro1 (Dro1-KP) and IR64 did not differ in root dry weight in the shallow soil layers (0-25 cm), but root dry weight of Dro1-KP in deep soil layers (25-50 cm) was significantly greater than that of IR64, suggesting that Dro1 plays a crucial role in increased deep rooting under upland field conditions.	DRO1
Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions	2013	Nat Genet	National Institute of Agrobiological Sciences, Tsukuba, Japan. yuga@nias.affrc.go.jp	The genetic improvement of drought resistance is essential for stable and adequate crop production in drought-prone areas. Here we demonstrate that alteration of root system architecture improves drought avoidance through the cloning and characterization of DEEPER ROOTING 1 (DRO1), a rice quantitative trait locus controlling root growth angle. DRO1 is negatively regulated by auxin and is involved in cell elongation in the root tip that causes asymmetric root growth and downward bending of the root in response to gravity. Higher expression of DRO1 increases the root growth angle, whereby roots grow in a more downward direction. Introducing DRO1 into a shallow-rooting rice cultivar by backcrossing enabled the resulting line to avoid drought by increasing deep rooting, which maintained high yield performance under drought conditions relative to the recipient cultivar. Our experiments suggest that control of root system architecture will contribute to drought avoidance in crops.	DRO1
A rice dihydrosphingosine C4 hydroxylase (DSH1) gene, which is abundantly expressed in the stigmas, vascular cells and apical meristem, may be involved in fertility	2007	Plant Cell Physiol	Department of Biological Science and Technology, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.	Dihydrosphingosine C4 hydroxylase is a key enzyme in the biosynthesis of phytosphingosine, a major constituent of sphingolipids in plants and yeasts. The rice genome contains five homologue genes for dihydrosphingosine C4 hydroxylase, DSH1-DSH5, whose gene products show high degrees of homology to the yeast counterpart, SUR2. Among them, expression of DSH1, DSH2 and DSH4 was detected, and DSH1 and DSH4 complement the yeast sur2 mutation. The DSH1 gene was specifically and abundantly expressed in vascular bundles and apical meristems. In particular, very strong expression was detected in the stigmas of flowers. Repression of DSH1 expression by the antisense gene or RNA interference (RNAi) resulted in a severe reduction of fertility. In the transformants in which DSH1 expression was suppressed, significantly increased expression of DSH2 was found in leaves but not in pistils, suggesting that there was tissue-specific correlation between DSH1 and DSH2 expression. Our results indicate that the product of DSH1 may be involved in plant viability or reproductive processes, and that the phenotype of sterility is apparently caused by loss of function of DSH1 in the stigma. It is also suggested that there is a complex mechanism controlling the tissue-specific expression of the DSH1 gene.	DSH1
A Raf-like MAPKKK gene DSM1 mediates drought resistance through reactive oxygen species scavenging in rice	2010	Plant Physiol	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.	Mitogen-activated protein kinase (MAPK) cascades have been identified in various signaling pathways involved in plant development and stress responses. We identified a drought-hypersensitive mutant (drought-hypersensitive mutant1 [dsm1]) of a putative MAPK kinase kinase (MAPKKK) gene in rice (Oryza sativa). Two allelic dsm1 mutants were more sensitive than wild-type plants to drought stress at both seedling and panicle development stages. The dsm1 mutants lost water more rapidly than wild-type plants under drought stress, which was in agreement with the increased drought-sensitivity phenotype of the mutant plants. DSM1-RNA interference lines were also hypersensitive to drought stress. The predicted DSM1 protein belongs to a B3 subgroup of plant Raf-like MAPKKKs and was localized in the nucleus. By real-time PCR analysis, the DSM1 gene was induced by salt, drought, and abscisic acid, but not by cold. Microarray analysis revealed that two peroxidase (POX) genes, POX22.3 and POX8.1, were sharply down-regulated compared to wild type, suggesting that DSM1 may be involved in reactive oxygen species (ROS) signaling. Peroxidase activity, electrolyte leakage, chlorophyll content, and 3,3'-diaminobenzidine staining revealed that the dsm1 mutant was more sensitive to oxidative stress due to an increase in ROS damage caused by the reduced POX activity. Overexpression of DSM1 in rice increased the tolerance to dehydration stress at the seedling stage. Together, these results suggest that DSM1 might be a novel MAPKKK functioning as an early signaling component in regulating responses to drought stress by regulating scavenging of ROS in rice.	DSM1
Characterization of the beta-carotene hydroxylase gene DSM2 conferring drought and oxidative stress resistance by increasing xanthophylls and abscisic acid synthesis in rice	2010	Plant Physiol	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.	Drought is a major limiting factor for crop production. To identify critical genes for drought resistance in rice (Oryza sativa), we screened T-DNA mutants and identified a drought-hypersensitive mutant, dsm2. The mutant phenotype was caused by a T-DNA insertion in a gene encoding a putative beta-carotene hydroxylase (BCH). BCH is predicted for the biosynthesis of zeaxanthin, a carotenoid precursor of abscisic acid (ABA). The amounts of zeaxanthin and ABA were significantly reduced in two allelic dsm2 mutants after drought stress compared with the wild type. Under drought stress conditions, the mutant leaves lost water faster than the wild type and the photosynthesis rate, biomass, and grain yield were significantly reduced, whereas malondialdehyde level and stomata aperture were increased in the mutant. The mutant is also hypersensitive to oxidative stresses. The mutant had significantly lower maximal efficiency of photosystem II photochemistry and nonphotochemical quenching capacity than the wild type, indicating photoinhibition in photosystem II and decreased capacity for eliminating excess energy by thermal dissipation. Overexpression of DSM2 in rice resulted in significantly increased resistance to drought and oxidative stresses and increases of the xanthophylls and nonphotochemical quenching. Some stress-related ABA-responsive genes were up-regulated in the overexpression line. DSM2 is a chloroplast protein, and the response of DSM2 to environmental stimuli is distinctive from the other two BCH members in rice. We conclude that the DSM2 gene significantly contributes to control of the xanthophyll cycle and ABA synthesis, both of which play critical roles in the establishment of drought resistance in rice.	DSM2
Characterization of an inositol 1,3,4-trisphosphate 5/6-kinase gene that is essential for drought and salt stress responses in rice	2011	Plant Mol Biol	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, China.	Drought and salt stresses are major limiting factors for crop production. To identify critical genes for stress resistance in rice (Oryza sativa L.), we screened T-DNA mutants and identified a drought- and salt-hypersensitive mutant dsm3. The mutant phenotype was caused by a T-DNA insertion in a gene encoding a putative inositol 1,3,4-trisphosphate 5/6-kinase previously named OsITPK2 with unknown function. Under drought stress conditions, the mutant had significantly less accumulation of osmolytes such as proline and soluble sugar and showed significantly reduced root volume, spikelet fertility, biomass, and grain yield; however, malondialdehyde level was increased in the mutant. Interestingly, overexpression of DSM3 (OsITPK2) in rice resulted in drought- and salt-hypersensitive phenotypes and physiological changes similar to those in the mutant. Inositol trisphosphate (IP3) level was decreased in the overexpressors under normal condition and drought stress. A few genes related to osmotic adjustment and reactive oxygen species scavenging were down-regulated in the mutant and overexpression lines. The expression level of DSM3 promoter-driven beta-glucuronidase (GUS) reporter gene in rice was induced by drought, salt and abscisic acid. Protoplast transient expression assay indicated that DSM3 is an endoplasmic reticulum protein. Sequence analysis revealed six putative ITPKs in rice. Transcript level analysis of OsITPK genes revealed that they had different tempo-spatial expression patterns, and the responses of DSM3 to abiotic stresses, including drought, salinity, cold, and high temperature, were distinct from the other five members in rice. These results together suggest that DSM3/OsITPK2 is an important member of the OsITPK family for stress responses, and an optimal expression level is essential for drought and salt tolerance in rice.	DSM3|OsITPK2
The SNAC1-targeted gene OsSRO1c modulates stomatal closure and oxidative stress tolerance by regulating hydrogen peroxide in rice	2013	J Exp Bot	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.	Abiotic stresses such as drought cause a reduction of plant growth and loss of crop yield. Stomatal aperture controls CO(2) uptake and water loss to the atmosphere, thus playing important roles in both the yield gain and drought tolerance of crops. Here, a rice homologue of SRO (similar to RCD one), termed OsSRO1c, was identified as a direct target gene of SNAC1 (stress-responsive NAC 1) involved in the regulation of stomatal aperture and oxidative response. SNAC1 could bind to the promoter of OsSRO1c and activate the expression of OsSRO1c. OsSRO1c was induced in guard cells by drought stress. The loss-of-function mutant of OsSRO1c showed increased stomatal aperture and sensitivity to drought, and faster water loss compared with the wild-type plant, whereas OsSRO1c overexpression led to decreased stomatal aperture and reduced water loss. Interestingly, OsSRO1c-overexpressing rice showed increased sensitivity to oxidative stress. Expression of DST, a reported zinc finger gene negatively regulating H(2)O(2)-induced stomatal closure, and the activity of H(2)O(2)-scavenging related enzymes were significantly suppressed, and H(2)O(2) in guard cells was accumulated in the overexpression lines. OsSRO1c interacted with various stress-related regulatory and functional proteins, and some of the OsSRO1c-interacting proteins are predicted to be involved in the control of stomatal aperture and oxidative stress tolerance. The results suggest that OsSRO1c has dual roles in drought and oxidative stress tolerance of rice by promoting stomatal closure and H(2)O(2) accumulation through a novel pathway involving regulators SNAC1 and DST.	DST,OsSRO1c,OsNAC19|SNAC1|OsNAC9
A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control	2009	Genes Dev	National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.	Abiotic stresses, such as drought and salinity, lead to crop growth damage and a decrease in crop yields. Stomata control CO(2) uptake and optimize water use efficiency, thereby playing crucial roles in abiotic stress tolerance. Hydrogen peroxide (H(2)O(2)) is an important signal molecule that induces stomatal closure. However, the molecular pathway that regulates the H(2)O(2) level in guard cells remains largely unknown. Here, we clone and characterize DST (drought and salt tolerance)-a previously unknown zinc finger transcription factor that negatively regulates stomatal closure by direct modulation of genes related to H(2)O(2) homeostasis-and identify a novel pathway for the signal transduction of DST-mediated H(2)O(2)-induced stomatal closure. Loss of DST function increases stomatal closure and reduces stomatal density, consequently resulting in enhanced drought and salt tolerance in rice. These findings provide an interesting insight into the mechanism of stomata-regulated abiotic stress tolerance, and an important genetic engineering approach for improving abiotic stress tolerance in crops.	DST
Rice zinc finger protein DST enhances grain production through controlling Gn1a/OsCKX2 expression	2013	Proc Natl Acad Sci U S A	State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	The phytohormone cytokinin (CK) positively regulates the activity and function of the shoot apical meristem (SAM), which is a major parameter determining seed production. The rice (Oryza sativa L.) Gn1a/OsCKX2 (Grain number 1a/Cytokinin oxidase 2) gene, which encodes a cytokinin oxidase, has been identified as a major quantitative trait locus contributing to grain number improvement in rice breeding practice. However, the molecular mechanism of how the expression of OsCKX2 is regulated in planta remains elusive. Here, we report that the zinc finger transcription factor DROUGHT AND SALT TOLERANCE (DST) directly regulates OsCKX2 expression in the reproductive meristem. DST-directed expression of OsCKX2 regulates CK accumulation in the SAM and, therefore, controls the number of the reproductive organs. We identify that DST(reg1), a semidominant allele of the DST gene, perturbs DST-directed regulation of OsCKX2 expression and elevates CK levels in the reproductive SAM, leading to increased meristem activity, enhanced panicle branching, and a consequent increase of grain number. Importantly, the DST(reg1) allele provides an approach to pyramid the Gn1a-dependent and Gn1a-independent effects on grain production. Our study reveals that, as a unique regulator of reproductive meristem activity, DST may be explored to facilitate the genetic enhancement of grain production in rice and other small grain cereals.	DST,Gn1a|OsCKX2
Association of functional nucleotide polymorphisms at DTH2 with the northward expansion of rice cultivation in Asia	2013	Proc Natl Acad Sci U S A	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.	Flowering time (i.e., heading date in crops) is an important ecological trait that determines growing seasons and regional adaptability of plants to specific natural environments. Rice (Oryza sativa L.) is a short-day plant that originated in the tropics. Increasing evidence suggests that the northward expansion of cultivated rice was accompanied by human selection of the heading date under noninductive long-day (LD) conditions. We report here the molecular cloning and characterization of DTH2 (for Days to heading on chromosome 2), a minor-effect quantitative trait locus that promotes heading under LD conditions. We show that DTH2 encodes a CONSTANS-like protein that promotes heading by inducing the florigen genes Heading date 3a and RICE FLOWERING LOCUS T 1, and it acts independently of the known floral integrators Heading date 1 and Early heading date 1. Moreover, association analysis and transgenic experiments identified two functional nucleotide polymorphisms in DTH2 that correlated with early heading and increased reproductive fitness under natural LD conditions in northern Asia. Our combined population genetics and network analyses suggest that DTH2 likely represents a target of human selection for adaptation to LD conditions during rice domestication and/or improvement, demonstrating an important role of minor-effect quantitative trait loci in crop adaptation and breeding.	DTH2,Hd3a,RFT1
Genetic interactions involved in the inhibition of heading by heading date QTL, Hd2 in rice under long-day conditions	2011	Theor Appl Genet	QTL Genomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.	Heading date is the one of the most important traits in rice breeding, because it defines where rice can be cultivated and influences the expression of various agronomic traits. To examine the inhibition of heading by Heading date 2 (Hd2), previously detected on the distal end of chromosome 7's long arm by quantitative trait locus (QTL) analysis, we developed backcross inbred lines (BILs) from Koshihikari, a leading Japanese cultivar, and Hayamasari, an extremely early heading cultivar. The BILs were cultivated under natural field conditions in Tsukuba Japan, and under long-day (14.5 h), extremely long-day (18 h), and short-day (10 h) conditions. Combinations of several QTLs near Hd1, Hd2, Ghd7, Hd5, and Hd16 were detected under these four conditions. Analysis of advanced backcross progenies revealed genetic interactions between Hd2 and Hd16 and between Hd2 and Ghd7. In the homozygous Koshihikari genetic background at Hd16, inhibition of heading by the Koshihikari allele at Hd2 was smaller than that with the Hayamasari Hd16 allele. Similarly, in the homozygous Koshihikari genetic background at Ghd7, the difference in heading date caused by different alleles at Hd2 was smaller than in plants homozygous for the Hayamasari Ghd7 allele. Based on these results, we conclude that Hd2 and its genetic interactions play an important role in controlling heading under long-day conditions. In addition, QTLs near Hd2, Hd16, and Ghd7, which are involved in inhibition of heading under long-day conditions, function in the same pathway that controls heading date.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,Ghd7,Hd1,CKI|EL1|Hd16
Roles of the Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation	2013	Theor Appl Genet	Agricultural Research Institute, HOKUREN Federation of Agricultural Cooperatives, Naganuma, Hokkaido, 067-1317, Japan. kfujino@affrc.go.jp	During the diversification of cultivated rice after domestication, rice was grown in diverse geographic regions using genetic variations attributed to the combination of alleles in loci for adaptability to various environmental conditions. To elucidate the key gene for adaptation in rice cultivars to the northern limit of rice cultivation, we conducted genetic analyses of heading date using extremely early-heading cultivars. The Hd5 gene controlling heading date (flowering time) generated variations in heading date among cultivars adapted to Hokkaido, where is the northernmost region of Japan and one of the northern limits of rice cultivation in the world. The association of the Hd5 genotype with heading date and genetical analysis clearly showed that the loss-of-function Hd5 has an important role in exhibiting earlier heading among a local population in Hokkaido. Distinct distribution of the loss-of-function Hd5 revealed that this mutation event of the 19-bp deletion occurred in a local landrace Bouzu and that this mutation may have been selected as an early-heading variety in rice breeding programs in Hokkaido in the early 1900s. The loss-of-function Hd5 was then introduced into the rice variety Fanny from France and contributed to its extremely early heading under the presence of functional Ghd7. These results demonstrated that Hd5 plays roles not only in generating early heading in variations of heading date among a local population in Hokkaido, but also in extremely early heading for adaptation to northern limits of rice cultivation.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,Ghd7
Identification, characterization and interaction of HAP family genes in rice	2008	Mol Genet Genomics	Genetic Strains Research Center, National Institute of Genetics, Shizuoka-ken, Japan.	A HAP complex, which consists of three subunits, namely HAP2 (also called NF-YA or CBF-B), HAP3 (NF-YB/CBF-A) and HAP5 (NF-YC/CBF-C), binds to CCAAT sequences in a promoter to control the expression of target genes. We identified 10 HAP2 genes, 11 HAP3 genes and 7 HAP5 genes in the rice genome. All the three HAP family genes encode a protein with a conserved domain in each family and various non-conserved regions in both length and amino acid sequence. These genes showed various expression patterns depending on genes, and various combinations of overlapped expression of the HAP2, HAP3 and HAP5 genes were observed. Furthermore, protein interaction analyses showed interaction of OsHAP3A, a ubiquitously expressed HAP3 subunit of rice, with specific members of HAP5. These results indicate that the formation of specific complex with various HAP subunits combinations can be achieved by both tissue specific expression of three subunit genes and specific interaction of three subunit proteins. This may suggest that the HAP complexes may control various aspects of rice growth and development through tissue specific expression and complex formation of three subunit members.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,OsHAP3A,OsHAP3B,OsHAP3C,OsHAP3E,OsNF-YB1
LHD1, an allele of DTH8/Ghd8, controls late heading date in common wild rice (Oryza rufipogon)	2012	J Integr Plant Biol	State Key Laboratory of Plant Physiology and Biochemistry, National Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.	Flowering at suitable time is very important for plants to adapt to complicated environments and produce their seeds successfully for reproduction. In rice (Oryza rufipogon Griff.) photoperiod regulation is one of the important factors for controlling heading date. Common wild rice, the ancestor of cultivated rice, exhibits a late heading date and a more sensitive photoperiodic response than cultivated rice. Here, through map-based cloning, we identified a major quantitative trait loci (QTL) LHD1 (Late Heading Date 1), an allele of DTH8/Ghd8, which controls the late heading date of wild rice and encodes a putative HAP3/NF-YB/CBF-A subunit of the CCAAT-box-binding transcription factor. Sequence analysis revealed that several variants in the coding region of LHD1 were correlated with a late heading date, and a further complementary study successfully rescued the phenotype. These results suggest that a functional site for LHD1 could be among those variants present in the coding region. We also found that LHD1 could down-regulate the expression of several floral transition activators such as Ehd1, Hd3a and RFT1 under long-day conditions, but not under short-day conditions. This indicates that LHD1 may delay flowering by repressing the expression of Ehd1, Hd3a and RFT1 under long-day conditions.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,Ehd1,Hd3a,RFT1
A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice	2011	Mol Plant	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Rice yield and heading date are two distinct traits controlled by quantitative trait loci (QTLs). The dissection of molecular mechanisms underlying rice yield traits is important for developing high-yielding rice varieties. Here, we report the cloning and characterization of Ghd8, a major QTL with pleiotropic effects on grain yield, heading date, and plant height. Two sets of near isogenic line populations were developed for the cloning of Ghd8. Ghd8 was narrowed down to a 20-kb region containing two putative genes, of which one encodes the OsHAP3 subunit of a CCAAT-box binding protein (HAP complex); this gene was regarded as the Ghd8 candidate. A complementary test confirmed the identity and pleiotropic effects of the gene; interestingly, the genetic effect of Ghd8 was dependent on its genetic background. By regulating Ehd1, RFT1, and Hd3a, Ghd8 delayed flowering under long-day conditions, but promoted flowering under short-day conditions. Ghd8 up-regulated MOC1, a key gene controlling tillering and branching; this increased the number of tillers, primary and secondary branches, thus producing 50% more grains per plant. The ectopic expression of Ghd8 in Arabidopsis caused early flowering by 10 d-a situation similar to the one observed by its homolog AtHAP3b, when compared to wild-type under long-day conditions; these findings indicate the conserved function of Ghd8 and AtHAP3b in flowering in Arabidopsis. Our results demonstrated the important roles of Ghd8 in rice yield formation and flowering, as well as its opposite functions in flowering between rice and Arabidopsis under long-day conditions.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,Ehd1,Hd3a,MOC1,RFT1
DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously	2010	Plant Physiol	State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China.	The three most important agronomic traits of rice (Oryza sativa), yield, plant height, and flowering time, are controlled by many quantitative trait loci (QTLs). In this study, a newly identified QTL, DTH8 (QTL for days to heading on chromosome 8), was found to regulate these three traits in rice. Map-based cloning reveals that DTH8 encodes a putative HAP3 subunit of the CCAAT-box-binding transcription factor and the complementary experiment increased significantly days to heading, plant height, and number of grains per panicle in CSSL61 (a chromosome segment substitution line that carries the nonfunctional DTH8 allele) with the Asominori functional DTH8 allele under long-day conditions. DTH8 is expressed in most tissues and its protein is localized to the nucleus exclusively. The quantitative real-time PCR assay revealed that DTH8 could down-regulate the transcriptions of Ehd1 (for Early heading date1) and Hd3a (for Heading date3a; a rice ortholog of FLOWERING LOCUS T) under long-day conditions. Ehd1 and Hd3a can also be down-regulated by the photoperiodic flowering genes Ghd7 and Hd1 (a rice ortholog of CONSTANS). Meanwhile, the transcription of DTH8 has been proved to be independent of Ghd7 and Hd1, and the natural mutation of this gene caused weak photoperiod sensitivity and shorter plant height. Taken together, these data indicate that DTH8 probably plays an important role in the signal network of photoperiodic flowering as a novel suppressor as well as in the regulation of plant height and yield potential.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,Ehd1,Ghd7,Hd1,Hd3a
Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response	2013	Plant J	National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.	The alteration of photoperiod sensitivity has let breeders diversify flowering time in Oryza sativa (rice) and develop cultivars adjusted to a range of growing season periods. Map-based cloning revealed that the rice flowering-time quantitative trait locus (QTL) Heading date 16 (Hd16) encodes a casein kinase-I protein. One non-synonymous substitution in Hd16 resulted in decreased photoperiod sensitivity in rice, and this substitution occurred naturally in an old rice cultivar. By using near-isogenic lines with functional or deficient alleles of several rice flowering-time genes, we observed significant digenetic interactions between Hd16 and four other flowering-time genes (Ghd7, Hd1, DTH8 and Hd2). In a near-isogenic line with the weak-photoperiod-sensitivity allele of Hd16, transcription levels of Ehd1, Hd3a, and RFT1 increased under long-day conditions, and transcription levels of Hd3a and RFT1 decreased under short-day conditions. Expression analysis under continuous light and dark conditions showed that Hd16 was not likely to be associated with circadian clock regulation. Biochemical characterization indicated that the functional Hd16 recombinant protein specifically phosphorylated Ghd7. These results demonstrate that Hd16 acts as an inhibitor in the rice flowering pathway by enhancing the photoperiod response as a result of the phosphorylation of Ghd7.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1,Ehd1,Ghd7,Hd1,CKI|EL1|Hd16,Hd3a,RFT1
Quantitative trait loci for panicle size, heading date and plant height co-segregating in trait-performance derived near-isogenic lines of rice (Oryza sativa)	2006	Theor Appl Genet	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Near-isogenic lines (NILs) are ideal materials for precise estimation of quantitative trait loci (QTL) effects and map-based gene isolation. With the completion of the rice genome sequence, QTL isolation based on NILs is becoming a routine. In this study, a trait-performance derived NIL strategy was adopted to develop NILs. Two plants were identified within one inbred line of recombinant inbred lines (RILs, F(7) generation), exhibiting a significant difference in panicle size. By marker screening of the whole genome the genetic background of the two plants was estimated to be 98.7% identical. These two plants were selected as parents to produce a near-isogenic F(2) (NIL-F(2)) population, consisting of 125 individuals, in which spikelets per panicle (SPP), grains per panicle (GPP), heading date (HD) and plant height (PH) were recorded. These four traits expressed discontinuous or bimodal distribution in the NIL-F(2) population and followed the expected segregation ratios for a single Mendelian factor by progeny tests. A partial dominant QTL for the four traits was mapped to the same interval flanked by RM310 and RM126 on chromosome 8. The QTL region explained 83.0, 80.2, 94.9 and 93.8% of trait variation of SPP, GPP, HD and PH in the progenies, respectively. Progeny tests also confirmed co-segregation of QTL for the four traits, tall plants consistently flowering late and carrying large panicles. Different NILs development strategies are discussed.	Hd5|DTH8|Ghd8|OsHAP3H|LHD1
The rice gene DEFECTIVE TAPETUM AND MEIOCYTES 1 (DTM1) is required for early tapetum development and meiosis	2012	Plant J	Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.	Tapetum development and meiosis play crucial roles in anther development. Here we identified a rice gene, DEFECTIVE TAPETUM AND MEIOCYTES 1 (DTM1), which controls the early stages of that development. This gene encodes for an endoplasmic reticulum (ER) membrane protein that is present only in cereals. Our T-DNA insertion mutations gave rise to abnormal tapetal formation. Cellular organelles, especially the ER, were underdeveloped, which led to hampered differentiation and degeneration of the tapetum. In addition, the development of pollen mother cells was arrested at the early stages of meiotic prophase I. RNA in-situ hybridization analyses showed that DTM1 transcripts were most abundant in tapetal cells at stages 6 and 7, and moderately in the pollen mother cells and meiocytes. Transcripts of UDT1, which functions in tapetum development during early meiosis, were reduced in dtm1 anthers, as were those of PAIR1, which is involved in chromosome pairing and synapsis during meiosis. However, expression of MSP1 and MEL1, which function in anther wall specification and germ cell division, respectively, was not altered in the dtm1 mutant. Moreover, transcripts of DTM1 were reduced in msp1 mutant anthers, but not in udt1 and pair1 mutants. These results, together with their mutant phenotypes, suggest that DTM1 plays important roles in the ER membrane during early tapetum development, functioning after MSP1 and before UDT1, and also in meiocyte development, after MEL1 and before PAIR1.	DTM1,MEL1,OsMSP1,PAIR1,Udt1
Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.)	2007	Plant Mol Biol	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Starch is the major component of cereal grains. In rice, starch properties determine the eating and cooking quality. The dull endosperm of rice grains is a classical morphological and agronomical trait that has long been exploited for breeding and genetics study. To understand the molecular mechanism that regulates the starch biosynthesis in rice grains, we characterized a classic rice mutant dull endosperm1 (du1) and isolated Du1 through a map-based cloning approach. Du1, encoding a member of pre-mRNA processing (Prp1) family, is expressed mainly in panicles. Du1 specifically affects the splicing efficiency of Wx(b) and regulates starch biosynthesis by mediating the expression of starch biosynthesis genes. Analysis of du1wx shows that Du1 acts upstream of Wx(b). These results strongly suggest that Du1 may function as a regulator of the starch biosynthesis by affecting the splicing of Wx(b) and the expression of other genes involved in the rice starch biosynthetic pathways.	Du1,Wx
Putative megaenzyme DWA1 plays essential roles in drought resistance by regulating stress-induced wax deposition in rice	2013	Proc Natl Acad Sci U S A	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Drought stress is a major limiting factor for crop production. Cuticular wax plays an important role in preventing water loss from drought stress. However, the genetic control of cuticular wax deposition under drought stress conditions has not been characterized. Here, we identified a rice gene Drought-Induced Wax Accumulation 1 (DWA1) encoding a very large protein (2,391 aa in length) containing multiple enzymatic structures, including an oxidoreductase-like domain; a prokaryotic nonribosomal peptide synthetase-like module, including an AMP-binding domain; and an allene oxide synthase-like domain. This previously unreported putative megaenzyme is conserved in vascular plants. A dwa1 KO mutant was highly sensitive to drought stress relative to the WT. DWA1 was preferentially expressed in vascular tissues and epidermal layers and strongly induced by drought stress. The dwa1 mutant was impaired in cuticular wax accumulation under drought stress, which significantly altered the cuticular wax composition of the plant, resulting in increased drought sensitivity. The mutant had reduced levels of very-long-chain fatty acids, and plants overexpressing DWA1 showed elevated levels of very-long-chain fatty acids relative to the WT. The expression of many wax-related genes was significantly suppressed in dwa1 under drought conditions. The AMP-binding domain exhibited in vitro enzymatic activity in activating long-chain fatty acids to form acyl-CoA. Our results suggest that DWA1 controls drought resistance by regulating drought-induced cuticular wax deposition in rice. This finding may have significant implications for improving the drought resistance of crop varieties.	DWA1
OsGSR1 is involved in crosstalk between gibberellins and brassinosteroids in rice	2009	Plant J	Research Center for Molecular & Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	Gibberellins (GAs) and brassinosteroids (BRs), two growth-promoting phytohormones, regulate many common physiological processes. Their interactions at the molecular level remain unclear. Here, we demonstrate that OsGSR1, a member of the GAST (GA-stimulated transcript) gene family, is induced by GA and repressed by BR. RNA interference (RNAi) transgenic rice plants with reduced OsGSR1 expression show phenotypes similar to plants deficient in BR, including short primary roots, erect leaves and reduced fertility. The OsGSR1 RNAi transgenic rice shows a reduced level of endogenous BR, and the dwarf phenotype could be rescued by the application of brassinolide. The yeast two-hybrid assay revealed that OsGSR1 interacts with DIM/DWF1, an enzyme that catalyzes the conversion from 24-methylenecholesterol to campesterol in BR biosynthesis. These results suggest that OsGSR1 activates BR synthesis by directly regulating a BR biosynthetic enzyme at the post-translational level. Furthermore, OsGSR1 RNAi plants show a reduced sensitivity to GA treatment, an increased expression of the GA biosynthetic gene OsGA20ox2, which is feedback inhibited by GA signaling, and an elevated level of endogenous GA: together, these suggest that OsGSR1 is a positive regulator of GA signaling. These results demonstrate that OsGSR1 plays important roles in both BR and GA pathways, and also mediates an interaction between the two signaling pathways.	OsGSR1,sd1|GA20ox2
Dwarf Tiller1, a Wuschel-related homeobox transcription factor, is required for tiller growth in rice	2014	PLoS Genet	State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China; Graduate University of the Chinese Academy of Sciences, Beijing, China.	Unlike many wild grasses, domesticated rice cultivars have uniform culm height and panicle size among tillers and the main shoot, which is an important trait for grain yield. However, the genetic basis of this trait remains unknown. Here, we report that Dwarf Tiller1 (DWT1) controls the developmental uniformity of the main shoot and tillers in rice (Oryza sativa). Most dwt1 mutant plants develop main shoots with normal height and larger panicles, but dwarf tillers bearing smaller panicles compared with those of the wild type. In addition, dwt1 tillers have shorter internodes with fewer and un-elongated cells compared with the wild type, indicating that DWT1 affects cell division and cell elongation. Map-based cloning revealed that DWT1 encodes a Wuschel-related homeobox (WOX) transcription factor homologous to the Arabidopsis WOX8 and WOX9. The DWT1 gene is highly expressed in young panicles, but undetectable in the internodes, suggesting that DWT1 expression is spatially or temporally separated from its effect on the internode growth. Transcriptomic analysis revealed altered expression of genes involved in cell division and cell elongation, cytokinin/gibberellin homeostasis and signaling in dwt1 shorter internodes. Moreover, the non-elongating internodes of dwt1 are insensitive to exogenous gibberellin (GA) treatment, and some of the slender rice1 (slr1) dwt1 double mutant exhibits defective internodes similar to the dwt1 single mutant, suggesting that the DWT1 activity in the internode elongation is directly or indirectly associated with GA signaling. This study reveals a genetic pathway synchronizing the development of tillers and the main shoot, and a new function of WOX genes in balancing branch growth in rice.	DWT1
Fine Mapping and Analysis of DWARF TILLER1 in Controlling Rice Architecture	2013	Journal of Genetics and Genomics	Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China	Rice is one of the most consumed staple food plants around the world, and its plant architecture is very important to improve the grain yield (Zhang et al., 2008). Plant height, leaf angle, tiller number and angle, and uniformity of panicle layer all can have strong effects on grain yield (Wang and Li, 2008). During the long history of domestication, rice has been selected to develop uniform tiller height architecture that ensures panicle layer uniformity and ease of harvesting (Ma et al., 2009), and is largely determined by the synchronic culm elongation. A large number of dwarf mutants deficient in culm elongation have been isolated and characterized, and gibberellin (GA) and brassinosteroid (BR) have been demonstrated as two major factors in promoting the culm development (Peng et al., 1997; Ikeda et al., 2001; Ashikari et al., 2002; Itoh et al., 2002; Spielmeyer et al., 2002). However, the mechanism of the coordinated elongation between the main shoot and tillers remains unknown. Here, we report a DWARF TILLER1 (DWT1) locus involved in the regulation of the uniform growth of main shoot and tillers in rice.	DWT1
EAT1 promotes tapetal cell death by regulating aspartic proteases during male reproductive development in rice	2013	Nat Commun	State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.	Programmed cell death is essential for the development of multicellular organisms, yet pathways of plant programmed cell death and its regulation remain elusive. Here we report that ETERNAL TAPETUM 1, a basic helix-loop-helix transcription factor conserved in land plants, positively regulates programmed cell death in tapetal cells in rice anthers. eat1 exhibits delayed tapetal cell death and aborted pollen formation. ETERNAL TAPETUM 1 directly regulates the expression of OsAP25 and OsAP37, which encode aspartic proteases that induce programmed cell death in both yeast and plants. Expression and genetic analyses revealed that ETERNAL TAPETUM 1 acts downstream of TAPETUM DEGENERATION RETARDATION, another positive regulator of tapetal programmed cell death, and that ETERNAL TAPETUM 1 can also interact with the TAPETUM DEGENERATION RETARDATION protein. This study demonstrates that ETERNAL TAPETUM 1 promotes aspartic proteases triggering plant programmed cell death, and reveals a dynamic regulatory cascade in male reproductive development in rice.	DTD|EAT1,OsAP25,OsAP37,OsAP19
A novel rice bHLH transcription factor, DTD, acts coordinately with TDR in controlling tapetum function and pollen development	2013	Mol Plant	State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China.	None	DTD|EAT1
Phytochrome-regulated EBL1 contributes to ACO1 upregulation in rice	2011	Biotechnol Lett	Division of Plant Sciences, Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602, Japan. iwamas@nias.affrc.go.jp	The 1-aminocyclopropane-1-carboxylate oxidase gene (ACO1) was upregulated in rice (Oryza sativa L.) phyAphyBphyC mutants lacking any phytochrome and containing the GCC box element, a binding site for rice ethylene-responsive element binding protein 1 (OsEREBP1), in its promoter region. Since the OsEREBP1-like gene EBL1 (OsEREBP1-LIKE 1) was significantly downregulated in phyAphyBphyC mutants, EBL1 was suspected to repress ACO1 expression in wild-type plants. However, ACO1 was downregulated in EBL1 RNA interference plants, and the total length of these plants was slightly shorter than that of wild-type plants. This study shows that EBL1 is positively regulated by phytochrome B and associated with ACO1 upregulation.	EBL1,OsACO1,OsEREBP1
A novel variant of translation elongation factor-1beta: isolation and characterization of the rice gene encoding EF-1beta2	1998	Biochim Biophys Acta	Cryobiosystem Research Center, Faculty of Agriculture, Iwate University, Ueda, Morioka, Iwate 020-8550, Japan.	A rice gene encoding a novel isoform of translation elongation factor-1beta subunit (termed EF-1beta2) was isolated and characterized. The gene comprises of eight exons, and encodes a 226-amino-acid protein. Expression of EF-1beta2 mRNA is abundant in seeds and cultured cells, but is considerably low in the tissues of the rice seedling. Antiserum raised against an EF-1beta2 synthetic peptide detected a protein with a relative molecular mass of about 32 kDa, indicating the EF-1beta2 gene is actually expressed in rice tissues. EF-1beta2 showed a close similarity to the cognate subunits from plant (beta and beta').	EF-1beta2
A putative lipase gene EXTRA GLUME1 regulates both empty-glume fate and spikelet development in rice	2009	Plant J	The State Key Laboratory of Rice Biology, College of Life Sciences, Zhejiang University, Hangzhou, 310029 China.	Recent studies have shown that molecular control of inner floral organ identity appears to be largely conserved between monocots and dicots, but little is known regarding the molecular mechanism underlying development of the monocot outer floral organ, a unique floral structure in grasses. In this study, we report the cloning of the rice EXTRA GLUME1 (EG1) gene, a putative lipase gene that specifies empty-glume fate and floral meristem determinacy. In addition to affecting the identity and number of empty glumes, mutations in EG1 caused ectopic floral organs to be formed at each organ whorl or in extra ectopic whorls. Iterative glume-like structures or new floral organ primordia were formed in the presumptive region of the carpel, resulting in an indeterminate floral meristem. EG1 is expressed strongly in inflorescence primordia and weakly in developing floral primordia. We also found that the floral meristem and organ identity gene OsLHS1 showed altered expression with respect to both pattern and levels in the eg1 mutant, and is probably responsible for the pleiotropic floral defects in eg1. As a putative class III lipase that functionally differs from any known plant lipase, EG1 reveals a novel pathway that regulates rice empty-glume fate and spikelet development.	EG1,OsMADS1|LHS1|AFO
Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls FT-like gene expression independently of Hd1	2004	Genes Dev	Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan. kdoi@agr.kyushu-u.ac.jp	Two evolutionarily distant plant species, rice (Oryza sativa L.), a short-day (SD) plant, and Arabidopsis thaliana, a long-day plant, share a conserved genetic network controlling photoperiodic flowering. The orthologous floral regulators-rice Heading date 1 (Hd1) and Arabidopsis CONSTANS (CO)-integrate circadian clock and external light signals into mRNA expression of the FLOWERING LOCUS T (FT) group floral inducer. Here, we report that the rice Early heading date 1 (Ehd1) gene, which confers SD promotion of flowering in the absence of a functional allele of Hd1, encodes a B-type response regulator that might not have an ortholog in the Arabidopsis genome. Ehd1 mRNA was induced by 1-wk SD treatment, and Ehd1 may promote flowering by inducing FT-like gene expression only under SD conditions. Microarray analysis further revealed a few MADS box genes downstream of Ehd1. Our results indicate that a novel two-component signaling cascade is integrated into the conserved pathway in the photoperiodic control of flowering in rice.	Ehd1
Knockdown of SAMS genes encoding S-adenosyl-l-methionine synthetases causes methylation alterations of DNAs and histones and leads to late flowering in rice	2011	J Plant Physiol	Research Center for Molecular and Developmental Biology, Key Laboratory of Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	S-Adenosyl-l-methionine synthetase (SAMS) [EC 2.5.1.6] catalyzes to produce SAM (S-adenosyl-l-methionine), a universal methyl group donor in biochemical reactions in cells. However, less is known how SAMS controls plant development. Here, we demonstrate that OsSAMS1, 2 and 3 are essential for histone H3K4me3 and DNA methylation to regulate gene expression related to flowering in Oryza sativa. RNA interference (RNAi) transgenic rice with downregulated transcripts of OsSAMS1, 2 and 3 showed pleiotropic phenotypes, including dwarfism, reduced fertility, delayed germination, as well as late flowering. Delayed germination was largely rescued by application of SAM in the knockdown lines. Knockdown of OsSAMS1, 2 and 3 led to distinguished late flowering and greatly reduced the expression of the flowering key genes, Early heading date 1 (Ehd1), Hd3a and RFT1 (rice FT-like genes). Moreover, the histone H3K4me3 and symmetric DNA methylation at these genes were greatly reduced. Thus, SAM deficiency suppressing DNA and H3K4me3 transmethylations at flowering key genes led to a late-flowering phenotype in rice. This information could help elucidate the mechanism of epigenetic control flowering transition.	Ehd1,Hd3a,OsSAMS1,OsSAM2,OsSAM3,RFT1
Heading date gene, dth3 controlled late flowering in O. Glaberrima Steud. by down-regulating Ehd1	2011	Plant Cell Rep	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.	Heading date in rice is an important agronomic trait controlled by several genes. In this study, flowering time of variety Dianjingyou 1 (DJY1) was earlier than a near-isogenic line (named NIL) carried chromosome segment from African rice on chromosome 3S, when grown in both long-day (LD) and short-day (SD) conditions. By analyzing a large F2 population from NIL x DJY1, the locus DTH3 (QTL for days to heading on chromosome 3) controlling early heading date in DJY1 was fine mapped to a 64-kb segment which contained only one annotated gene, a MIKC-type MADS-box protein. We detected a 6-bp deletion and a single base substitution in the C-domain by sequencing DTH3 in DJY1 compared with dth3 in NIL, and overexpression of DTH3 caused early flowering in callus. Quantitative real-time PCR revealed that the transcript level of dth3 in NIL was lower than that DTH3 in DJY1 in both LD and SD conditions. The Early heading date 1 (Ehd1) which promotes the RFT1, was up-regulated by DTH3 in both LD and SD conditions. Based on Indel and dCAPs marker analysis, the dth3 allele was only present in African rice accessions. A phylogenetic analysis based on microsatellite genotyping suggested that African rice had a close genetic relationship to O. rufipogon and O. latifolia, and was similar to japonica cultivars. DTH3 affected flowering time and had no significant effect on the main agronomic traits.	Ehd1,Hd1,OsMADS50|OsSOC1|DTH3,RFT1
OsCO3, a CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of FT-like genes under SD conditions in rice	2008	Planta	Plant Signaling Network Research Center, School of Life Sciences and Biotechnology, Korea University, Seoul 136-701, South Korea.	The photoperiod is an important environmental stress that determines flowering time. The CONSTANS (CO) and Heading date 1 (Hd1) genes are known to be central integrators of the photoperiod pathway in Arabidopsis and rice, respectively. Although they are both members of the CONSTANS-LIKE (COL) family and have two B-boxes and a CCT domain, rice also possesses novel COL genes that are not found in Arabidopsis. Here, we demonstrate that a novel COL gene, OsCO3, containing a single B-box and a CCT domain, modulates photoperiodic flowering in rice. The circadian expression pattern of OsCO3 mRNA oscillated in a different phase from Hd1 and was similar to that of OsCO3 pre-mRNA, suggesting that the diurnal expression pattern of OsCO3 transcripts may be regulated at the transcriptional level. Overexpression of OsCO3 specifically caused late flowering under short day (SD) conditions relative to wild-type rice plants. The expression of Hd3a and FTL decreased in these transgenic plants, whereas the expression of Hd1, Early heading date 1 (Ehd1), OsMADS51, and OsMADS50 did not significantly change. Our results suggest that OsCO3 primarily controls flowering time under SD conditions by negatively regulating Hd3a and FTL expression, independent of the SD-promotion pathway.	Ehd1,Hd1,Hd3a,OsCO3,OsMADS50|OsSOC1|DTH3,OsMADS51|OsMADS65
Functional characterization of rice OsDof12	2009	Planta	State Key Laboratory of Plant Genomics and National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 5 Datun Road, Chaoyang District, 100101, Beijing, China. djli@genetics.ac.cn	DNA-binding with one finger (Dof) proteins are a large family of transcription factors involved in a variety of biological processes in plants. In rice, 30 different Dof genes have been identified through genome analysis. Here we report the functional characteristics of a rice Dof gene, OsDof12, which encodes a predicted Dof protein. The nuclear localization of OsDof12 was investigated by the transient expression assays of the OsDof12-GFP fusion protein in onion epidermal cells. Trans-activation assays in a yeast one-hybrid system indicated that OsDof12 had transcriptional activity. RNA expression analyses showed that the expression of OsDof12 was not tissue-specific in general and fluctuated at different development stages in rice. In addition, OsDof12 was strongly inhibited by dark treatments. The transgenic lines overexpressing OsDof12 showed early flowering under long-day (LD) conditions, whereas OsDof12 overexpression had no effect on flowering time under short-day (SD) conditions. In transgenic lines overexpressing OsDof12, the transcription levels of Hd3a and OsMADS14 were up-regulated under LD conditions but not SD conditions, whereas the expression of Hd1, OsMADS51, Ehd1 and OsGI did not change under LD and SD conditions. These results suggested that OsDof12 might regulate flowering by controlling the expression of Hd3a and OsMADS14.	Ehd1,Hd1,Hd3a,OsDof12,OsGI,OsMADS14,OsMADS51|OsMADS65
Epistasis among the three major flowering time genes in rice: coordinate changes of photoperiod sensitivity, basic vegetative growth and optimum photoperiod	2007	Euphytica	Plant Breeding Laboratory, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan	Flowering time is affected not only by photoperiod sensitivity (PS) but also by basic vegetative growth (BVG) and optimum photoperiod (OP), although their developmental and genetic relationships are not well understood. The present study was carried out in rice to examine to what extent these three developmental components are modified by the three flowering time genes, Se1 (= Hd1), Ef1 and e1 (= m-Ef1), which are known to contribute to flowering time in temperate and tropical regions of rice cultivation. Photoperiodic response curves were estimated under controlled conditions of different growth regimes, using eight near-isogenic lines possessing different combinations of the alleles at the three loci. The results showed that each of the components is greatly affected by the main effect of the genes, temperature and their epistasis, indicating that none of the three genes controls flowering time by altering any single component in PS, BVG or OP. Epistasis was detected more frequently among the three genes than reported before, suggesting that epistasis contributes to flowering time by changing PS, BVG and OP differently. The comparison of the nucleotide sequences suggested that Ef1 is the same as Early heading date 1 (Ehd1). Since the two genes Se1 (= Hd1) and Ef1 (= Ehd1) are known to up-regulate the rice homolog of Arabidopsis FT, it is suggested that the detected epistasis may respond to diverse environments by modulating the CO/FT system conserved in flowering plants.	Ehd1,Hd1
Molecular dissection of the roles of phytochrome in photoperiodic flowering in rice	2011	Plant Physiol	Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8561, Japan.	Phytochromes mediate the photoperiodic control of flowering in rice (Oryza sativa), a short-day plant. Recent molecular genetics studies have revealed a genetic network that enables the critical daylength response of florigen gene expression. Analyses using a rice phytochrome chromophore-deficient mutant, photoperiod sensitivity5, have so far revealed that within this network, phytochromes are required for expression of Grain number, plant height and heading date7 (Ghd7), a floral repressor gene in rice. There are three phytochrome genes in rice, but the roles of each phytochrome family member in daylength response have not previously been defined. Here, we revealed multiple action points for each phytochrome in the critical daylength response of florigen expression by using single and double phytochrome mutant lines of rice. Our results show that either phyA alone or a genetic combination of phyB and phyC can induce Ghd7 mRNA, whereas phyB alone causes some reduction in levels of Ghd7 mRNA. Moreover, phyB and phyA can affect Ghd7 activity and Early heading date1 (a floral inducer) activity in the network, respectively. Therefore, each phytochrome gene of rice has distinct roles, and all of the phytochrome actions coordinately control the critical daylength response of florigen expression in rice.	Ehd1,Ghd7,Hd3a,OsCOL4,PHYA,PHYB|OsphyB,PHYC,RFT1
Ectopic expression of OsLFL1 in rice represses Ehd1 by binding on its promoter	2007	Biochem Biophys Res Commun	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	B3 domain was identified as a novel DNA-binding motif specific to higher plant species. The B3 proteins play important roles in plant development. In the mutant W378, the mutant gene coding OsLFL1, a putative B3 transcription factor gene, was ectopically expressed. In this study, it was found that the flowering promoting gene Ehd1 and its putative downstream genes were all repressed by OsLFL1. Electrophoretic mobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) analyses suggest that OsLFL1 binds to the RY cis-elements (CATGCATG) in the promoter of the Ehd1 gene. Thus, ectopically expressed OsLFL1 might repress Ehd1 via binding directly to the RY cis-elements in its promoter.	Ehd1,OsLFL1
A gene network for long-day flowering activates RFT1 encoding a mobile flowering signal in rice	2009	Development	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology (NAIST), Takayama, Ikoma, Japan.	Although some genes that encode sensory or regulatory elements for photoperiodic flowering are conserved between the long-day (LD) plant Arabidopsis thaliana and the short-day (SD) plant rice, the gene networks that control rice flowering, and particularly flowering under LD conditions, are not well understood. We show here that RICE FLOWERING LOCUS T 1 (RFT1), the closest homolog to Heading date 3a (Hd3a), is a major floral activator under LD conditions. An RFT1:GFP fusion protein localized in the shoot apical meristem (SAM) under LD conditions, suggesting that RFT1 is a florigen gene in rice. Furthermore, mutants in OsMADS50, a rice ortholog of Arabidopsis SUPPRESOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) did not flower up to 300 days after sowing under LD conditions, indicating that OsMADS50, which acts upstream of RFT1, promotes flowering under LD conditions. We propose that both positive (OsMADS50 and Ehd1) and negative (Hd1, phyB and Ghd7) regulators of RFT1 form a gene network that regulates LD flowering in rice. Among these regulators, Ehd1, a rice-specific floral inducer, integrates multiple pathways to regulate RFT1, leading to flowering under appropriate photoperiod conditions. A rice ortholog of Arabidopsis APETALA1, OsMADS14, was expressed in the floral meristem in wild-type but not in RFT1 RNAi plants, suggesting that OsMADS14 is activated by RFT1 protein in the SAM after the transition to flowering. We have thus exposed a network of genes that regulate LD flowering in rice.	Ehd1,Ghd7,Hd1,OsMADS14,OsMADS50|OsSOC1|DTH3,PHYB|OsphyB,RFT1
OsMADS50 and OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice	2009	Plant Cell Environ	Department of Life Science and Functional Genomic Center, Pohang University of Science and Technology (POSTECH), Pohang, Korea.	In much of the tropics and subtropics, rice (Oryza sativa L.) is grown under long days (LDs). Therefore, LD must play a major role in inducing flowering signal in rice. However, little is known on LD-dependent flowering signal in the species. We previously reported that OsMADS50, which is highly homologous to Arabidopsis SOC1, functions as a positive regulator for flowering. However, its detailed photoperiodic mechanism was not yet elucidated. Here, we report the functional analysis of OsMADS50 and its closely related gene OsMADS56. Knock-out of OsMADS50 caused a late-flowering phenotype only under LD conditions. Overexpression of OsMADS56 (56OX) also resulted in delayed flowering under LD. In the osmads50 mutants and 56OX transgenic plants, transcripts of Ehd1, Hd3a and RFT1 were reduced, although that of OsLFL1 increased. On the other hand, mRNA levels of OsGI, Hd1, OsId1, OsDof12, Ghd7, Hd6 and SE5 were unchanged. These observations imply that OsMADS50 and OsMADS56 function antagonistically through OsLFL1-Ehd1 in regulating LD-dependent flowering. Yeast two-hybrid and co-immunoprecipitation analyses indicated an interaction between those two proteins as well as their formation of homodimers. These results suggest that OsMADS50 and OsMADS56 may form a complex that regulates downstream target genes.	Ehd1,Ghd7,Hd1,Hd3a,Hd6|CK2,OsDof12,OsGI,OsLFL1,OsMADS50|OsSOC1|DTH3,OsMADS56,RFT1
Rice Indeterminate 1 (OsId1) is necessary for the expression of Ehd1 (Early heading date 1) regardless of photoperiod	2008	Plant J	Division of Applied Life Science (BK21 Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju 660-701, Korea.	Indeterminate 1 (Id1), a classical flowering gene first reported in 1946, is one of the earliest genes whose expression in leaf tissues affects the floral transition in the shoot meristem. How Id1 is integrated into the flowering process is largely unknown. In this study, we examined the genetic action of the rice (Oryza sativa) ortholog OsId1. In rice, OsId1 is preferentially expressed in young leaves, but the overall expression pattern is broader than that in maize (Zea mays). OsId1 is able to activate transcription in yeast. RNAi mutants show a delay in flowering under both short-day (SD) and long-day (LD) conditions. OsId1 regulates the expression of Ehd1 (Early heading date 1) and its downstream genes, including Hd3a (a rice ortholog of FT) and RFT1 (Rice Flowering Locus T1), under both SD and LD conditions. In rice, the expression of Ehd1 is also controlled by the photoperiodic flowering genes OsGI (a rice ortholog of GI) and OsMADS51. However, the expression of OsId1 is independent of OsGI, OsMADS51, and OsMADS50 (a rice SOC1 ortholog). This study demonstrates that the activation of Ehd1 by OsId1 is required for the promotion of flowering.	Ehd1,OsMADS51|OsMADS65,RFT1
OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB	2010	Plant J	Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea.	Plants recognize environmental factors to determine flowering time. CONSTANS (CO) plays a central role in the photoperiod flowering pathway of Arabidopsis, and CO protein stability is modulated by photoreceptors. In rice, Hd1, an ortholog of CO, acts as a flowering promoter, and phytochromes repress Hd1 expression. Here, we investigated the functioning of OsCOL4, a member of the CONSTANS-like (COL) family in rice. OsCOL4 null mutants flowered early under short or long days. In contrast, OsCOL4 activation-tagging mutants (OsCOL4-D) flowered late in either environment. Transcripts of Ehd1, Hd3a, and RFT1 were increased in the oscol4 mutants, but reduced in the OsCOL4-D mutants. This finding indicates that OsCOL4 is a constitutive repressor functioning upstream of Ehd1. By comparison, levels of Hd1, OsID1, OsMADS50, OsMADS51, and OsMADS56 transcripts were not significantly changed in oscol4 or OsCOL4-D, suggesting that OsCOL4 functions independently from previously reported flowering pathways. In osphyB mutants, OsCOL4 expression was decreased and osphyB oscol4 double mutants flowered at the same time as the osphyB single mutants, indicating OsCOL4 functions downstream of OsphyB. We also present evidence for two independent pathways through which OsPhyB controls flowering time. These pathways are: (i) night break-sensitive, which does not need OsCOL4; and (ii) night break-insensitive, in which OsCOL4 functions between OsphyB and Ehd1.	Ehd1,Hd3a,OsCOL4,PHYB|OsphyB,RFT1
Ehd3, encoding a plant homeodomain finger-containing protein, is a critical promoter of rice flowering	2011	Plant J	National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.	Oryza sativa (rice) flowers in response to photoperiod, and is a facultative short-day (SD) plant. Under SD conditions, flowering is promoted through the activation of FT-like genes (rice florigens) by Heading date 1 (Hd1, a rice CONSTANS homolog) and Early heading date 1 (Ehd1, with no ortholog in the Arabidopsis genome). On the other hand, under long-day (LD) conditions, flowering is delayed by the repressive function of Hd1 on FT-like genes and by downregulation of Ehd1 by the flowering repressor Ghd7 - a unique pathway in rice. We report here that an early heading date 3 (ehd3) mutant flowered later than wild-type plants, particularly under LD conditions, regardless of the Hd1-deficient background. Map-based cloning revealed that Ehd3 encodes a nuclear protein that contains a putative transcriptional regulator with two plant homeodomain (PHD) finger motifs. To identify the role of Ehd3 within the gene regulatory network for rice flowering, we compared the transcript levels of genes related to rice flowering in wild-type plants and ehd3 mutants. Increased transcription of Ghd7 under LD conditions and reduced transcription of downstream Ehd1 and FT-like genes in the ehd3 mutants suggested that Ehd3 normally functions as an LD downregulator of Ghd7 in floral induction. Furthermore, Ehd3 ghd7 plants flowered earlier and show higher Ehd1 transcript levels than ehd3 ghd7 plants, suggesting a Ghd7-independent role of Ehd3 in the upregulation of Ehd1. Our results demonstrate that the PHD-finger gene Ehd3 acts as a promoter in the unique genetic pathway responsible for photoperiodic flowering in rice.	Ehd1,Ehd3,Ghd7,Hd1
Footprints of natural and artificial selection for photoperiod pathway genes in Oryza	2012	Plant J	Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.	Asian rice, Oryza sativa, consists of two major subspecies, indica and japonica, which are physiologically differentiated and adapted to different latitudes. Genes for photoperiod sensitivity are likely targets of selection along latitude. We examined the footprints of natural and artificial selections for four major genes of the photoperiod pathway, namely PHYTOCHROME B (PhyB), HEADING DATE 1 (Hd1), HEADING DATE 3a (Hd3a), and EARLY HEADING DATE 1 (Ehd1), by investigation of the patterns of nucleotide polymorphisms in cultivated and wild rice. Geographical subdivision between tropical and subtropical O. rufipogon was found for all of the photoperiod genes in plants divided by the Tropic of Cancer (TOC). All of these genes, except for PhyB, were characterized by the existence of clades that split a long time ago and that corresponded to latitudinal subdivisions, and revealed a likely diversifying selection. Ssp. indica showed close affinity to tropical O. rufipogon for all genes, while ssp. japonica, which has a much wider range of distribution, displayed complex patterns of differentiation from O. rufipogon, which reflected various agricultural needs in relation to crop yield. In japonica, all genes, except Hd3a, were genetically differentiated at the TOC, while geographical subdivision occurred at 31 degrees N in Hd3a, probably the result of varying photoperiods. Many other features of the photoperiod genes revealed domestication signatures, which included high linkage disequilibrium (LD) within genes, the occurrence of frequent and recurrent non-functional Hd1 mutants in cultivated rice, crossovers between subtropical and tropical alleles of Hd1, and significant LD between Hd1 and Hd3a in japonica and indica.	Ehd1,Hd1,Hd3a,PHYB|OsphyB
Ehd4 encodes a novel and Oryza-genus-specific regulator of photoperiodic flowering in rice	2013	PLoS Genet	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, China.	Land plants have evolved increasingly complex regulatory modes of their flowering time (or heading date in crops). Rice (Oryza sativa L.) is a short-day plant that flowers more rapidly in short-day but delays under long-day conditions. Previous studies have shown that the CO-FT module initially identified in long-day plants (Arabidopsis) is evolutionary conserved in short-day plants (Hd1-Hd3a in rice). However, in rice, there is a unique Ehd1-dependent flowering pathway that is Hd1-independent. Here, we report isolation and characterization of a positive regulator of Ehd1, Early heading date 4 (Ehd4). ehd4 mutants showed a never flowering phenotype under natural long-day conditions. Map-based cloning revealed that Ehd4 encodes a novel CCCH-type zinc finger protein, which is localized to the nucleus and is able to bind to nucleic acids in vitro and transactivate transcription in yeast, suggesting that it likely functions as a transcriptional regulator. Ehd4 expression is most active in young leaves with a diurnal expression pattern similar to that of Ehd1 under both short-day and long-day conditions. We show that Ehd4 up-regulates the expression of the "florigen" genes Hd3a and RFT1 through Ehd1, but it acts independently of other known Ehd1 regulators. Strikingly, Ehd4 is highly conserved in the Oryza genus including wild and cultivated rice, but has no homologs in other species, suggesting that Ehd4 is originated along with the diversification of the Oryza genus from the grass family during evolution. We conclude that Ehd4 is a novel Oryza-genus-specific regulator of Ehd1, and it plays an essential role in photoperiodic control of flowering time in rice.	Ehd1,Ehd4,Hd3a,RFT1
OsELF3-1, an ortholog of Arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering	2012	PLoS One	Rice Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China.	Arabidopsis thaliana early flowering 3 (ELF3) as a zeitnehmer (time taker) is responsible for generation of circadian rhythm and regulation of photoperiodic flowering. There are two orthologs (OsELF3-1 and OsELF3-2) of ELF3 in rice (Oryza sativa), but their roles have not yet been fully identified. Here, we performed a functional characterization of OsELF3-1 and revealed it plays a more predominant role than OsELF3-2 in rice heading. Our results suggest OsELF3-1 can affect rice circadian systems via positive regulation of OsLHY expression and negative regulation of OsPRR1, OsPRR37, OsPRR73 and OsPRR95 expression. In addition, OsELF3-1 is involved in blue light signaling by activating early heading date 1 (Ehd1) expression to promote rice flowering under short-day (SD) conditions. Moreover, OsELF3-1 suppresses a flowering repressor grain number, plant height and heading date 7 (Ghd7) to indirectly accelerate flowering under long-day (LD) conditions. Taken together, our results indicate OsELF3-1 is essential for circadian regulation and photoperiodic flowering in rice.	Ehd1,Ghd7,Hd17|Ef7|OsELF3-1,OsEF3|OsELF3-2,OsPRR1
A pair of floral regulators sets critical day length for Hd3a florigen expression in rice	2010	Nat Genet	Photosynthesis and Photobiology Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Japan.	The critical day length triggering photoperiodic flowering is set as an acute, accurate threshold in many short-day plants, including rice. Here, we show that, unlike the Arabidopsis florigen gene FT, the rice florigen gene Hd3a (Heading date 3a) is toggled by only a 30-min day-length reduction. Hd3a expression is induced by Ehd1 (Early heading date 1) expression when blue light coincides with the morning phase set by OsGIGANTEA(OsGI)-dependent circadian clocks. Ehd1 expression is repressed by both night breaks under short-day conditions and morning light signals under long-day conditions. Ghd7 (Grain number, plant height and heading date 7) was acutely induced when phytochrome signals coincided with a photosensitive phase set differently by distinct photoperiods and this induction repressed Ehd1 the next morning. Thus, two distinct gating mechanisms--of the floral promoter Ehd1 and the floral repressor Ghd7--could enable manipulation of slight differences in day length to control Hd3a transcription with a critical day-length threshold.	Ehd1,Ghd7,Hd3a,OsGI
Flowering time genes Heading date 1 and Early heading date 1 together control panicle development in rice	2011	Plant Cell Physiol	University of Tsukuba, Tsukuba, Japan.	Although flowering time is often associated with plant size, little is known about how flowering time genes affect plant architecture. We grew four rice lines having different flowering time genotypes (hd1 ehd1, hd1 Ehd1, Hd1 ehd1 and Hd1 Ehd1) under distinct photoperiod conditions. By using genotype-treatment combinations that resulted in similar flowering times, we were able to compare the effects of flowering time genes on traits related to plant architecture. The results revealed that the combination of Heading-date 1 (Hd1) and Early heading date 1 (Ehd1) can reduce the number of primary branches in a panicle, resulting in smaller spikelet numbers per panicle; this occurs independently of the control of flowering time. In addition, expression of the Hd3a and Rice Flowering-locus T 1 (RFT1) florigen genes was up-regulated in leaves of the Hd1 Ehd1 line at the time of the floral transition. We further revealed that Hd1 and/or Ehd1 caused up-regulation of Terminal Flower 1-like genes and precocious expression of panicle formation-related genes at shoot apical meristems during panicle development. Therefore, two key flowering time genes, Hd1 and Ehd1, can control panicle development in rice; this may affect crop yields in the field through florigen expression in leaf.	Ehd1,Hd1,Hd3a,RFT1
OsMADS51 is a short-day flowering promoter that functions upstream of Ehd1, OsMADS14, and Hd3a	2007	Plant Physiol	Division of Molecular and Life Sciences and Biotechnology Research Center, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea.	Although flowering regulatory mechanisms have been extensively studied in Arabidopsis (Arabidopsis thaliana), those in other species have not been well elucidated. Here, we investigated the role of OsMADS51, a type I MADS-box gene in the short-day (SD) promotion pathway in rice (Oryza sativa). In SDs OsMADS51 null mutants flowered 2 weeks later than normal, whereas in long days loss of OsMADS51 had little effect on flowering. Transcript levels of three flowering regulators-Ehd1, OsMADS14, and Hd3a-were decreased in these mutants, whereas those of OsGI and Hd1 were unchanged. Ectopic expression of OsMADS51 caused flowering to occur about 7 d earlier only in SDs. In ectopic expression lines, transcript levels of Ehd1, OsMADS14, and Hd3a were increased, but those of OsGI and Hd1 remained the same. These results indicate that OsMADS51 is a flowering promoter, particularly in SDs, and that this gene functions upstream of Ehd1, OsMADS14, and Hd3a. To further investigate the relationship with other flowering promoters, we generated transgenic plants in which expression of Ehd1 or OsGI was suppressed. In Ehd1 RNA interference plants, OsMADS51 expression was not affected, supporting our conclusion that the MADS-box gene functions upstream of Ehd1. However, in OsGI antisense plants, the OsMADS51 transcript level was reduced. In addition, the circadian expression pattern for this MADS-box gene was similar to that for OsGI. These results demonstrate that OsMADS51 functions downstream of OsGI. In summary, OsMADS51 is a novel flowering promoter that transmits a SD promotion signal from OsGI to Ehd1.	Ehd1,Hd3a,OsGI,OsMADS14,OsMADS51|OsMADS65
Ehd2, a rice ortholog of the maize INDETERMINATE1 gene, promotes flowering by up-regulating Ehd1	2008	Plant Physiol	National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.	Recent research into the flowering of rice (Oryza sativa) has revealed both unique and conserved genetic pathways in the photoperiodic control of flowering compared with those in Arabidopsis (Arabidopsis thaliana). We discovered an early heading date2 (ehd2) mutant that shows extremely late flowering under both short- and long-day conditions in line with a background deficient in Heading date1 (Hd1), a rice CONSTANS ortholog that belongs to the conserved pathway. This phenotype in the ehd2 mutants suggests that Ehd2 is pivotal for the floral transition in rice. Map-based cloning revealed that Ehd2 encodes a putative transcription factor with zinc finger motifs orthologous to the INDETERMINATE1 (ID1) gene, which promotes flowering in maize (Zea mays). Ehd2 mRNA in rice tissues accumulated most abundantly in developing leaves, but was present at very low levels around the shoot apex and in roots, patterns that are similar to those of ID1. To assign the position of Ehd2 within the flowering pathway of rice, we compared transcript levels of previously isolated flowering-time genes, such as Ehd1, a member of the unique pathway, Hd3a, and Rice FT-like1 (RFT1; rice florigens), between the wild-type plants and the ehd2 mutants. Severely reduced expression of these genes in ehd2 under both short- and long-day conditions suggests that Ehd2 acts as a flowering promoter mainly by up-regulating Ehd1 and by up-regulating the downstream Hd3a and RFT1 genes in the unique genetic network of photoperiodic flowering in rice.	Ehd1,Hd1,Hd3a,RFT1,Ehd2|RID1
Analysis of PHOTOPERIOD SENSITIVITY5 sheds light on the role of phytochromes in photoperiodic flowering in rice	2009	Plant Physiol	Instituto Valenciano de Investigaciones Agrarias, Carretera Moncada-Naquera Km 7.5, 46113 Moncada, Spain.	A great number of plants synchronize flowering with day length. In rice (Oryza sativa), photoperiod is the primary environmental cue that triggers flowering. Here, we show that the s73 mutant, identified in a gamma-irradiated Bahia collection, displays early flowering and photoperiodic insensitivity due to a null mutation in the PHOTOPERIOD SENSITIVITY5 (SE5) gene, which encodes an enzyme implicated in phytochrome chromophore biosynthesis. s73 mutant plants show a number of alterations in the characteristic diurnal expression patterns of master genes involved in photoperiodic control of flowering, resulting in up-regulation of the floral integrator Heading date3a (Hd3a). Early heading date1 (Ehd1), an additional rice floral activator, was also highly expressed in the s73 mutant, suggesting that SE5 represses Ehd1 in wild-type plants. Silencing of Ehd1 in both Bahia and s73 backgrounds indicated that SE5 regulates Ehd1 expression. The data also indicate that SE5 confers photoperiodic sensitivity through regulation of Hd1. These results provide direct evidence that phytochromes inhibit flowering by affecting both Hd1 and Ehd1 flowering pathways.	Ehd1,Hd3a,Se5|OsHY1|OsHO1|YGL2
Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice	2009	Proc Natl Acad Sci U S A	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.	Rice is a facultative short-day plant, and molecular genetic studies have identified the major genes involved in short-day flowering. However, the molecular mechanisms promoting the diversity of flowering time in cultivated rice are not known. We used a core collection of 64 rice cultivars that represent the genetic diversity of 332 accessions from around the world and studied the expression levels and polymorphisms of 6 genes in the short-day flowering pathway. The RNA levels of Heading date 3a (Hd3a), encoding a floral activator, are highly correlated with flowering time, and there is a high degree of polymorphism in the Heading date 1 (Hd1) protein, which is a major regulator of Hd3a expression. Functional and nonfunctional alleles of Hd1 are associated with early and late flowering, respectively, suggesting that Hd1 is a major determinant of variation in flowering time of cultivated rice. We also found that the type of Hd3a promoter and the level of Ehd1 expression contribute to the diversity in flowering time and Hd3a expression level. We evaluated the contributions of these 3 factors by a statistical analysis using a simple linear model, and the results supported our experimental observations.	Ehd1,Hd1,Hd3a
OsVIL2 functions with PRC2 to induce flowering by repressing OsLFL1 in rice	2013	Plant J	Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.	Flowering is exquisitely regulated by both promotive and inhibitory factors. Molecular genetic studies with Arabidopsis have verified several epigenetic repressors that regulate flowering time. However, the roles of chromatin remodeling factors in developmental processes have not been well explored in Oryza sativa (rice). We identified a chromatin remodeling factor OsVIL2 (O. sativa VIN3-LIKE 2) that promotes flowering. OsVIL2 contains a plant homeodomain (PHD) finger, which is a conserved motif of histone binding proteins. Insertion mutations in OsVIL2 caused late flowering under both long and short days. In osvil2 mutants OsLFL1 expression was increased, but that of Ehd1, Hd3a and RFT1 was reduced. We demonstrated that OsVIL2 is bound to native histone H3 in vitro. Chromatin immunoprecipitation analyses showed that OsVIL2 was directly associated with OsLFL1 chromatin. We also observed that H3K27me3 was significantly enriched by OsLFL1 chromatin in the wild type, but that this enrichment was diminished in the osvil2 mutants. These results indicated that OsVIL2 epigenetically represses OsLFL1 expression. We showed that OsVIL2 physically interacts with OsEMF2b, a component of polycomb repression complex 2. As observed from osvil2, a null mutation of OsEMF2b caused late flowering by increasing OsLFL1 expression and decreasing Ehd1 expression. Thus, we conclude that OsVIL2 functions together with PRC2 to induce flowering by repressing OsLFL1.	Ehd1,Hd3a,OsEMF2b,OsLFL1,OsVIL2,RFT1
Trithorax group protein Oryza sativa Trithorax1 controls flowering time in rice via interaction with early heading date3	2014	Plant Physiol	Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.	Trithorax group proteins are chromatin-remodeling factors that activate target gene expression by antagonistically functioning against the Polycomb group. In Arabidopsis (Arabidopsis thaliana), Arabidopsis Trithorax protein1 (ATX1) regulates flowering time and floral organ identity. Here, we observed that suppression of Oryza sativa Trithorax1 (OsTrx1), an ortholog of ATX1, delayed flowering time in rice (Oryza sativa). Because the delay occurred only under long-day conditions, we evaluated the flowering signal pathways that specifically function under long-day conditions. Among them, the OsMADS50 and Heading date1 pathways were not affected by the mutation. However, the Grain number, plant height, and heading date7 (Ghd7) pathway was altered in ostrx1. Transcript levels of OsGI, phytochrome genes, and Early heading date3 (Ehd3), which function upstream of Ghd7, were unchanged in the mutant. Because Trx group proteins form a complex with other proteins to modify the chromatin structure of target genes, we investigated whether OsTrx1 interacts with a previously identified protein that functions upstream of Ghd7. We demonstrated that the plant homeodomain motif of OsTrx1 binds to native histone H3 from the calf thymus and that OsTrx1 binds to Ehd3 through the region between the plant homeodomain and SET domains. Finally, we showed that the SET domain at the C-terminal end of OsTrx1 has histone H3 methyltransferase activity when incubated with oligonucleosomes. Our results suggest that OsTrx1 plays an important role in regulating flowering time in rice by modulating chromatin structure.	Ehd3,Ghd7,Hd1,OsGI,OsMADS50|OsSOC1|DTH3,OsTrx1|SDG723
The SUI-homologous translation initiation factor eIF-1 is involved in regulation of ion homeostasis in rice	2008	Plant Biol (Stuttg)	Department of Physiology and Biochemistry of Plants, Faculty of Biology, University of Bielefeld, Bielefeld, Germany.	Halophytes survive high salinity by using complex adaptive mechanisms. In a search for novel molecular mechanisms involved in salt acclimation, transcript analyses revealed increased expression of a SUI-homologous translation initiation factor eIF-1 in the salt-tolerant grass species Festuca rubra ssp. littoralis but not in rice. Upon analysis of the cell specificity of eIF-1 transcription by in situ polymerase chain reaction (PCR), predominant signals were detected in rice leaf mesophyll. To further examine the role of eIF-1 in salt tolerance, transgenic rice plants were generated that over-express this factor under the control of the CaMV-35S promoter. The eIF-1 over-expressing lines showed improved growth under salt stress that was correlated with maintenance of photosynthetic activity and reduced Na(+) and Cl(-) accumulation in leaves. The transgenic rice lines also activated expression of the vacuolar H(+)-ATPase. In addition, an oxidoreductase that belongs to the aldo/keto reductase family was identified as a gene with modified expression in the eIF-1 over-expressing lines, compared with wild-type rice. Our data suggest that eIF-1 has a central function in salt-stress adaptation in rice by regulating ion accumulation and the intracellular redox status.	eIF-1
Inhibition of a basal transcription factor 3-like gene Osj10gBTF3 in rice results in significant plant miniaturization and typical pollen abortion	2012	Plant Cell Physiol	Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, PR China.	BTF3, which was originally recognized as a basal transcription factor, has been known to be involved in transcription initiation, translational regulation and protein localization in many eukaryotic organisms. However, its function remains largely unknown in plant species. In the present study, we analyzed a BTF3-related sequence in Oryza sativa L. subsp. japonica, which shares the conserved domain of a nascent polypeptide-associated complex with human BTF3, and was referred to as Osj10gBTF3. The expression of Osj10gBTF3 was primarily constitutive and generally modulated by salt, high temperature and exogenous phytohormone stress. The Osj10gBTF3::EGFP (enhanced green fluorescence protein) fusion protein was localized in both the nucleus and cytoplasmic membrane system. Inhibition of Osj10gBTF3 led to significant morphological changes in all detected tissues and organs, with a reduced size of between 25% and 52%. Furthermore, the pollen that developed was completely sterile, which was correlated with the altered expression of two Rf (fertility restorer)-like genes that encode pentatricopeptide repeat-containing proteins OsPPR676 and OsPPR920, translational initiation factors OseIF3e and OseIF3h, and the heat shock protein OsHSP82. These findings were verified through a yeast two-hybrid assay using a Nipponbare callus cDNA library as bait followed by the reverse transcription-PCR analysis of total leaf or anther RNAs. Our demonstration of the important role of Osj10gBTF3 in rice growth and development provides new insights showing that more complex regulatory functions are associated with BTF3 in plants.	EIF3E,EIF3H,OsBTF3|Osj10gBTF3,Osj3g2BTF3
Two novel genes rapidly and transiently activated in suspension-cultured rice cells by treatment with N-acetylchitoheptaose, a biotic elicitor for phytoalexin production	1996	Plant Cell Physiol	Department of Cell Biology, National Institute of Agrobiological Resources, Japan.	By using subtracted probes, two cDNA clones of rice, EL2 and EL3, were isolated as genes responsive within 6 min to N-acetylchitoheptaose, a potent biotic elicitor for phytoalexin biosynthesis. Analyses of the sequence of the cDNAs showed that both of EL2 and EL3 encoded basic proteins with no significant similarities to those of known genes.	EL2
Novel plant-specific cyclin-dependent kinase inhibitors induced by biotic and abiotic stresses	2007	J Biol Chem	CropDesign N.V., B-9052 Ghent, Belgium.	The EL2 gene of rice (Oryza sativa), previously classified as early response gene against the potent biotic elicitor N-acetylchitoheptaose and encoding a short polypeptide with unknown function, was identified as a novel cell cycle regulatory gene related to the recently reported SIAMESE (SIM) gene of Arabidopsis thaliana. Iterative two-hybrid screens, in vitro pull-down assays, and fluorescence resonance energy transfer analyses showed that Orysa; EL2 binds the cyclin-dependent kinase (CDK) CDKA1;1 and D-type cyclins. No interaction was observed with the plant-specific B-type CDKs. The amino acid motif ELERFL was identified to be essential for cyclin, but not for CDK binding. Orysa;EL2 impaired the ability of Orysa; CYCD5;3 to complement a budding yeast (Saccharomyces cerevisiae) triple CLN mutant, whereas recombinant protein inhibited CDK activity in vitro. Moreover, Orysa;EL2 was able to rescue the multicellular trichome phenotype of sim mutants of Arabidopsis, unequivocally demonstrating that Orysa;EL2 operates as a cell cycle inhibitor. Orysa;EL2 mRNA levels were induced by cold, drought, and propionic acid. Our data suggest that Orysa;EL2 encodes a new type of plant CDK inhibitor that links cell cycle progression with biotic and abiotic stress responses.	EL2
Isolation and analysis of expression mechanisms of a rice gene, EL5, which shows structural similarity to ATL family from Arabidopsis, in response to N-acetylchitooligosaccharide elicitor	2001	Plant Science	Institute of Applied Biochemistry, University of Tsukuba, 305-8072, Tsukuba, Japan	Two rice cDNAs, EL5 and RRF1, were isolated and characterized. EL5 was responsive to N-acetylchitooligosaccharide, a biotic elicitor active in suspension-cultured rice cells. The structural specificity of the elicitor required for the expression of EL5 was consistent with other defense reactions observed in the experimental system, indicating that the elicitor signal to EL5 is transmitted through a single class of receptor-mediated recognition events. However, the intracellular signaling pathway to EL5 was distinct from those to other elicitor-responsive genes. Sequence analysis and alignment showed that a genomic sequence stored in rice genome databases in addition to EL5 and RRF1 belongs to the ATL family of RING-H2 finger motif proteins first isolated from Arabidopsis.	EL5
EL5, a rice N-acetylchitooligosaccharide elicitor-responsive RING-H2 finger protein, is a ubiquitin ligase which functions in vitro in co-operation with an elicitor-responsive ubiquitin-conjugating enzyme, OsUBC5b	2002	The Plant Journal	Institute of Applied Biochemistry, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8572, Japan.	EL5, a rice gene responsive to N-acetylchitooligosaccharide elicitor, encodes a RING-H2 finger protein with structural features common to the plant-specific ATL family. We show that the fusion protein of EL5 with maltose binding protein (MBP) was polyubiquitinated by incubation with ubiquitin, ubiquitin-activating enzyme (E1), and the Ubc4/5 subfamily of the ubiquitin-conjugating enzyme (E2). EL5 possesses the activity to catalyse the transfer of ubiquitin to the MBP moiety, and the RING-H2 finger motif of EL5 is necessary for this activity. Thus, we concluded that EL5 represents a ubiquitin ligase (E3). We also show that two rice E2s (OsUBC5a, OsUBC5b) of the Ubc4/5 subfamily function as E2 which catalyses EL5-mediated ubiquitination, and OsUBC5b was induced by elicitor, as well as EL5. These results strongly suggest that EL5 and OsUBC5b have roles in plant defense response through the turnover of protein(s) via the ubiquitin/proteasome system.	EL5,OsUBC5b,OsUBC5a
RING-H2 type ubiquitin ligase EL5 is involved in root development through the maintenance of cell viability in rice	2007	Plant J	Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai, 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.	Rice EL5 is an ATL family gene characterized by a transmembrane domain at the N-terminal and a RING-H2 finger domain (RFD), which exhibits ubiquitin ligase (E3) activity. To elucidate the physiological roles of EL5, we analyzed transgenic rice plants overexpressing mutant EL5 proteins that are impaired in E3 activity to various degrees. Plants expressing EL5C153A and EL5W165A, which encode an inactive E3, showed a rootless phenotype accompanied by cell death in root primordia, and those expressing EL5V162A, with moderately impaired E3 activity, formed short crown roots with necrotic lateral roots. The dominant-negative phenotype was specifically observed in root meristems where EL5 is expressed, and not recovered by exogenous auxin. When wild-type EL5 was transcriptionally overexpressed, the EL5 protein was barely detected by Western blotting. Neither treatment with a proteasome inhibitor nor mutation of the sole lysine residue, a potential target of ubiquitination, resulted in increased EL5 accumulation, whereas mutations in the RFD led to increased EL5 accumulation. The stabilized EL5 without the RFD was localized in the plasma membrane. Deletion of the transmembrane domain prevented the EL5 from localizing in the membrane and from exerting an inhibitory effect on root formation. Deletion of the C-terminal region also neutralized the negative effect. We concluded that EL5 plays a major role as a membrane-anchored E3 for the maintenance of cell viability after the initiation of root primordial formation. In addition, we propose that EL5 is an unstable protein, of which degradation is regulated by the RFD in a proteasome-independent manner.	EL5
EL5 is involved in root development as an anti-cell death ubiquitin ligase	2008	Plant Signal Behav	Division of Plant Sciences; National Institute of Agrobiological Sciences; Tsukuba, Japan.	Ubiquitin ligase (E3) plays a central role in substrate recognition during ubiquitination, a post-translational modification of proteins. Rice EL5 is an E3 with a RING-H2 finger domain (RFD) and its transcript is upregulated by a chitin elicitor. The EL5-RFD has been intensively studied and demonstrated to exhibit E3 activity. Its three-dimensional structure was determined for the first time in plant E3, and the amino acid residues required for the interaction with the ubiquitin-conjugating enzyme (E2) were identified. Recent analyses revealed that EL5 plays a crucial role as an E3 in the maintenance of cell viability during root development in rice. In this addendum, we report that the EL5-RFD catalyzes polyubiquitination via the Lys48 residue of ubiquitin. We also discuss the possible role of EL5 as an anti-cell death enzyme. We hypothesize that EL5 might be responsible for mediating the degradation of cytotoxic proteins produced in root cells after the actions of phytohormones.	EL5
Overexpression of the trehalose-6-phosphate synthase gene OsTPS1 enhances abiotic stress tolerance in rice	2011	Planta	Key Laboratory of Gene Engineering Drug and Biotechnology, College of Life Sciences, Beijing Normal University, Beijing, 100875, People's Republic of China.	Trehalose plays an important role in metabolic regulation and abiotic stress tolerance in a variety of organisms. In plants, its biosynthesis is catalyzed by two key enzymes: trehalose-6-phosphate synthase (TPS) and trehalose-6-phosphate phosphatase (TPP). The genome of rice (Oryza sativa) contains 11 OsTPS genes, and only OsTPS1 shows TPS activity. To demonstrate the physiological function of OsTPS1, we introduced it into rice and found that OsTPS1 overexpression improved the tolerance of rice seedling to cold, high salinity and drought treatments without other significant phenotypic changes. In transgenic lines overexpressing OsTPS1, trehalose and proline concentrations were higher than in the wild type and some stress-related genes were up-regulated, including WSI18, RAB16C, HSP70, and ELIP. These results demonstrate that OsTPS1 may enhance the abiotic stress tolerance of plants by increasing the amount of trehalose and proline, and regulating the expression of stress-related genes. Furthermore, we found that overexpression of some Class II TPSs also enhanced plant tolerance of abiotic stress. This work will help to clarify the role of trehalose metabolism in abiotic stress response in higher plants.	ELIP,OsTPS1,pwsi18|WSI18,CRP,OsLEA25,OsTRE
Cloning of cDNA encoding the rice 22 kDa protein of Photosystem II (PSII-S) and analysis of light-induced expression of the gene	1997	Gene	National Institute of Agrobiological Resources, Ibaraki, Japan.	Cloning of rice cDNA encoding the chlorophyll-binding 22 kDa protein of Photosystem II (PSII-S) and the light-induced expression of the gene are reported. One of the light-responsive cDNA clones, isolated by screening with a light-specific subtracted cDNA probe, was shown to encode PSII-S of rice. Genomic Southern analysis suggested that the PSII-S gene, psbS, is a single-copy gene in rice. A brief exposure to red light induced a severalfold increase in the steady state level of PSII-S transcripts in etiolated seedlings. The red light effect was reversed by far-red light, suggesting involvement of phytochrome in the PSII-S gene regulation. Prolonged exposure (3 h) to blue light, however, revealed a much stronger effect than red light on the accumulation of PSII-S transcripts in the etiolated seedlings. In dark-adapted green plants, prolonged exposure to blue light induced re-accumulation of transcripts encoding PSII-S, whereas red light had little effect.	ELIP,ASCAB9-A|CP26|Lhcb5
Empty pericarp5 encodes a pentatricopeptide repeat protein that is required for mitochondrial RNA editing and seed development in maize	2013	Plant Cell	State Key Lab of Agrobiotechnology, Institute of Plant Molecular Biology and Agrobiotechnology, School of Life Science, Chinese University of Hong Kong, Shatin, N.T., Hong Kong, China.	In flowering plants, RNA editing is a posttranscriptional mechanism that converts specific cytidines to uridines in both mitochondrial and plastidial transcripts, altering the information encoded by these genes. Here, we report the molecular characterization of the empty pericarp5 (emp5) mutants in maize (Zea mays). Null mutation of Emp5 results in abortion of embryo and endosperm development at early stages. Emp5 encodes a mitochondrion-targeted DYW subgroup pentatricopeptide repeat (PPR) protein. Analysis of the mitochondrial transcripts revealed that loss of the EMP5 function abolishes the C-to-U editing of ribosomal protein L16 at the rpl16-458 site (100% edited in the wild type), decreases the editing at nine sites in NADH dehydrogenase9 (nad9), cytochrome c oxidase3 (cox3), and ribosomal protein S12 (rps12), and surprisingly increases the editing at five sites of ATP synthase F0 subunit a (atp6), apocytochrome b (cob), nad1, and rpl16. Mutant EMP5-4 lacking the E+ and DYW domains still retains the substrate specificity and editing function, only at reduced efficiency. This suggests that the E+ and DYW domains of EMP5 are not essential to the EMP5 editing function but are necessary for efficiency. Analysis of the ortholog in rice (Oryza sativa) indicates that rice EMP5 has a conserved function in C-to-U editing of the rice mitochondrial rpl16-458 site. EMP5 knockdown expression in transgenics resulted in slow growth and defective seeds. These results demonstrate that Emp5 encodes a PPR-DYW protein that is required for the editing of multiple transcripts in mitochondria, and the editing events, particularly the C-to-U editing at the rpl16-458 site, are critical to the mitochondrial functions and, hence, to seed development in maize.	EMP5|OsEMP5
Phytosiderophore efflux transporters are crucial for iron acquisition in graminaceous plants	2011	J Biol Chem	Department of Global Agricultural Sciences, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657 Japan.	Eukaryotic organisms have developed diverse mechanisms for the acquisition of iron, which is required for their survival. Graminaceous plants use a chelation strategy. They secrete phytosiderophore compounds, which solubilize iron in the soil, and then take up the resulting iron-phytosiderophore complexes. Bacteria and mammals also secrete siderophores to acquire iron. Although phytosiderophore secretion is crucial for plant growth, its molecular mechanism remains unknown. Here, we show that the efflux of deoxymugineic acid, the primary phytosiderophore from rice and barley, involves the TOM1 and HvTOM1 genes, respectively. Xenopus laevis oocytes expressing TOM1 or HvTOM1 released (14)C-labeled deoxymugineic acid but not (14)C-labeled nicotianamine, a structural analog and biosynthetic precursor of deoxymugineic acid, indicating that the TOM1 and HvTOM1 proteins are the phytosiderophore efflux transporters. Under conditions of iron deficiency, rice and barley roots express high levels of TOM1 and HvTOM1, respectively, and the overexpression of these genes increased tolerance to iron deficiency. In rice roots, the efficiency of deoxymugineic acid secretion was enhanced by overexpression of TOM1 and decreased by its repression, providing further evidence that TOM1 encodes the efflux transporter of deoxymugineic acid. We have also identified two genes encoding efflux transporters of nicotianamine, ENA1 and ENA2. Our identification of phytosiderophore efflux transporters has revealed the final piece in the molecular machinery of iron acquisition in graminaceous plants.	OsENA1,TOM1|OsZIFL4
ENAC1, a NAC transcription factor, is an early and transient response regulator induced by abiotic stress in rice (Oryza sativa L.)	2012	Mol Biotechnol	State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.	The plant-specific NAC (NAM, ATAF, and CUC)-domain proteins play important roles in plant development and stress responses. In this research, a full-length cDNA named ENAC1 (early NAC-domain protein induced by abiotic stress 1) was isolated from rice. ENAC1 possess one NAC domain in the N-terminus. Comparative time-course expression analysis indicated that ENAC1 expression, similar with OsDREB1A, was induced very quickly by various abiotic stresses including salt, drought, cold, and exogenous abscisic acid. However, the induction of ENAC1 by abiotic stress was transient and lasted up to 3 h, whereas that of OsDREB1A maintained longer. The promoter sequence of ENAC1 harbors several cis-elements including ABA response elements, but the well-known dehydration responsive element/C-repeat element is absent. The ENAC1-GFP (green fluorescent protein) fusion protein was localized in the nucleus of rice protoplast cell. Yeast hybrid assays revealed that ENAC1 was a transcription activator and bound to NAC recognition sequence (NACRS). Co-expression analysis suggested that ENAC1 co-expressed with a number of stress-related genes. Taken together, ENAC1 may be an early transcription activator of stress responses and function in the regulation of NACRS-mediated gene expression under abiotic stress.	ENAC1,OsDREB1A|OsDREBL
Rice SNF2 family helicase ENL1 is essential for syncytial endosperm development	2014	Plant J	Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan.	The endosperm of cereal grains represents the most important source of human nutrition. In addition, the endosperm provides many investigatory opportunities for biologists because of the unique processes that occur during its ontogeny, including syncytial development at early stages. Rice endospermless 1 (enl1) develops seeds lacking an endosperm but carrying a functional embryo. The enl1 endosperm produces strikingly enlarged amoeboid nuclei. These abnormal nuclei result from a malfunction in mitotic chromosomal segregation during syncytial endosperm development. The molecular identification of the causal gene revealed that ENL1 encodes an SNF2 helicase family protein that is orthologous to human PICH, which has been implicated in the resolution of persistent DNA catenation during anaphase. ENL1-Venus (enhanced YFP) localizes to the cytoplasm during interphase but moves to the chromosome arms during mitosis. ENL1-Venus is also detected on a thread-like structure that connects separating sister chromosomes. These observations indicate the functional conservation between PICH and ENL1 and confirm the proposed role of PICH. Although ENL1 dysfunction also affects karyokinesis in the root meristem, enl1 plants can grow in a field and set seeds, indicating that its indispensability is tissue-dependent. Notably, despite the wide conservation of ENL1/PICH among eukaryotes, the loss of function of the ENL1 ortholog in Arabidopsis (CHR24) has only marginal effects on endosperm nuclei and results in normal plant development. Our results suggest that ENL1 is endowed with an indispensable role to secure the extremely rapid nuclear cycle during syncytial endosperm development in rice.	ENL1
Identification and characterization of the erect-pose panicle gene EP conferring high grain yield in rice (Oryza sativa L.)	2009	Theor Appl Genet	Key Laboratory of Crop Physiology, Ecology, Genetics and Breeding, Ministry of Agriculture/Key Laboratory of Northern Japonica Rice Breeding of Liaoning, Shenyang Agricultural University, Shenyang, China.	The breeding of japonica varieties with erect-pose panicle (EP) has recently progressed in the northern part of China, because these varieties exhibit a far higher grain yield than the varieties with normal-pose panicle (NP). A genetic analysis using the F(2) population from the cross between Liaojing5, the first japonica EP variety in China, and the Japanese japonica NP variety Toyonishiki revealed that EP is governed by a single dominant gene EP. Based on previous studies, map-based cloning of EP locus was conducted using Liaojing5, Toyonishiki, their F(2) population, and a pair of near-isogenic lines for EP locus (ZF14 and WF14) derived from the cross between the two varieties; consequently, the STS marker H90 was found to completely cosegregate with panicle pose. The H90 is located in the coding sequence AK101247 in the database, and the AK101247 of Liaojing5 has a 12 bp sequence in exon 5 replaced with a 637 bp sequence of its wild type allele. It was therefore considered that the AK101247 encodes the protein of the wild type allele at EP locus, and that the sequence substitution in exon 5 of Liaojing5 is crucial for expression of the EP phenotype. The effects of EP gene on agronomic traits were investigated using two pairs of near-isogenic lines (ZF6 vs. WF6 and ZF14 vs. WF14) derived from the cross between the two varieties. Experimental results showed that EP gene markedly enhanced grain yield, chiefly by increasing number of secondary branches and number of grains on the secondary branch. EP gene also produced a remarkable increase in grain density.	EP
Evidence for an evolutionary force that prevents epigenetic silencing between tail-to-tail rice genes with a short spacer	2005	Gene	Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.	During the course of evolution, the genome should have toned down various types of genomic noise, such as those that cause the unstable expression or gene silencing observed in transgenic organisms. We found a rice genomic segment where two genes, encoding 5-enolpyruvylshikimate-3-phosphate synthase (EPSPs) and ribosomal protein small subunit 20 (rps20), are located in a tail-to-tail orientation and separated by only 300 bp of spacer. It is possible that this kind of structure would give rise to unstable expression due to antisense RNA derived from the neighboring gene. We examined this possibility using Northern blot, reverse transcription-polymerase chain reaction (RT-PCR), and 3' RACE analyses, but obtained no evidence for instability or antisense RNAs of these housekeeping genes. Comparison of the sequences in the corresponding regions among related rice species revealed a lower level of genetic divergence of both the 3'-untranslated region (3'-UTRs) than of the other noncoding regions; in particular both of the boundaries between the 3'-UTRs and the spacer were markedly conserved. The conservation of both the terminal regions is most likely the result of purifying selection, implying a functional role for the strict termination of the transcription of these genes to prevent gene-silencing-related events.	EPSPs
Whole-genome analysis of Oryza sativa reveals similar architecture of two-component signaling machinery with Arabidopsis	2006	Plant Physiol	Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India. ashwanip@mail.jnu.ac.in	The two-component system (TCS), which works on the principle of histidine-aspartate phosphorelay signaling, is known to play an important role in diverse physiological processes in lower organisms and has recently emerged as an important signaling system in plants. Employing the tools of bioinformatics, we have characterized TCS signaling candidate genes in the genome of Oryza sativa L. subsp. japonica. We present a complete overview of TCS gene families in O. sativa, including gene structures, conserved motifs, chromosome locations, and phylogeny. Our analysis indicates a total of 51 genes encoding 73 putative TCS proteins. Fourteen genes encode 22 putative histidine kinases with a conserved histidine and other typical histidine kinase signature sequences, five phosphotransfer genes encoding seven phosphotransfer proteins, and 32 response regulator genes encoding 44 proteins. The variations seen between gene and protein numbers are assumed to result from alternative splicing. These putative proteins have high homology with TCS members that have been shown experimentally to participate in several important physiological phenomena in plants, such as ethylene and cytokinin signaling and phytochrome-mediated responses to light. We conclude that the overall architecture of the TCS machinery in O. sativa and Arabidopsis thaliana is similar, and our analysis provides insights into the conservation and divergence of this important signaling machinery in higher plants.	ERS1,ERS2,ETR3,ETR4,HK1
Nomenclature for two-component signaling elements of rice	2007	Plant Physiol	Department of Biological Sciences, Dartmouth College, Hanover, NH 03755	None	ERS1,ERS2,ETR3,ETR4,HK1
Differential expression of three genes encoding an ethylene receptor in rice during development, and in response to indole-3-acetic acid and silver ions	2004	J Exp Bot	Department of Botany, University of Hong Kong, Pokfulam Road, Hong Kong.	Five ethylene receptor genes, OS-ERS1, OS-ERS2, OS-ETR2, OS-ETR3, and OS-ETR4 were isolated and characterized from rice. The genomic structure of OS-ERS1 and OS-ERS2 revealed that the introns within the coding sequences occurred in conserved positions to those of At-ETR1 and At-ERS1, whereas each of the OS-ETR2, OS-ETR3, and OS-ETR4 genes contained 1 intron within its coding region located at a position equivalent to those of At-ERS2, At-ETR2, and At-EIN4. Deduced amino acid sequences of OS-ERS1, OS-ERS2, OS-ETR2, OS-ETR3, and OS-ETR4 showed that they exhibited significant homology to the prokaryotic two-component signal transducer and a wide range of ethylene receptors in a variety of plant species. Northern analysis revealed that the level of OS-ETR2 mRNA was markedly elevated either by the exogenous application of IAA or by ethylene treatment in young etiolated rice seedlings, whereas the OS-ERS1 transcript level was only slightly induced under the same experimental conditions. Pretreatment with silver prevented IAA-induced and ethylene-induced accumulation of both mRNAs (OS-ERS1 and OS-ETR2). However, the abundance of OS-ERS2 mRNA was shown to be down-regulated by both IAA and ethylene treatments, indicating that it was not positively regulated by ethylene. Analysis of the expression of the three ethylene receptor genes in different tissues of rice has unravelled their corresponding tissue-specificity in which OS-ERS1 was constitutively expressed in considerable amounts in all tissues studied, while OS-ERS2 and OS-ETR2 exhibited differential expression patterns in different tissues of rice. Moreover, higher levels of these three mRNAs were commonly observed in anthers when compared with their corresponding levels in other tissues, suggesting the important role played by ethylene involved in the regulation of pollen development in rice. Among the five ethylene receptor genes, the expression levels of both OS-ETR3 and OS-ETR4 were too low to be detected by the northern blot analysis. Results from RT-PCR illustrated that both mRNAs were present in young green rice seedlings and anthers.	ERS1,ERS2,ETR3,ETR4
The ethylene receptor ETR2 delays floral transition and affects starch accumulation in rice	2009	Plant Cell	Plant Gene Research Center, National Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Ethylene regulates multiple aspects of plant growth and development in dicotyledonous plants; however, its roles in monocotyledonous plants are poorly known. Here, we characterized a subfamily II ethylene receptor, ETHYLENE RESPONSE2 (ETR2), in rice (Oryza sativa). The ETR2 receptor with a diverged His kinase domain is a Ser/Thr kinase, but not a His kinase, and can phosphorylate its receiver domain. Mutation of the N box of the kinase domain abolished the kinase activity of ETR2. Overexpression of ETR2 in transgenic rice plants reduced ethylene sensitivity and delayed floral transition. Conversely, RNA interference (RNAi) plants exhibited early flowering and the ETR2 T-DNA insertion mutant etr2 showed enhanced ethylene sensitivity and early flowering. The effective panicles and seed-setting rate were reduced in the ETR2-overexpressing plants, while thousand-seed weight was substantially enhanced in both the ETR2-RNAi plants and the etr2 mutant compared with controls. Starch granules accumulated in the internodes of the ETR2-overexpressing plants, but not in the etr2 mutant. The GIGANTEA and TERMINAL FLOWER1/CENTRORADIALIS homolog (RCN1) that cause delayed flowering were upregulated in ETR2-overexpressing plants but downregulated in the etr2 mutant. Conversely, the alpha-amylase gene RAmy3D was suppressed in ETR2-overexpressing plants but enhanced in the etr2 mutant. Thus, ETR2 may delay flowering and cause starch accumulation in stems by regulating downstream genes.	ETR3,ETR4,ETR2|Os-ERL1,Rcn1
Identification of a 98-kb DNA segment containing the rice Eui gene controlling uppermost internode elongation, and construction of a TAC transgene sublibrary	2004	Mol Genet Genomics	College of Life Sciences, Zhejiang University, 310029, Hangzhou, China.	The recessive 'tall rice' phenotype associated with the mutation eui (elongated upper-most internode) is an important agronomic trait that has been introduced into hybrid rice to eliminate panicle enclosure in all types of male-sterile lines and produce good-quality seeds in high yield and at low cost. Based on our previous Eui mapping data, we conducted fine-structure mapping and positional cloning of the gene using an F2 population comprising more than 5000 individuals derived from a cross of the near-isogenic lines 307T (eui/eui) with the recurrent parent Zhenshan 97 (Eui/Eui). In total 45 CAPS (cleaved amplified polymorphic sequences) markers located within an interval of 14.5 cM were analyzed in the subpopulation of 1298 homozygous recessive plants. The resulting high-resolution map defined a 98-kb interval containing the Eui locus flanked by the markers M0387 and M01, and three markers were found to co-segregate with Eui. In order to facilitate the identification of the Eui gene, we used a transformation-competent artificial chromosome (TAC) vector to construct a set of contiguous TAC clones from the Nipponbare BACs (obtained from the Clemson University Genome Institute; CUGI) spanning this region. These clones can be used to streamline complementation testing. The markers tightly linked to the Eui locus can also be used in breeding male-sterile lines with the elongated uppermost internode.	EUI1
Gibberellin homeostasis and plant height control by EUI and a role for gibberellin in root gravity responses in rice	2008	Cell Res	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	The rice Eui (ELONGATED UPPERMOST INTERNODE) gene encodes a cytochrome P450 monooxygenase that deactivates bioactive gibberellins (GAs). In this study, we investigated controlled expression of the Eui gene and its role in plant development. We found that Eui was differentially induced by exogenous GAs and that the Eui promoter had the highest activity in the vascular bundles. The eui mutant was defective in starch granule development in root caps and Eui overexpression enhanced starch granule generation and gravity responses, revealing a role for GA in root starch granule development and gravity responses. Experiments using embryoless half-seeds revealed that RAmy1A and GAmyb were highly upregulated in eui aleurone cells in the absence of exogenous GA. In addition, the GA biosynthesis genes GA3ox1 and GA20ox2 were downregulated and GA2ox1 was upregulated in eui seedlings. These results indicate that EUI is involved in GA homeostasis, not only in the internodes at the heading stage, but also in the seedling stage, roots and seeds. Disturbing GA homeostasis affected the expression of the GA signaling genes GID1 (GIBBERELLIN INSENSITIVE DWARF 1), GID2 and SLR1. Transgenic RNA interference of the Eui gene effectively increased plant height and improved heading performance. By contrast, the ectopic expression of Eui under the promoters of the rice GA biosynthesis genes GA3ox2 and GA20ox2 significantly reduced plant height. These results demonstrate that a slight increase in Eui expression could dramatically change rice morphology, indicating the practical application of the Eui gene in rice molecular breeding for a high yield potential.	EUI1,GF14e|GID2,OsGA2ox1,OsGA3ox1,GID1|OsGID1,SLR1|OsGAI
Altered disease development in the eui mutants and Eui overexpressors indicates that gibberellins negatively regulate rice basal disease resistance	2008	Mol Plant	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.	Gibberellins (GAs) form a group of important plant tetracyclic diterpenoid hormones that are involved in many aspects of plant growth and development. Emerging evidence implicates that GAs also play roles in stress responses. However, the role of GAs in biotic stress is largely unknown. Here, we report that knockout or overexpression of the Elongated uppermost internode (Eui) gene encoding a GA deactivating enzyme compromises or increases, respectively, disease resistance to bacterial blight (Xanthomonas oryzae pv. oyrzae) and rice blast (Magnaporthe oryzae). Exogenous application of GA(3) and the inhibitor of GA synthesis (uniconazol) could increase disease susceptibility and resistance, respectively, to bacterial blight. Similarly, uniconazol restored disease resistance of the eui mutant and GA(3) decreased disease resistance of the Eui overexpressors to bacterial blight. Therefore, the change of resistance attributes to GA levels. In consistency with this, the GA metabolism genes OsGA20ox2 and OsGA2ox1 were down-regulated during pathogen challenge. We also found that PR1a induction was enhanced but the SA level was decreased in the Eui overexpressor, while the JA level was reduced in the eui mutant. Together, our current study indicates that GAs play a negative role in rice basal disease resistance, with EUI as a positive modulator through regulating the level of bioactive GAs.	EUI1,OsGA20ox1
The APETALA-2-Like Transcription Factor OsAP2-39 Controls Key Interactions between Abscisic Acid and Gibberellin in Rice	2010	PLoS Genet	Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada	The interaction between phytohormones is an important mechanism which controls growth and developmental processes in plants. Deciphering these interactions is a crucial step in helping to develop crops with enhanced yield and resistance to environmental stresses. Controlling the expression level of OsAP2-39 which includes an APETALA 2 (AP2) domain leads to phenotypic changes in rice. Overexpression of OsAP2-39 leads to a reduction in yield by decreasing the biomass and the number of seeds in the transgenic rice lines. Global transcriptome analysis of the OsAP2-39 overexpression transgenic rice revealed the upregulation of a key Abscisic Acid (ABA) biosynthetic gene OsNCED-I which codes for 9-cis-epoxycarotenoid dioxygenase and leads to an increase in the endogenous ABA level. In addition to OsNCED-1, the gene expression analysis revealed the upregulation of a gene that codes for the Elongation of Upper most Internode (EUI) protein, an enzyme that catalyzes 16a, 17-epoxidation of non-13-hydroxylated GAs, which has been shown to deactivate gibberellins (GAs) in rice. The exogenous application of GA restores the wild-type phenotype in the transgenic line and ABA application induces the expression of EUI and suppresses the expression of OsAP2-39 in the wild-type line. These observations clarify the antagonistic relationship between ABA and GA and illustrate a mechanism that leads to homeostasis of these hormones. In vivo and in vitro analysis showed that the expression of both OsNCED-1 and EUI are directly controlled by OsAP2-39. Together, these results reveal a novel mechanism for the control of the ABA/GA balance in rice which is regulated by OsAP2-39 that in turn regulates plant growth and seed production.	EUI1,OsAP2-39,OsNCED1
ELONGATED UPPERMOST INTERNODE encodes a cytochrome P450 monooxygenase that epoxidizes gibberellins in a novel deactivation reaction in rice	2006	Plant Cell	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	The recessive tall rice (Oryza sativa) mutant elongated uppermost internode (eui) is morphologically normal until its final internode elongates drastically at the heading stage. The stage-specific developmental effect of the eui mutation has been used in the breeding of hybrid rice to improve the performance of heading in male sterile cultivars. We found that the eui mutant accumulated exceptionally large amounts of biologically active gibberellins (GAs) in the uppermost internode. Map-based cloning revealed that the Eui gene encodes a previously uncharacterized cytochrome P450 monooxygenase, CYP714D1. Using heterologous expression in yeast, we found that EUI catalyzed 16alpha,17-epoxidation of non-13-hydroxylated GAs. Consistent with the tall and dwarfed phenotypes of the eui mutant and Eui-overexpressing transgenic plants, respectively, 16alpha,17-epoxidation reduced the biological activity of GA(4) in rice, demonstrating that EUI functions as a GA-deactivating enzyme. Expression of Eui appeared tightly regulated during plant development, in agreement with the stage-specific eui phenotypes. These results indicate the existence of an unrecognized pathway for GA deactivation by EUI during the growth of wild-type internodes. The identification of Eui as a GA catabolism gene provides additional evidence that the GA metabolism pathway is a useful target for increasing the agronomic value of crops.	EUI1
EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice	2006	Plant Cell Physiol	National Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, PR China.	Elongation of rice internodes is one of the most important agronomic traits, which determines the plant height and underlies the grain yield. It has been shown that the elongation of internodes is under genetic control, and various factors are implicated in the process. Here, we report a detailed characterization of an elongated uppermost internode1 (eui1) mutant, which has been used in hybrid rice breeding. In the eui1-2 mutant, the cell lengths in the uppermost internodes are significantly longer than that of wild type and thus give rise to the elongated uppermost internode. It was found that the level of active gibberellin was elevated in the mutant, whereas its growth in response to gibberellin is similar to that of the wild type, suggesting that the higher level accumulation of gibberellin in the eui1 mutant causes the abnormal elongation of the uppermost internode. Consistently, the expression levels of several genes which encode gibberellin biosynthesis enzymes were altered. We cloned the EUI1 gene, which encodes a putative cytochrome P450 monooxygenase, by map-based cloning and found that EUI1 was weakly expressed in most tissues, but preferentially in young panicles. To confirm its function, transgenic experiments with different constructs of EUI1 were conducted. Overexpression of EUI1 gave rise to the gibberellin-deficient-like phenotypes, which could be partially reversed by supplementation with gibberellin. Furthermore, apart from the alteration of expression levels of the gibberellin biosynthesis genes, accumulation of SLR1 protein was found in the overexpressing transgenic plants, indicating that the expression level of EUI1 is implicated in both gibberellin-mediated SLR1 destruction and a feedback regulation in gibberellin biosynthesis. Therefore, we proposed that EUI1 plays a negative role in gibberellin-mediated regulation of cell elongation in the uppermost internode of rice.	EUI1,SLR1|OsGAI
Fine mapping and in silico isolation of the EUI1 gene controlling upper internode elongation in rice	2006	Plant Mol Biol	Institute of Genetics and Crop Breeding, Fujian Agriculture and Forestry University, 350002, Fuzhou, China.	Upper internode elongation in rice is an important agronomic trait. Well-known mutants with an elongated uppermost internode (eui) are important germplasms for developing unsheathed-panicle male-sterile lines in hybrid rice breeding. We finely mapped the eui1 gene and identified its candidate gene using in silico analysis based on previous research work and rice genomic sequence data. The rice eui1 gene was mapped to two overlapping BAC clones, OSJNBa0095J22 and OSJNBb0099O15, between the markers AC40 and AC46, that were 0.64 cM apart and spanned approximately 152 kb. A simple sequence repeat (SSR) marker AC41 that cosegregated with eui1 was located in an intron of a putative cytochrome P450-related gene. In silico analysis suggested that this encoded the cytochrome CYP714D1. Allelic sequencing confirmed that EUI1 corresponded to this P450 gene. A gamma ray-induced eui1 mutant carried a deletion in exon II of the EUI1 gene, and resulted in a frame-shift deletion that produced a truncated polypeptide. We conclude that the EUI1 gene controlling the upper internode elongation in rice is 9,804 bp long, and comprises two exons and one intron. The length of the cDNA is 1,931 bp containing a 1,734 bp ORF, a 110 bp 5'-UTR and a 87 bp 3'-UTR. The ORF encodes an unknown 577 amino acid functional protein, that appears to be a member of the cytochrome P450 family.	EUI1
FLEXIBLE CULM 1 encoding a cinnamyl-alcohol dehydrogenase controls culm mechanical strength in rice	2009	Plant Mol Biol	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Culm mechanical strength is an important agronomic trait in crop breeding. To understand the molecular mechanisms that control culm mechanical strength, we identified a flexible culm1 (fc1) mutant by screening a rice T-DNA insertion mutant library. This mutant exhibited an abnormal development phenotype, including late heading time, semi-dwarf habit, and flexible culm. In this study, we cloned the FLEXIBLE CULM1 (FC1) gene in rice using a T-DNA tagging approach. FC1 encodes a cinnamyl-alcohol dehydrogenase and is mainly expressed in the sclerenchyma cells of the secondary cell wall and vascular bundle region. In these types of cells, a deficiency of FC1 in the fc1 mutant caused a reduction in cell wall thickness, as well as a decrease in lignin. Extracts from the first internodes and panicles of the fc1 plants exhibited drastically reduced cinnamyl-alcohol dehydrogenase activity. Further histological and biochemical analyses revealed that the p-hydroxyphenyl and guaiacyl monomers in fc1 cell wall were reduced greatly. Our results indicated that FC1 plays an important role in the biosynthesis of lignin and the control of culm strength in rice.	FC1|OsCAD7
FINE CULM1 (FC1) works downstream of strigolactones to inhibit the outgrowth of axillary buds in rice	2010	Plant Cell Physiol	Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo, 113-8657 Japan.	Recent studies of highly branched mutants of pea, Arabidopsis and rice have demonstrated that strigolactones (SLs) act as hormones that inhibit shoot branching. The identification of genes that work downstream of SLs is required for a better understanding of how SLs control the growth of axillary buds. We found that the increased tillering phenotype of fine culm1 (fc1) mutants of rice is not rescued by the application of 1 microM GR24, a synthetic SL analog. Treatment with a high concentration of GR24 (10 microM) causes suppression of tiller growth in wild-type plants, but is not effective on fc1 mutants, implying that proper FC1 functioning is required for SLs to inhibit bud growth. Overexpression of FC1 partially rescued d3-2 defects in the tiller growth and plant height. An in situ hybridization analysis showed that FC1 mRNA accumulates in axillary buds, the shoot apical meristem, young leaves, vascular tissues and the tips of crown roots. FC1 mRNA expression was not significantly affected by GR24, suggesting that transcriptional induction may not be the mechanism by which SLs affect FC1 functioning. On the other hand, the expression level of FC1 is negatively regulated by cytokinin treatment. We propose that FC1 acts as an integrator of multiple signaling pathways and is essential to the fine-tuning of shoot branching in rice.	FC1|OsCAD7,OsTB1|FC1
Functional diversification of CLAVATA3-related CLE proteins in meristem maintenance in rice	2008	Plant Cell	Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan.	Postembryonic development in plants depends on the activity of the shoot apical meristem (SAM) and root apical meristem (RAM). In Arabidopsis thaliana, CLAVATA signaling negatively regulates the size of the stem cell population in the SAM by repressing WUSCHEL. In other plants, however, studies of factors involved in stem cell maintenance are insufficient. Here, we report that two proteins closely related to CLAVATA3, FLORAL ORGAN NUMBER2 (FON2) and FON2-LIKE CLE PROTEIN1 (FCP1/Os CLE402), have functionally diversified to regulate the different types of meristem in rice (Oryza sativa). Unlike FON2, which regulates the maintenance of flower and inflorescence meristems, FCP1 appears to regulate the maintenance of the vegetative SAM and RAM. Constitutive expression of FCP1 results in consumption of the SAM in the vegetative phase, and application of an FCP1 CLE peptide in vitro disturbs root development by misspecification of cell fates in the RAM. FON1, a putative receptor of FON2, is likely to be unnecessary for these FCP1 functions. Furthermore, we identify a key amino acid residue that discriminates between the actions of FCP1 and FON2. Our results suggest that, although the basic framework of meristem maintenance is conserved in the angiosperms, the functions of the individual factors have diversified during evolution.	FCP1|OsCLE402,FON1,FON2|FON4
WUSCHEL-RELATED HOMEOBOX4 is involved in meristem maintenance and is negatively regulated by the CLE gene FCP1 in rice	2013	Plant Cell	Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-8654, Japan.	The shoot apical meristem is the ultimate source of the cells that constitute the entire aboveground portion of the plant body. In Arabidopsis thaliana, meristem maintenance is regulated by the negative feedback loop of WUSCHEL-CLAVATA (WUS-CLV). Although CLV-like genes, such as FLORAL ORGAN NUMBER1 (FON1) and FON2, have been shown to be involved in maintenance of the reproductive meristems in rice (Oryza sativa), current understanding of meristem maintenance remains insufficient. In this article, we demonstrate that the FON2-LIKE CLE PROTEIN1 (FCP1) and FCP2 genes encoding proteins with similar CLE domains are involved in negative regulation of meristem maintenance in the vegetative phase. In addition, we found that WUSCHEL-RELATED HOMEOBOX4 (WOX4) promotes the undifferentiated state of the meristem in rice and that WOX4 function is associated with cytokinin action. Consistent with similarities in the shoot apical meristem phenotypes caused by overexpression of FCP1 and downregulation of WOX4, expression of WOX4 was negatively regulated by FCP1 (FCP2). Thus, FCP1/2 and WOX4 are likely to be involved in maintenance of the vegetative meristem in rice.	FCP1|OsCLE402,FCP2,OsWOX4
A CLE-WOX signalling module regulates root meristem maintenance and vascular tissue development in rice	2013	J Exp Bot	School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	CLAVATA3 (CLV3)/ENDOSPERM SURROUNDING REGION (ESR)-related (CLE) proteins belong to a small peptide family conserved in plants. Recent studies in Arabidopsis and rice have revealed a key role for CLEs in mediating cell-cell communication and stem cell maintenance during plant development, but how CLE signalling controls root development in the rice remains largely unknown. Here it is shown that exogenous application of a synthetic dodeca-amino acid peptide corresponding to the CLE motif of the rice FON2-LIKE CLE PROTEIN2 (FCP2p) protein or overexpression of FCP2 terminates root apical meristem (RAM) activity and impairs late metaxylem formation. FCP2p treatment suppresses the expression of the rice QUIESCENT-CENTER-SPECIFIC HOMEOBOX (QHB) gene, a putative orthologue of Arabidopsis WUSCHEL (WUS)-RELATED HOMEOBOX 5 (WOX5) gene, in both quiescent centre and late metaxylem cells; whereas inducible overexpression of QHB reduces the sensitivity of rice to FCP2p treatment. These results together suggest that in rice RAM maintenance and late metaxylem development are probably controlled by the mutual regulation between FCP2 and QHB. Moreover, a cross-species peptide treatment experiment in Arabidopsis implies that FCP2 has both evolutionarily conserved and species-specific roles in root development.	FCP2
Isolation and characterization of IRO2, a novel iron-regulated bHLH transcription factor in graminaceous plants	2006	J Exp Bot	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Tokyo 113-8657, Japan.	To clarify the molecular mechanism that regulates iron (Fe) acquisition in graminaceous plants, a time-course analysis of gene expression during Fe deficiency stress was conducted using a rice 22K oligo-DNA microarray. Twenty-one genes for proteins that function in gene regulation were induced by Fe deficiency. Of these genes, a putative basic helix-loop-helix (bHLH) transcription factor gene, named OsIRO2, was strongly expressed in both roots and shoots during Fe deficiency stress. The expression of OsIRO2 was induced exclusively by Fe deficiency, and not by deficiencies in other metals. Expression of the barley HvIRO2 gene, which is a homologue of OsIRO2, was also induced by Fe deficiency. An in silico search revealed that IRO2 is highly conserved among graminaceous plants, which include wheat, sorghum, and maize. The cyclic amplification and selection of targets (CASTing) technique revealed that OsIRO2 bound preferentially to the sequence 5'-ACCACGTGGTTTT-3', and the electrophoretic mobility shift assay revealed 5'-CACGTGG-3' as the core sequence for OsIRO2 binding. Sequences similar to the OsIRO2-binding sequence were found upstream of several genes that are involved in Fe acquisition, such as OsNAS1, OsNAS3, OsIRT1, OsFDH, OsAPT1, and IDS3. The core sequence of the OsIRO2-binding sequence occurred more frequently in the upstream regions of Fe deficiency-inducible genes than in the corresponding regions of non-inducible genes. These results suggest that IRO2 is involved in the regulation of gene expression under Fe-deficient conditions.	FDH,OsAPT1|APRT,OsIRO2,OsIRT1,OsNAS1,OsNAS3
Expression profiling of Oryza sativa metal homeostasis genes in different rice cultivars using a cDNA macroarray	2007	Plant Physiol Biochem	USDA-ARS Children's Nutrition Research Center, Department of Pediatrics, Baylor College of Medicine, 1100 Bates Street, Houston, TX 77030, USA.	Rice is an important food crop, but it is a poor source of essential micronutrients such as iron and zinc. In order to improve the metal ion content of rice grains through breeding or biotechnology, more information is needed on the molecular players that help mobilize metals from leaves to developing seeds. To profile several genes simultaneously, a cDNA macroarray was developed using 36 metal-related genes from rice, including ZIPs, NRAMPs, and YSLs (coding for known or potential metal transporters), as well as NAS, FER, FRO, NAAT, FDH, GSTU, and PDR (involved in metal homeostasis). Because flag leaves are the major source of phloem-delivered photoassimilates and remobilized metals for developing seeds, we analyzed the expression of these metal-related genes in flag and non-flag leaves of four different rice cultivars (Cocodrie, Taipei 309, IR58, and IR68144) during the period of mid-grain fill. Genes (24 of 36) exhibited low to non-detectable signals in the macroarray, while 12 genes (OsIRT1, OsZIP1, OsZIP5, OsZIP8, OsYSL5, OsYSL6, OsYSL7, OsYSL8, OsYSL18, OsNRAMP2, OsNRAMP4 and OsNRAMP7) were found to be highly expressed in both flag and non-flag leaves of all four cultivars. Additional expression analysis using semi-quantitative or quantitative PCR provided results that were generally consistent with the macroarray, but semi-quantitative PCR confirmed that OsFDH, OsFER1, OsNAAT, OsNAS1, OsPDR9, OsYSL12, OsYSL13, OsZIP7, and OsZIP10 were also expressed in leaves. This specialized macroarray has provided a short list of potential candidate genes, expressed in leaves, which might contribute to the process of metal transport to distant sinks, such as seeds.	FDH,OsZIP1,OsZIP3,OsZIP6
BENT UPPERMOST INTERNODE1 encodes the class II formin FH5 crucial for actin organization and rice development	2011	Plant Cell	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.	The actin cytoskeleton is an important regulator of cell expansion and morphogenesis in plants. However, the molecular mechanisms linking the actin cytoskeleton to these processes remain largely unknown. Here, we report the functional analysis of rice (Oryza sativa) FH5/BENT UPPERMOST INTERNODE1 (BUI1), which encodes a formin-type actin nucleation factor and affects cell expansion and plant morphogenesis in rice. The bui1 mutant displayed pleiotropic phenotypes, including bent uppermost internode, dwarfism, wavy panicle rachis, and enhanced gravitropic response. Cytological observation indicated that the growth defects of bui1 were caused mainly by inhibition of cell expansion. Map-based cloning revealed that BUI1 encodes the class II formin FH5. FH5 contains a phosphatase tensin-like domain at its amino terminus and two highly conserved formin-homology domains, FH1 and FH2. In vitro biochemical analyses indicated that FH5 is capable of nucleating actin assembly from free or profilin-bound monomeric actin. FH5 also interacts with the barbed end of actin filaments and prevents the addition and loss of actin subunits from the same end. Interestingly, the FH2 domain of FH5 could bundle actin filaments directly and stabilize actin filaments in vitro. Consistent with these in vitro biochemical activities of FH5/BUI1, the amount of filamentous actin decreased, and the longitudinal actin cables almost disappeared in bui1 cells. The FH2 or FH1FH2 domains of FH5 could also bind to and bundle microtubules in vitro. Thus, our study identified a rice formin protein that regulates de novo actin nucleation and spatial organization of the actin filaments, which are important for proper cell expansion and rice morphogenesis.	FH5|RMD|BUI1
RICE MORPHOLOGY DETERMINANT encodes the type II formin FH5 and regulates rice morphogenesis	2011	Plant Cell	School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.	Multicellular organisms contain a large number of formins; however, their physiological roles in plants remain poorly understood. Here, we reveal that formin homology 5 (FH5), a type II formin mutated in rice morphology determinant (rmd), plays a crucial role in determining rice (Oryza sativa) morphology. FH5/RMD encodes a formin-like protein consisting of an N-terminal phosphatase tensin (PTEN)-like domain, an FH1 domain, and an FH2 domain. The rmd mutants display a bending growth pattern in seedlings, are stunted as adult plants, and have aberrant inflorescence (panicle) and seed shape. Cytological analysis showed that rmd mutants have severe cell elongation defects and abnormal microtubule and microfilament arrays. FH5/RMD is ubiquitously expressed in rice tissues, and its protein localization to the chloroplast surface is mediated by the PTEN domain. Biochemical assays demonstrated that recombinant FH5 protein can nucleate actin polymerization from monomeric G-actin or actin/profilin complexes, cap the barbed end of actin filaments, and bundle actin filaments in vitro. Moreover, FH5 can directly bind to and bundle microtubules through its FH2 domain in vitro. Our findings suggest that the rice formin protein FH5 plays a critical role in determining plant morphology by regulating actin dynamics and proper spatial organization of microtubules and microfilaments.	FH5|RMD|BUI1
Rice actin-binding protein RMD is a key link in the auxin–actin regulatory loop that controls cell growth	2014	Proceedings of the National Academy of Sciences	State Key Laboratory of Hybrid Rice, Shanghai Jiao Tong University, Shanghai 20040, China	The plant hormone auxin plays a central role in plant growth and development. Auxin transport and signaling depend on actin organization. Despite its functional importance, the mechanistic link between actin filaments (F-actin) and auxin intracellular signaling remains unclear. Here, we report that the actin-organizing protein Rice Morphology Determinant (RMD), a type II formin from rice (Oryza sativa), provides a key link. Mutants lacking RMD display abnormal cell growth and altered configuration of F-actin array direction. The rmd mutants also exhibit an inhibition of auxin-mediated cell elongation, decreased polar auxin transport, altered auxin distribution gradients in root tips, and suppression of plasma membrane localization of auxin transporters O. sativa PIN-FORMED 1b (OsPIN1b) and OsPIN2 in root cells. We demonstrate that RMD is required for endocytosis, exocytosis, and auxin-mediated OsPIN2 recycling to the plasma membrane. Moreover, RMD expression is directly regulated by heterodimerized O. sativa auxin response factor 23 (OsARF23) and OsARF24, providing evidence that auxin modulates the orientation of F-actin arrays through RMD. In support of this regulatory loop, osarf23 and lines with reduced expression of both OsARF23 and OsARF24 display reduced RMD expression, disrupted F-actin organization and cell growth, less sensitivity to auxin response, and altered auxin distribution and OsPIN localization. Our findings establish RMD as a crucial component of the auxin–actin self-organizing regulatory loop from the nucleus to cytoplasm that controls rice cell growth and morphogenesis.	FH5|RMD|BUI1,OsARF24,UBQ
The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin-related processes	2014	Plant J	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, 113-8657, Japan.	Auxin is a fundamental plant hormone and its localization within organs plays pivotal roles in plant growth and development. Analysis of many Arabidopsis mutants that were defective in auxin biosynthesis revealed that the indole-3-pyruvic acid (IPA) pathway, catalyzed by the TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) families, is the major biosynthetic pathway of indole-3-acetic acid (IAA). In contrast, little information is known about the molecular mechanisms of auxin biosynthesis in rice. In this study, we identified a auxin-related rice mutant, fish bone (fib). FIB encodes an orthologue of TAA genes and loss of FIB function resulted in pleiotropic abnormal phenotypes, such as small leaves with large lamina joint angles, abnormal vascular development, small panicles, abnormal organ identity and defects in root development, together with a reduction in internal IAA levels. Moreover, we found that auxin sensitivity and polar transport activity were altered in the fib mutant. From these results, we suggest that FIB plays a pivotal role in IAA biosynthesis in rice and that auxin biosynthesis, transport and sensitivity are closely interrelated.	FIB
Genetic analysis of endosperm mutants in rice Oryza sativa L	1991	Theor Appl Genet	Division of Plant Breeding, Genetics, and Biochemistry, International Rice Research Institute, P.O. Box 933, Manila, Philippines.	Sugary, shrunken, floury, white core, amylose extender and dull mutants induced in japonica varieties were used in this study. The results of an allelic analysis conducted in japonica background indicated that the two sugary mutants 82GF and EM5 are allelic. The two amylose extender mutants 2064 and EM16 are also allelic. The opaque mutant ESD7-3(0) and floury mutants 2047, EM17 and EM28 are allelic as well and have the flo-1 gene. The three white core mutants EM3, EM24 and EM66 were found to be non-allelic. Eleven dull mutants were investigated. Dull mutants 2057, 2083, 2091 and EM15 were found to be allelic to each other. Similarly, dull mutants 2077, 2078 and 2120 have allelic genes. Dull mutants 2035, EM12, EM47, and EM98 are non-allelic to the above loci. Dull genes in EM12, EM15, and EM98 were designated earlier as du-1, du-2 and du-4, respectively.The mutant genes were transferred to indica background by two backcrosses to IR36. Some of the mutant genes were located to respective chromosomes through trisomic analysis using primary trisomics of IR36. In this way the amylose extender gene ae was located to chromosome 2, the flo-1 was located to chromosome 5 and the flo-2 to chromosome 4. Dull genes of EM47, 2120, and 2035 were assigned to chromosomes 6, 9, and 6, respectively.	FLO2
A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality	2010	Plant Cell	Department of Biological Science and Technology, Tokyo University of Science, Noda, Japan.	Rice (Oryza sativa) endosperm accumulates a massive amount of storage starch and storage proteins during seed development. However, little is known about the regulatory system involved in the production of storage substances. The rice flo2 mutation resulted in reduced grain size and starch quality. Map-based cloning identified FLOURY ENDOSPERM2 (FLO2), a member of a novel gene family conserved in plants, as the gene responsible for the rice flo2 mutation. FLO2 harbors a tetratricopeptide repeat motif, considered to mediate a protein-protein interactions. FLO2 was abundantly expressed in developing seeds coincident with production of storage starch and protein, as well as in leaves, while abundant expression of its homologs was observed only in leaves. The flo2 mutation decreased expression of genes involved in production of storage starch and storage proteins in the endosperm. Differences between cultivars in their responsiveness of FLO2 expression during high-temperature stress indicated that FLO2 may be involved in heat tolerance during seed development. Overexpression of FLO2 enlarged the size of grains significantly. These results suggest that FLO2 plays a pivotal regulatory role in rice grain size and starch quality by affecting storage substance accumulation in the endosperm.	FLO2
FLOURY ENDOSPERM6 encodes a CBM48 domain-containing protein involved in compound granule formation and starch synthesis in rice endosperm	2014	Plant J	State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, China.	Starch is the most widespread form of energy storage in the plant kingdom. Although many enzymes and related factors have been identified for starch biosynthesis, unknown players remain to be identified, given that it is a complicated and sophisticated process. The endosperm of rice (Oryza sativa) has been used for the study of starch synthesis. Here, we report the cloning and characterization of the FLOURY ENDOSPERM6 (FLO6) gene in rice. In the flo6 mutant, the starch content is decreased and the normal physicochemical features of starch are changed. Significantly, flo6 mutant endosperm cells show obvious defects in compound granule formation. Map-based cloning showed that FLO6 encodes a protein of unknown function. It harbors an N-terminal transit peptide that ensures its correct localization and functions in the plastid, and a C-terminal carbohydrate-binding module 48 (CBM48) domain that binds to starch. Furthermore, FLO6 can interact with isoamylase1 (ISA1) both in vitro and in vivo, whereas ISA1 does not bind to starch directly. We thus propose that FLO6 may act as a starch-binding protein involved in starch synthesis and compound granule formation through a direct interaction with ISA1 in developing rice seeds. Our data provide a novel insight into the role of proteins with the CBM48 domain in plant species.	FLO6
The rice FON1 gene controls vegetative and reproductive development by regulating shoot apical meristem size	2006	Mol Cells	National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea.	Most plant organs develop from meristems. Rice FON1, which is an ortholog of Clv1, regulates stem cell proliferation and organ initiation. The point muta-tions, fon1-1 and fon1-2, disrupt meristem balance, resulting in alteration of floral organ numbers and the architecture of primary rachis branches. In this study, we identified two knockout alleles, fon1-3 and fon1-4, generated by T-DNA and Tos17 insertion, respectively. Unlike the previously isolated point mutants, the null mutants have alterations not only of the reproductive organs but also of vegetative tissues, producing fewer tillers and secondary rachis branches. The mutant plants are semi-dwarfs due to delayed leaf emergence, and leaf senescence is delayed. SEM analysis showed that the shoot apical meristems of fon1-3 mutants are enlarged. These results indicate that FON1 controls vegetative as well as reproductive development by regulating meristem size.	FON1
The gene FLORAL ORGAN NUMBER1 regulates floral meristem size in rice and encodes a leucine-rich repeat receptor kinase orthologous to Arabidopsis CLAVATA1	2004	Development	Graduate School of Agricultural and Life Sciences, University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.	The regulation of floral organ number is closely associated with floral meristem size. Mutations in the gene FLORAL ORGAN NUMBER1 (FON1) cause enlargement of the floral meristem in Oryza sativa (rice), resulting in an increase in the number of all floral organs. Ectopic floral organs develop in the whorl of each organ and/or in the additional whorls that form. Inner floral organs are more severely affected than outer floral organs. Many carpel primordia develop indeterminately, and undifferentiated meristematic tissues remain in the center in almost-mature flowers. Consistent with this result, OSH1, a molecular marker of meristematic indeterminate cells in rice, continues to be expressed in this region. Although floral meristems are strongly affected by the fon1-2 mutation, vegetative and inflorescence meristems are largely normal, even in this strong allele. We isolated the FON1 gene by positional cloning and found that it encodes a leucine-rich repeat receptor-like kinase most similar to CLAVATA1 (CLV1) in Arabidopsis thaliana. This suggests that a pathway similar to the CLV signaling system that regulates meristem maintenance in Arabidopsis is conserved in the grass family. Unlike CLV1, which is predominantly expressed in the L3 layer of the shoot meristem, FON1 is expressed throughout the whole floral meristem, suggesting that small modifications to the CLV signaling pathway may be required to maintain the floral meristem in rice. In addition, FON1 transcripts are detected in all meristems responsible for development of the aerial part of rice, suggesting that genes sharing functional redundancy with FON1 act in the vegetative and inflorescence meristems to mask the effects of the fon1 mutation.	FON1,OSH1|Oskn1
The floral organ number4 gene encoding a putative ortholog of Arabidopsis CLAVATA3 regulates apical meristem size in rice	2006	Plant Physiol	Shanghai Jiaotong University, Shanghai Institutes for Biological Sciences, Shanghai, China.	To understand the molecular mechanism regulating meristem development in the monocot rice (Oryza sativa), we describe here the isolation and characterization of three floral organ number4 (fon4) alleles and the cloning of the FON4 gene. The fon4 mutants showed abnormal enlargement of the embryonic and vegetative shoot apical meristems (SAMs) and the inflorescence and floral meristems. Likely due to enlarged SAMs, fon4 mutants produced thick culms (stems) and increased numbers of both primary rachis branches and floral organs. We identified FON4 using a map-based cloning approach and found it encodes a small putatively secreted protein, which is the putative ortholog of the Arabidopsis (Arabidopsis thaliana) CLAVATA3 (CLV3) gene. FON4 transcripts mainly accumulated in the small group of cells at the apex of the SAMs, whereas the rice ortholog of CLV1 (FON1) is expressed throughout the SAMs, suggesting that the putative FON4 ligand might be sequestered as a possible mechanism for rice meristem regulation. Exogenous application of the peptides FON4p and CLV3p corresponding to the CLV3/ESR-related (CLE) motifs of FON4 and CLV3, respectively, resulted in termination of SAMs in rice, and treatment with CLV3p caused consumption of both rice and Arabidopsis root meristems, suggesting that the CLV pathway in limiting meristem size is conserved in both rice and Arabidopsis. However, exogenous FON4p did not have an obvious effect on limiting both rice and Arabidopsis root meristems, suggesting that the CLE motifs of Arabidopsis CLV3 and FON4 are potentially functionally divergent.	FON1,FON2|FON4
FON2 SPARE1 redundantly regulates floral meristem maintenance with FLORAL ORGAN NUMBER2 in rice	2009	PLoS Genet	Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan.	CLAVATA signaling restricts stem cell identity in the shoot apical meristem (SAM) in Arabidopsis thaliana. In rice (Oryza sativa), FLORAL ORGAN NUMBER2 (FON2), closely related to CLV3, is involved as a signaling molecule in a similar pathway to negatively regulate stem cell proliferation in the floral meristem (FM). Here we show that the FON2 SPARE1 (FOS1) gene encoding a CLE protein functions along with FON2 in maintenance of the FM. In addition, FOS1 appears to be involved in maintenance of the SAM in the vegetative phase, because constitutive expression of FOS1 caused termination of the vegetative SAM. Genetic analysis revealed that FOS1 does not need FON1, the putative receptor of FON2, for its action, suggesting that FOS1 and FON2 may function in meristem maintenance as signaling molecules in independent pathways. Initially, we identified FOS1 as a suppressor that originates from O. sativa indica and suppresses the fon2 mutation in O. sativa japonica. FOS1 function in japonica appears to be compromised by a functional nucleotide polymorphism (FNP) at the putative processing site of the signal peptide. Sequence comparison of FOS1 in about 150 domesticated rice and wild rice species indicates that this FNP is present only in japonica, suggesting that redundant regulation by FOS1 and FON2 is commonplace in species in the Oryza genus. Distribution of the FNP also suggests that this mutation may have occurred during the divergence of japonica from its wild ancestor. Stem cell maintenance may be regulated by at least three negative pathways in rice, and each pathway may contribute differently to this regulation depending on the type of the meristem. This situation contrasts with that in Arabidopsis, where CLV signaling is the major single pathway in all meristems.	FON2|FON4,FOS1
Conservation and diversification of meristem maintenance mechanism in Oryza sativa: Function of the FLORAL ORGAN NUMBER2 gene	2006	Plant Cell Physiol	Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, 113-0033 Japan.	To elucidate the genetic mechanism that regulates meristem maintenance in monocots, here we have examined the function of the gene FLORAL ORGAN NUMBER2 (FON2) in Oryza sativa (rice). Mutations in FON2 cause enlargement of the floral meristem, resulting in an increase in the number of floral organs, although the vegetative and inflorescence meristems are largely normal. Molecular cloning reveals that FON2 encodes a small secreted protein, containing a CLE domain, that is closely related to CLAVATA3 in Arabidopsis thaliana. FON2 transcripts are localized at the apical region in all meristems in the aerial parts of rice plants, showing an expression pattern similar to that of Arabidopsis CLV3. Constitutive expression of FON2 causes a reduction in the number of floral organs and flowers, suggesting that both the flower and inflorescence meristems are reduced in size. This action of FON2 requires the function of FON1, an ortholog of CLV1. Constitutive expression of FON2 also causes premature termination of the shoot apical meristem in Arabidopsis, a phenotype similar to that caused by constitutive expression of CLV3. Together with our previous study of FON1, these results clearly indicate that the FON1-FON2 system in rice corresponds to the CLV signaling system in Arabidopsis and suggest that the negative regulation of stem cell identity by these systems may be principally conserved in a wide range of plants within the Angiosperms. In addition, we propose a model of the genetic regulation of meristem maintenance in rice that includes an alternative pathway independent of FON2-FON1.	FON2|FON4
The rice flattened shoot meristem, encoding CAF-1 p150 subunit, is required for meristem maintenance by regulating the cell-cycle period	2008	Dev Biol	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.	We isolated flattened shoot meristem (fsm) mutants in rice that showed defective seedling growth and died in the vegetative phase. Since most fsm plants had flat and small shoot apical meristems (SAMs), we suggest that FSM is required for proper SAM maintenance. FSM encodes a putative ortholog of Arabidopsis FASCIATA1 (FAS1) that corresponds to the p150 subunit of chromatin assembly factor-1 (CAF-1). FSM is expressed patchily in tissues with actively dividing cells, suggesting a tight association of FSM with specific cell-cycle phases. Double-target in situ hybridization counterstained with cell-cycle marker genes revealed that FSM is expressed mainly in the G(1) phase. In fsm, expressions of the two marker genes representing S- and G(2)- to M-phases were enhanced in SAM, despite a reduced number of cells in SAM, suggesting that S- and G(2)-phases are prolonged in fsm. In addition, developmental events in fsm leaves took place at the proper time, indicating that the temporal regulation of development occurs independently of the cell-cycle period. In contrast to the fasciated phenotype of Arabidopsis fas1, fsm showed size reduction of SAM. The opposite phenotypes between fsm and fas1 indicate that the SAM maintenance is regulated differently between rice and Arabidopsis.	FSM|CAF-1
A novel frameshift mutant allele, fzp-10, affecting the panicle architecture of rice	2011	Euphytica	Faculty of Biology-Oriented Science and Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan	The rice FRIZZY PANICLE (FZP) locus on chromosome 7, in which an ERF and acidic domain are present, is concerned with the regulation of spikelet meristem identity and the determination of panicle architecture. Many fzp mutants drastically alter panicle morphology with higher-order rachis-branches developing successively instead of the development of floral organs in these mutants. A new mutant showing the same fzp phenotype was induced by γ-ray irradiation of seeds of a rice cultivar “Gimbozu”. Examination of this fzp-like mutant for its allelism to a known allele of fzp-1, nucleotide sequence, and panicle and agronomic characteristics clearly indicated that the allele of this fzp-like mutant is located in FZP. Because there is a previously identified allele called fzp-9, we designated this new allele as fzp-10. fzp-10 has a single nucleotide (cytosine) deletion between the ERF domain and the acidic domain, which results in a frameshift mutation and a premature stop codon, thereby altering the C-terminus of the encoded protein. The degree of higher-order branching in the panicles was significantly reduced in the fzp-10 mutant compared with that of fzp-1. Moreover, the fzp-10 mutant showed highly depressed culm and panicle lengths and panicle number, as well as delayed heading dates compared with its wild type and also with fzp-1. fzp-10 has several new characteristics, its altered nucleotide position and severity of phenotype alteration, and, therefore, could be a new gene resource to examine the function of FZP and the determination of rice panicle architecture.	FZP|BFL1
Ds tagging of BRANCHED FLORETLESS 1 (BFL1) that mediates the transition from spikelet to floret meristem in rice (Oryza sativa L)	2003	BMC Plant Biol	CSIRO Plant Industry, GPO Box 1600, Canberra, ACT 2601, Australia. qianhao.zhu@csiro.au	BACKGROUND: The genetics of spikelet formation, a feature unique to grasses such as rice and maize, is yet to be fully understood, although a number of meristem and organ identity mutants have been isolated and investigated in Arabidopsis and maize. Using a two-element Ac/Ds transposon tagging system we have isolated a rice mutant, designated branched floretless 1 (bfl1) which is defective in the transition from spikelet meristem to floret meristem. RESULTS: The bfl1 mutant shows normal differentiation of the primary rachis-branches leading to initial spikelet meristem (bract-like structure equivalent to rudimentary glumes) formation but fails to develop empty glumes and florets. Instead, axillary meristems in the bract-like structure produce sequential alternate branching, thus resulting in a coral shaped morphology of the branches in the developing panicle. The bfl1 mutant harbours a single Ds insertion in the upstream region of the BFL1 gene on chromosome 7 corresponding to PAC clone P0625E02 (GenBank Acc No. message URL http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uid s=34395191&dopt=GenBank&term=ap004570AP004570). RT-PCR analyses revealed a drastic reduction of BFL1 transcript levels in the bfl1 mutant compared to that in the wild-type. In each of the normal panicle-bearing progeny plants, from occasional revertant seeds of the vegetatively-propagated mutant plant, Ds was shown to be excised from the bfl1 locus. BFL1 contains an EREBP/AP2 domain and is most likely an ortholog of the maize transcription factor gene BRANCHED SILKLESS1 (BD1). CONCLUSIONS: bfl1 is a Ds-tagged rice mutant defective in the transition from spikelet meristem (SM) to floret meristem (FM). BFL1 is most probably a rice ortholog of the maize ERF (EREBP/AP2) transcription factor gene BD1. Based on the similarities in mutant phenotypes bfl1 is likely to be an allele of the previously reported frizzy panicle locus.	FZP|BFL1
FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets	2003	Development	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.	Inflorescences of grass species have a distinct morphology in which florets are grouped in compact branches called spikelets. Although many studies have shown that the molecular and genetic mechanisms that control floret organ formation are conserved between monocots and dicots, little is known about the genetic pathway leading to spikelet formation. In the frizzy panicle (fzp) mutant of rice, the formation of florets is replaced by sequential rounds of branching. Detailed analyses revealed that several rudimentary glumes are formed in each ectopic branch, indicating that meristems acquire spikelet identity. However, instead of proceeding to floret formation, axillary meristems are formed in the axils of rudimentary glumes and they either arrest or develop into branches of higher order. The fzp mutant phenotype suggests that FZP is required to prevent the formation of axillary meristems within the spikelet meristem and permit the subsequent establishment of floral meristem identity. The FZP gene was isolated by transposon tagging. FZP encodes an ERF transcription factor and is the rice ortholog of the maize BD1 gene. Consistent with observations from phenotypic analyses, FZP expression was found to be restricted to the time of rudimentary glumes differentiation in a half-ring domain at the base of which the rudimentary glume primordium emerged.	FZP|BFL1
Two AP2 family genes, supernumerary bract (SNB) and Osindeterminate spikelet 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice	2012	Plant J	Department of Plant Molecular Systems Biotechnology, Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea.	Meristem identity is crucial in determining the inflorescence architecture of grass species. We previously reported that SUPERNUMERARY BRACT (SNB) regulates the transition of spikelet meristems into floral meristems in rice (Oryza sativa). Here we demonstrated that SNB and Oryza sativa INDETERMINATE SPIKELET 1 (OsIDS1) together play important roles in inflorescence architecture and the establishment of floral meristems. In snb osids1 double mutants, the numbers of branches and spikelets within a panicle are significantly decreased, and the transition to a floral meristem is further delayed compared with the snb single mutant. Expression analyses showed that SNB and OsIDS1 are required for spatio-temporal expression of B- and E-function floral organ identity genes in the lodicules. In addition, the AP2 family genes are important for determining the degree of ramification in branch meristems, regulating the spatio-temporal expression of spikelet meristem genes, such as FRIZZY PANICLE (FZP). Furthermore, overexpression of microRNA172 (miR172) causes reductions in SNB and OsIDS1 transcript levels, and phenotypes of the transgenic plants are more severe than for snb osids1. This indicates that additional gene(s) participate in the development of branch and floral meristems. Preferential expression of mature miR172s in the area around the spikelet meristems implies that depletion of the AP2 family genes in those meristems via miR172 is an important step in controlling inflorescence branching and the formation of floral organs.	FZP|BFL1,OsIDS1,SNB
Morphological and molecular characterization of a new frizzy panicle mutant, "fzp-9(t)", in rice (Oryza sativa L.)	2005	Hereditas	Yeongnam Agricultural Research Institute, NICS, RDA, Milyang, Korea.	The spikelet identity gene "fzp'' (frizzy panicle) is required for transformation of the floral meristems to inflorescent shoots. In fzp mutants, spikelets are replaced by branches and spikelet meristems produce massive numbers of branch meristems. We have isolated and characterized a new fzp mutant derived from anther culture lines in rice and designated as fzp-9 (t). The fzp-9 (t) mutant showed retarded growth habit and developed fewer tillers than those of the wild- type plant. The primary and secondary rachis branches of fzp-9 (t) appeared to be normal, but higher-order branches formed continuous bract- like structures without developing spikelets. The genetic segregation of fzp-9 (t) showed a good fit to the expected ratio of 3:1. The sequence analysis of fzp-9(t) revealed that there is a single nucleotide base change upstream of the ERF (ethylene-responsive element-binding factor) domain compare to wild-type plant. The mutation point of fzp-9 (t) (W66G) was one of the six amino acids of the ERF domain that contributed to GCC box-specific binding. The premature formation of a stop codon at the beginning of the ERF domain might cause a non-functional product.	FZP|BFL1
The homeotic gene long sterile lemma (G1) specifies sterile lemma identity in the rice spikelet	2009	Proc Natl Acad Sci U S A	Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo 113-8654, Japan.	The mechanism of floral organ specification is principally conserved in angiosperms, as demonstrated by the ABC model. By contrast, mechanisms that regulate the development of organs or structures specific to a group of species remain unclear. Grasses have unique inflorescence units, comprising spikelets and florets. In the genus Oryza (rice), the single spikelet consists of a fertile floret subtended by a lemma and a palea, two sterile lemmas, and rudimentary glumes. Each sterile lemma is a tiny glume-like organ with a smooth surface. Here, we have examined a long sterile lemma1 (g1) mutant, in which the sterile lemma is enlarged like the lemma. Detailed phenotypic analysis reveals that the large sterile lemma in the g1 mutant appears to be caused by homeotic transformation of the sterile lemma into a lemma, suggesting that G1 is involved in the repression of lemma identity to specify the sterile lemma. Gene isolation reveals that G1 is a member of a plant-specific gene family that encodes proteins with a previously uncharacterized domain, named here ALOG (Arabidopsis LSH1 and Oryza G1). G1 mRNA is expressed in sterile lemma primordia throughout their development, and G1 protein is localized in the nucleus. A trans-activation assay using the yeast GAL4 system suggests that G1 is involved in transcriptional regulation. Repression of lemma identity by G1 is consistent with a hypothesis proposed to explain the morphological evolution of rice spikelets. We also show that a wild rice species, Oryza grandiglumis, that forms large sterile lemmas has serious mutations in the G1 gene.	G1
Molecular cloning of plant transcripts encoding protein kinase homologs	1989	Proc Natl Acad Sci U S A	Plant Biology Laboratory, Salk Institute for Biological Studies, San Diego, CA 92138-9216.	Oligonucleotides, corresponding to conserved regions of animal protein-serine/threonine kinases, were used to isolate cDNAs encoding plant homologs in the dicot bean (Phaseolus vulgaris L.) and the monocot rice (Oryzae sativa L.). The C-terminal regions of the deduced polypeptides encoded by the bean (PVPK-1) and rice (G11A) cDNAs, prepared from mRNAs of suspension cultures and leaves, respectively, contain features characteristic of the catalytic domains of eukaryotic protein-serine/threonine kinases, indicating that these cDNAs encode plant protein kinases. The putative catalytic domains are most closely related to cyclic nucleotide-dependent protein kinases and the protein kinase C family, suggesting the plant homologs may likewise transduce extracellular signals. However, outside these domains, PVPK-1 and G11A exhibit no homology either to each other or to regulatory domains of other protein kinases, indicating the plant homologs are modulated by other signals. PVPK-1 corresponds to a 2.4-kb transcript in suspension cultured bean cells. Southern blots of genomic DNA indicate that PVPK-1 and G11A correspond to single copy genes that form part of a family of related plant sequences.	G11A
Overexpression of a type-A response regulator alters rice morphology and cytokinin metabolism	2007	Plant Cell Physiol	RIKEN Plant Science Center, 1-7-22, Suehiro, Tsurumi, Yokohama, 230-0045, Japan.	Genome-wide analyses of rice (Oryza sativa L.) cytokinin (CK)-responsive genes using the Affymetrix GeneChip(R) rice genome array were conducted to define the spectrum of genes subject to regulation by CK in monocotyledonous plants. Application of trans-zeatin modulated the expression of a wide variety of genes including those involved in hormone signaling and metabolism, transcriptional regulation, macronutrient transport and protein synthesis. To understand further the function of CK in rice plants, we examined the effects of in planta manipulation of a putative CK signaling factor on morphology, CK metabolism and expression of CK-responsive genes. Overexpression of the CK-inducible type-A response regulator OsRR6 abolished shoot regeneration, suggesting that OsRR6 acts as a negative regulator of CK signaling. Transgenic lines overexpressing OsRR6 (OsRR6-ox) had dwarf phenotypes with poorly developed root systems and panicles. Increased content of trans-zeatin-type CKs in OsRR6-ox lines indicates that homeostatic control of CK levels is regulated by OsRR6 signaling. Expression of genes encoding CK oxidase/dehydrogenase decreased in OsRR6-ox plants, possibly accounting for elevated CK levels in transgenic lines. Expression of a number of stress response genes was also altered in OsRR6-ox plants.	GA20OX4,GA2OX3,OsRR3,OsRR5,OsRR6,OsTMK
Cryptochrome and phytochrome cooperatively but independently reduce active gibberellin content in rice seedlings under light irradiation	2012	Plant Cell Physiol	Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan. fumih@affrc.go.jp	In contrast to a wealth of knowledge about the photoregulation of gibberellin metabolism in dicots, that in monocots remains largely unclear. In this study, we found that a blue light signal triggers reduction of active gibberellin content in rice seedlings with simultaneous repression of two gibberellin 20-oxidase genes (OsGA20ox2 and OsGA20ox4) and acute induction of four gibberellin 2-oxidase genes (OsGA2ox4-OsGA2ox7). For further examination of the regulation of these genes, we established a series of cryptochrome-deficient lines through reverse genetic screening from a Tos17 mutant population and construction of knockdown lines based on an RNA interference technique. By using these lines and phytochrome mutants, we elucidated that cryptochrome 1 (cry1), consisting of two species in rice plants (cry1a and cry1b), is indispensable for robust induction of the GA2ox genes. On the other hand, repression of the GA20ox genes is mediated by phytochromes. In addition, we found that the phytochromes also mediate the repression of a gibberellin 3-oxidase gene (OsGA3ox2) in the light. These results imply that, in rice seedlings, phytochromes mediate the repression of gibberellin biosynthesis capacity, while cry1 mediates the induction of gibberellin inactivation capacity. The cry1 action was demonstrated to be dominant in the reduction of active gibberellin content, but, in rice seedlings, the cumulative effects of these independent actions reduced active gibberellin content in the light. This pathway design in which different types of photoreceptors independently but cooperatively regulate active gibberellin content is unique from the viewpoint of dicot research. This redundancy should provide robustness to the response in rice plants.	GA20OX4,GA2OX3,OsCRY1a,OsCRY1b,OsCRY2|CRY2,PHYA,PHYB|OsphyB,PHYC
Differences and similarities in the photoregulation of gibberellin metabolism between rice and dicots	2013	Plant Signal Behav	Functional Plant Research Unit; National Institute of Agrobiological Sciences; Tsukuba, Ibaraki Japan.	In rice seedlings, elongation of leaf sheaths is suppressed by light stimuli. The response is mediated by two classes of photoreceptors, phytochromes and cryptochromes. However, it remains unclear how these photoreceptors interact in the process. Our recent study using phytochrome mutants and novel cryptochrome RNAi lines revealed that cryptochromes and phytochromes function cooperatively, but independently to reduce active GA contents in seedlings in visible light. Blue light captured by cryptochrome 1 (cry1a and cry1b) induces robust expression of GA 2-oxidase genes (OsGA2ox4-7). In parallel, phytochrome B with auxiliary action of phytochrome A mediates repression of GA 20-oxidase genes (OsGA20ox2 and OsGA20ox4). The independent effects cumulatively reduce active GA contents, leading to a suppression of leaf sheath elongation. These regulatory mechanisms are distinct from phytochrome B function in dicots. We discuss reasons why the distinct system appeared in rice, and advantages of the rice system in early photomorphogenesis.	GA20OX4,OsCRY2|CRY2
An overview of gibberellin metabolism enzyme genes and their related mutants in rice	2004	Plant Physiol	Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188-0002, Japan.	To enhance our understanding of GA metabolism in rice (Oryza sativa), we intensively screened and identified 29 candidate genes encoding the following GA metabolic enzymes using all available rice DNA databases: ent-copalyl diphosphate synthase (CPS), ent-kaurene synthase (KS), ent-kaurene oxidase (KO), ent-kaurenoic acid oxidase (KAO), GA 20-oxidase (GA20ox), GA 3-oxidase (GA3ox), and GA 2-oxidase (GA2ox). In contrast to the Arabidopsis genome, multiple CPS-like, KS-like, and KO-like genes were identified in the rice genome, most of which are contiguously arranged. We also identified 18 GA-deficient rice mutants at six different loci from rice mutant collections. Based on the mutant and expression analyses, we demonstrated that the enzymes catalyzing the early steps in the GA biosynthetic pathway (i.e. CPS, KS, KO, and KAO) are mainly encoded by single genes, while those for later steps (i.e. GA20ox, GA3ox, and GA2ox) are encoded by gene families. The remaining CPS-like, KS-like, and KO-like genes were likely to be involved in the biosynthesis of diterpene phytoalexins rather than GAs because the expression of two CPS-like and three KS-like genes (OsCPS2, OsCPS4, OsKS4, OsKS7, and OsKS8) were increased by UV irradiation, and four of these genes (OsCPS2, OsCPS4, OsKS4, and OsKS7) were also induced by an elicitor treatment.	GA20OX4,GA2OX3,KAO,KS2,OsKS1,OsCPS3
Global gene profiling of laser-captured pollen mother cells indicates molecular pathways and gene subfamilies involved in rice meiosis	2010	Plant Physiol	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	Pollen mother cells (PMCs) represent a critical early stage in plant sexual reproduction in which the stage is set for male gamete formation. Understanding the global molecular genetics of this early meiotic stage has so far been limited to whole stamen or floret transcriptome studies, but since PMCs are a discrete population of cells in developmental synchrony, they provide the potential for precise transcriptome analysis and for enhancing our understanding of the transition to meiosis. As a step toward identifying the premeiotic transcriptome, we performed microarray analysis on a homogenous population of rice (Oryza sativa) PMCs isolated by laser microdissection and compared them with those of tricellular pollen and seedling. Known meiotic genes, including OsSPO11-1, PAIR1, PAIR2, PAIR3, OsDMC1, OsMEL1, OsRAD21-4, OsSDS, and ZEP1, all showed preferential expression in PMCs. The Kyoto Encyclopedia of Genes and Genomes pathways significantly enriched in PMC-preferential genes are DNA replication and repair pathways. Our genome-wide survey showed that, in the buildup to meiosis, PMCs accumulate the molecular machinery for meiosis at the mRNA level. We identified 1,158 PMC-preferential genes and suggested candidate genes and pathways involved in meiotic recombination and meiotic cell cycle control. Regarding the developmental context for meiosis, the DEF-like, AGL2-like, and AGL6-like subclades of MADS box transcription factors are PMC-preferentially expressed, the trans-zeatin type of cytokinin might be preferentially synthesized, and the gibberellin signaling pathway is likely active in PMCs. The ubiquitin-mediated proteolysis pathway is enriched in the 127 genes that are expressed in PMCs but not in tricellular pollen or seedling.	GA20OX4,GA2OX3,KAO
The rice R2R3-MYB transcription factor OsMYB55 is involved in the tolerance to high temperature and modulates amino acid metabolism	2012	PLoS One	Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada.	Temperatures higher than the optimum negatively affects plant growth and development. Tolerance to high temperature is a complex process that involves several pathways. Understanding this process, especially in crops such as rice, is essential to prepare for predicted climate changes due to global warming. Here, we show that OsMYB55 is induced by high temperature and overexpression of OsMYB55 resulted in improved plant growth under high temperature and decreased the negative effect of high temperature on grain yield. Transcriptome analysis revealed an increase in expression of several genes involved in amino acids metabolism. We demonstrate that OsMYB55 binds to the promoter regions of target genes and directly activates expression of some of those genes including glutamine synthetase (OsGS1;2) glutamine amidotransferase (GAT1) and glutamate decarboxylase 3 (GAD3). OsMYB55 overexpression resulted in an increase in total amino acid content and of the individual amino acids produced by the activation of the above mentioned genes and known for their roles in stress tolerance, namely L-glutamic acid, GABA and arginine especially under high temperature condition. In conclusion, overexpression of OsMYB55 improves rice plant tolerance to high temperature, and this high tolerance is associated with enhanced amino acid metabolism through transcription activation.	GAD3,GAT1,GLN1;2|GS1;2,OsMYB55
GIANT EMBRYO encodes CYP78A13, required for proper size balance between embryo and endosperm in rice	2013	Plant J	DuPont Agricultural Biotechnology, Experimental Station E353, PO Box 80353, Wilmington, DE 19880, USA.	Among angiosperms there is a high degree of variation in embryo/endosperm size in mature seeds. However, little is known about the molecular mechanism underlying size control between these neighboring tissues. Here we report the rice GIANT EMBRYO (GE) gene that is essential for controlling the size balance. The function of GE in each tissue is distinct, controlling cell size in the embryo and cell death in the endosperm. GE, which encodes CYP78A13, is predominantly expressed in the interfacing tissues of the both embryo and endosperm. GE expression is under negative feedback regulation; endogenous GE expression is upregulated in ge mutants. In contrast to the loss-of-function mutant with large embryo and small endosperm, GE overexpression causes a small embryo and enlarged endosperm. A complementation analysis coupled with heterofertilization showed that complementation of ge mutation in either embryo or endosperm failed to restore the wild-type embryo/endosperm ratio. Thus, embryo and endosperm interact in determining embryo/endosperm size balance. Among genes associated with embryo/endosperm size, REDUCED EMBRYO genes, whose loss-of-function causes a phenotype opposite to ge, are revealed to regulate endosperm size upstream of GE. To fully understand the embryo-endosperm size control, the genetic network of the related genes should be elucidated.	GE|CYP78A13
Control of rice embryo development, shoot apical meristem maintenance, and grain yield by a novel cytochrome p450	2013	Mol Plant	National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research (Shanghai), Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	Angiosperm seeds usually consist of two major parts: the embryo and the endosperm. However, the molecular mechanism(s) underlying embryo and endosperm development remains largely unknown, particularly in rice, the model cereal. Here, we report the identification and functional characterization of the rice GIANT EMBRYO (GE) gene. Mutation of GE resulted in a large embryo in the seed, which was caused by excessive expansion of scutellum cells. Post-embryonic growth of ge seedling was severely inhibited due to defective shoot apical meristem (SAM) maintenance. Map-based cloning revealed that GE encodes a CYP78A subfamily P450 monooxygenase that is localized to the endoplasmic reticulum. GE is expressed predominantly in the scutellar epithelium, the interface region between embryo and endosperm. Overexpression of GE promoted cell proliferation and enhanced rice plant growth and grain yield, but reduced embryo size, suggesting that GE is critical for coordinating rice embryo and endosperm development. Moreover, transgenic Arabidopsis plants overexpressing AtCYP78A10, a GE homolog, also produced bigger seeds, implying a conserved role for the CYP78A subfamily of P450s in regulating seed development. Taken together, our results indicate that GE plays critical roles in regulating embryo development and SAM maintenance.	GE|CYP78A13
The rice 14-3-3 gene family and its involvement in responses to biotic and abiotic stress	2006	DNA Res	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences 300 Fenglin Road, Shanghai 200032, China.	14-3-3 proteins function as major regulators of primary metabolism and cellular signal transduction in plants. However, their involvement in plant defense and stress responses is largely unknown. In order to better address functions of the rice 14-3-3/GF14 proteins in defense and abiotic stress responses, we examined the rice GF14 family that comprises eight numbers. The phylogenetic comparison with the Arabidopsis 14-3-3 family revealed that the majority of rice GF14s might have evolved as an independent branch. At least four rice GF14 genes, GF14b, GF14c, GF14e and Gf14f were differentially regulated in the interactions of rice-Magnaporthe grisea and rice-Xanthomonas oryzae pv. oryzae, and the incompatible interactions stronger induced the genes than the compatible interactions. These GF14 genes were also induced by the defense compounds, benzothiadiazole, methyl jasmonate, ethephon and hydrogen peroxide. Similarly, they were differentially regulated by salinity, drought, wounding and abscisic acid. Tissue-specific analysis and expression of GF14-YFP fusions revealed that the four GF14 isoforms were expressed with tissue specificity and accumulated differentially in the cytoplasm and nucleus. Our current study provides fundamental information for the further investigation of the rice GF14 proteins.	GF14b,GF14c,GF14f,GF14e|GID2
14-3-3 proteins act as intracellular receptors for rice Hd3a florigen	2011	Nature	Laboratory of Plant Molecular Genetics, Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan.	'Florigen' was proposed 75 years ago to be synthesized in the leaf and transported to the shoot apex, where it induces flowering. Only recently have genetic and biochemical studies established that florigen is encoded by FLOWERING LOCUS T (FT), a gene that is universally conserved in higher plants. Nonetheless, the exact function of florigen during floral induction remains poorly understood and receptors for florigen have not been identified. Here we show that the rice FT homologue Hd3a interacts with 14-3-3 proteins in the apical cells of shoots, yielding a complex that translocates to the nucleus and binds to the Oryza sativa (Os)FD1 transcription factor, a rice homologue of Arabidopsis thaliana FD. The resultant ternary 'florigen activation complex' (FAC) induces transcription of OsMADS15, a homologue of A. thaliana APETALA1 (AP1), which leads to flowering. We have determined the 2.4 A crystal structure of rice FAC, which provides a mechanistic basis for florigen function in flowering. Our results indicate that 14-3-3 proteins act as intracellular receptors for florigen in shoot apical cells, and offer new approaches to manipulate flowering in various crops and trees.	GF14c,Hd3a,OsKANADI1|OsKANADI2,OsBIP116b
The 14-3-3 protein GF14c acts as a negative regulator of flowering in rice by interacting with the florigen Hd3a	2009	Plant Cell Physiol	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0101, Japan.	Hd3a and FT proteins have recently been proposed to act as florigens in rice and Arabidopsis, respectively; however, the molecular mechanisms of their function remain to be determined. In this study, we identified GF14c (a 14-3-3 protein) as an Hd3a-interacting protein in a yeast two-hybrid screen. In vitro and in vivo experiments, using a combination of pull-down assays and bimolecular fluorescence complementation, confirmed the interaction between Hd3a and GF14c. Functional analysis using either GF14c overexpression or knockout transgenic rice plants indicated that this interaction plays a role in the regulation of flowering. GF14c-overexpressing plants exhibited a delay in flowering and the knockout mutants displayed early flowering relative to the wild-type plants under short-day conditions. These results suggest that GF14c acts as a negative regulator of flowering by interacting with Hd3a. Since the 14-3-3 protein has been shown to interact with FT protein in tomato and Arabidopsis, our results in rice provide important findings about FT signaling in plants.	GF14c,Hd3a
Sugar starvation- and GA-inducible calcium-dependent protein kinase 1 feedback regulates GA biosynthesis and activates a 14-3-3 protein to confer drought tolerance in rice seedlings	2013	Plant Mol Biol	Department of Agronomy, National Chiayi University, Chiayi, 600, Taiwan, ROC. slho@mail.ncyu.edu.tw	Germination followed by seedling growth constitutes two essential steps in the initiation of a new life cycle in plants, and in cereals, completion of these steps is regulated by sugar starvation and the hormone gibberellin. A calcium-dependent protein kinase 1 gene (OsCDPK1) was identified by differential screening of a cDNA library derived from sucrose-starved rice suspension cells. The expression of OsCDPK1 was found to be specifically activated by sucrose starvation among several stress conditions tested as well as activated transiently during post-germination seedling growth. In gain- and loss-of-function studies performed with transgenic rice overexpressing a constitutively active or RNA interference gene knockdown construct, respectively, OsCDPK1 was found to negatively regulate the expression of enzymes essential for GA biosynthesis. In contrast, OsCDPK1 activated the expression of a 14-3-3 protein, GF14c. Overexpression of either constitutively active OsCDPK1 or GF14c enhanced drought tolerance in transgenic rice seedlings. Hence, our studies demonstrated that OsCDPK1 transduces the post-germination Ca(2+) signal derived from sugar starvation and GA, refines the endogenous GA concentration and prevents drought stress injury, all essential functions to seedling development at the beginning of the life cycle in rice.	GF14c,OsCDPK13|OsCDPK11|OsCPK11
A mutation in the rice chalcone isomerase gene causes the golden hull and internode 1 phenotype	2012	Planta	State Key Laboratory of Plant Genomics, Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, People's Republic of China.	The biosynthesis of flavonoids, important secondary plant metabolites, has been investigated extensively, but few mutants of genes in this pathway have been identified in rice (Oryza sativa). The rice gold hull and internode (gh) mutants exhibit a reddish-brown pigmentation in the hull and internode and their phenotype has long been used as a morphological marker trait for breeding and genetic study. Here, we characterized that the gh1 mutant was a mutant of the rice chalcone isomerase gene (OsCHI). The result showed that gh1 had a Dasheng retrotransposon inserted in the 5' UTR of the OsCHI gene, which resulted in the complete loss of OsCHI expression. gh1 exhibited golden pigmentation in hulls and internodes once the panicles were exposed to light. The total flavonoid content in gh1 hulls was increased threefold compared to wild type. Consistent with the gh1 phenotype, OsCHI transcripts were expressed in most tissues of rice and most abundantly in internodes. It was also expressed at high levels in panicles before heading, distributed mainly in lemmas and paleae, but its expression decreased substantially after the panicles emerged from the sheath. OsCHI encodes a protein functionally and structurally conserved to chalcone isomerases in other species. Our findings demonstrated that the OsCHI gene was indispensable for flux of the flavonoid pathway in rice.	gh1|OsCHI
Structure of the cinnamyl-alcohol dehydrogenase gene family in rice and promoter activity of a member associated with lignification	2005	Planta	Agricultural Research Service, Western Regional Research Center, United States Department of Agriculture, 800 Buchanan Street, Albany, CA 94710, USA. ctobias@pw.usda.gov	Analysis of lignification in rice has been facilitated by the availability of the recently completed rice genome sequence, and rice will serve as an important model for understanding the relationship of grass lignin composition to cell wall digestibility. Cinnamyl-alcohol dehydrogenase (CAD) is an enzyme important in lignin biosynthesis. The rice genome contains 12 distinct genes present at nine different loci that encode products with significant similarity to CAD. The rice gene family is diverse with respect to other angiosperm and gymnosperm CAD genes isolated to date and includes one member (OsCAD6) that contains a peroxisomal targeting signal and is substantially diverged relative to other family members. Four closely related family members (OsCAD8A-D) are present at the same locus and represent the product of a localized gene duplication and inversion. Promoter-reporter gene fusions to OsCAD2, an orthologue of the CAD gene present at the bm1 (brown midrib 1) locus of maize, reveal that in rice expression is associated with vascular tissue in aerial parts of the plant and is correlated with the onset of lignification. In root tissue, expression is primarily in the cortical parenchyma adjacent to the exodermis and in vascular tissue.	GH2|OsCAD2
GOLD HULL AND INTERNODE2 encodes a primarily multifunctional cinnamyl-alcohol dehydrogenase in rice	2006	Plant Physiol	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, People's Republic of China.	Lignin content and composition are two important agronomic traits for the utilization of agricultural residues. Rice (Oryza sativa) gold hull and internode phenotype is a classical morphological marker trait that has long been applied to breeding and genetics study. In this study, we have cloned the GOLD HULL AND INTERNODE2 (GH2) gene in rice using a map-based cloning approach. The result shows that the gh2 mutant is a lignin-deficient mutant, and GH2 encodes a cinnamyl-alcohol dehydrogenase (CAD). Consistent with this finding, extracts from roots, internodes, hulls, and panicles of the gh2 plants exhibited drastically reduced CAD activity and undetectable sinapyl alcohol dehydrogenase activity. When expressed in Escherichia coli, purified recombinant GH2 was found to exhibit strong catalytic ability toward coniferaldehyde and sinapaldehyde, while the mutant protein gh2 completely lost the corresponding CAD and sinapyl alcohol dehydrogenase activities. Further phenotypic analysis of the gh2 mutant plants revealed that the p-hydroxyphenyl, guaiacyl, and sinapyl monomers were reduced in almost the same ratio compared to the wild type. Our results suggest GH2 acts as a primarily multifunctional CAD to synthesize coniferyl and sinapyl alcohol precursors in rice lignin biosynthesis.	GH2|OsCAD2
Increased lodging resistance in long-culm, low-lignin gh2 rice for improved feed and bioenergy production	2014	Sci Rep	Institute of Agriculture, Graduate School, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183-8509, Japan.	Lignin modification has been a breeding target for the improvements of forage digestibility and energy yields in forage and bioenergy crops, but decreased lignin levels are often accompanied by reduced lodging resistance. The rice mutant gold hull and internode2 (gh2) has been identified to be lignin deficient. GH2 has been mapped to the short arm of chromosome 2 and encodes cinnamyl-alcohol dehydrogenase (CAD). We developed a long-culm variety, 'Leaf Star', with superior lodging resistance and a gh phenotype similar to one of its parents, 'Chugoku 117'. The gh loci in Leaf Star and Chugoku 117 were localized to the same region of chromosome 2 as the gh2 mutant. Leaf Star had culms with low lignin concentrations due to a natural mutation in OsCAD2 that was not present in Chugoku 117. However, this variety had high culm strength due to its strong, thick culms. Additionally, this variety had a thick layer of cortical fiber tissue with well-developed secondary cell walls. Our results suggest that rice can be improved for forage and bioenergy production by combining superior lodging resistance, which can be obtained by introducing thick and stiff culm traits, with low lignin concentrations, which can be obtained using the gh2 variety.	GH2|OsCAD2
A stress-induced rice (Oryza sativa L.) beta-glucosidase represents a new subfamily of glycosyl hydrolase family 5 containing a fascin-like domain	2007	Biochem J	School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.	GH5BG, the cDNA for a stress-induced GH5 (glycosyl hydrolase family 5) beta-glucosidase, was cloned from rice (Oryza sativa L.) seedlings. The GH5BG cDNA encodes a 510-amino-acid precursor protein that comprises 19 amino acids of prepeptide and 491 amino acids of mature protein. The protein was predicted to be extracellular. The mature protein is a member of a plant-specific subgroup of the GH5 exoglucanase subfamily that contains two major domains, a beta-1,3-exoglucanase-like domain and a fascin-like domain that is not commonly found in plant enzymes. The GH5BG mRNA is highly expressed in the shoot during germination and in leaf sheaths of mature plants. The GH5BG was up-regulated in response to salt stress, submergence stress, methyl jasmonate and abscisic acid in rice seedlings. A GUS (glucuronidase) reporter tagged at the C-terminus of GH5BG was found to be secreted to the apoplast when expressed in onion (Allium cepa) cells. A thioredoxin fusion protein produced from the GH5BG cDNA in Escherichia coli hydrolysed various pNP (p-nitrophenyl) glycosides, including beta-D-glucoside, alpha-L-arabinoside, beta-D-fucoside, beta-D-galactoside, beta-D-xyloside and beta-D-cellobioside, as well as beta-(1,4)-linked glucose oligosaccharides and beta-(1,3)-linked disaccharide (laminaribiose). The catalytic efficiency (kcat/K(m)) for hydrolysis of beta-(1,4)-linked oligosaccharides by the enzyme remained constant as the DP (degree of polymerization) increased from 3 to 5. This substrate specificity is significantly different from fungal GH5 exoglucanases, such as the exo-beta-(1,3)-glucanase of the yeast Candida albicans, which may correlate with a marked reduction in a loop that makes up the active-site wall in the Candida enzyme.	GH5BG
Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice	2013	Cell Res	None	None	Ghd7.1|Hd2|OsPRR37
Validation and characterization of Ghd7.1, a major quantitative trait locus with pleiotropic effects on spikelets per panicle, plant height, and heading date in rice (Oryza sativa L.)	2013	J Integr Plant Biol	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China.	A quantitative trait locus (QTL) that affects heading date (HD) and the number of spikelets per panicle (SPP) was previously identified in a small region on chromosome 7 in rice (Oryza sativa L.). In order to further characterize the QTL region, near isogenic lines (NILs) were quickly obtained by self-crossing recombinant inbred line 189, which is heterozygous in the vicinity of the target region. The pleiotropic effects of QTL Ghd7.1 on plant height (PH), SPP, and HD, were validated using an NIL-F2 population. Ghd7.1 explained 50.2%, 45.3%, and 76.9% of phenotypic variation in PH, SPP, and HD, respectively. Ghd7.1 was precisely mapped to a 357-kb region on the basis of analysis of the progeny of the NIL-F2 population. Day-length treatment confirmed that Ghd7.1 is sensitive to photoperiod, with long days delaying heading up to 12.5 d. Identification of panicle initiation and development for the pair of NILs showed that Ghd7.1 elongated the photoperiod-sensitive phase more than 10 d, but did not change the basic vegetative phase and the reproductive growth phase. These findings indicated that Ghd7.1 regulates SPP by controlling the rate of panicle differentiation rather than the duration of panicle development.	Ghd7.1|Hd2|OsPRR37
Natural variation in OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes	2013	Mol Plant	Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.	Heading date and photoperiod sensitivity are fundamental traits that determine rice adaptation to a wide range of geographic environments. By quantitative trait locus (QTL) mapping and candidate gene analysis using whole-genome re-sequencing, we found that Oryza sativa Pseudo-Response Regulator37 (OsPRR37; hereafter PRR37) is responsible for the Early heading7-2 (EH7-2)/Heading date2 (Hd2) QTL which was identified from a cross of late-heading rice 'Milyang23 (M23)' and early-heading rice 'H143'. H143 contains a missense mutation of an invariantly conserved amino acid in the CCT (CONSTANS, CO-like, and TOC1) domain of PRR37 protein. In the world rice collection, different types of nonfunctional PRR37 alleles were found in many European and Asian rice cultivars. Notably, the japonica varieties harboring nonfunctional alleles of both Ghd7/Hd4 and PRR37/Hd2 flower extremely early under natural long-day conditions, and are adapted to the northernmost regions of rice cultivation, up to 53 degrees N latitude. Genetic analysis revealed that the effects of PRR37 and Ghd7 alleles on heading date are additive, and PRR37 down-regulates Hd3a expression to suppress flowering under long-day conditions. Our results demonstrate that natural variations in PRR37/Hd2 and Ghd7/Hd4 have contributed to the expansion of rice cultivation to temperate and cooler regions.	Ghd7.1|Hd2|OsPRR37,Ghd7
Evolution and association analysis of Ghd7 in rice	2012	PLoS One	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan, China.	Plant height, heading date, and yield are the main targets for rice genetic improvement. Ghd7 is a pleiotropic gene that controls the aforementioned traits simultaneously. In this study, a rice germplasm collection of 104 accessions (Oryza sativa) and 3 wild rice varieties (O.rufipogon) was used to analyze the evolution and association of Ghd7 with plant height, heading date, and yield. Among the 104 accessions, 76 single nucleotide polymorphisms (SNPs) and six insertions and deletions were found within a 3932-bp DNA fragment of Ghd7. A higher pairwise pi and theta in the promoter indicated a highly diversified promoter of Ghd7. Sixteen haplotypes and 8 types of Ghd7 protein were detected. SNP changes between haplotypes indicated that Ghd7 evolved from two distinct ancestral gene pools, and independent domestication processes were detected in indica and japonica varietals respectively. In addition to the previously reported premature stop mutation in the first exon of Ghd7, which caused phenotypic changes of multiple traits, we found another functional C/T mutation (SNP S_555) by structure-based association analysis. SNP S_555 is located in the promoter and was related to plant height probably by altering gene expression. Moreover, another seven SNP mutations in complete linkage were found to be associated with the number of spikelets per panicle, regardless of the photoperiod. These associations provide the potential for flexibility of Ghd7 application in rice breeding programs.	Ghd7
Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice	2008	Nat Genet	National Key Laboratory of Crop Genetic Improvement, National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Yield potential, plant height and heading date are three classes of traits that determine the productivity of many crop plants. Here we show that the quantitative trait locus (QTL) Ghd7, isolated from an elite rice hybrid and encoding a CCT domain protein, has major effects on an array of traits in rice, including number of grains per panicle, plant height and heading date. Enhanced expression of Ghd7 under long-day conditions delays heading and increases plant height and panicle size. Natural mutants with reduced function enable rice to be cultivated in temperate and cooler regions. Thus, Ghd7 has played crucial roles for increasing productivity and adaptability of rice globally.	Ghd7
Natural variation in Hd17, a homolog of Arabidopsis ELF3 that is involved in rice photoperiodic flowering	2012	Plant Cell Physiol	National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.	Flowering time of rice depends strongly on photoperiodic responses. We previously identified a quantitative trait locus, Heading date 17 (Hd17), that is associated with a difference in flowering time between Japanese rice (Oryza sativa L.) cultivars. Here, we show that the difference may result from a single nucleotide polymorphism within a putative gene that encodes a homolog of the Arabidopsis EARLY FLOWERING 3 protein, which plays important roles in maintaining circadian rhythms. Our results demonstrate that natural variation in Hd17 may change the transcription level of a flowering repressor, Grain number, plant height and heading date 7 (Ghd7), suggesting that Hd17 is part of rice's photoperiodic flowering pathway.	Ghd7,Hd17|Ef7|OsELF3-1
Ghd7 is a central regulator for growth, development, adaptation and responses to biotic and abiotic stresses	2014	Plant physiology	National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University	Ghd7 has been regarded as an important regulator of heading date and yield potential in rice. In the study reported in this paper, we investigated new functions of Ghd7 in rice growth, development and environmental response. As a long-day dependent negative regulator of heading date, the degree of phenotypic effect of Ghd7 on heading date and yield traits is quantitatively related to the transcript level, and was also influenced by both environmental conditions and genetic backgrounds. Ghd7 regulates yield traits through modulating panicle branching independent of heading date. Ghd7 also regulates plasticity of tiller branching by mediating the PHYB-OsTB1 pathway as adaption to shade signal. The expression of Ghd7 was strongly repressed by ABA, JA and drought stress while enhanced by low temperature. Over-expression of Ghd7 increased drought sensitivity while knock-down of Ghd7 enhanced drought tolerance. Analysis of expression profiles using gene chip revealed that Ghd7 was involved in regulation of multiple processes, including flowering time, hormone metabolism, biotic and abiotic stresses. This study suggested that Ghd7 functions to link the dynamic environmental inputs with phase transition, architecture regulation and stress response to maximize the reproductive success of the rice plant.	Ghd7
Characterization of the molecular mechanism underlying gibberellin perception complex formation in rice	2010	Plant Cell	Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.	The DELLA protein SLENDER RICE1 (SLR1) is a repressor of gibberellin (GA) signaling in rice (Oryza sativa), and most of the GA-associated responses are induced upon SLR1 degradation. It is assumed that interaction between GIBBERELLIN INSENSITIVE DWARF1 (GID1) and the N-terminal DELLA/TVHYNP motif of SLR1 triggers F-box protein GID2-mediated SLR1 degradation. We identified a semidominant dwarf mutant, Slr1-d4, which contains a mutation in the region encoding the C-terminal GRAS domain of SLR1 (SLR1(G576V)). The GA-dependent degradation of SLR1(G576V) was reduced in Slr1-d4, and compared with SLR1, SLR1(G576V) showed reduced interaction with GID1 and almost none with GID2 when tested in yeast cells. Surface plasmon resonance of GID1-SLR1 and GID1-SLR1(G576V) interactions revealed that the GRAS domain of SLR1 functions to stabilize the GID1-SLR1 interaction by reducing its dissociation rate and that the G576V substitution in SLR1 diminishes this stability. These results suggest that the stable interaction of GID1-SLR1 through the GRAS domain is essential for the recognition of SLR1 by GID2. We propose that when the DELLA/TVHYNP motif of SLR1 binds with GID1, it enables the GRAS domain of SLR1 to interact with GID1 and that the stable GID1-SLR1 complex is efficiently recognized by GID2.	GF14e|GID2,GID1|OsGID1,SLR1|OsGAI
GID2, an F-box subunit of the SCF E3 complex, specifically interacts with phosphorylated SLR1 protein and regulates the gibberellin-dependent degradation of SLR1 in rice	2004	The Plant Journal	Bioscience and Biotechnology Center, Nagoya University, Chikusa, Nagoya 464-8601, Japan.	The phytohormone gibberellin (GA) controls growth and development in plants. Previously, we identified a rice F-box protein, gibberellin-insensitive dwarf2 (GID2), which is essential for GA-mediated DELLA protein degradation. In this study, we analyzed the biological and molecular biological properties of GID2. Expression of GID2 preferentially occurred in rice organs actively synthesizing GA. Domain analysis of GID2 revealed that the C-terminal regions were essential for the GID2 function, but not the N-terminal region. Yeast two-hybrid assay and immunoprecipitation experiments demonstrated that GID2 is a component of the SCF complex through an interaction with a rice ASK1 homolog, OsSkp15. Furthermore, an in vitro pull-down assay revealed that GID2 specifically interacted with the phosphorylated Slender Rice 1 (SLR1). Taken these results together, we conclude that the phosphorylated SLR1 is caught by the SCFGID2 complex through an interacting affinity between GID2 and phosphorylated SLR1, triggering the ubiquitin-mediated degradation of SLR1.	GF14e|GID2,SLR1|OsGAI
Rice 14-3-3 protein (GF14e) negatively affects cell death and disease resistance	2011	Plant J	Bioagricultural Sciences and Pest Management and Program in Plant Molecular Biology, Colorado State University, Fort Collins, CO 80523-1177, USA.	Plant 14-3-3 proteins regulate important cellular processes, including plant immune responses, through protein-protein interactions with a wide range of target proteins. In rice (Oryza sativa), the GF14e gene, which encodes a 14-3-3 protein, is induced during effector-triggered immunity (ETI) associated with pathogens such as Xanthomonas oryzae pv. oryzae (Xoo). To determine whether the GF14e gene plays a direct role in resistance to disease in rice, we suppressed its expression by RNAi silencing. GF14e suppression was correlated with the appearance of a lesion-mimic (LM) phenotype in the transgenic plants at 3 weeks after sowing. This indicates inappropriate regulation of cell death, a phenotype that is frequently associated with enhanced resistance to pathogens. GF14e-silenced rice plants showed high levels of resistance to a virulent strain of Xoo compared with plants that were not silenced. Enhanced resistance was correlated with GF14e silencing prior to and after development of the LM phenotype, higher basal expression of a defense response peroxidase gene (POX22.3), and accumulation of reactive oxygen species (ROS). In addition, GF14e-silenced plants also exhibit enhanced resistance to the necrotrophic fungal pathogen Rhizoctonia solani. Together, our findings suggest that GF14e negatively affects the induction of plant defense response genes, cell death and broad-spectrum resistance in rice.	GF14e|GID2
Release of the repressive activity of rice DELLA protein SLR1 by gibberellin does not require SLR1 degradation in the gid2 mutant	2008	Plant Cell	Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan. makoto@nuagr1.agr.nagoya-u.ac.jp	The rice (Oryza sativa) DELLA protein SLR1 acts as a repressor of gibberellin (GA) signaling. GA perception by GID1 causes SLR1 protein degradation involving the F-box protein GID2; this triggers GA-associated responses such as shoot elongation and seed germination. In GA-insensitive and GA biosynthesis mutants, SLENDER RICE1 (SLR1) accumulates to high levels, and the severity of dwarfism is usually correlated with the level of SLR1 accumulation. An exception is the GA-insensitive F-box mutant gid2, which shows milder dwarfism than mutants such as gid1 and cps even though it accumulates higher levels of SLR1. The level of SLR1 protein in gid2 was decreased by loss of GID1 function or treatment with a GA biosynthesis inhibitor, and dwarfism was enhanced. Conversely, overproduction of GID1 or treatment with GA(3) increased the SLR1 level in gid2 and reduced dwarfism. These results indicate that derepression of SLR1 repressive activity can be accomplished by GA and GID1 alone and does not require F-box (GID2) function. Evidence for GA signaling without GID2 was also provided by the expression behavior of GA-regulated genes such as GA-20oxidase1, GID1, and SLR1 in the gid2 mutant. Based on these observations, we propose a model for the release of GA suppression that does not require DELLA protein degradation.	GF14e|GID2,GID1|OsGID1,SLR1|OsGAI
Accumulation of Phosphorylated Repressor for Gibberellin Signaling in an F-box Mutant	2003	Science	BioScience Center, Nagoya University, Nagoya 464-8601, Japan.	Gibberellin (GA) regulates growth and development in plants. We isolated and characterized a rice GA-insensitive dwarf mutant, gid2. The GID2 gene encodes a putative F-box protein, which interacted with the rice Skp1 homolog in a yeast two-hybrid assay. In gid2, a repressor for GA signaling, SLR1, was highly accumulated in a phosphorylated form and GA increased its concentration, whereas SLR1 was rapidly degraded by GA through ubiquitination in the wild type. We conclude that GID2 is a positive regulator of GA signaling and that regulated degradation of SLR1 is initiated through GA-dependent phosphorylation and finalized by an SCF(GID2)-proteasome pathway.	GF14e|GID2
Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication	2010	BMC Evol Biol	National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	BACKGROUND: Various evolutionary models have been proposed to interpret the fate of paralogous duplicates, which provides substrates on which evolution selection could act. In particular, domestication, as a special selection, has played important role in crop cultivation with divergence of many genes controlling important agronomic traits. Recent studies have indicated that a pair of duplicate genes was often sub-functionalized from their ancestral functions held by the parental genes. We previously demonstrated that the rice cell-wall invertase (CWI) gene GIF1 that plays an important role in the grain-filling process was most likely subjected to domestication selection in the promoter region. Here, we report that GIF1 and another CWI gene OsCIN1 constitute a pair of duplicate genes with differentiated expression and function through independent selection. RESULTS: Through synteny analysis, we show that GIF1 and another cell-wall invertase gene OsCIN1 were paralogues derived from a segmental duplication originated during genome duplication of grasses. Results based on analyses of population genetics and gene phylogenetic tree of 25 cultivars and 25 wild rice sequences demonstrated that OsCIN1 was also artificially selected during rice domestication with a fixed mutation in the coding region, in contrast to GIF1 that was selected in the promoter region. GIF1 and OsCIN1 have evolved into different expression patterns and probable different kinetics parameters of enzymatic activity with the latter displaying less enzymatic activity. Overexpression of GIF1 and OsCIN1 also resulted in different phenotypes, suggesting that OsCIN1 might regulate other unrecognized biological process. CONCLUSION: How gene duplication and divergence contribute to genetic novelty and morphological adaptation has been an interesting issue to geneticists and biologists. Our discovery that the duplicated pair of GIF1 and OsCIN1 has experienced sub-functionalization implies that selection could act independently on each duplicate towards different functional specificity, which provides a vivid example for evolution of genetic novelties in a model crop. Our results also further support the established hypothesis that gene duplication with sub-functionalization could be one solution for genetic adaptive conflict.	GIF1|OsCIN2,OsCIN1
Sugar homeostasis mediated by cell wall invertase GRAIN INCOMPLETE FILLING 1 (GIF1) plays a role in pre-existing and induced defence in rice	2014	Mol Plant Pathol	College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China; National Key Laboratory of Plant Molecular Genetics and National Center of Plant Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.	Sugar metabolism and sugar signalling are not only critical for plant growth and development, but are also important for stress responses. However, how sugar homeostasis is involved in plant defence against pathogen attack in the model crop rice remains largely unknown. In this study, we observed that the grains of gif1, a loss-of-function mutant of the cell wall invertase gene GRAIN INCOMPLETE FILLING 1 (GIF1), were hypersusceptible to postharvest fungal pathogens, with decreased levels of sugars and a thinner glume cell wall in comparison with the wild-type. Interestingly, constitutive expression of GIF1 enhanced resistance to both the rice bacterial pathogen Xanthomonas oryzae pv. oryzae and the fungal pathogen Magnaporthe oryzae. The GIF1-overexpressing (GIF1-OE) plants accumulated higher levels of glucose, fructose and sucrose compared with the wild-type plants. More importantly, higher levels of callose were deposited in GIF1-OE plants during pathogen infection. Moreover, the cell wall was much thicker in the infection sites of the GIF1-OE plants when compared with the wild-type plants. We also found that defence-related genes were constitutively activated in the GIF1-OE plants. Taken together, our study reveals that sugar homeostasis mediated by GIF1 plays an important role in constitutive and induced physical and chemical defence.	GIF1|OsCIN2
Control of rice grain-filling and yield by a gene with a potential signature of domestication	2008	Nat Genet	Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	Grain-filling, an important trait that contributes greatly to grain weight, is regulated by quantitative trait loci and is associated with crop domestication syndrome. However, the genes and underlying molecular mechanisms controlling crop grain-filling remain elusive. Here we report the isolation and functional analysis of the rice GIF1 (GRAIN INCOMPLETE FILLING 1) gene that encodes a cell-wall invertase required for carbon partitioning during early grain-filling. The cultivated GIF1 gene shows a restricted expression pattern during grain-filling compared to the wild rice allele, probably a result of accumulated mutations in the gene's regulatory sequence through domestication. Fine mapping with introgression lines revealed that the wild rice GIF1 is responsible for grain weight reduction. Ectopic expression of the cultivated GIF1 gene with the 35S or rice Waxy promoter resulted in smaller grains, whereas overexpression of GIF1 driven by its native promoter increased grain production. These findings, together with the domestication signature that we identified by comparing nucleotide diversity of the GIF1 loci between cultivated and wild rice, strongly suggest that GIF1 is a potential domestication gene and that such a domestication-selected gene can be used for further crop improvement.	GIF1|OsCIN2
A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice	2012	J Integr Plant Biol	State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China.	A thorough understanding of the genetic basis of rice grain traits is critical for the improvement of rice (Oryza sativa L.) varieties. In this study, we generated an F(2) population by crossing the large-grain japonica cultivar CW23 with Peiai 64 (PA64), an elite indica small-grain cultivar. Using QTL analysis, 17 QTLs for five grain traits were detected on four different chromosomes. Eight of the QTLs were newly-identified in this study. In particular, qGL3-1, a newly-identified grain length QTL with the highest LOD value and largest phenotypic variation, was fine-mapped to the 17 kb region of chromosome 3. A serine/threonine protein phosphatase gene encoding a repeat domain containing two Kelch motifs was identified as the unique candidate gene corresponding to this QTL. A comparison of PA64 and CW23 sequences revealed a single nucleotide substitution (C-->A) at position 1092 in exon 10, resulting in replacement of Asp (D) in PA64 with Glu (E) in CW23 for the 364(th) amino acid. This variation is located at the D position of the conserved sequence motif AVLDT of the Kelch repeat. Genetic analysis of a near-isogenic line (NIL) for qGL3-1 revealed that the allele qGL3-1 from CW23 has an additive or partly dominant effect, and is suitable for use in molecular marker-assisted selection.	GL3.1|qGL3-1|qGL3|OsPPKL1
Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice	2012	Proc Natl Acad Sci U S A	State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.	Grain size and shape are important components determining rice grain yield, and they are controlled by quantitative trait loci (QTLs). Here, we report the cloning and functional characterization of a major grain length QTL, qGL3, which encodes a putative protein phosphatase with Kelch-like repeat domain (OsPPKL1). We found a rare allele qgl3 that leads to a long grain phenotype by an aspartate-to-glutamate transition in a conserved AVLDT motif of the second Kelch domain in OsPPKL1. The rice genome has other two OsPPKL1 homologs, OsPPKL2 and OsPPKL3. Transgenic studies showed that OsPPKL1 and OsPPKL3 function as negative regulators of grain length, whereas OsPPKL2 as a positive regulator. The Kelch domains are essential for the OsPPKL1 biological function. Field trials showed that the application of the qgl3 allele could significantly increase grain yield in both inbred and hybrid rice varieties, due to its favorable effect on grain length, filling, and weight.	GL3.1|qGL3-1|qGL3|OsPPKL1,OsPPKL2,OsPPKL3
Influence of different nitrogen inputs on the members of ammonium transporter and glutamine synthetase genes in two rice genotypes having differential responsiveness to nitrogen	2012	Mol Biol Rep	Department of Molecular Biology and Genetic Engineering, College of Basic Sciences and Humanities, G. B. Pant University of Agriculture and Technology, Pantnagar, Uttarakhand, India.	Two aromatic rice genotypes, Pusa Basmati 1 (PB1) and Kalanamak 3119 (KN3119) having 120 and 30 kg/ha optimum nitrogen requirement respectively, to produce optimal yield, were chosen to understand their differential nitrogen responsiveness. Both the genotypes grown under increasing nitrogen inputs showed differences in seed/panicle, 1,000 seed weight, %nitrogen in the biomass and protein content in the seeds. All these parameters in PB1 were found to be in the increasing order in contrast to KN3119 which showed declined response on increasing nitrogen dose exceeding the normal dose indicating that both the genotypes respond differentially to the nitrogen inputs. Gene expression analysis of members of ammonium transporter gene family in flag leaves during active grain filling stage revealed that all the three members of OsAMT3 family genes (OsAMT1;1-3), only one member of OsAMT2 family i.e., OsAMT2;3 and the high affinity OsAMT1;1 were differentially expressed and were affected by different doses of nitrogen. In both the genotypes, both increase and decline in seed protein contents matched with the expressions levels of OsAMT1;1, OsGS1;1 and OsGS1;2 in the flag leaves during grain filling stage indicating that high nitrogen nutrition in KN3119 probably causes the repression of these genes which might be important during grain filling.	GLN1;2|GS1;2,OsAMT1;1|OsAMT1.1,OsAMT2;1,OsAMT2;3,OsGS|OsGS1|GS1|OsGS1;1|OsGLN1;1
Biochemical background and compartmentalized functions of cytosolic glutamine synthetase for active ammonium assimilation in rice roots	2004	Plant Cell Physiol	RIKEN Plant Science Center, 1-7-22 Suehiro, Tsurumi-ku, Yokohama, 230-0045 Japan.	Rice plants in paddy fields prefer to utilize ammonium as a major nitrogen source. Glutamine synthetase (GS) serves for assimilation of ammonium in rice root, and ameliorates the toxic effect of ammonium excess. Among the three isoenzymes of the cytosolic GS1 gene family in rice, OsGLN1;1 and OsGLN1;2 were abundantly expressed in roots. Analysis of the purified enzymes showed that OsGLN1;1 and OsGLN1;2 can be classified into high-affinity subtypes with relatively high V(max) values, as compared with the major high-affinity isoenzyme, GLN1;1, in Arabidopsis. Low-affinity forms of GS1 comparable to those in Arabidopsis (GLN1;2 and GLN1;3) were absent in rice roots. The OsGLN1;1 and OsGLN1;2 transcripts showed reciprocal responses to ammonium supply in the surface cell layers of roots. OsGLN1;1 accumulated in dermatogen, epidermis and exodermis under nitrogen-limited condition. By contrast, OsGLN1;2 was abundantly expressed in the same cell layers under nitrogen-sufficient conditions, replenishing the loss of OsGLN1;1 following ammonium treatment. Within the central cylinder of elongating zone, OsGLN1;1 and OsGLN1;2 were both induced by ammonium, which was distinguishable from the response observed in the surface cell layers. The high-capacity Gln synthetic activities of OsGLN1;1 and OsGLN1;2 facilitate active ammonium assimilation in specific cell types in rice roots.	GLN1;2|GS1;2,OsGS1;3|OsGLN1;3,OsGS|OsGS1|GS1|OsGS1;1|OsGLN1;1,OsGS2|lambdaGS31
Severe reduction in growth rate and grain filling of rice mutants lacking OsGS1;1, a cytosolic glutamine synthetase1;1	2005	Plant J	Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan.	Rice (Oryza sativa L.) plants possess three homologous but distinct genes for cytosolic glutamine synthetase (GS1): these are OsGS1;1, OsGS1;2, and OsGS1;3. OsGS1;1 was expressed in all organs tested with higher expression in leaf blades, while OsGS1;2, and OsGS1;3 were expressed mainly in roots and spikelets, respectively. We characterized knockout mutants caused by insertion of endogenous retrotransposon Tos17 into the exon-8 (lines ND8037 and ND9801) or the exon-10 (line NC2327) of OsGS1;1. Mendelian segregation occurred in each progeny. Homozygously inserted mutants showed severe retardation in growth rate and grain filling when grown at normal nitrogen concentrations. Abnormal mRNA for GS1;1 was transcribed, and the GS1 protein and its activity in the leaf blades were barely detectable in these mutants. The glutamine pool in the roots and leaf blades of the mutants was lower than that of the wild type. Re-introduction of OsGS1;1 cDNA under the control of its own promoter into the mutants successfully complemented these phenotypes. Progeny where Tos17 was heterozygously inserted or deleted during segregation showed normal phenotypes. The results indicate that GS1;1 is important for normal growth and grain filling in rice; GS1;2 and GS1;3 were not able to compensate for GS1;1 function.	GLN1;2|GS1;2,OsGS1;3|OsGLN1;3,OsGS|OsGS1|GS1|OsGS1;1|OsGLN1;1
Metabolomics data reveal a crucial role of cytosolic glutamine synthetase 1;1 in coordinating metabolic balance in rice	2011	Plant J	RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.	Rice plants grown in paddy fields preferentially use ammonium as a source of inorganic nitrogen. Glutamine synthetase (GS) catalyses the conversion of ammonium to glutamine. Of the three genes encoding cytosolic GS in rice, OsGS1;1 is critical for normal growth and grain filling. However, the basis of its physiological function that may alter the rate of nitrogen assimilation and carbon metabolism within the context of metabolic networks remains unclear. To address this issue, we carried out quantitative comparative analyses between the metabolite profiles of a rice mutant lacking OsGS1;1 and its background wild type (WT). The mutant plants exhibited severe retardation of shoot growth in the presence of ammonium compared with the WT. Overaccumulation of free ammonium in the leaf sheath and roots of the mutant indicated the importance of OsGS1;1 for ammonium assimilation in both organs. The metabolite profiles of the mutant line revealed: (i) an imbalance in levels of sugars, amino acids and metabolites in the tricarboxylic acid cycle, and (ii) overaccumulation of secondary metabolites, particularly in the roots under a continuous supply of ammonium. Metabolite-to-metabolite correlation analysis revealed the presence of mutant-specific networks between tryptamine and other primary metabolites in the roots. These results demonstrated a crucial function of OsGS1;1 in coordinating the global metabolic network in rice plants grown using ammonium as the nitrogen source.	GLN1;2|GS1;2,OsGDH2,OsGS|OsGS1|GS1|OsGS1;1|OsGLN1;1
Assimilation of ammonium ions and reutilization of nitrogen in rice (Oryza sativa L.)	2007	J Exp Bot	Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai 981-8555, Japan.	A major source of inorganic nitrogen for rice plants grown in paddy soil is ammonium ions. The ammonium ions are actively taken up by the roots via ammonium transporters and subsequently assimilated into the amide residue of glutamine (Gln) by the reaction of glutamine synthetase (GS) in the roots. The Gln is converted into glutamate (Glu), which is a central amino acid for the synthesis of a number of amino acids, by the reaction of glutamate synthase (GOGAT). Although a small gene family for both GS and GOGAT is present in rice, ammonium-dependent and cell type-specific expression suggest that cytosolic GS1;2 and plastidic NADH-GOGAT1 are responsible for the primary assimilation of ammonium ions in the roots. In the plant top, approximately 80% of the total nitrogen in the panicle is remobilized through the phloem from senescing organs. Since the major form of nitrogen in the phloem sap is Gln, GS in the senescing organs and GOGAT in developing organs are important for nitrogen remobilization and reutilization, respectively. Recent work with a knock-out mutant of rice clearly showed that GS1;1 is responsible for this process. Overexpression studies together with age- and cell type-specific expression strongly suggest that NADH-GOGAT1 is important for the reutilization of transported Gln in developing organs. The overall process of nitrogen utilization within the plant is discussed.	GLN1;2|GS1;2
Comparison of ion balance and nitrogen metabolism in old and young leaves of alkali-stressed rice plants	2012	PLoS One	Key laboratory of Molecular Epigenetics of MOE, Northeast Normal University, Changchun, Jilin Province, China.	BACKGROUND: Alkali stress is an important agricultural contaminant and has complex effects on plant metabolism. The aim of this study was to investigate whether the alkali stress has different effects on the growth, ion balance, and nitrogen metabolism in old and young leaves of rice plants, and to compare functions of both organs in alkali tolerance. METHODOLOGY/PRINCIPAL FINDINGS: The results showed that alkali stress only produced a small effect on the growth of young leaves, whereas strongly damaged old leaves. Rice protected young leaves from ion harm via the large accumulation of Na(+) and Cl(-) in old leaves. The up-regulation of OsHKT1;1, OsAKT1, OsHAK1, OsHAK7, OsHAK10 and OsHAK16 may contribute to the larger accumulation of Na(+) in old leaves under alkali stress. Alkali stress mightily reduced the NO(3)(-) contents in both organs. As old leaf cells have larger vacuole, under alkali stress these scarce NO(3)(-) was principally stored in old leaves. Accordingly, the expression of OsNRT1;1 and OsNRT1;2 in old leaves was up-regulated by alkali stress, revealing that the two genes might contribute to the accumulation of NO(3)(-) in old leaves. NO(3)(-) deficiency in young leaves under alkali stress might induce the reduction in OsNR1 expression and the subsequent lacking of NH(4)(+), which might be main reason for the larger down-regulation of OsFd-GOGAT and OsGS2 in young leaves. CONCLUSIONS/SIGNIFICANCE: Our results strongly indicated that, during adaptation of rice to alkali stress, young and old leaves have distinct mechanisms of ion balance and nitrogen metabolism regulation. We propose that the comparative studies of young and old tissues may be important for abiotic stress tolerance research.	GLN1;2|GS1;2,NRT1,OsGDH2,OsGDH3
Reduced expression of glycolate oxidase leads to enhanced disease resistance in rice	2013	PeerJ	Department of Plant Pathology , University of California Davis , California , USA.	Glycolate oxidase (GLO) is a key enzyme in photorespiration, catalyzing the oxidation of glycolate to glyoxylate. Arabidopsis GLO is required for nonhost defense responses to Pseudomonas syringae and for tobacco Pto/AvrPto-mediated defense responses. We previously described identification of rice GLO1 that interacts with a glutaredoxin protein, which in turn interacts with TGA transcription factors. TGA transcription factors are well known to participate in NPR1/NH1-mediated defense signaling, which is crucial to systemic acquired resistance in plants. Here we demonstrate that reduction of rice GLO1 expression leads to enhanced resistance to Xanthomonas oryzae pv oryzae (Xoo). Constitutive silencing of GLO1 leads to programmed cell death, resulting in a lesion-mimic phenotype and lethality or reduced plant growth and development, consistent with previous reports. Inducible silencing of GLO1, employing a dexamethasone-GVG (Gal4 DNA binding domain-VP16 activation domain-glucocorticoid receptor fusion) inducible system, alleviates these detrimental effects. Silencing of GLO1 results in enhanced resistance to Xoo, increased expression of defense regulators NH1, NH3, and WRKY45, and activation of PR1 expression.	GLO1,GLO2,GLO3,GLO4,OsNPR1|NH1,OsWRKY45
Glycolate oxidase isozymes are coordinately controlled by GLO1 and GLO4 in rice	2012	PLoS One	State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, China.	Glycolate oxidase (GLO) is a key enzyme in photorespiratory metabolism. Four putative GLO genes were identified in the rice genome, but how each gene member contributes to GLO activities, particularly to its isozyme profile, is not well understood. In this study, we analyzed how each gene plays a role in isozyme formation and enzymatic activities in both yeast cells and rice tissues. Five GLO isozymes were detected in rice leaves. GLO1 and GLO4 are predominately expressed in rice leaves, while GLO3 and GLO5 are mainly expressed in the root. Enzymatic assays showed that all yeast-expressed GLO members except GLO5 have enzymatic activities. Further analyses suggested that GLO1, GLO3 and GLO4 interacted with each other, but no interactions were observed for GLO5. GLO1/GLO4 co-expressed in yeast exhibited the same isozyme pattern as that from rice leaves. When either GLO1 or GLO4 was silenced, expressions of both genes were simultaneously suppressed and most of the GLO activities were lost, and consistent with this observation, little GLO isozyme protein was detected in the silenced plants. In contrast, no observable effect was detected when GLO3 was suppressed. Comparative analyses between the GLO isoforms expressed in yeast and the isozymes from rice leaves indicated that two of the five isozymes are homo-oligomers composed of either GLO1 or GLO4, and the other three are hetero-oligomers composed of both GLO1 and GLO4. Our current data suggest that GLO isozymes are coordinately controlled by GLO1 and GLO4 in rice, and the existence of GLO isozymes and GLO molecular and compositional complexities implicate potential novel roles for GLO in plants.	GLO1,GLO3,GLO4
Glabrous Rice 1, encoding a homeodomain protein, regulates trichome development in rice	2012	Rice (N Y)	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China. gsxiong@genetics.ac.cn.	BACKGROUND: Glabrous rice, which lacks trichomes on the rice epidermis, is regarded as an important germplasm resource in rice breeding. Trichomes are derived from aerial epidermal cells and used as a model to study the cell fate determination in plant. In Arabidopsis, the molecular mechanisms of trichome development have been well studied. However, little is known about the molecular basis of trichome development in rice. RESULTS: In this study, near isogenic lines harboring the glabrous rice 1 locus were developed. By a map-based approach, we narrowed down the locus to a 21-kb DNA region harboring two genes. One of the genes named Glabrous Rice 1 (GLR1), which is most likely the candidate, encodes a homeodomain protein containing the WOX motif. Constitutive Expression of GLR1 could partially complement the glabrous phenotype of NILglr1. The knock down of GLR1 by RNA interference led to a significant decrease in trichome number on the leaves and glumes of the RNAi transgenic plants. CONCLUSION: GLR1 plays an important role in rice trichome development and will contribute to breeding of glabrous elite rice varieties.	GLR1
A rice glutamate receptor-like gene is critical for the division and survival of individual cells in the root apical meristem	2006	Plant Cell	State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310029, China.	Glu receptors are known to function as Glu-activated ion channels that mediate mostly excitatory neurotransmission in animals. Glu receptor-like genes have also been reported in higher plants, although their function is largely unknown. We have identified a rice (Oryza sativa) Glu receptor-like gene, designated GLR3.1, in which mutation by T-DNA insertion caused a short-root mutant phenotype. Histology and DNA synthesis analyses revealed that the mutant root meristematic activity is distorted and is accompanied by enhanced programmed cell death. Our results supply genetic evidence that a plant Glu receptor-like gene, rice GLR3.1, is essential for the maintenance of cell division and individual cell survival in the root apical meristem at the early seedling stage.	GLR3.1
Identification of cis-regulatory elements required for endosperm expression of the rice storage protein glutelin gene GluB-1	1999	Plant Mol Biol	Department of Biotechnology, National Institute of Agrobiological Resources, Tsukuba, Ibaraki, Japan.	Rice storage protein glutelin genes are coordinately regulated during seed development. A previous 5' deletion analysis using transgenic tobacco revealed that the minimum 5' region necessary for endosperm specificity was within -245 bp of the transcription start site, and included the AACA and GCN4 motifs that are highly conserved in the 5'-flanking regions of all glutelin genes. In this paper, the sequence elements essential for endosperm-specific expression are characterized in stable transgenic tobacco plants by both loss-of-function and gain-of-function experiments using this minimum promoter. Base substitution analysis shows that the proximal AACA motif between -73 and -61, and the GCN4 motif between -165 and -158 act as critical elements. An ACGT motif between -81 and -75, and Skn-I-like elements between -173 and -169 also play important roles in controlling the seed-specific expression. When the distal region between -245 and -145 containing the AACA and the GCN4 motifs or the proximal region between -113 and -46 containing the ACGT and AACA motifs is fused to a truncated promoter (-90 to +9) of the CaMV 35S gene fused to the beta-glucuronidase (GUS) reporter gene, high levels of seed-specific expression are observed in these fusions, thereby indicating that either pair of motifs is sufficient to confer seed expression in these fusions. However, when substituted for by the CaMV 35S core promoter (-46 to +1), seed expression is abolished, suggesting that the sequence between -90 and -46 of the CaMV 35S promoter containing G-box-like motif (as-1 element) is required for such specific expression in addition to AACA and GCN4 motifs. Therefore, we conclude that at least three cis-regulatory elements, the AACA motif, GCN4 motif and ACGT motif, are necessary to mediate endosperm expression of the GluB-1 glutelin gene.	GluB-1
The 3'-untranslated region of rice glutelin GluB-1 affects accumulation of heterologous protein in transgenic rice	2009	Biotechnol Lett	Transgenic Crop Research and Development Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan.	We compared the effect of the rice storage protein glutelin B-1 (GluB-1) terminator with the nopaline synthase (Nos) terminator on the accumulation of the modified house dust mite allergen mDer f 2 driven by the maize ubiquitin promoter in transgenic rice. Accumulation of mDer f 2 in transgenic seed and leaf using the GluB-1 terminator was greater than when using the Nos terminator construct. The mDer f 2 mRNA containing the GluB-1 3'UTR was processed and polyadenylated at the same sites as the native GluB-1 mRNA in the seeds but diverged in leaves of the transgenic plants. In contrast, the poly(A) sites of mDer f 2 containing Nos 3'UTR were more divergent in both seed and leaf. These results suggest that GluB-1 3'UTR functions as a faithful terminator and that termination at the specific sites may play an important role in mRNA stability and/or translatability, resulting in higher levels of protein accumulation.	GluB-1
Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice	2014	Plant Mol Biol	Sylvius Laboratory, Institute of Biology (IBL), Leiden University, Sylviusweg 72, 2333 BE, PO Box 9505, 2300 RA, Leiden, The Netherlands.	Glutelins are the most abundant storage proteins in rice grain and can make up to 80 % of total protein content. The promoter region of GluB-1, one of the glutelin genes in rice, has been intensively used as a model to understand regulation of seed-storage protein accumulation. In this study, we describe a zinc finger gene of the Cys3His1 (CCCH or C3H) class, named OsGZF1, which was identified in a yeast one-hybrid screening using the core promoter region of GluB-1 as bait and cDNA expression libraries prepared from developing rice panicles and grains as prey. The OsGZF1 protein binds specifically to the bait sequence in yeast and this interaction was confirmed in vitro. OsGZF1 is predominantly expressed in a confined domain surrounding the scutellum of the developing embryo and is localised in the nucleus. Transient expression experiments demonstrated that OsGZF1 can down-regulate a GluB-1-GUS (beta-glucuronidase) reporter and OsGZF1 was also able to significantly reduce activation conferred by RISBZ1 which is a known strong GluB-1 activator. Furthermore, down-regulation of OsGZF1 by an RNAi approach increased grain nitrogen concentration. We propose that OsGZF1 has a function in regulating the GluB-1 promoter and controls accumulation of glutelins during grain development.	GluB-1,OsGZF1
Development of Simple Functional Markers for Low Glutelin Content Gene 1 (Lgc1) in Rice (Oryza sativa)	2010	Rice Science	Jiangsu High Quality Rice Research and Development Center, Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China	Rice with low glutelin content is suitable as functional food for patients affected by kidney failure. Low glutelin-content gene Lgc1 in rice has a 3.5-kb deletion between two highly similar glutelin genes GluB4 and GluB5, which locates on the short arm of chromosome 2. To improve the selection efficiency in low glutelin-content rice breeding, two molecular markers designated as InDel-Lgc1-1 and InDel-Lgc1-2 were developed to detect the low glutelin-content gene Lgc1. A double PCR detection indicated that combined use of the two markers could easily distinguish the genotypes of Lgc1 from different rice varieties. Therefore, as a simple and low-cost technique, the molecular marker could be widely used to identify different varieties with Lgc1 gene and applied in marker-assisted selection of low glutelin-content rice.	GluB4,GluB5
Low glutelin content1: A Dominant Mutation That Suppresses the Glutelin Multigene Family via RNA Silencing in Rice	2003	The Plant Cell Online	Institute of Radiation Breeding, National Institute of Agrobiological Sciences, Ohmiya-machi, Naka-gun, Ibaraki 319-2293, Japan. 	Low glutelin content1 (Lgc1) is a dominant mutation that reduces glutelin content in rice grains. Glutelin is a major seed storage protein encoded by a multigene family. RNA gel blot and reverse transcriptase-mediated PCR analyses revealed that Lgc1 acts at the mRNA level in a similarity-dependent manner. In Lgc1 homozygotes, there is a 3.5-kb deletion between two highly similar glutelin genes that forms a tail-to-tail inverted repeat, which might produce a double-stranded RNA molecule, a potent inducer of RNA silencing. The hypothesis that Lgc1 suppresses glutelin expression via RNA silencing is supported by transgenic analysis using this Lgc1 candidate region, by reporter gene analysis, and by the detection of small interfering RNAs. In this context, Lgc1 provides an interesting example of RNA silencing occurring among genes that exhibit various levels of similarity to an RNA-silencing-inducing gene. Possible mechanisms for gene silencing of the glutelin multigene family by Lgc1 are discussed.	GluB4,GluB5
Gene-gene interactions between mutants that accumulate abnormally high amounts of proglutelin in rice seed	2010	Breeding Science	Faculty of Agriculture, Kyushu University	We had previously identified eight mutants, esp2 and g(G)lups1 to 7, which accumulated abnormally high amounts of proglutelin, the major storage protein in rice seeds. Analysis of their seed proteins by SDS-PAGE, their levels of the luminal chaperone BiP and gene-gene interactions indicated that these mutants fell into four classes. The most epistatic class consisted of esp2, which encodes a defective protein disulfide isomerase (PDI). A second class consisting of Glup1, glup2 and glup7 was hypostatic to esp2, and showed abnormally high levels of BiP, suggesting that maturation and export of proglutelins from the ER are inhibited in this class of mutants. The third class containing glup4, Glup5 and glup6 mutations was hypostatic to esp2, Glup1, glup2 and glup7. Since the glup4 allele encodes the small GTPase Rab5a, which participates in the trafficking of proglutelin from Golgi apparatus to the protein storage vacuole (PSV), this third class of mutants is likely affected in this process. Lastly, glup3, which encodes a vacuolar processing enzyme, which proteolytically processes proglutelin into acidic and basic subunits within the PSV, was hypostatic to the other mutants. Overall, these gene relationships are consistent with the sequential intracellular transport and processing of proglutelin and provide novel insights on the trafficking of proglutelin to the PSV.	Glup3|OsVPE1,OsRab5a|gpa1|glup4
The vacuolar processing enzyme OsVPE1 is required for efficient glutelin processing in rice	2009	Plant J	Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, China.	Rice (Oryza sativa L.) accumulates prolamines and glutelins as its major storage proteins. Glutelins are synthesized on rough endoplasmic reticulum as 57-kDa precursors; they are then sorted into protein storage vacuoles where they are processed into acidic and basic subunits. We report a novel rice glutelin mutant, W379, which accumulates higher levels of the 57-kDa glutelin precursor. Genetic analysis revealed that the W379 phenotype is controlled by a single recessive nuclear gene. Using a map-based cloning strategy, we identified this gene, OsVPE1, which is a homolog of the Arabidopsis betaVPE gene. OsVPE1 encodes a 497-amino-acid polypeptide. Nucleotide sequence analysis revealed a missense mutation in W379 that changes Cys269 to Gly. Like the wild-type protein, the mutant protein is sorted into vacuoles; however, the enzymatic activity of the mutant OsVPE1 is almost completely eliminated. Further, we show that OsVPE1 is incorrectly cleaved, resulting in a mature protein that is smaller than the wild-type mature protein. Taken together, these results demonstrate that OsVPE1 is a cysteine protease that plays a crucial role in the maturation of rice glutelins. Further, OsVPE1 Cys269 is a key residue for maintaining the Asn-specific cleavage activity of OsVPE1.	Glup3|OsVPE1
Bcl-2 suppresses hydrogen peroxide-induced programmed cell death via OsVPE2 and OsVPE3, but not via OsVPE1 and OsVPE4, in rice	2011	FEBS J	State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory for Cell and Gene Engineering of Zhejiang province, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China.	Hydrogen peroxide (H(2)O(2)) is known to be a key player in apoptosis in animals. The components and pathways regulating H(2)O(2)-induced programmed cell death in plants, however, remain largely unknown. In the present study, rice transgenic lines overexpressing Bcl-2, a human apoptotic suppressor, were obtained. These transgenic lines showed increased tolerance to high levels of H(2)O(2), resulting in increased seed germination rates, root elongation, root tip cell viability and chlorophyll retention compared to control lines. In the control lines, treatment with H(2)O(2) resulted in DNA laddering and a clear terminal transferase dUTP nick end labeling signal, which are the hallmarks of programmed cell death. However, this effect was not detected in the Bcl-2-overexpressing transgenic lines. Further investigations indicated that Bcl-2 suppressed H(2)O(2)-induced programmed cell death but did not inhibit stress-elicited reactive oxygen species production in rice. RT-PCR revealed that the expression of the two vacuolar processing enzyme genes (i.e. OsVPE2 and OsVPE3) was dramatically induced by H(2)O(2) in the wild-type line but not in the Bcl-2-overexpressing line. Moreover, treatment with H(2)O(2) resulted in the disruption of the vacuolar membrane in the wild-type line. The expression levels of OsVPE1 and OsVPE4 did not significantly differ between the wild-type line and the transgenic line that was treated or untreated with H(2)O(2). The similar roles of Bcl-2 and OsVPEs during endogenous reactive oxygen species-triggered programmed cell death were also confirmed by NaCl stress in rice. To our knowledge, the present study is the first to demonsatrate that Bcl-2 overexpression inhibits H(2)O(2)-induced programmed cell death and enhances H(2)O(2) tolerance. We propose that Bcl-2 overexpression in rice suppresses the transcriptional activation of OsVPE2 and OsVPE3, but not of OsVPE1 or OsVPE4.	Glup3|OsVPE1,OsVPE2,OsVPE4,OsVPE3|REP-2
Vacuolar processing enzyme plays an essential role in the crystalline structure of glutelin in rice seed	2010	Plant Cell Physiol	Faculty of Agriculture, Kyushu University, Fukuoka, Japan. kumamaru@agr.kyushu-u.ac.jp	To identify the function of genes that regulate the processing of proglutelin, we performed an analysis of glup3 mutants, which accumulates excess amounts of proglutelin and lack the vacuolar processing enzyme (VPE). VPE activity in developing seeds from glup3 lines was reduced remarkably compared with the wild type. DNA sequencing of the VPE gene in glup3 mutants revealed either amino acid substitutions or the appearance of a stop codon within the coding region. Microscopic observations showed that alpha-globulin and proglutelin were distributed homogeneously within glup3 protein storage vacuoles (PSVs), and that glup3 PSVs lacked the crystalline lattice structure typical of wild-type PSVs. This suggests that the processing of proglutelin by VPE in rice is essential for proper PSV structure and compartmentalization of storage proteins. Growth retardation in glup3 seedlings was also observed, indicating that the processing of proglutelin influences early seedling development. These findings indicate that storage of glutelin in its mature form as a crystalline structure in PSVs is required for the rapid use of glutelin as a source of amino acids during early seedling development. In conclusion, VPE plays an important role in the formation of protein crystalline structures in PSVs.	Glup3|OsVPE1
A guanine nucleotide exchange factor for Rab5 proteins is essential for intracellular transport of the proglutelin from the Golgi apparatus to the protein storage vacuole in rice endosperm	2013	Plant Physiol	Kyushu University, Fukuoka 812-8581, Japan.	Rice (Oryza sativa) glutelins are synthesized on the endoplasmic reticulum as a precursor, which are then transported via the Golgi to protein storage vacuoles (PSVs), where they are proteolytically processed into acidic and basic subunits. The glutelin precursor mutant6 (glup6) accumulates abnormally large amounts of proglutelin. Map-base cloning studies showed that glup6 was a loss-of-function mutant of guanine nucleotide exchange factor (GEF), which activates Rab GTPase, a key regulator of membrane trafficking. Immunofluorescence studies showed that the transport of proglutelins and alpha-globulins to PSV was disrupted in glup6 endosperm. Secreted granules of glutelin and alpha-globulin were readily observed in young glup6 endosperm, followed by the formation of large dilated paramural bodies (PMBs) containing both proteins as the endosperm matures. The PMBs also contained membrane biomarkers for the Golgi and prevacuolar compartment as well as the cell wall component, beta-glucan. Direct evidence was gathered showing that GLUP6/GEF activated in vitro GLUP4/Rab5 as well as several Arabidopsis (Arabidopsis thaliana) Rab5 isoforms to the GTP-bound form. Therefore, loss-of-function mutations in GEF or Rab5 disrupt the normal transport of proglutelin from the Golgi to PSVs, resulting in the initial extracellular secretion of these proteins followed, in turn, by the formation of PMBs. Overall, our results indicate that GLUP6/GEF is the activator of Rab5 GTPase and that the cycling of GTP- and GDP-bound forms of this regulatory protein is essential for the intracellular transport of proglutelin and alpha-globulin from the Golgi to PSVs and in the maintenance of the general structural organization of the endomembrane system in rice seeds.	GLUP6
A loss-of-function mutation of rice DENSE PANICLE 1 causes semi-dwarfness and slightly increased number of spikelets	2011	Breeding Science	QTL Genomics Research Center, National Institute of Agrobiological Sciences	In cereal breeding, semi-dwarfness and an increased spikelet number are favorable characteristics. We show that the rice DENSE PANICLE 1 (DN1) mutant allele Dn1-1 causes both of these characteristics and that Dn1-1 is a loss-of-function mutation. DN1 is allelic to DENSE AND ERECT PANICLE 1 (DEP1) (=qPE(9-1)). The expression level of OsCKX2 in the shoot apex of Dn1-1 plants is similar to that in the wild type, indicating that OsCKX2 does not contribute to an increased number of spikelets. A comparison of the Dn1-1 and Dn1-3 alleles suggests that the N-terminal region of DN1 contains a coiled-coil domain and a nuclear localization signal that might be responsible for semi-dwarfness. This comparison also revealed that a single transmembrane alpha-helix, a VWFC module, and a four-disulfide core domain can further increase spikelet number. Subcellular localization analysis of the DN1 protein fused with green fluorescent protein (GFP) implies that DN1 is located in the nucleus and cell membrane and that its N-terminal fragment is cleaved. Dn1-1 plants have normal sensitivity to gibberellin, brassinolide, and kinetin, and we observed no genetic epistasis with brassinolide-related mutants, suggesting that DN1 does not function in the signaling pathways of these phytohormones.	Gn1a|OsCKX2,DEP1|DN1|qPE9-1|OsDEP1
Mutations in the F-box gene LARGER PANICLE improve the panicle architecture and enhance the grain yield in rice	2011	Plant Biotechnol J	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.	Panicle architecture is one of the most important agronomical traits that directly contribute to grain yield in rice (Oryza sativa L.). We report herein an in-depth characterization of two allelic larger panicle (lp) mutants that show significantly increased panicle size as well as improved plant architecture. Morphological analyses reveal that panicles of two mutants produced more inflorescence branches, especially the primary branches, and contained more grains. Moreover, mutant plants also display more lodging resistance than the wild type. The grain yield per plant in mutants is also increased, suggesting that mutant plants have useful potential for high grain yield in rice breeding. Map-based cloning reveals that LARGER PANICLE (LP) encodes a Kelch repeat-containing F-box protein. RNA in situ hybridization studies display that LP expression was enriched in the branch primordial region. Subcellular localization analyses demonstrate that LP is an endoplasmic reticulum (ER) localized protein, suggesting that LP might be involved in ER-associated protein degradation (ERAD). Using yeast two-hybrid assay and bimolecular fluorescence complementation analysis, we confirm that LP is an F-box protein and could interact with rice SKP1-like protein in an F-box domain-dependent manner. Quantitative real-time PCR results show that OsCKX2, which encodes cytokinin oxidase/dehydrogenase, is down-regulated evidently in mutants, implying that LP might be involved in modulating cytokinin level in plant tissues. These results suggest that LP plays an important role in regulating plant architecture, particularly in regulating panicle architecture, thereby representing promising targets for genetic improvement of grain production plants.	Gn1a|OsCKX2,EP3|LP
Cytokinin oxidase regulates rice grain production	2005	Science	Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan.	Most agriculturally important traits are regulated by genes known as quantitative trait loci (QTLs) derived from natural allelic variations. We here show that a QTL that increases grain productivity in rice, Gn1a, is a gene for cytokinin oxidase/dehydrogenase (OsCKX2), an enzyme that degrades the phytohormone cytokinin. Reduced expression of OsCKX2 causes cytokinin accumulation in inflorescence meristems and increases the number of reproductive organs, resulting in enhanced grain yield. QTL pyramiding to combine loci for grain number and plant height in the same genetic background generated lines exhibiting both beneficial traits. These results provide a strategy for tailormade crop improvement.	Gn1a|OsCKX2
New perspectives on the endo-beta-glucanases of glycosyl hydrolase Family 17	2000	Int J Biol Macromol	Section of Molecular and Cellular Biology, University of California, Davis, CA 95616-8535, USA. brthomas@ucdavis.edu	Isozymes of glycosyl hydrolase Family 17 hydrolyze 1,3-beta-glucan polysaccharides found in the cell wall matrix of plants and fungi, enabling these plant enzymes to serve diverse roles in plant defense and plant development. Fourteen genes from Family 17 have been characterized in the genome of rice. A sequence dendrogram analysis divided these genes into four subfamilies. The recombinant GNS1 enzyme from subfamily B had 1,3;1,4-beta-glucanase activity, suggesting a role for this isozyme in plant development.	Gns1
Characterization of transgenic rice plants over-expressing the stress-inducible beta-glucanase gene Gns1	2003	Plant Mol Biol	National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba 305-8602, Japan. ynishi@nias.affrc.go.jp	The Gns1 gene of rice (Oryza sativa L. japonica) encodes 1,3;1,4-beta glucanase (EC 3.2.1.73), which hydrolyzes 1,3;1,4-beta-glucosidic linkages on 1,3;1,4-beta-glucan, an important component of cell walls in the Poaceae family. RNA and protein gel blot analyses demonstrated that blast disease or dark treatment induced the expression of the Gns1 gene. To assess the function of the Gns1 gene in disease resistance, we characterized transgenic rice plants constitutively expressing the Gns1 gene. The introduced Gns1 gene was driven by the CaMV 35S promoter and its products were found in the apoplast and accumulated in up to 0.1% of total soluble protein in leaves. Although transgenic plants showed stunted growth and impaired root formation, fertility, germination, and coleoptile elongation appeared unaffected compared to non-transgenic control plants, indicating that Gns1 does not play a crucial role in rice germination and coleoptile elongation. When transgenic plants were inoculated with virulent blast fungus (Magnaporthe grisea), they developed many resistant-type lesions on the inoculated leaf accompanying earlier activation of defense-related genes PR-1 and PBZ1 than in control plants. Transgenic plants spontaneously produced brown specks, similar in appearance to those reported for an initiation type of disease-lesion-mimic mutants, on the third and fourth leaves and occasionally on older leaves without inoculation of pathogens. Expression of the two defense-related genes was drastically increased after the emergence of the lesion-mimic phenotype.	Gns1,OsPR10a|PBZ1
N-glycan maturation is crucial for cytokinin-mediated development and cellulose synthesis in Oryza sativa	2013	Plant J	Division of Applied Life Science (BK21 Program) and PMBBRC, Gyeongsang National University, 501 Jinju-daero, Jinju, 660-701, Korea.	To explore the physiological significance of N-glycan maturation in the plant Golgi apparatus, gnt1, a mutant with loss of N-acetylglucosaminyltransferase I (GnTI) function, was isolated in Oryza sativa. gnt1 exhibited complete inhibition of N-glycan maturation and accumulated high-mannose N-glycans. Phenotypic analyses revealed that gnt1 shows defective post-seedling development and incomplete cell wall biosynthesis, leading to symptoms such as failure in tiller formation, brittle leaves, reduced cell wall thickness, and decreased cellulose content. The developmental defects of gnt1 ultimately resulted in early lethality without transition to the reproductive stage. However, callus induced from gnt1 seeds could be maintained for periods, although it exhibited a low proliferation rate, small size, and hypersensitivity to salt stress. Shoot regeneration and dark-induced leaf senescence assays indicated that the loss of GnTI function results in reduced sensitivity to cytokinin in rice. Reduced expression of A-type O. sativa response regulators that are rapidly induced by cytokinins in gnt1 confirmed that cytokinin signaling is impaired in the mutant. These results strongly support the proposed involvement of N-glycan maturation in transport as well as in the function of membrane proteins that are synthesized via the endomembrane system.	GnT1
Expression profiling of rice cultivars differing in their tolerance to long-term drought stress	2009	Plant Mol Biol	Max-Planck-Institut fur Molekulare Pflanzenphysiologie, Am Muhlenberg 1, 14476 Potsdam, Germany.	Understanding the molecular basis of plant performance under water-limiting conditions will help to breed crop plants with a lower water demand. We investigated the physiological and gene expression response of drought-tolerant (IR57311 and LC-93-4) and drought-sensitive (Nipponbare and Taipei 309) rice (Oryza sativa L.) cultivars to 18 days of drought stress in climate chamber experiments. Drought stressed plants grew significantly slower than the controls. Gene expression profiles were measured in leaf samples with the 20 K NSF oligonucleotide microarray. A linear model was fitted to the data to identify genes that were significantly regulated under drought stress. In all drought stressed cultivars, 245 genes were significantly repressed and 413 genes induced. Genes differing in their expression pattern under drought stress between tolerant and sensitive cultivars were identified by the genotype x environment (G x E) interaction term. More genes were significantly drought regulated in the sensitive than in the tolerant cultivars. Localizing all expressed genes on the rice genome map, we checked which genes with a significant G x E interaction co-localized with published quantitative trait loci regions for drought tolerance. These genes are more likely to be important for drought tolerance in an agricultural environment. To identify the metabolic processes with a significant G x E effect, we adapted the analysis software MapMan for rice. We found a drought stress induced shift toward senescence related degradation processes that was more pronounced in the sensitive than in the tolerant cultivars. In spite of higher growth rates and water use, more photosynthesis related genes were down-regulated in the tolerant than in the sensitive cultivars.	gp1
bZIP transcription factor OsbZIP52/RISBZ5: a potential negative regulator of cold and drought stress response in rice	2011	Planta	Key Laboratory of Cell Proliferation and Regulation of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, People's Republic of China.	OsbZIP52/RISBZ5 is a member of the basic leucine zipper (bZIP) transcription factor (TF) family in rice (Oryza sativa) isolated from rice (Zhonghua11) panicles. Expression of the OsbZIP52 gene was strongly induced by low temperature (4°C) but not by drought, PEG, salt, or ABA. The subcellular localization of OsbZIP52-GFP in onion (Allium cepa) epidermis cells revealed that OsbZIP52 is a nuclear localized protein. A transactivation assay in yeast demonstrated that OsbZIP52 functions as a transcriptional activator and can specifically bind to the G-box promoter motif. In a yeast two-hybrid (Y-2-H) experiment, OsbZIP52 was able to form homodimeric complexes. Rice plants overexpressing OsbZIP52 showed significantly increased sensitivity to cold and drought stress. Real-time PCR analysis revealed that some abiotic stress-related genes, such as OsLEA3, OsTPP1, Rab25, gp1 precursor, beta-gal, LOC_Os05g11910 and LOC_Os05g39250, were down-regulated in OsbZIP52 overexpression lines. These results suggest that OsbZIP52/RISBZ5 could function as a negative regulator in cold and drought stress environments.	gp1
GLUTELIN PRECURSOR ACCUMULATION3 encodes a regulator of post-Golgi vesicular traffic essential for vacuolar protein sorting in rice endosperm	2014	Plant Cell	State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing 210095, China.	In seed plants, a major pathway for sorting of storage proteins to the protein storage vacuole (PSV) depends on the Golgi-derived dense vesicles (DVs). However, the molecular mechanisms regulating the directional trafficking of DVs to PSVs remain largely elusive. Here, we report the functional characterization of the rice (Oryza sativa) glutelin precursor accumulation3 (gpa3) mutant, which exhibits a floury endosperm phenotype and accumulates excess proglutelins in dry seeds. Cytological and immunocytochemistry studies revealed that in the gpa3 mutant, numerous proglutelin-containing DVs are misrouted to the plasma membrane and, via membrane fusion, release their contents into the apoplast to form a new structure named the paramural body. Positional cloning of GPA3 revealed that it encodes a plant-specific kelch-repeat protein that is localized to the trans-Golgi networks, DVs, and PSVs in the developing endosperm. In vitro and in vivo experiments verified that GPA3 directly interacts with the rice Rab5a-guanine exchange factor VPS9a and forms a regulatory complex with Rab5a via VPS9a. Furthermore, our genetic data support the notion that GPA3 acts synergistically with Rab5a and VPS9a to regulate DV-mediated post-Golgi traffic in rice. Our findings provide insights into the molecular mechanisms regulating the plant-specific PSV pathway and expand our knowledge of vesicular trafficking in eukaryotes.	GPA3
Rice G-protein coupled receptor (GPCR): In silico analysis and transcription regulation under abiotic stress	2011	Plant Signal Behav	International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, India.	Majority of transmembrane signal transduction in response to diverse external stimuli is mediated by G-protein coupled receptors (GPCRs) and are the principal signal transducers. GPCRs are characterized by seven membrane-spanning domains with an extracellular N-terminus and a cytoplasmic C-terminus which functions along with GTP-binding protein in a highly coordinated fashion. Role of heterotrimeric G-proteins in abiotic stresses has been reported, but the response of GPCR is not yet well characterized. In the present study we report the isolation of one putative GPCR (966 bp) from Indica rice (Oryza sativa cv. Indica group Swarna) and described its transcriptional regulation under abiotic stresses. Amino acid sequence analyses shows the presence of typical heptahelical transmembrane spanning domains with extracellular N-terminus involved in ligand binding and cytoplasm facing C-terminus that binds with heterotrimeric G-protein. Sequence analysis also confirmed the presence of all signature motifs required for functional GPCR. Domain and site prediction shows the presence of myristoylation sites for membrane association, and protein kinase C sites for its desensitization. The transcript levels of rice GPCR was induced following NaCl and ABA treatments. However, in drought condition the expression profile of GPCR up regulated during early exposure which subsequently decreased. On the other hand it seems no significant effect due to cold and heat stress. These findings provide a direct evidence for transcriptional regulation of rice GPCR under abiotic stress conditions. These findings also suggest that GPCR can be exploited for promoting stress tolerance in plants.	OsGPCR
The rice pentatricopeptide repeat protein RF5 restores fertility in Hong-Lian cytoplasmic male-sterile lines via a complex with the glycine-rich protein GRP162	2012	Plant Cell	Key Laboratory of the Ministry of Education for Plant Developmental Biology, College of Life Sciences, Wuhan University, Wuhan 430072, China.	The cytoplasmic male sterility (CMS) phenotype in plants can be reversed by the action of nuclear-encoded fertility restorer (Rf) genes. The molecular mechanism involved in Rf gene-mediated processing of CMS-associated transcripts is unclear, as are the identities of other proteins that may be involved in the CMS-Rf interaction. In this study, we cloned the restorer gene Rf5 for Hong-Lian CMS in rice and studied its fertility restoration mechanism with respect to the processing of the CMS-associated transcript atp6-orfH79. RF5, a pentatricopeptide repeat (PPR) protein, was unable to bind to this CMS-associated transcript; however, a partner protein of RF5 (GRP162, a Gly-rich protein encoding 162 amino acids) was identified to bind to atp6-orfH79. GRP162 was found to physically interact with RF5 and to bind to atp6-orfH79 via an RNA recognition motif. Furthermore, we found that RF5 and GRP162 are both components of a restoration of fertility complex (RFC) that is 400 to 500 kD in size and can cleave CMS-associated transcripts in vitro. Evidence that a PPR protein interacts directly with a Gly-rich protein to form a subunit of the RFC provides a new perspective on the molecular mechanisms underlying fertility restoration.	GRP162,OsSUT2|OsSUT2M,Rf1a|Rf5
GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein	2006	Theor Appl Genet	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, 430070 Wuhan, China.	The GS3 locus located in the pericentromeric region of rice chromosome 3 has been frequently identified as a major QTL for both grain weight (a yield trait) and grain length (a quality trait) in the literature. Near isogenic lines of GS3 were developed by successive crossing and backcrossing Minghui 63 (large grain) with Chuan 7 (small grain), using Minghui 63 as the recurrent parent. Analysis of a random subpopulation of 201 individuals from the BC3F2 progeny confirmed that the GS3 locus explained 80-90% of the variation for grain weight and length in this population. In addition, this locus was resolved as a minor QTL for grain width and thickness. Using 1,384 individuals with recessive phenotype (large grain) from a total of 5,740 BC3F2 plants and 11 molecular markers based on sequence information, GS3 was mapped to a DNA fragment approximately 7.9 kb in length. A full-length cDNA corresponding to the target region was identified, which provided complete sequence information for the GS3 candidate. This gene consists of five exons and encodes 232 amino acids with a putative PEBP-like domain, a transmembrane region, a putative TNFR/NGFR family cysteine-rich domain and a VWFC module. Comparative sequencing analysis identified a nonsense mutation, shared among all the large-grain varieties tested in comparison with the small grain varieties, in the second exon of the putative GS3 gene. This mutation causes a 178-aa truncation in the C-terminus of the predicted protein, suggesting that GS3 may function as a negative regulator for grain size. Cloning of such a gene provided the opportunity for fully characterizing the regulatory mechanism and related processes during grain development.	GS3
Evolutionary history of GS3, a gene conferring grain length in rice	2009	Genetics	Faculty of Agriculture, Kyushu University, Fukuoka 812-8581, Japan.	Unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. Here we clone and characterize GS3, an evolutionarily important gene controlling grain size in rice. We show that GS3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to demonstrate that the dominant allele for short grain complements the long-grain phenotype. An association study revealed that a C to A mutation in the second exon of GS3 (A allele) was associated with enhanced grain length in Oryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (theta(pi)) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to a Japonica-like ancestor and demonstrated introgression into the Indica gene pool. This study indicates a critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativa and enhances the potential for genetic manipulation of grain size in rice.	GS3
Multiple and independent origins of short seeded alleles of GS3 in rice	2013	Breed Sci	Faculty of Agriculture, Graduate School, Kyushu University , 6-10-1, Hakozaki, Higashi, Fukuoka 812-8581, Japan.	GRAIN SIZE 3 (GS3) is a cloned gene that is related to seed length. Here we report the discovery of new deletion alleles at the GS3 locus, each of which confer short seed. We selected ten short seeded cultivars from a collection of 282 diverse cultivars. Sequence analysis across the GS3 gene in these ten cultivars identified three novel alleles and a known allele that contain several independent deletion(s) in the fifth exon of GS. These independent deletion variants each resulted in a frameshift mutation that caused a premature stop codon, and they were functionally similar to one another. Each coded for a truncated gene product that behaved as an incomplete dominant allele and conferred a short seeded phenotype. Haplotype analysis of these sequence variants indicated that two of the variants were of japonica origin, and two were from indica. Transformation experiments demonstrated that one of the deletion alleles of GS3 decrease the cell number in the upper epidermis of the glume, resulting in a significant reduction in seed length. The multiple and independent origins of these short seeded alleles indicate that farmers and early breeders imposed artificial selection favoring short seeds.	GS3
GS3 participates in stigma exsertion as well as seed length in rice	2011	Breeding Science	Plant Breeding Laboratory, Faculty of Agriculture, Graduate School, Kyushu University	Stigma exsertion is an important trait that contributes to the improvement of seed production in hybrid rice. We demonstrate that GS3, one of the genes regulating seed length, also regulates stigma length and participates in stigma exsertion in rice. GS3 mRNA is expressed in the basal part of the young stigma, and a nonsense mutation in the second exon of GS3 causes an increase in cell number, resulting in elongation of the stigma. Manipulation of GS3 should contribute to the improvement of hybrid seed-production efficiency.	GS3
A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker	2009	Theor Appl Genet	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, 430070, Wuhan, China.	Comparative sequencing of GS3, the most important grain length (GL) QTL, has shown that differentiation of rice GL might be principally due to a single nucleotide polymorphism (SNP) between C and A in the second exon. A total of 180 varieties representing a wide range of rice germplasm were used for association analysis between C-A mutation and GL in order to confirm the potential causal mutation. A cleaved amplified polymorphic sequence (CAPS) marker, SF28, was developed based on the C-A polymorphism in the GS3 gene. A total of 142 varieties carried allele C with GL from 6.4 to 8.8 mm, while the remaining 38 varieties carried allele A with GL from 8.8 to 10.7 mm. Twenty-four unlinked SSR markers were selected to genotype 180 varieties for population structure analysis. Population structure was observed when the population was classified to three subpopulations. Average GL of either genotype A or genotype C within japonica among the three subpopulations had no significant difference from that in indica, respectively, although indica rice had longer grains on average than japonica in the 180 varieties. However, genotype C always had longer grain length on average than genotype A among three subpopulations. The mutation could explain 79.1, 66.4 and 34.7% of GL variation in the three subpopulations, respectively. These results clearly confirmed the mutation between C and A was highly associated with GL. The SF28 could be a functional marker for improvement of rice grain length.	GS3
Antagonistic actions of HLH/bHLH proteins are involved in grain length and weight in rice	2012	PLoS One	Graduate School of Horticulture, Chiba University, Chiba, Japan.	Grain size is a major yield component in rice, and partly controlled by the sizes of the lemma and palea. Molecular mechanisms controlling the sizes of these organs largely remain unknown. In this study, we show that an antagonistic pair of basic helix-loop-helix (bHLH) proteins is involved in determining rice grain length by controlling cell length in the lemma/palea. Overexpression of an atypical bHLH, named POSITIVE REGULATOR OF GRAIN LENGTH 1 (PGL1), in lemma/palea increased grain length and weight in transgenic rice. PGL1 is an atypical non-DNA-binding bHLH and assumed to function as an inhibitor of a typical DNA-binding bHLH through heterodimerization. We identified the interaction partner of PGL1 and named it ANTAGONIST OF PGL1 (APG). PGL1 and APG interacted in vivo and localized in the nucleus. As expected, silencing of APG produced the same phenotype as overexpression of PGL1, suggesting antagonistic roles for the two genes. Transcription of two known grain-length-related genes, GS3 and SRS3, was largely unaffected in the PGL1-overexpressing and APG-silenced plants. Observation of the inner epidermal cells of lemma revealed that are caused by increased cell length. PGL1-APG represents a new grain length and weight-controlling pathway in which APG is a negative regulator whose function is inhibited by PGL1.	GS3,APG|OsPIL16,PGL1,SRS3
Linking differential domain functions of the GS3 protein to natural variation of grain size in rice	2010	Proc Natl Acad Sci U S A	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Grain yield in many cereal crops is largely determined by grain size. Here we report the genetic and molecular characterization of GS3, a major quantitative trait locus for grain size. It functions as a negative regulator of grain size and organ size. The wild-type isoform is composed of four putative domains: a plant-specific organ size regulation (OSR) domain in the N terminus, a transmembrane domain, a tumor necrosis factor receptor/nerve growth factor receptor (TNFR/NGFR) family cysteine-rich domain, and a von Willebrand factor type C (VWFC) in the C terminus. These domains function differentially in grain size regulation. The OSR domain is both necessary and sufficient for functioning as a negative regulator. The wild-type allele corresponds to medium grain. Loss of function of OSR results in long grain. The C-terminal TNFR/NGFR and VWFC domains show an inhibitory effect on the OSR function; loss-of-function mutations of these domains produced very short grain. This study linked the functional domains of the GS3 protein to natural variation of grain size in rice.	GS3
The plant-specific G protein gamma subunit AGG3 influences organ size and shape in Arabidopsis thaliana	2012	New Phytol	State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	* Control of organ size and shape by cell proliferation and cell expansion is a fundamental developmental process, but the mechanisms that set the size and shape of determinate organs are largely unknown in plants. * Molecular, genetic, cytological and biochemical approaches were used to characterize the roles of the Arabidopsis thaliana G protein gamma subunit (AGG3) gene in organ growth. * Here, we describe A. thaliana AGG3, which promotes petal growth by increasing the period of cell proliferation. Both the N-terminal region and the C-terminal domains of AGG3 are necessary for the function of AGG3. By contrast, analysis of a series of AGG3 derivatives with deletions in specific domains showed that the deletion of any of these domains cannot completely abolish the function of AGG3. The GFP-AGG3 fusion protein is localized to the plasma membrane. The predicted transmembrane domain plays an important role in the plasma membrane localization of AGG3. Genetic analyses revealed that AGG3 action requires a functional G protein alpha subunit (GPA1) and G protein beta subunit (AGB1). * Our findings demonstrate that AGG3, GPA1 and AGB1 act in the same genetic pathway to influence organ size and shape in A. thaliana.	GS3,DEP1|DN1|qPE9-1|OsDEP1
Natural variation in GS5 plays an important role in regulating grain size and yield in rice	2011	Nat Genet	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China.	Increasing crop yield is one of the most important goals of plant science research. Grain size is a major determinant of grain yield in cereals and is a target trait for both domestication and artificial breeding(1). We showed that the quantitative trait locus (QTL) GS5 in rice controls grain size by regulating grain width, filling and weight. GS5 encodes a putative serine carboxypeptidase and functions as a positive regulator of grain size, such that higher expression of GS5 is correlated with larger grain size. Sequencing of the promoter region in 51 rice accessions from a wide geographic range identified three haplotypes that seem to be associated with grain width. The results suggest that natural variation in GS5 contributes to grain size diversity in rice and may be useful in improving yield in rice and, potentially, other crops(2).	GS5
Identification and characterization of dwarf 62, a loss-of-function mutation in DLT/OsGRAS-32 affecting gibberellin metabolism in rice	2010	Planta	Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310029, China.	A dwarf mutant, dwarf 62 (d62), was isolated from rice cultivar 93-11 by mutagenesis with gamma-rays. Under normal growth conditions, the mutant had multiple abnormal phenotypes, such as dwarfism, wide and dark-green leaf blades, reduced tiller numbers, late and asynchronous heading, short roots, partial male sterility, etc. Genetic analysis indicated that the abnormal phenotypes were controlled by the recessive mutation of a single nuclear gene. Using molecular markers, the D62 gene was fine mapped in 131-kb region at the short arm of chromosome 6. Positional cloning of D62 gene revealed that it was the same locus as DLT/OsGRAS-32, which encodes a member of the GRAS family. In previous studies, the DLT/OsGRAS-32 is confirmed to play positive roles in brassinosteroid (BR) signaling. Sequence analysis showed that the d62 carried a 2-bp deletion in ORF region of D62 gene which led to a loss-of-function mutation. The function of D62 gene was confirmed by complementation experiment. RT-PCR analysis and promoter activity analysis showed that the D62 gene expressed in all tested tissues including roots, stems, leaves and panicles of rice plant. The d62 mutant exhibited decreased activity of alpha-amylase in endosperm and reduced content of endogenous GA(1). The expression levels of gibberellin (GA) biosynthetic genes including OsCPS1, OsKS1, OsKO1, OsKAO, OsGA20ox2/SD1 and OsGA2ox3 were significantly increased in d62 mutant. Briefly, these results demonstrated that the D62 (DLT/OsGRAS-32) not only participated in the regulation of BR signaling, but also influenced GA metabolism in rice.	DLT|OsGRAS-32|D62|GS6,OsCPS|OsCPS1,OsKOS4|OsKO1,OsKS1,sd1|GA20ox2
DWARF AND LOW-TILLERING acts as a direct downstream target of a GSK3/SHAGGY-like kinase to mediate brassinosteroid responses in rice	2012	Plant Cell	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	In Arabidopsis thaliana, the GSK3/SHAGGY-like kinase BRASSINOSTEROID-INSENSITIVE2 (BIN2) plays a critical role in the brassinosteroid (BR) signaling pathway by negatively regulating the activities of bri1-EMS-SUPPRESSOR1/BRASSINAZOLE-RESISTANT1 family transcription factors that regulate the expression of downstream BR-responsive genes. In this study, we analyzed the function of a rice (Oryza sativa) GSK3/SHAGGY-like kinase (GSK2), which is one of the orthologs of BIN2. Overexpression of GSK2 (Go) led to plants with typical BR loss-of-function phenotypes, and suppression of GSK2 resulted in enhanced BR signaling phenotypes. DWARF AND LOW-TILLERING (DLT) is a positive regulator that mediates several BR responses in rice. Suppression of DLT can enhance the phenotypes of BR receptor mutant d61-1, and overexpression of DLT obviously suppressed the BR loss-of-function phenotypes of both d61-1 and Go, suggesting that DLT functions downstream of GSK2 to modulate BR responses. Indeed, GSK2 can interact with DLT and phosphorylate DLT. Moreover, brassinolide treatment can induce the dephosphorylation of DLT, leading to the accumulation of dephosphorylated DLT protein. In GSK2 transgenic plants, the DLT phosphorylation level is dictated by the GSK2 level. These results demonstrate that DLT is a GSK2 substrate, further reinforcing that the BIN2/GSK2 kinase has multiple substrates that carry out various BR responses.	DLT|OsGRAS-32|D62|GS6,GSK2,OsGSK4
DWARF AND LOW-TILLERING, a new member of the GRAS family, plays positive roles in brassinosteroid signaling in rice	2009	The Plant Journal	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.	Rapid progress has been made regarding the understanding of brassinosteroid (BR) signaling in Arabidopsis. However, little is known about BR signaling in monotyledons. Here, we characterized a rice dwarf and low-tillering (dlt) mutant and cloned the corresponding gene via map-based cloning. DLT encodes a new member of the plant-specific GRAS family. The dwarf phenotype of dlt is similar to BR-deficient or signaling mutants in rice. In addition, both lamina bending and coleoptile elongation assays show that dlt is insensitive or much less responsive to brassinolide (BL), the most active BR, suggesting that DLT is involved in BR signaling. Consistent with this conclusion, the accumulation of transcripts of BR biosynthesis genes in the dlt mutant indicated that DLT is involved in feedback inhibition of BR biosynthesis genes. In addition, transcription of several other BR-regulated genes is altered in the dlt mutant. Finally, consistent with the fact that DLT is also negatively feedback-regulated by BR treatment, a gel mobility shift assay showed that OsBZR1 can bind to the DLT promoter through the BR-response element. Taken together, these studies have enabled us to identify a new signaling component that is involved in several specific BR responses in rice.	DLT|OsGRAS-32|D62|GS6,OsBZR1
GS6, a member of the GRAS gene family, negatively regulates grain size in rice	2013	J Integr Plant Biol	State Key Laboratory of Plant Physiology and Biochemistry, National Center for Evaluation of Agricultural Wild Plants (Rice), MOE Key Laboratory of Crop Heterosis and Utilization, Beijing 100193, China; Key Laboratory of Crop Genetic Improvement, Department of Plant Genetics and Breeding, China Agricultural University, Beijing 100193, China.	Grain size is an important yield-related trait in rice. Intensive artificial selection for grain size during domestication is evidenced by the larger grains of most of today's cultivars compared with their wild relatives. However, the molecular genetic control of rice grain size is still not well characterized. Here, we report the identification and cloning of Grain Size 6 (GS6), which plays an important role in reducing grain size in rice. A premature stop at the +348 position in the coding sequence (CDS) of GS6 increased grain width and weight significantly. Alignment of the CDS regions of GS6 in 90 rice materials revealed three GS6 alleles. Most japonica varieties (95%) harbor the Type I haplotype, and 62.9% of indica varieties harbor the Type II haplotype. Association analysis revealed that the Type I haplotype tends to increase the width and weight of grains more than either of the Type II or Type III haplotypes. Further investigation of genetic diversity and the evolutionary mechanisms of GS6 showed that the GS6 gene was strongly selected in japonica cultivars. In addition, a "ggc" repeat region identified in the region that encodes the GRAS domain of GS6 played an important historic role in the domestication of grain size in rice. Knowledge of the function of GS6 might aid efforts to elucidate the molecular mechanisms that control grain development and evolution in rice plants, and could facilitate the genetic improvement of rice yield.	DLT|OsGRAS-32|D62|GS6
Grain setting defect 1, encoding a remorin protein, affects the grain setting in rice through regulating plasmodesmatal conductance	2014	Plant Physiol	Institute of Plant Physiology and Ecology, CAS.	Effective grain filling is one of the key determinants of grain setting in rice. Grain setting defect 1 (GSD1), which encodes a putative remorin protein, was found to affect grain setting in rice. Investigation of the phenotype of a T-DNA insertion mutant (grain setting defect 1-Dominant, gsd1-D) with enhanced GSD1 expression revealed abnormalities including a reduced grain setting rate, accumulation of carbohydrates in leaves, and lower soluble sugar content in the phloem exudates. GSD1 was found to be specifically expressed in the plasma membrane and plasmodesmata (PD) of phloem companion cells. Experimental evidence suggests the phenotype of the gsd1-D mutant is caused by defects in the grain filling process as a result of the impaired transport of carbohydrates from the photosynthetic site to the phloem. GSD1 functioned in affecting PD conductance by interacting with OsACT1 in association with the PD callose binding protein PDCB1. Together, our results suggest that GSD1 may play a role in regulating photoassimilate translocation through the symplastic pathway to impact grain setting in rice.	GSD1,OsACT1
GT-2: a transcription factor with twin autonomous DNA-binding domains of closely related but different target sequence specificity	1992	EMBO J	University of California, Berkeley.	A triplet of adjacent, highly similar GT motifs in the phyA promoter of rice functions to support maximal expression of this gene. We have obtained a recombinant clone that encodes a full-length nuclear protein, designated GT-2, which binds specifically to these target sequences. This novel protein contains acidic, basic and proline- + glutamine-rich regions, as well as two autonomous DNA-binding domains, one NH2-terminal and the other COOH-terminal, that discriminate with high resolution between the three GT motifs. A duplicated sequence of 75 amino acids, present once in each DNA-binding domain, appears likely to mediate DNA target element recognition. Each copy of this duplicated protein sequence is predicted to form three amphipathic alpha-helices separated from each other by two short loops. The absence of sequence similarity to other known proteins suggests that this predicted structural unit, which we term the trihelix motif, might be representative of a new class of DNA-binding proteins.	GT-2
The HMG-I/Y protein PF1 stimulates binding of the transcriptional activator GT-2 to the PHYA gene promoter	1999	The Plant Journal	Department of Plant and Microbial Biology, University of California, Berkeley 94720, USA.	The DNA-binding proteins PF1 and GT-2 are factors that bind to different functionally defined, positively acting cis-elements in the PHYA genes of oat and rice, respectively. PF1 is an HMG-I/Y protein, with its cognate cis-element being an AT-rich sequence, designated PE1, whereas GT-2 is a transcriptional activator with twin DNA binding domains that recognize a triplet of GT-boxes in a complex motif designated GTE. To further define the DNA-binding activity of PF1 and to explore potential inter-relationships between the two factors, we have performed a series of in vitro DNA-binding experiments with both PE1 and GTE target sites. The data show that, consistent with its membership of the HMG-I/Y protein family, PF1 can bend DNA when bound to PE1. In addition, PF1 can bind promiscuously, with varying affinity, to other AT-containing motifs, including GTE. When co-incubated with GT-2, PF1 enhances the specific DNA-binding activity of GT-2 toward GTE, the first report of such activity for a plant HMG-I/Y protein. This enhancement takes place without demonstrable physical contact between the two proteins, suggesting the possibility of a novel, indirect mechanism of recruitment involving DNA target-site pre-conditioning. The evidence indicates therefore that PF1 and GT-2 do not perform functionally equivalent roles in positively regulating oat and rice PHYA gene expression. However, the data suggest the possibility that PF1 may act as an architectural factor, promiscuously recognizing a spectrum of AT-containing elements in plant promoters, with the general function of catalyzing enhanced binding of conventional cognate transcriptional regulators to these elements via DNA bending.	GT-2,PF1,PHYA
Transcript profiling of crown rootless1 mutant stem base reveals new elements associated with crown root development in rice	2011	BMC Genomics	Universite Montpellier 2, UMR DAP, Place Eugene Bataillon, 34095 Montpellier Cedex 5, France.	BACKGROUND: In rice, the major part of the post-embryonic root system is made of stem-derived roots named crown roots (CR). Among the few characterized rice mutants affected in root development, crown rootless1 mutant is unable to initiate crown root primordia. CROWN ROOTLESS1 (CRL1) is induced by auxin and encodes an AS2/LOB-domain transcription factor that acts upstream of the gene regulatory network controlling CR development. RESULTS: To identify genes involved in CR development, we compared global gene expression profile in stem bases of crl1 mutant and wild-type (WT) plants. Our analysis revealed that 250 and 236 genes are down- and up-regulated respectively in the crl1 mutant. Auxin induces CRL1 expression and consequently it is expected that auxin also alters the expression of genes that are early regulated by CRL1. To identify genes under the early control of CRL1, we monitored the expression kinetics of a selected subset of genes, mainly chosen among those exhibiting differential expression, in crl1 and WT following exogenous auxin treatment. This analysis revealed that most of these genes, mainly related to hormone, water and nutrient, development and homeostasis, were likely not regulated directly by CRL1. We hypothesized that the differential expression for these genes observed in the crl1 mutant is likely a consequence of the absence of CR formation. Otherwise, three CRL1-dependent auxin-responsive genes: FSM (FLATENNED SHOOT MERISTEM)/FAS1 (FASCIATA1), GTE4 (GENERAL TRANSCRIPTION FACTOR GROUP E4) and MAP (MICROTUBULE-ASSOCIATED PROTEIN) were identified. FSM/FAS1 and GTE4 are known in rice and Arabidopsis to be involved in the maintenance of root meristem through chromatin remodelling and cell cycle regulation respectively. CONCLUSION: Our data showed that the differential regulation of most genes in crl1 versus WT may be an indirect consequence of CRL1 inactivation resulting from the absence of CR in the crl1 mutant. Nevertheless some genes, FAS1/FSM, GTE4 and MAP, require CRL1 to be induced by auxin suggesting that they are likely directly regulated by CRL1. These genes have a function related to polarized cell growth, cell cycle regulation or chromatin remodelling. This suggests that these genes are controlled by CRL1 and involved in CR initiation in rice.	GTE4|OsGTE4,MAP,BTBN18,GIL1,ZOS8-11
A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase	2007	Nat Genet	National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, The Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	Grain weight is one of the most important components of grain yield and is controlled by quantitative trait loci (QTLs) derived from natural variations in crops. However, the molecular roles of QTLs in the regulation of grain weight have not been fully elucidated. Here, we report the cloning and characterization of GW2, a new QTL that controls rice grain width and weight. Our data show that GW2 encodes a previously unknown RING-type protein with E3 ubiquitin ligase activity, which is known to function in the degradation by the ubiquitin-proteasome pathway. Loss of GW2 function increased cell numbers, resulting in a larger (wider) spikelet hull, and it accelerated the grain milk filling rate, resulting in enhanced grain width, weight and yield. Our results suggest that GW2 negatively regulates cell division by targeting its substrate(s) to proteasomes for regulated proteolysis. The functional characterization of GW2 provides insight into the mechanism of seed development and is a potential tool for improving grain yield in crops.	GW2
Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight	2008	Cell Res	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.	Grain weight is a major determinant of crop grain yield and is controlled by naturally occurring quantitative trait loci (QTLs). We earlier identified a major QTL that controls rice grain width and weight, GW5, which was mapped to a recombination hotspot on rice chromosome 5. To gain a better understanding of how GW5 controls rice grain width, we conducted fine mapping of this locus and uncovered a 1 212-bp deletion associated with the increased grain width in the rice cultivar Asominori, in comparison with the slender grain rice IR24. In addition, genotyping analyses of 46 rice cultivars revealed that this deletion is highly correlated with the grain-width phenotype, suggesting that the GW5 deletion might have been selected during rice domestication. GW5 encodes a novel nuclear protein of 144 amino acids that is localized to the nucleus. Furthermore, we show that GW5 physically interacts with polyubiquitin in a yeast two-hybrid assay. Together, our results suggest that GW5 represents a major QTL underlying rice width and weight, and that it likely acts in the ubiquitin-proteasome pathway to regulate cell division during seed development. This study provides novel insights into the molecular mechanisms controlling rice grain development and suggests that GW5 could serve as a potential tool for high-yield breeding of crops.Cell Research (2008) 18:1199-1209. doi: 10.1038/cr.2008.307; published online 18 November 2008.	GW5|qSW5
Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on chromosome 5	2008	Genetics	National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China.	Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F(7) recombinant inbred line (RIL) population derived from a single cross between Asominori (japonica) and IR24 (indica). QTL by environment interactions were evaluated in four environments. Chromosome segment substitution lines (CSSLs) harboring the six additive effect QTL were used to evaluate gene action across eight environments. A major, stable QTL, qGW-5, consistently decreased rice grain width in both the Asominori/IR24 RIL and CSSL populations with the genetic background Asominori. By investigating the distorted segregation of phenotypic values of rice grain width and genotypes of molecular markers in BC(4)F(2) and BC(4)F(3) populations, qGW-5 was dissected into a single recessive gene, gw-5, which controlled both grain width and length-width ratio. gw-5 was narrowed down to a 49.7-kb genomic region with high recombination frequencies on chromosome 5 using 6781 BC(4)F(2) individuals and 10 newly developed simple sequence repeat markers. Our results provide a basis for map-based cloning of the gw-5 gene and for marker-aided gene/QTL pyramiding in rice quality breeding.	GW5|qSW5
Deletion in a gene associated with grain size increased yields during rice domestication	2008	Nat Genet	Institute of the Society for Techno-Innovation of Agriculture, Forestry, and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan.	The domestication of crops involves a complex process of selection in plant evolution and is associated with changes in the DNA regulating agronomically important traits. Here we report the cloning of a newly identified QTL, qSW5 (QTL for seed width on chromosome 5), involved in the determination of grain width in rice. Through fine mapping, complementation testing and association analysis, we found that a deletion in qSW5 resulted in a significant increase in sink size owing to an increase in cell number in the outer glume of the rice flower; this trait might have been selected by ancient humans to increase yield of rice grains. In addition, we mapped two other defective functional nucleotide polymorphisms of rice domestication-related genes with genome-wide RFLP polymorphisms of various rice landraces. These analyses show that the qSW5 deletion had an important historical role in artificial selection, propagation of cultivation and natural crossings in rice domestication, and shed light on how the rice genome was domesticated.	GW5|qSW5
Histone acetyltransferases in rice (Oryza sativa L.): phylogenetic analysis, subcellular localization and expression	2012	BMC Plant Biol	South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.	BACKGROUND: Histone acetyltransferases (HATs) play an important role in eukaryotic transcription. Eight HATs identified in rice (OsHATs) can be organized into four families, namely the CBP (OsHAC701, OsHAC703, and OsHAC704), TAFII250 (OsHAF701), GNAT (OsHAG702, OsHAG703, and OsHAG704), and MYST (OsHAM701) families. The biological functions of HATs in rice remain unknown, so a comprehensive protein sequence analysis of the HAT families was conducted to investigate their potential functions. In addition, the subcellular localization and expression patterns of the eight OsHATs were analyzed. RESULTS: On the basis of a phylogenetic and domain analysis, monocotyledonous CBP family proteins can be subdivided into two groups, namely Group I and Group II. Similarly, dicotyledonous CBP family proteins can be divided into two groups, namely Group A and Group B. High similarities of protein sequences, conserved domains and three-dimensional models were identified among OsHATs and their homologs in Arabidopsis thaliana and maize. Subcellular localization predictions indicated that all OsHATs might localize in both the nucleus and cytosol. Transient expression in Arabidopsis protoplasts confirmed the nuclear and cytosolic localization of OsHAC701, OsHAG702, and OsHAG704. Real-time quantitative polymerase chain reaction analysis demonstrated that the eight OsHATs were expressed in all tissues examined with significant differences in transcript abundance, and their expression was modulated by abscisic acid and salicylic acid as well as abiotic factors such as salt, cold, and heat stresses. CONCLUSIONS: Both monocotyledonous and dicotyledonous CBP family proteins can be divided into two distinct groups, which suggest the possibility of functional diversification. The high similarities of protein sequences, conserved domains and three-dimensional models among OsHATs and their homologs in Arabidopsis and maize suggested that OsHATs have multiple functions. OsHAC701, OsHAG702, and OsHAG704 were localized in both the nucleus and cytosol in transient expression analyses with Arabidopsis protoplasts. OsHATs were expressed constitutively in rice, and their expression was regulated by exogenous hormones and abiotic stresses, which suggested that OsHATs may play important roles in plant defense responses.	OsHAF701,OsHAM701
Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5	2008	Plant Physiol Biochem	Laboratorio de Biofisica y Biologia Molecular, Facultad de Ciencias, Universidad Autonoma del Estado de Morelos, Avenida Universidad 1001, Colonia Chamilpa, 62210 Cuernavaca, Morelos, Mexico.	This work reports the analysis of an additional hemoglobin (hb) gene copy, hb5, in the genome of rice. The amino acid sequence of Hb5 differs from the previously determined rice Hbs 1-4 in missing 11 residues in helix E. Transcripts of hb5 were found to be ubiquitous in rice organs, and hormone- and stress-response promoters exist upstream of the rice hb5 gene. Furthermore, the modeled structure of Hb5 based on the known crystal structure of rice Hb1 is unusual in that the putative distal His is distant from the heme Fe. This observation suggests that Hb5 binds and releases O(2) easily and thus that it functions as an O(2)-carrier or in some aspects of the O(2) metabolism.	Hb5
Identification and linkage mapping of complementary recessive genes causing hybrid breakdown in an intraspecific rice cross	2007	Theor Appl Genet	National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki, 305-8602, Japan.	One outcome of hybrid breakdown is poor growth, which we observed as a reduction in the number of panicles per plant and in culm length in an F(2) population derived from a cross between the genetically divergent rice (Oryza sativa L.) cultivars 'Sasanishiki' (japonica) and 'Habataki' (indica). Quantitative trait locus (QTL) analysis of the two traits and two-way ANOVA of the detected QTLs suggested that the poor growth was due mainly to an epistatic interaction between genes at QTLs located on chromosomes 2 and 11. The poor growth was likely to result when a plant was homozygous for the 'Habataki' allele at the QTL on chromosome 2 and homozygous for the 'Sasanishiki' allele at the QTL on chromosome 11. The results suggest that the poor growth found in the F(2) population was due to hybrid breakdown of a set of complementary genes. To test this hypothesis and determine the precise chromosomal location of the genes causing the hybrid breakdown, we performed genetic analyses using a chromosome segment substitution line, in which a part of chromosome 2 from 'Habataki' was substituted into the genetic background of 'Sasanishiki'. The segregation patterns of poor growth in plants suggested that both of the genes underlying the hybrid breakdown were recessive. The gene on chromosome 2, designated hybrid breakdown 2 (hbd2), was mapped between simple sequence repeat markers RM3515 and RM3730. The gene on chromosome 11, hbd3, was mapped between RM5824 and RM1341.	hbd2|OsCKI1
Interaction of two recessive genes, hbd2 and hbd3, induces hybrid breakdown in rice	2007	Theor Appl Genet	Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan.	Reproductive barriers are important for the maintenance of species identity. We discovered a reproductive barrier via hybrid breakdown among the progeny of a cross between the japonica rice cultivar Koshihikari and the indica rice cultivar Habataki. Genetic analysis indicated that the hybrid breakdown is regulated by the interaction of two recessive genes: hbd2 in Habataki and hbd3 in Koshihikari. Linkage mapping showed that hbd2 is located near the 100 cM region of chromosome 2 in Habataki, whereas hbd3 is located near the 60 cM region of chromosome 11 in Koshihikari. Construction of nearly isogenic lines for hbd2 and Hbd3 (NIL-hbd2 and NIL-Hbd3), as well as a pyramiding line (NIL-hbd2 + Hbd3), confirmed that the hybrid breakdown is induced by the interaction of these two recessive genes. Our results indicate that these genes are novel for the induction of hybrid breakdown in rice.	hbd2|OsCKI1
Gain of deleterious function causes an autoimmune response and Bateson-Dobzhansky-Muller incompatibility in rice	2010	Mol Genet Genomics	Bioscience and Biotechnology Center, Nagoya University, Nagoya, 464-8601, Japan.	Reproductive isolation plays an important role in speciation as it restricts gene flow and accelerates genetic divergence between formerly interbreeding population. In rice, hybrid breakdown is a common reproductive isolation observed in both intra and inter-specific crosses. It is a type of post-zygotic reproductive isolation in which sterility and weakness are manifested in the F(2) and later generations. In this study, the physiological and molecular basis of hybrid breakdown caused by two recessive genes, hbd2 and hbd3, in a cross between japonica variety, Koshihikari, and indica variety, Habataki, were investigated. Fine mapping of hbd2 resulted in the identification of the causal gene as casein kinase I (CKI1). Further analysis revealed that hbd2-CKI1 allele gains its deleterious function that causes the weakness phenotype by a change of one amino acid. As for the other gene, hbd3 was mapped to the NBS-LRR gene cluster region. It is the most common class of R-gene that triggers the immune signal in response to pathogen attack. Expression analysis of pathogen response marker genes suggested that weakness phenotype in this hybrid breakdown can be attributed to an autoimmune response. So far, this is the first evidence linking autoimmune response to post-zygotic isolation in rice. This finding provides a new insight in understanding the molecular and evolutionary mechanisms establishing post-zygotic isolation in plants.	hbd2|OsCKI1
Roles of OsCKI1, a rice casein kinase I, in root development and plant hormone sensitivity	2003	The Plant Journal	National Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.	Casein kinases are critical in cell division and differentiation across species. A rice cDNA fragment encoding a putative casein kinase I (CKI) was identified via cDNA macroarray under brassinosteroid (BR) treatment, and a 1939-bp full-length cDNA, OsCKI1, was isolated and found to encode a putative 463-aa protein. RT-PCR and Northern blot analysis indicated that OsCKI1 was constitutively expressed in various rice tissues and upregulated by treatments with BR and abscisic acid (ABA). Enzymatic assay of recombinant OsCKI1 proteins expressed in Escherichia coli showed that the protein was capable of phosphorylating casein. The physiological roles of OsCKI1 were studied through antisense transgenic approaches, and homozygous transgenic plants showed abnormal root development, including fewer lateral and adventitious roots, and shortened primary roots as a result of reduced cell elongation. Treatment of wild-type plants with CKI-7, a specific inhibitor of CKI, also confirmed these functions of OsCKI1. Interestingly, in transgenic and CKI-7-treated plants, exogenously supplied IAA could restore normal root development, and measurement of free IAA content in CKI-deficient primary and adventitious roots revealed altered auxin content, indicating that OsCKI1 is involved in auxin metabolism or that it may affect auxin levels. Transgenic plants were less sensitive than control plants to ABA or BR treatment during germination, suggesting that OsCKI1 may be involved in various hormone-signaling pathways. OsCKI1-GFP fusion studies revealed the localization of OsCKI1 to the nucleus, suggesting a possible involvement in regulation of gene expression. In OsCKI1-deficient plants, differential gene expression was investigated using cDNA chip technology, and results indicated that genes related to signal transduction and hormone metabolism were indeed with altered expression.	hbd2|OsCKI1
Systematic identification of novel protein domain families associated with nuclear functions	2002	Genome Res	European Molecular Biology Laboratory, 69114 Heidelberg, Germany. doerks@embl-heidelberg.de	A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic lineages, but 3 are species specific. For about 500 of the 1200 proteins that contain these new domains, nuclear localization could be inferred, and for 700, additional features could be predicted. For example, we identified a new domain, likely to have a role downstream of the unfolded protein response; a nematode-specific signalling domain; and a widespread domain, likely to be a noncatalytic homolog of ubiquitin-conjugating enzymes.	Hd1
An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15	2011	N Biotechnol	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	In plants, flowering as a crucial developmental event is highly regulated by both genetic programs and environmental signals. Genetic analysis of flowering time mutants is instrumental in dissecting the regulatory pathways of flowering induction. In this study, we isolated the OsLF gene by its association with the T-DNA insertion in the rice late flowering mutant named A654. The OsLF gene encodes an atypical HLH protein composed of 419 amino acids (aa). Overexpression of the OsLF gene in wild type rice recapitulated the late flowering phenotype of A654, indicating that the OsLF gene negatively regulates flowering. Flowering genes downstream of OsPRR1 such as OsGI and Hd1 were down regulated in the A654 mutant. Yeast two hybrid and colocalization assays revealed that OsLF interacts strongly with OsPIL13 and OsPIL15 that are potentially involved in light signaling. In addition, OsPIL13 and OsPIL15 colocalize with OsPRR1, an ortholog of the Arabidopsis APRR1 gene that controls photoperiodic flowering response through clock function. Together, these results suggest that overexpression of OsLF might repress expression of OsGI and Hd1 by competing with OsPRR1 in interacting with OsPIL13 and OsPIL15 and thus induce late flowering.	Hd1,OsGI,OsLF,OsPIL13|OsPIL1,OsPIL15,OsPRR1
Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map	1997	TAG Theoretical and Applied Genetics	Rice Genome Research Program (RGP), National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305, Japan 	Quantitative trait locus (QTL) analysis has been carried out to identify genes conferring heading date in rice. One hundred and eighty six F2 plants derived from a cross between a japonica variety, Nipponbare, and an indica variety, Kasalath, were used as a segregating population for QTL mapping and more than 850 markers were employed to identify QTLs. Scan-analysis revealed the existence of two QTLs with large effects, Hd-1 and Hd-2, one in the middle of chromosome 6 and one at the end of chromosome 7, respectively. For both loci, the Kasalath alleles reduced days-to-heading. In addition, three QTLs with minor effects, Hd-3, Hd-4 and Hd-5, were found to be located on chromosomes 6, 7 and 8 based on a secondary scan analysis which was carried out by removing the phenotypic effects of Hd-1 and Hd-2. For the three secondary loci, the Nipponbare alleles reduced days-to-heading. The five QTLs explained 84% of the total phenotypic variation in the F2 population based on a multiple-QTL model. The presence of a digenic interaction between Hd-1 and Hd-2 was clearly suggested.	Hd1
Fine mapping of quantitative trait loci Hd-1 , Hd-2 and Hd-3 , controlling heading date of rice, as single Mendelian factors	1998	TAG Theoretical and Applied Genetics	Rice Genome Research Program, Institute of Society for Techno-innovation of Agriculture, Forestry and Fisheries (STAFF), Tsukuba, Ibaraki 305, Japan, JP	Fine mapping was carried out on three putative QTLs (tentatively designated as Hd-1 to Hd-3) of five such QTLs controlling heading date in rice that had been earlier identified using an F2 population derived from a cross between a japonica variety, ‘Nipponbare’, and an indica variety, ‘Kasalath’, using progeny backcrossed with ‘Nipponbare’ as the recurrent parent. One BC3F2 and two BC3F1 plants, in which the target QTL regions were heterozygous and most other chromosomal regions were homozygous for the ‘Nipponbare’ allele, were selected as the experimental material. Self-pollinated progeny (BC3F2 and BC3F3) of the BC3F1 or BC3F2 showed continuous variation in days to heading. By means of progeny testing based on BC3F3 or BC3F4 lines, we determined the genotypes of each BC3F2 or BC3F3 individual at target QTLs. Their segregation patterns fitted Mendelian inheritance ratios. When the results obtained by RFLP analysis and progeny tests were combined, Hd-1, Hd-2 and Hd-3 were mapped precisely on chromosomes 6, 7 and 6, respectively, of a rice RFLP linkage map. The results demonstrated that QTLs can be treated as Mendelian factors. Moreover, these precise locations were in good agreement with the regions estimated by QTL analysis of the initial F2 population, demonstrating the high reliability of QTL mapping using a high-density linkage map.	Hd1,Hd3a
Characterization and detection of epistatic interactions of 3 QTLs, Hd1 , Hd2 , and Hd3, controlling heading date in rice using nearly isogenic lines	2000	TAG Theoretical and Applied Genetics	Bio-oriented Technology Research Advancement Institution, Omiya, Saitama 331-8537, Japan, JP	To characterize quantitative trait loci (QTLs), we used marker-assisted selection (MAS) to develop three nearly isogenic lines (NILs) differing only for the presence of a single, specific QTL (QTL-NILs) –Hd1, Hd2, and Hd3 – for heading date in rice. The three lines contained the chromosomal region of the target QTL from donor variety Kasalath(indica) in the genetic background of var. Nipponbare (japonica). To analyze epistatic interactions in pairs of these QTLs, we also used MAS to develop four combined QTL-NILs with 2 of the 3 QTLs or with all 3. Different daylength treatment testing of the QTL-NILs revealed that the three QTLs control photoperiod sensitivity. Genetic analysis of F2 populations derived from crosses between the three QTL-NILs with a single QTL using molecular markers revealed the existence of epistatic interactions between Hd1 and Hd2, and Hd2 and Hd3. These interactions were also confirmed by the analysis of combined QTL-NILs under different daylength conditions. The existence of an epistatic interaction between Hd1 and Hd3 was also clarified. Based on these results, we suggest that the Kasalath allele of Hd3 does not affect photoperiod sensitivity by itself but that it is involved in enhancement of the expression of the Nipponbare alleles of Hd1 and Hd2.	Hd1
Phytochrome B regulates Heading date 1 (Hd1)-mediated expression of rice florigen Hd3a and critical day length in rice	2011	Mol Genet Genomics	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, 630-0192, Japan.	Many plants require circadian clock and light information for the photoperiodic control of flowering. In Arabidopsis, a long-day plant (LDP), flowering is triggered by the circadian clock-controlled expression of CONSTANS (CO) and light stabilization of the CO protein to induce FT (FLOWERING LOCUS T). In rice, a short-day plant (SDP), the CO ortholog Heading date 1 (Hd1) regulates FT ortholog Hd3a, but regulation of Hd3a by Hd1 differs from that in Arabidopsis. Here, we report that phytochrome B (phyB)-mediated suppression of Hd3a is a primary cause of long-day suppression of flowering in rice, based on the three complementary discoveries. First, overexpression of Hd1 causes a delay in flowering under SD conditions and this effect requires phyB, suggesting that light modulates Hd1 control of Hd3a transcription. Second, a single extension of day length decreases Hd3a expression proportionately with the length of daylight. Third, Hd1 protein levels in Hd1-overexpressing plants are not altered in the presence of light. These results also suggest that phyB-mediated suppression of Hd3a expression is a component of the molecular mechanism for critical day length in rice.	Hd1,Hd3a,PHYB|OsphyB
Interactive effects of two heading-time loci, Se1 and Ef1, on pre-flowering developmental phases in rice (Oryza sativa L.)	2002	Euphytica	Faculty of Agriculture, Kagoshima University, Kagoshima, 890-0065, Japan	The interaction between the Se1 and the Ef1 loci, which chiefly control the photoperiod sensitivity (PS) and the basic vegetative growth (BVG) period of rice (Oryza sativa L.) respectively, was investigated using four tester lines different in genotype for the two heading time loci from each other. The four tester lines were grown under 10, 13, 14, 15, and 16h daylengths to estimate their BVG period and PS. The Taiwanese cultivar Taichung 65 (T65), one of the tester lines, has an extremely long BVG period that has been considered to be conferred by a late heading-time allele ef1 at the Ef1 locus. Experimental results, however, showed that the extremely long BVG of T65 was conferred not by a single effect of ef1 but by a complementary effect of ef1 and Se1-e, a photoperiod insensitivity allele, at the Se1 locus. It was also found that a complementary effect of a PS allele Se1-n at the Se1 locus and ef1 stimulates the PS of rice. Gene analysis for heading time under an optimum daylength (10 h) as well as under natural daylength confirmed the presence of the complementary effect of the two nonallelic genes on BVG, which was found only with homozygosity of both the genes. Based on these results and earlier reports on the Se1 locus, the roles of the Se1 and Ef1 loci on the durations of pre-flowering developmental phases in rice were discussed.	Hd1
Heading date 1 (Hd1), an ortholog of Arabidopsis CONSTANS, is a possible target of human selection during domestication to diversify flowering times of cultivated rice	2011	Genes Genet Syst	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology	During the domestication of rice (Oryza sativa L.), diversification of flowering time was important in expanding the areas of cultivation. Rice is a facultative short day (SD) plant and requires certain periods of dark to induce flowering. Heading date 1 (Hd1), a regulator of the florigen gene Hd3a, is one of the main factors used to generate diversity in flowering. Loss-of-function alleles of Hd1 are common in cultivated rice and cause the diversity of flowering time. However, it is unclear how these functional nucleotide polymorphisms of Hd1 accumulated in the course of evolution. Nucleotide polymorphisms within Hd1 and Hd3a were analyzed in 38 accessions of ancestral wild rice Oryza rufipogon and compared with those of cultivated rice. In contrast to cultivated rice, no nucleotide changes affecting Hd1 function were found in 38 accessions of wild rice ancestors. No functional changes were found in Hd3a in either cultivated or ancestral rice. A phylogenetic analysis indicated that evolution of the Hd1 alleles may have occurred independently in cultivars descended from various accessions of ancestral rice. The non-functional Hd1 alleles found in cultivated rice may be selected during domestication, because they were not found or very rare in wild ancestral rice. In contrast with Hd3a, which has been highly conserved, Hd1 may have undergone human selection to diversify the flowering times of rice during domestication or the early stage of the cultivation period.	Hd1
Functional analyses of the flowering time gene OsMADS50, the putative SUPPRESSOR OF OVEREXPRESSION OF CO 1/AGAMOUS-LIKE 20 (SOC1/AGL20) ortholog in rice	2004	Plant J	National Research Laboratory of Plant Functional Genomics, Division of Molecular and Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea.	A late-flowering mutant was isolated from rice T-DNA-tagging lines. T-DNA had been integrated into the K-box region of Oryza sativa MADS50 (OsMADS50), which shares 50.6% amino acid identity with the Arabidopsis MADS-box gene SUPPRESSOR OF OVEREXPRESSION OF CO 1/AGAMOUS-LIKE 20 (SOC1/AGL20). While overexpression of OsMADS50 caused extremely early flowering at the callus stage, OsMADS50 RNAi plants exhibited phenotypes of late flowering and an increase in the number of elongated internodes. This confirmed that the phenotypes observed in the knockout (KO) plants are because of the mutation in OsMADS50. RT-PCR analyses of the OsMADS50 KO and ubiquitin (ubi):OsMADS50 plants showed that OsMADS50 is an upstream regulator of OsMADS1, OsMADS14, OsMADS15, OsMADS18, and Hd (Heading date)3a, but works either parallel with or downstream of Hd1 and O. sativa GIGANTEA (OsGI). These results suggest that OsMADS50 is an important flowering activator that controls various floral regulators in rice.	Hd1,Hd3a,OsGI,OsMADS1|LHS1|AFO,OsMADS14,OsMADS15|DEP,OsMADS18,OsMADS50|OsSOC1|DTH3
The effect of the crosstalk between photoperiod and temperature on the heading-date in rice	2009	PLoS One	Department of Biological Sciences and Biotechnology, Tsinghua University, Beijing, People's Republic of China.	Photoperiod and temperature are two important environmental factors that influence the heading-date of rice. Although the influence of the photoperiod on heading has been extensively reported in rice, the molecular mechanism for the temperature control of heading remains unknown. This study reports an early heading mutant derived from tissue culture lines of rice and investigates the heading-date of wild type and mutant in different photoperiod and temperature treatments. The linkage analysis showed that the mutant phenotype cosegregated with the Hd1 locus. Sequencing analysis found that the mutant contained two insertions and several single-base substitutions that caused a dramatic reduction in Hd1mRNA levels compared with wild type. The expression patterns of Hd1 and Hd3a were also analyzed in different photoperiod and temperature conditions, revealing that Hd1 mRNA levels displayed similar expression patterns for different photoperiod and temperature treatments, with high expression levels at night and reduced levels in the daytime. In addition, Hd1 displayed a slightly higher expression level under long-day and low temperature conditions. Hd3a mRNA was present at a very low level under low temperature conditions regardless of the day-length. This result suggests that suppression of Hd3a expression is a principle cause of late heading under low temperature and long-day conditions.	Hd1,Hd3a
Pleiotropism of the photoperiod-insensitive allele of Hd1 on heading date, plant height and yield traits in rice	2012	PLoS One	State Key Laboratory of Rice Biology and Chinese National Center for Rice Improvement, China National Rice Research Institute, Hangzhou, China.	Five populations segregated in isogenic backgrounds and three sets of near isogenic lines (NILs) overlapping in a 362.3-kb region covering heading date gene Hd1 were developed from the indica rice cross Zhenshan97 (ZS97)/Milyang 46 (MY46). They were used to analyze the effects of Hd1 on heading date, plant height and yield traits. In a background of the parental mixtures, the photoperiod-sensitive allele derived from ZS97 functioned in promoting and delaying flowering in the natural short-day and long-day conditions, respectively. In the background of ZS97, no response to the photoperiod was observed, whereas the photoperiod-insensitive allele derived from MY46 functioned in delaying flowering, increasing plant height, and enhancing grain productivity. The additive effects estimated in two NIL sets were 6.14 and 6.14 d for heading date, 4.46 and 5.55 cm for plant height, 10.82 and 11.54 for the number of spikelets per panicle, 6.82 and 8.00 for the number of grains per panicle, and 2.16 and 2.23 g for grain yield per plant, which explained 94.1% and 96.3%, 70.5% and 84.8%, 52.4% and 55.2%, 28.9% and 39.2%, and 36.5% and 26.9% of the phenotypic variances, respectively. Since the photoperiod-insensitive allele of Hd1 confers a long vegetative phase, it is a good candidate for breeding rice varieties with high yielding potential for low latitudes.	Hd1
Hd1, a Major Photoperiod Sensitivity Quantitative Trait Locus in Rice, Is Closely Related to the Arabidopsis Flowering Time Gene CONSTANS	2000	The Plant Cell Online	National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602, Japan.	A major quantitative trait locus (QTL) controlling response to photoperiod, Hd1, was identified by means of a map-based cloning strategy. High-resolution mapping using 1505 segregants enabled us to define a genomic region of approximately 12 kb as a candidate for Hd1. Further analysis revealed that the Hd1 QTL corresponds to a gene that is a homolog of CONSTANS in Arabidopsis. Sequencing analysis revealed a 43-bp deletion in the first exon of the photoperiod sensitivity 1 (se1) mutant HS66 and a 433-bp insertion in the intron in mutant HS110. Se1 is allelic to the Hd1 QTL, as determined by analysis of two se1 mutants, HS66 and HS110. Genetic complementation analysis proved the function of the candidate gene. The amount of Hd1 mRNA was not greatly affected by a change in length of the photoperiod. We suggest that Hd1 functions in the promotion of heading under short-day conditions and in inhibition under long-day conditions.	Hd1
Suppression of the floral activator Hd3a is the principal cause of the night break effect in rice	2005	Plant Cell	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, Takayama, Ikoma, Japan.	A short exposure to light in the middle of the night causes inhibition of flowering in short-day plants. This phenomenon is called night break (NB) and has been used extensively as a tool to study the photoperiodic control of flowering for many years. However, at the molecular level, very little is known about this phenomenon. In rice (Oryza sativa), 10 min of light exposure in the middle of a 14-h night caused a clear delay in flowering. A single NB strongly suppressed the mRNA of Hd3a, a homolog of Arabidopsis thaliana FLOWERING LOCUS T (FT), whereas the mRNAs of OsGI and Hd1 were not affected. The NB effect on Hd3a mRNA was maximal in the middle of the 14-h night. The phyB mutation abolished the NB effect on flowering and Hd3a mRNA, indicating that the NB effect was mediated by phytochrome B. Because expression of the other FT-like genes was very low and not appreciably affected by NB, our results strongly suggest that the suppression of Hd3a mRNA is the principal cause of the NB effect on flowering in rice.	Hd1,Hd3a
Identification of dynamin as an interactor of rice GIGANTEA by tandem affinity purification (TAP)	2008	Plant Cell Physiol	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan.	GIGANTEA (GI), CONSTANS (CO) and FLOWERING LOCUS T (FT) regulate photoperiodic flowering in Arabidopsis. In rice, OsGI, Hd1 and Hd3a were identified as orthologs of GI, CO and FT, respectively, and are also important regulators of flowering. Although GI has roles in both flowering and the circadian clock, our understanding of its biochemical functions is still limited. In this study, we purified novel OsGI-interacting proteins by using the tandem affinity purification (TAP) method. The TAP method has been used effectively in a number of model species to isolate proteins that interact with proteins of interest. However, in plants, the TAP method has been used in only a few studies, and no novel proteins have previously been isolated by this method. We generated transgenic rice plants and cell cultures expressing a TAP-tagged version of OsGI. After a two-step purification procedure, the interacting proteins were analyzed by mass spectrometry. Seven proteins, including dynamin, were identified as OsGI-interacting proteins. The interaction of OsGI with dynamin was verified by co-immunoprecipitation using a myc-tagged version of OsGI. Moreover, an analysis of Arabidopsis dynamin mutants indicated that although the flowering times of the mutants were not different from those of wild-type plants, an aerial rosette phenotype was observed in the mutants. We also found that OsGI is present in both the nucleus and the cytosol by Western blot analysis and by transient assays. These results indicate that the TAP method is effective for the isolation of novel proteins that interact with target proteins in plants.	Hd1,Hd3a,OsGI
Breeding strategies for optimum heading date using genotypic information in rice	2009	Molecular Breeding	State Key Laboratory for Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, 210095, Nanjing, China	Heading date (HD) is a key trait for the adaptation of rice cultivar to a specific growing region. Here, we report conventional and marker-assisted breeding strategies using genetic information related to the determination of HD, where the breeding objectives were to avoid the delayed heading common in indica × japonica hybrids, to increase the efficiency in selecting hybrid rice combinations having a suitable growth duration, and to develop cultivars with target growth duration by quantitative trait locus (QTL) pyramiding. The allelic constitution at the major HD loci was determined for a set of 109 leading Chinese rice cultivars by crossing them with HD tester lines. It was shown that the late heading in indica × japonica hybrids can be overcome by replacing the strong photoperiod-sensitivity allele Se-1 n with Se-1 e . A breeding strategy to enable the selection of hybrid combinations with suitable growth duration was proposed, based on HD genotypic information in rice. Meanwhile, a QTL analysis for HD was conducted over five years based on a recombinant inbred line population, derived from two parents Asominori (japonica) and IR24 (indica). Four QTLs, located on chromosomes 2, 3, 6, and 8, respectively, could be detected in all five years, indicating they were stably expressed QTL. According to this QTL information, and taking Asominori as an example, the HD genotypes for improving the growth duration were designed, and the best breeding selection schemes were determined by use of a genetic breeding simulation tool. Results obtained in this study demonstrate that genetic information related to HD can make a significant contribution to rice breeding.	Hd1
SPIN1, a K homology domain protein negatively regulated and ubiquitinated by the E3 ubiquitin ligase SPL11, is involved in flowering time control in rice	2008	Plant Cell	Department of Plant Pathology, Plant Molecular Biology and Biotechnology Program, Ohio State University, Columbus, Ohio 43210, USA.	The rice (Oryza sativa) E3 ligase SPOTTED LEAF11 (SPL11) negatively regulates programmed cell death and disease resistance. We demonstrate here that SPL11 also regulates flowering via interaction with SPIN1 (for SPL11-interacting protein1), a Signal Transduction and Activation of RNA family member. SPIN1 binds RNA and DNA in vitro and interacts with SPL11 in the nucleus. Spl11 mutants have delayed flowering under long-day conditions. Spin1 overexpression causes late flowering independently of daylength; expression analyses of flowering marker genes in these lines suggested that SPIN1 represses flowering by downregulating the flowering promoter gene Heading date3a (Hd3a) via Hd1-dependent mechanisms in short days and by targeting Hd1-independent factors in long days. Both Spin1 and Spl11 are regulated diurnally in opposing phases. SPL11 negatively regulates Spin1 transcript levels, while SPIN1 also affects Spl11 expression. Moreover, we show that coincidence of high accumulation of Spin1 mRNA with the light in the morning and early evening is needed to repress flowering. SPIN1 is monoubiquitinated by SPL11, suggesting that it is not targeted for degradation. Our data are consistent with a model in which SPIN1 acts as a negative regulator of flowering that itself is negatively regulated by SPL11, possibly via ubiquitination.	Hd1,Hd3a,SPIN1,SPL11
Rice early flowering1, a CKI, phosphorylates DELLA protein SLR1 to negatively regulate gibberellin signalling	2010	EMBO J	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China.	The plant hormone gibberellin (GA) is crucial for multiple aspects of plant growth and development. To study the relevant regulatory mechanisms, we isolated a rice mutant earlier flowering1, el1, which is deficient in a casein kinase I that has critical roles in both plants and animals. el1 had an enhanced GA response, consistent with the suppression of EL1 expression by exogenous GA(3). Biochemical characterization showed that EL1 specifically phosphorylates the rice DELLA protein SLR1, proving a direct evidence for SLR1 phosphorylation. Overexpression of SLR1 in wild-type plants caused a severe dwarf phenotype, which was significantly suppressed by EL1 deficiency, indicating the negative effect of SLR1 on GA signalling requires the EL1 function. Further studies showed that the phosphorylation of SLR1 is important for maintaining its activity and stability, and mutation of the candidate phosphorylation site of SLR1 results in the altered GA signalling. This study shows EL1 a novel and key regulator of the GA response and provided important clues on casein kinase I activities in GA signalling and plant development.	CKI|EL1|Hd16,SLR1|OsGAI
Rice homeobox transcription factor HOX1a positively regulates gibberellin responses by directly suppressing EL1	2011	J Integr Plant Biol	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institute for Biological Sciences, the Chinese Academy of Sciences, Shanghai 200032, China.	Homeobox transcription factors are involved in various aspects of plant development, including maintenance of the biosynthesis and signaling pathways of different hormones. However, few direct targets of homeobox proteins have been identified. We here show that overexpression of rice homeobox gene HOX1a resulted in enhanced gibberellin (GA) response, indicating a positive effect of HOX1a in GA signaling. HOX1a is induced by GA and encodes a homeobox transcription factor with transcription repression activity. In addition, HOX1a suppresses the transcription of early flowering1 (EL1), a negative regulator of GA signaling, and further electrophoretic mobility shift assay and chromatin immunoprecipitation analysis revealed that HOX1a directly bound to the promoter region of EL1 to suppress its expression and stimulate GA signaling. These results demonstrate that HOX1a functions as a positive regulator of GA signaling by suppressing EL1, providing informative hints on the study of GA signaling.	CKI|EL1|Hd16,HAZ1|HOX1a
Identification of a novel gene ef7 conferring an extremely long basic vegetative growth phase in rice	2009	Theor Appl Genet	Graduate School of Agriculture, Kyoto University, Kitashirakawa, Sakyou, Kyoto, 606-8502, Japan.	A late heading-time mutant line, HS276, which was induced by gamma-irradiation of seeds of the japonica rice (Oryza sativa L.) variety Gimbozu, exhibits an extremely long basic vegetative growth phase (BVP). A genetic analysis using the F(2) population from the cross between HS276 and Gimbozu revealed that the late heading of HS276 is governed by a single recessive mutant gene. The subsequent analysis on heading responses of HS276 and Gimbozu to four photoperiods (12, 13, 14, and 15 h) and to the photoperiodic transfer treatment from a short photoperiod to a long photoperiod revealed that the mutant gene confers an extremely long BVP and increases photoperiod sensitivity under long photoperiod (14 and 15 h). The BVP durations of HS276 and Gimbozu were estimated at 30.1 and 16.0 days, respectively; the mutant gene, compared with its wild type allele, elongates the duration of BVP by 14 days. Linkage analysis showed that the mutant gene is located in the 129 kb region between the two INDEL markers, INDELAP0399_6 and INDELAP3487_2, on the distal part of the short arm of chromosome 6. None of the other BVP genes are located in this region; therefore, we declared this a newly detected mutant gene and designated it ef7. A recently established program to breed rice suitable for low latitudes, where short photoperiodic conditions continue throughout the year, aims to develop varieties with extremely long BVPs and weak photoperiod sensitivities; the mutant gene ef7, therefore, will be quite useful in these programs because it confers an extremely long BVP and little enhances photoperiod sensitivity under short photoperiod.	Hd17|Ef7|OsELF3-1
OsELF3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice	2013	Mol Plant	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research-Wuhan, Huazhong Agricultural University, Wuhan 430070, China.	Heading date is a critical trait that determines cropping seasons and regional adaptability in rice (Oryza sativa). Research efforts during the last decade have identified some important photoperiod pathway genes that are conserved between Arabidopsis and rice. In this study, we identified a novel gene, Oryza sativa ELF3 (OsELF3), which is a putative homolog of the ELF3 gene in Arabidopsis thaliana. OsELF3 was required for the control of heading date under long-day conditions. Its Tos17-tagging mutants exhibited a delayed heading date phenotype only under long-day, but not short-day, conditions. OsELF3 was highly expressed in leaf blades, and the OsELF3 protein was localized in the nucleolus. An obvious diurnal rhythm of OsELF3 transcript level was observed, with a trough in the early day and a peak in the late night in wild-type plants. However, this expression pattern was disrupted in oself3 mutants. Further investigations showed that the expression of OsGI and Ghd7 was up-regulated in the oself3 mutant, indicating that OsELF3 acts as a negative regulator upstream of OsGI and Ghd7 in the flowering-time control under long-day conditions. The rhythmic expression of circadian clock-related genes, including some OsPRR members, was obviously affected in oself3 mutants. Our results indicated that OsELF3 acts as a floral activator in the long-day photoperiodic pathway via its crosstalk with the circadian clock in rice.	Hd17|Ef7|OsELF3-1,OsGI
Ef7 encodes an ELF3-like protein and promotes rice flowering by negatively regulating the floral repressor gene Ghd7 under both short- and long-day conditions	2012	Plant Cell Physiol	Graduate School of Agriculture, Kyoto University, Kyoto, Japan.	Much progress has been made in our understanding of photoperiodic flowering of rice and the mechanisms underlying short-day (SD) promotion and long-day (LD) repression of floral induction. In this study, we identified and characterized the Ef7 gene, one of the rice orthologs of Arabidopsis EARLY FLOWERING 3 (ELF3). The ef7 mutant HS276, which was induced by gamma-irradiation of the japonica rice cultivar 'Gimbozu', flowers late under both SD and LD conditions. Expression analyses of flowering time-related genes demonstrated that Ef7 negatively regulates the expression of Ghd7, which is a repressor of the photoperiodic control of rice flowering, and consequently up-regulates the expression of the downstream Ehd1 and FT-like genes under both SD and LD conditions. Genetic analyses with a non-functional Ghd7 allele provided further evidence that the delayed flowering of ef7 is mediated through the Ghd7 pathway. The analysis of light-induced expression of Ghd7 revealed that the ef7 mutant was more sensitive to red light than the wild-type plant, but the gate of Ghd7 expression was unchanged. Thus, our results show that Ef7 functions as a floral promoter by repressing Ghd7 expression under both SD and LD conditions.	Hd17|Ef7|OsELF3-1
Phytochrome dependent quantitative control of Hd3a transcription is the basis of the night break effect in rice flowering	2009	Genes Genet Syst	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology	A short exposure to light during relative night (night break; NB) delays flowering in the short day plant rice. NB acts by downregulating Heading date 3a (Hd3a) expression. Because phytochrome B mutants do not respond to NB and their flowering time is not affected even under NB conditions, phyB is required for the suppression of Hd3a expression. The effect of NB is quantitatively controlled by light quality and by either light intensity or duration. However, the molecular mechanisms that regulate these interactions are poorly understood. Here, we examine the roles of phytochromes in the regulation of Hd3a transcription under NB conditions using monochromatic red, far-red and blue light. Red and blue light downregulated Hd3a expression, but far-red light NB did not. The effect of red light NB on Hd3a is dependent on photon fluence and is restored by subsequent far-red light irradiation. Our results suggest that quantitative effect of light on flowering in rice NB is mediated by the regulation of Hd3a transcription by phyB.	Hd3a
NECK LEAF 1, a GATA type transcription factor, modulates organogenesis by regulating the expression of multiple regulatory genes during reproductive development in rice	2009	Cell Res	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Graduate School of the Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	In the monocot rice species Oryza sativa L., one of the most striking morphological processes during reproductive development is the concurrence of panicle development with the sequential elongation of upper internodes (UPIs). To elucidate the underlying molecular mechanisms, we cloned the rice gene NECK LEAF 1 (NL1), which when mutated results in delays in flowering time, smaller panicles with overgrown bracts and abnormal UPI elongation patterns. The NL1 gene encodes a GATA-type transcription factor with a single zinc finger domain, and its transcripts are detected predominantly in the bract primordia, which normally degenerate in the wild-type plants. Overexpression of NL1 in transgenic plants often gives rise to severe growth retardation, less vegetative phytomers and smaller leaves, suggesting that NL1 plays an important role in organ differentiation. A novel mutant allele of PLASTOCHRON1 (PLA1), a gene known to play a key role in regulating leaf initiation, was identified in this study. Genetic analysis demonstrated an interaction between nl1 and pla1, with NL1 acting upstream of PLA1. The expression level and spatial pattern of PLA1 were found to be altered in the nl1 mutant. Furthermore, the expression of two regulators of flowering, Hd3a and OsMADS1, was also affected in the nl1 mutant. On the basis of these findings, we propose that NL1 is an intrinsic factor that modulates and coordinates organogenesis through regulating the expression of PLA1 and other regulatory genes during reproductive development in rice.	Hd3a,NL1,OsMADS1|LHS1|AFO,PLA1
Hd3a and RFT1 are essential for flowering in rice	2008	Development	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan.	RICE FLOWERING LOCUS T 1 (RFT1/FT-L3) is the closest homologue of Heading date 3a (Hd3a), which is thought to encode a mobile flowering signal and promote floral transition under short-day (SD) conditions. RFT1 is located only 11.5 kb from Hd3a on chromosome 6. Although RFT1 RNAi plants flowered normally, double RFT1-Hd3a RNAi plants did not flower up to 300 days after sowing (DAS), indicating that Hd3a and RFT1 are essential for flowering in rice. RFT1 expression was very low in wild-type plants, but there was a marked increase in RFT1 expression by 70 DAS in Hd3a RNAi plants, which flowered 90 DAS. H3K9 acetylation around the transcription initiation site of the RFT1 locus had increased by 70 DAS but not at 35 DAS. In the absence of Hd3a and RFT1 expression, transcription of OsMADS14 and OsMADS15, two rice orthologues of Arabidopsis APETALA1, was strongly reduced, suggesting that they act downstream of Hd3a and RFT1. These results indicate that Hd3a and RFT1 act as floral activators under SD conditions, and that RFT1 expression is partly regulated by chromatin modification.	Hd3a,OsMADS14,OsMADS15|DEP,RFT1
RBS1, an RNA Binding Protein, Interacts with SPIN1 and Is Involved in Flowering Time Control in Rice	2014	PLoS One	State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China ; College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.	The rice U-box/ARM E3 ubiquitin ligase SPL11 negatively regulates programmed cell death (PCD) and disease resistance, and controls flowering time through interacting with the novel RNA/DNA binding KH domain protein SPIN1. Overexpression of Spin1 causes late flowering in transgenic rice under short-day (SD) and long-day (LD) conditions. In this study, we characterized the function of the RNA-binding and SPIN1-interacting 1 (RBS1) protein in flowering time regulation. Rbs1was identified in a yeast-two-hybrid screen using the full-length Spin1 cDNA as a bait and encodes an RNA binding protein with three RNA recognition motifs. The protein binds RNA in vitro and interacts with SPIN1 in the nucleus. Rbs1 overexpression causes delayed flowering under SD and LD conditions in rice. Expression analyses of flowering marker genes show that Rbs1 overexpression represses the expression of Hd3a under SD and LD conditions. Rbs1 is upregulated in both Spin1 overexpression plants and in the spl11 mutant. Interestingly, Spin1 expression is increased but Spl11 expression is repressed in the Rbs1 overexpression plants. Western blot analysis revealed that the SPIN1 protein level is increased in the Rbs1 overexpression plants and that the RBS1 protein level is also up-regulated in the Spin1 overexpression plants. These results suggest that RBS1 is a new negative regulator of flowering time that itself is positively regulated by SPIN1 but negatively regulated by SPL11 in rice.	Hd3a,RBS1,SPIN1,SPL11
Inflorescence meristem identity in rice is specified by overlapping functions of three AP1/FUL-like MADS box genes and PAP2, a SEPALLATA MADS box gene	2012	Plant Cell	Graduate School of Agriculture and Life Sciences, University of Tokyo, Tokyo, Japan.	In plants, the transition to reproductive growth is of particular importance for successful seed production. Transformation of the shoot apical meristem (SAM) to the inflorescence meristem (IM) is the crucial first step in this transition. Using laser microdissection and microarrays, we found that expression of PANICLE PHYTOMER2 (PAP2) and three APETALA1 (AP1)/FRUITFULL (FUL)-like genes (MADS14, MADS15, and MADS18) is induced in the SAM during meristem phase transition in rice (Oryza sativa). PAP2 is a MADS box gene belonging to a grass-specific subclade of the SEPALLATA subfamily. Suppression of these three AP1/FUL-like genes by RNA interference caused a slight delay in reproductive transition. Further depletion of PAP2 function from these triple knockdown plants inhibited the transition of the meristem to the IM. In the quadruple knockdown lines, the meristem continued to generate leaves, rather than becoming an IM. Consequently, multiple shoots were formed instead of an inflorescence. PAP2 physically interacts with MAD14 and MADS15 in vivo. Furthermore, the precocious flowering phenotype caused by the overexpression of Hd3a, a rice florigen gene, was weakened in pap2-1 mutants. Based on these results, we propose that PAP2 and the three AP1/FUL-like genes coordinately act in the meristem to specify the identity of the IM downstream of the florigen signal.	Hd3a,OsMADS14,OsMADS15|DEP,OsMADS18,OsMADS34|PAP2
The histone methyltransferase SDG724 mediates H3K36me2/3 deposition at MADS50 and RFT1 and promotes flowering in rice	2012	Plant Cell	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Chromatin modifications affect flowering time in the long-day plant Arabidopsis thaliana, but the role of histone methylation in flowering time regulation of rice (Oryza sativa), a short-day plant, remains to be elucidated. We identified a late-flowering long vegetative phase1 (lvp1) mutant in rice and used map-based cloning to reveal that lvp1 affects the SET domain group protein 724 (SDG724). SDG724 functions as a histone methyltransferase in vitro and contributes to a major fraction of global histone H3 lysine 36 (H3K36) methylation in vivo. Expression analyses of flowering time genes in wild-type and lvp1 mutants revealed that Early heading date1, but not Heading date1, are misregulated in lvp1 mutants. In addition, the double mutant of lvp1 with photoperiod sensitivity5 (se5) flowered later than the se5 single mutant, indicating that lvp1 delays flowering time irrespective of photoperiod. Chromatin immunoprecipitation assays showed that lvp1 had reduced levels of H3K36me2/3 at MADS50 and RFT1. This suggests that the divergent functions of paralogs RFT1 and Hd3a, and of MADS50 and MADS51, are in part due to differential H3K36me2/3 deposition, which also correlates with higher expression levels of MADS50 and RFT1 in flowering promotion in rice.	Hd3a,OsMADS50|OsSOC1|DTH3,OsMADS51|OsMADS65,RFT1,SDG724|lvp1,SDG736|OsSET9
Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions	2002	Plant Cell Physiol	Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki, 305-0854 Japan.	Heading date 3a (Hd3a) has been detected as a heading-date-related quantitative trait locus in a cross between rice cultivars Nipponbare and Kasalath. A previous study revealed that the Kasalath allele of Hd3a promotes heading under short-day (SD) conditions. High-resolution linkage mapping located the Hd3a locus in a approximately 20-kb genomic region. In this region, we found a candidate gene that shows high similarity to the FLOWERING LOCUS T (FT) gene, which promotes flowering in Arabidopsis: Introduction of the gene caused an early-heading phenotype in rice. The transcript levels of Hd3a were increased under SD conditions. The rice Heading date 1 (Hd1) gene, a homolog of CONSTANS (CO), has been shown to promote heading under SD conditions. By expression analysis, we showed that the amount of Hd3a mRNA is up-regulated by Hd1 under SD conditions, suggesting that Hd3a promotes heading under the control of Hd1. These results indicate that Hd3a encodes a protein closely related to Arabidopsis FT and that the function and regulatory relationship with Hd1 and CO, respectively, of Hd3a and FT are conserved between rice (an SD plant) and Arabidopsis (a long-day plant).	Hd3a
Genetic dissection of a genomic region for a quantitative trait locus, Hd3, into two loci, Hd3a and Hd3b, controlling heading date in rice	2002	Theor Appl Genet	Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan.	The rice photoperiod sensitivity gene Hd3 was originally detected as a heading date-related quantitative trait locus localized on chromosome 6 of rice. High-resolution linkage mapping of Hd3 was performed using a large segregating population derived from advanced backcross progeny between a japonica variety, Nipponbare, and an indica variety, Kasalath. To determine the genotype of Hd3, we employed progeny testing under natural field and short-day conditions. As a result, two tightly linked loci, Hd3a and Hd3b, were identified in the Hd3 region. Nearly-isogenic lines for Hd3a and Hd3b were selected from progeny using marker-assisted selection. The inheritance mode of both Hd3a and Hd3b was found to be additive. Analysis of daylength response in nearly-isogenic lines of Hd3a and Hd3b showed that the Kasalath allele at Hd3a promotes heading under short-day conditions while that at Hd3b causes late heading under long-day and natural field conditions.	Hd3a
Hd3a Protein Is a Mobile Flowering Signal in Rice	2007	Science	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma 630-0101, Japan.	Florigen, the mobile signal that moves from an induced leaf to the shoot apex and causes flowering, has eluded identification since it was first proposed 70 years ago. Understanding the nature of the mobile flowering signal would provide a key insight into the molecular mechanism of floral induction. Recent studies suggest that the Arabidopsis FLOWERING LOCUS T (FT) gene is a candidate for encoding florigen. We show that the protein encoded by Hd3a, a rice ortholog of FT, moves from the leaf to the shoot apical meristem and induces flowering in rice. These results suggest that the Hd3a protein may be the rice florigen.	Hd3a
Identification of Heading Date Quantitative Trait Locus Hd6 and Characterization of Its Epistatic Interactions With Hd2 in Rice Using Advanced Backcross Progeny	2000	Genetics	Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan	A backcrossed population (BC4F2) derived from a cross between a japonica rice variety, Nipponbare, as the recurrent parent and an indica rice variety, Kasalath, as the donor parent showed a long-range variation in days to heading. Quantitative trait loci (QTL) analysis revealed that two QTL, one on chromosome 3, designated Hd6, and another on chromosome 2, designated Hd7, were involved in this variation; and Hd6 was precisely mapped as a single Mendelian factor by using progeny testing (BC4F3). The nearly isogenic line with QTL (QTL-NIL) that carries the chromosomal segment from Kasalath for the Hd6 region in Nipponbare's genetic background was developed by marker-assisted selection. In a day-length treatment test, the QTL-NIL for Hd6 prominently increased days to heading under a 13.5-hr day length compared with the recurrent parent, Nipponbare, suggesting that Hd6 controls photoperiod sensitivity. QTL analysis of the F2 population derived from a cross between the QTL-NILs revealed existence of an epistatic interaction between Hd2, which is one of the photoperiod sensitivity genes detected in a previous analysis, and Hd6. The day-length treatment tests of these QTL-NILs, including the line introgressing both Hd2 and Hd6, also indicated an epistatic interaction for photoperiod sensitivity between them.	Hd6|CK2
The role of casein kinase II in flowering time regulation has diversified during evolution	2010	Plant Physiol	University of Tsukuba, Tsukuba, Japan 305-8577.	Casein kinase II (CK2) is a protein kinase with an evolutionarily conserved function as a circadian clock component in several organisms, including the long-day plant Arabidopsis (Arabidopsis thaliana). The circadian clock component CIRCADIAN CLOCK ASSOCIATED1 (CCA1) is a CK2 target in Arabidopsis, where it influences photoperiodic flowering. In rice (Oryza sativa), a short-day plant, Heading date6 (Hd6) encodes a CK2alpha subunit that delays flowering time under long-day conditions. Here, we demonstrate that control of flowering time in rice by the Hd6 CK2alpha subunit requires a functional Hd1 gene (an Arabidopsis CONSTANS ortholog) and is independent of the circadian clock mechanism. Our findings from overexpressing the dominant-negative CK2 allele in rice support the independence of CK2 function from the circadian clock. This lack of control of the circadian clock by Hd6 CK2alpha might be due to the presence of glutamate in OsLHY (a CCA1 ortholog in rice) instead of the serine at the corresponding CK2 target site in CCA1. However, this glutamate is critical for the control of the OsPRR1 gene (a rice ortholog of the Arabidopsis TOC1/PRR1 gene) by OsLHY for regulation of the circadian clock. We also demonstrated that the other conserved CK2 target sites in OsLHY conferred robust rhythmic expression of OsLHY-LUC under diurnal conditions. These findings imply that the role of CK2 in flowering-time regulation in higher plants has diversified during evolution.	Hd6|CK2,OsLHY,OsPRR1
Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2	2001	Proc Natl Acad Sci U S A	Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-0854, Japan.	Hd6 is a quantitative trait locus involved in rice photoperiod sensitivity. It was detected in backcross progeny derived from a cross between the japonica variety Nipponbare and the indica variety Kasalath. To isolate a gene at Hd6, we used a large segregating population for the high-resolution and fine-scale mapping of Hd6 and constructed genomic clone contigs around the Hd6 region. Linkage analysis with P1-derived artificial chromosome clone-derived DNA markers delimited Hd6 to a 26.4-kb genomic region. We identified a gene encoding the alpha subunit of protein kinase CK2 (CK2 alpha) in this region. The Nipponbare allele of CK2 alpha contains a premature stop codon, and the resulting truncated product is undoubtedly nonfunctional. Genetic complementation analysis revealed that the Kasalath allele of CK2 alpha increases days-to-heading. Map-based cloning with advanced backcross progeny enabled us to identify a gene underlying a quantitative trait locus even though it exhibited a relatively small effect on the phenotype.	Hd6|CK2
The role of rice HEI10 in the formation of meiotic crossovers	2012	PLoS Genet	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.	HEI10 was first described in human as a RING domain-containing protein that regulates cell cycle and cell invasion. Mice HEI10(mei4) mutant displays no obvious defect other than meiotic failure from an absence of chiasmata. In this study, we characterize rice HEI10 by map-based cloning and explore its function during meiotic recombination. In the rice hei10 mutant, chiasma frequency is markedly reduced, and those remaining chiasmata exhibit a random distribution among cells, suggesting possible involvement of HEI10 in the formation of interference-sensitive crossovers (COs). However, mutation of HEI10 does not affect early recombination events and synaptonemal complex (SC) formation. HEI10 protein displays a highly dynamic localization on the meiotic chromosomes. It initially appears as distinct foci and co-localizes with MER3. Thereafter, HEI10 signals elongate along the chromosomes and finally restrict to prominent foci that specially localize to chiasma sites. The linear HEI10 signals always localize on ZEP1 signals, indicating that HEI10 extends along the chromosome in the wake of synapsis. Together our results suggest that HEI10 is the homolog of budding yeast Zip3 and Caenorhabditis elegans ZHP-3, and may specifically promote class I CO formation through modification of various meiotic components.	HEI10,MER3|RCK
The role of OsMSH5 in crossover formation during rice meiosis	2013	Mol Plant	College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China.	MSH5, a meiosis-specific member of the MutS-homolog family, is required for normal level of recombination in budding yeast, mice, Caenorhabditis elegans, and Arabidopsis. Here, we report the identification and characterization of its rice homolog, OsMSH5, and demonstrate its function in rice meiosis. Five independent Osmsh5 mutants exhibited normal vegetative growth and severe sterility. The synaptonemal complex is well installed in Osmsh5, while the chiasma frequency is greatly reduced to approximately 10% of that observed in the wild-type, leading to the homologous non-disjunction and complete sterile phenotype. OsMSH5 is predominantly expressed in panicles. Immunofluorescence studies indicate that OsMSH5 chromosomal localization is limited to the early meiotic prophase I. OsMSH5 can be loaded onto meiotic chromosomes in Oszip4, Osmer3, and hei10. However, those ZMM proteins cannot be localized normally in the absence of OsMSH5. Furthermore, the residual chiasmata were shown to be the least frequent among the zmm mutants, including Osmer3, Oszip4, hei10, and Osmsh5. Taken together, we propose that OsMSH5 functions upstream of OsZIP4, OsMER3, and HEI10 in class I crossover formation.	HEI10,OsMSH5,MER3|RCK,ZIP4|SPO22
The Rice HGW Gene Encodes a Ubiquitin-Associated (UBA) Domain Protein That Regulates Heading Date and Grain Weight	2012	PLoS One	National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China	Heading date and grain weight are two determining agronomic traits of crop yield. To date, molecular factors controlling both heading date and grain weight have not been identified. Here we report the isolation of a hemizygous mutation, heading and grain weight (hgw), which delays heading and reduces grain weight in rice. Analysis of hgw mutant phenotypes indicate that the hemizygous hgw mutation decreases latitudinal cell number in the lemma and palea, both composing the spikelet hull that is known to determine the size and shape of brown grain. Molecular cloning and characterization of the HGW gene showed that it encodes a novel plant-specific ubiquitin-associated (UBA) domain protein localized in the cytoplasm and nucleus, and functions as a key upstream regulator to promote expressions of heading date-and grain weight-related genes. Moreover, co-expression analysis in rice and Arabidopsis indicated that HGW and its Arabidopsis homolog are co-expressed with genes encoding various components of ubiquitination machinery, implying a fundamental role for the ubiquitination pathway in heading date and grain weight control.	HGW
Two types of HKT transporters with different properties of Na+ and K+ transport in Oryza sativa	2001	The Plant Journal	Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma-shi, Nara 630-0101, Japan.	It is thought that Na+ and K+ homeostasis is crucial for salt-tolerance in plants. To better understand the Na+ and K+ homeostasis in important crop rice (Oryza sativa L.), a cDNA homologous to the wheat HKT1 encoding K+-Na+ symporter was isolated from japonica rice, cv Nipponbare (Ni-OsHKT1). We also isolated two cDNAs homologous to Ni-OsHKT1 from salt-tolerant indica rice, cv Pokkali (Po-OsHKT1, Po-OsHKT2). The predicted amino acid sequence of Ni-OsHKT1 shares 100% identity with Po-OsHKT1 and 91% identity with Po-OsHKT2, and they are 66-67% identical to wheat HKT1. Low-K+ conditions (less than 3 mM) induced the expression of all three OsHKT genes in roots, but mRNA accumulation was inhibited by the presence of 30 mM Na+. We further characterized the ion-transport properties of OsHKT1 and OsHKT2 using an expression system in the heterologous cells, yeast and Xenopus oocytes. OsHKT2 was capable of completely rescuing a K+-uptake deficiency mutation in yeast, whereas OsHKT1 was not under K+-limiting conditions. When OsHKTs were expressed in Na+-sensitive yeast, OsHKT1 rendered the cells more Na+-sensitive than did OsHKT2 in high NaCl conditions. The electrophysiological experiments for OsHKT1 expressed in Xenopus oocytes revealed that external Na+, but not K+, shifted the reversal potential toward depolarization. In contrast, for OsHKT2 either Na+ or K+ in the external solution shifted the reversal potential toward depolarization under the mixed Na+ and K+ containing solutions. These results suggest that two isoforms of HKT transporters, a Na+ transporter (OsHKT1) and a Na+- and K+-coupled transporter (OsHKT2), may act harmoniously in the salt tolerant indica rice.	HKT2,OsHKT2;2
Molecular characterization of Hmg2 gene encoding a 3-hydroxy-methylglutaryl-CoA reductase in rice	2001	Mol Cells	Division of Biochemistry, National Institute of Agricultural Science and Technology, Rural Development Administration, Suwon, Korea. shha@rda.go.kr	Three genes encoding 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR, EC1.1.1.34), which converts HMG-CoA into mevalonate in the early key step of the plant isoprenoid pathway, were isolated by RT-PCR and rice cDNA and genomic library screening. A genomic Southern blot analysis confirmed that HMGR genes are present in three copies in rice. Of the three, the HMGR 2 gene (Hmg2) obtained as a cDNA clone and its genomic clone had 4 exons and 3 introns, and encoded a 576 amino acid peptide containing an open reading frame of 1,728 bp with a calculated Mw. of 61,150. The structure of rice Hmg2 had common features, based on its nucleotide and deduced amino acid sequence homologies, with other plant HMGR genes published to date. Rice Hmg2 transcripts were constitutively detected in all parts of the rice plant, except in lamina and their levels were high particularly in the leaf part of the dark-grown seedlings and mature flowers. Our result showed that mRNA levels of rice Hmg2 were strongly induced in seedlings and influorescence in the early development stage. Rice Hmg2 possibly has a housekeeping role involved in the sterol biosynthesis, among the possible roles of plant HMGR genes that have been suggested in other plants [Weissenborn et al. (1995)].	HMG2
Rice HMGB1 protein recognizes DNA structures and bends DNA efficiently	2003	Archives of Biochemistry and Biophysics	Department of Biological Sciences, Faculty of Science, National University of Singapore, 10 Science Drive 4, 117543, Singapore, Singapore.	We analyzed the DNA-binding and DNA-bending properties of recombinant HMGB1 proteins based on a rice HMGB1 cDNA. Electrophoretic mobility shift assay demonstrated that rice HMGB1 can bind synthetic four-way junction (4H) DNA and DNA minicircles efficiently but the binding to 4H can be completed out by HMGA and histone H1. Conformational changes were detected by circular dichroism analysis with 4H DNA bound to various concentrations of HMGB1 or its truncated forms. T4 ligase-mediated circularization assays with short DNA fragments of 123 bp showed that the protein is capable of increasing DNA flexibility. The 123-bp DNA formed closed circular monomers efficiently in its presence, similar to that in an earlier study on maize HMG. Additionally, our results show for the first time that the basic N-terminal domain enhances the affinity of the plant HMGB1 protein for 4H DNA, while the acidic C-terminal domain has the converse effects.	HMGB1
Cloning and characterization of rice HMGB1 gene	2003	Gene	Department of Biological Sciences, National University of Singapore, 10 Science Drive 4, Singapore 117543, Singapore.	We isolated a 918 bp long full-length rice HMGB1 cDNA, which has an open reading frame of 471 bp encoding 157 amino acids, with a central domain of high sequence similarity to the HMG-box domain of other plant HMGB1 proteins. RNA gel blot analysis indicated that rice HMGB1 gene is constitutively expressed in various tissues and organs. Southern hybridization and sequence analyses suggested that a single copy of the HMGB1 gene composed of seven exons and six introns exists in rice. We have also cloned a 1755 bp long 5' flanking region of the rice HMGB1 gene, which can be regarded as its promoter. 5' deletion analysis of this promoter indicated that positive cis-elements residing between -1400 and -1115 are important to enhance quantitative expression, whereas negative cis-elements between -1755 and -1400 and between -1115 and -351 inhibit expression.	HMGB1
Radial axis differentiation in a globular embryo is marked by HAZ1, a PHD-finger homeobox gene of rice	2004	Gene	Plant Genetics Laboratory, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan.	Homeobox genes that encode transcription factors play important roles in development and differentiation of both plant and animal systems. From a cDNA library of 3-day after-pollination (DAP) rice embryos we cloned a HAZ1 cDNA that encodes a protein with a PHD-finger domain and a homeodomain. A database search showed that HAZ1 was most similar in its entire amino acid sequence to Zmhox1a (52% identity) and Zmhox1b (50%), PHD-finger family homeodomain proteins of maize. Differing from Zmhox1, overexpression of HAZ1 brought no morphological change either in tobacco or in rice. In situ hybridization showed that HAZ1 was expressed at a higher level in the outer layers of a developing embryo than in the inner parts of the embryo at 3 DAP. At 4 and 5 DAPs, the expression of HAZ1 was concentrated at the ventral part of an embryo. These results indicate that HAZ1 marks outer layer cells of a globular embryo before any morphological differentiation is discerned in it. Radial axis differentiation marked by HAZ1 is then collapsed dynamically along with embryo morphogenesis, and HAZ1 later marks the ventral surface of the embryo.	HAZ1|HOX1a
A positive feedback loop between HEAT SHOCK PROTEIN101 and HEAT STRESS-ASSOCIATED 32-KD PROTEIN modulates long-term acquired thermotolerance illustrating diverse heat stress responses in rice varieties	2014	Plant Physiol	Agricultural Biotechnology Research Center , Academia Sinica, Taipei 11529, Taiwan, Republic of China;	Heat stress is an important factor that has a negative impact on rice (Oryza sativa) production. To alleviate this problem, it is necessary to extensively understand the genetic basis of heat tolerance and adaptability to heat stress in rice. Here, we report the molecular mechanism underlying heat acclimation memory that confers long-term acquired thermotolerance (LAT) in this monocot plant. Our results showed that a positive feedback loop formed by two heat-inducible genes, HEAT SHOCK PROTEIN101 (HSP101) and HEAT STRESS-ASSOCIATED 32-KD PROTEIN (HSA32), at the posttranscriptional level prolongs the effect of heat acclimation in rice seedlings. The interplay between HSP101 and HSA32 also affects basal thermotolerance of rice seeds. These findings are similar to those reported for the dicot plant Arabidopsis (Arabidopsis thaliana), suggesting a conserved function in plant heat stress response. Comparison between two rice cultivars, japonica Nipponbare and indica N22 showed opposite performance in basal thermotolerance and LAT assays. 'N22' seedlings have a higher basal thermotolerance level than cv Nipponbare and vice versa at the LAT level, indicating that these two types of thermotolerance can be decoupled. The HSP101 and HSA32 protein levels were substantially higher in cv Nipponbare than in cv N22 after a long recovery following heat acclimation treatment, at least partly explaining the difference in the LAT phenotype. Our results point out the complexity of thermotolerance diversity in rice cultivars, which may need to be taken into consideration when breeding for heat tolerance for different climate scenarios.	HSA32,HSP101|OsClpB-cyt|HSP100
Heat-inducible rice hsp82 and hsp70 are not always co-regulated	1994	Planta	Laboratorium voor Genetica, Universiteit Gent, K.L. Ledeganckstraat 35, B-9000, Gent, Belgium	We have characterized several heat-shock-induced genes in rice (Oryza sativa L.) and compared their expression under a variety of conditions. Three of these genes, which are analogs of the hsp82/90 family, lie within a cloned 18-kilobase (kb) region of the genome. The middle member of this cluster, designated hsp82B, has been fully sequenced. The gene uses a promoter containing six putative heat-shock elements as well as several unusual sequence motifs including a stretch of 11 thymidines alternating with 11 adenosines. The mRNA for this gene reaches its highest relative level of expression within 120 min after plants are shifted to 42 degrees C; no other conditions induce this gene. By contrast, we found that during heat stress the expression of hsp70 correlates well with increases in internal ion concentrations, and can also be induced by excess salt or ethanol at normal growth temperatures. These results appear to indicate that whereas hsp70 is induced by all stresses that lead to protein denaturation-including heat stress-HSP82 mRNA accumulates only upon heat stress.	HSP70,hsp82A,hsp82B,hsp82D
Mechanisms of plant adaptation/memory in rice seedlings under arsenic and heat stress: expression of heat-shock protein gene HSP70	2010	AoB Plants	Centre for Applied Mathematics and Computational Science , Saha Institute of Nuclear Physics , 1/AF Bidhan Nagar , Kolkata- 700064 , India.	BACKGROUND AND AIMS: Plants can withstand many abiotic stresses. Stress adaptation through retention of imprints of previous stress exposure has also been described in plants. We have characterized the imprint or memory of adaptive stress responses of rice seedlings to arsenic (As) and heat stress. METHODOLOGY: Two-week-old rice seedlings (both with and without As) were given a 45 degrees C heat shock for 3 h. While under heat shock, the leafy portion of the seedlings was harvested at regular intervals. Subsequently, the seedlings were kept at room temperature for recovery and sampling continued over 3 h. Total RNA and protein were extracted from the leafy portion of the seedlings and complementary DNA (cDNA) was prepared from total RNA. The cDNA was used as a template for the polymerase chain reaction to identify the transcription level of HSP70. Protein extracted from the seedlings was western-blotted. HSP70 and actin (loading control) antibodies were used to recognize the proteins on the same blot. PRINCIPAL RESULTS: Our studies reveal that HSP70, a cellular chaperone gene, is over-expressed at the mRNA and protein levels when rice seedlings are exposed to As and heat. The effect is cumulative and increases with the duration of stress for 3 h. During 3 h recovery from heat stress at ambient temperatures for 3 h, the chaperone remains expressed at higher levels in plants pre-exposed to As. CONCLUSIONS: Our findings demonstrate a retention of the imprint of previous stress exposure, perhaps through sustained activation of the signalling pathways upstream of over-expression of HSP70. Furthermore, stress-induced HSP70 expression was additive/cumulative for continued exposure to similar or different kinds of stress, indicating that a commonality of signal transduction networks is adopted when plants experience more than one stress.	HSP70
Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.)	2005	Planta	National Plant Gene Research Centre (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Science, Beijing, 100101, China.	A rice htd-1 mutant, related to tillering and dwarfing, was characterized. We show that the htd-1 mutant increases its tiller number by releasing axillary buds from dormant stage rather than by initiating more axillary buds. The dwarf is caused by averagely reducing each internode and panicle. Based on this dwarfing pattern, the htd-1 mutant could be grouped into dn-type dwarf defined by Takeda (Gamma Field Symp 16:1, 1977). In addition, the dwarfing of the htd-1 mutant was found independent of GA based on the analyses of two GA-mediated processes. Based on the quantitative determination of IAA and ABA and application of the two hormones exogenously to the seedlings, we inferred that the high tillering capacity of the htd-1 mutant should not be attributed to a defect in the synthesis of IAA or ABA. The genetic analysis of the htd-1 mutant indicated that the phenotypes of high tillering and dwarf were controlled by a recessive gene, termed htd1. By map-based cloning, the htd1 gene was fine mapped in a 30-kb DNA region on chromosome 4. Sequencing the target DNA region and comparing the counterpart DNA sequences between the htd-1 mutant and other rice varieties revealed a nucleotide substitution corresponding to an amino acid substitution from prolin to leucine in a predicted rice gene, OsCCD7, the rice orthologous gene of AtMAX3/CCD7. With the evidence of the association between the presence of one amino acid change in OsCCD7 and the abnormal phenotypes of the htd-1 mutant, OsCCD7 was identified as the candidate of the HTD1 gene.	HTD1|OsCCD7
Carotenoid oxygenases involved in plant branching catalyse a highly specific conserved apocarotenoid cleavage reaction	2008	Biochem J	Albert-Ludwigs University of Freiburg, Faculty of Biology, Institute of Biology II, Schaenzlestrasse 1, D-79104 Freiburg, Germany.	Recent studies with the high-tillering mutants in rice (Oryza sativa), the max (more axillary growth) mutants in Arabidopsis thaliana and the rms (ramosus) mutants in pea (Pisum sativum) have indicated the presence of a novel plant hormone that inhibits branching in an auxin-dependent manner. The synthesis of this inhibitor is initiated by the two CCDs [carotenoid-cleaving (di)oxygenases] OsCCD7/OsCCD8b, MAX3/MAX4 and RMS5/RMS1 in rice, Arabidopsis and pea respectively. MAX3 and MAX4 are thought to catalyse the successive cleavage of a carotenoid substrate yielding an apocarotenoid that, possibly after further modification, inhibits the outgrowth of axillary buds. To elucidate the substrate specificity of OsCCD8b, MAX4 and RMS1, we investigated their activities in vitro using naturally accumulated carotenoids and synthetic apocarotenoid substrates, and in vivo using carotenoid-accumulating Escherichia coli strains. The results obtained suggest that these enzymes are highly specific, converting the C27 compounds beta-apo-10'-carotenal and its alcohol into beta-apo-13-carotenone in vitro. Our data suggest that the second cleavage step in the biosynthesis of the plant branching inhibitor is conserved in monocotyledonous and dicotyledonous species.	HTD1|OsCCD7,D10|OsCCD8|OsCCD8b
Dwarf 88, a novel putative esterase gene affecting architecture of rice plant	2009	Plant Mol Biol	National Center for Gene Research/Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200233 Shanghai, China.	Rice architecture is an important agronomic trait that affects grain yield. We characterized a tillering dwarf mutant d88 derived from Oryza sativa ssp. japonica cultivar Lansheng treated with EMS. The mutant had excessive shorter tillers and smaller panicles and seeds compared to the wild-type. A reduction in number and size of parenchyma cells around stem marrow cavity as well as a delay in the elongation of parenchyma cells caused slender tillers and dwarfism in the d88 mutant. The D88 gene was isolated via map-based cloning and identified to encode a putative esterase. The gene was expressed in most rice organs, with especially high levels in the vascular tissues. The mutant carried a nucleotide substitution in the first exon of the gene that led to the substitution of arginine for glycine, which presumably disrupted the functionally conserved N-myristoylation domain of the protein. The function of the gene was confirmed by complementation test and antisense analysis. D88, thus, represents a new category of genes that regulates cell growth and organ development and consequently plant architecture. The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development.	HTD2|D88|D14
The interaction between OsMADS57 and OsTB1 modulates rice tillering via DWARF14	2013	Nat Commun	The Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	Rice tillering is a multigenic trait that influences grain yield, but its regulation molecular module is poorly understood. Here we report that OsMADS57 interacts with OsTB1 (TEOSINTE BRANCHED1) and targets D14 (Dwarf14) to control the outgrowth of axillary buds in rice. An activation-tagged mutant osmads57-1 and OsMADS57-overexpression lines showed increased tillers, whereas OsMADS57 antisense lines had fewer tillers. OsMIR444a-overexpressing lines exhibited suppressed OsMADS57 expression and tillering. Furthermore, osmads57-1 was insensitive to strigolactone treatment to inhibit axillary bud outgrowth, and OsMADS57's function in tillering was dependent on D14. D14 expression was downregulated in osmads57-1, but upregulated in antisense and OsMIR444a-overexpressing lines. OsMADS57 bound to the CArG motif [C(A/T)TTAAAAAG] in the promoter and directly suppressed D14 expression. Interaction of OsMADS57 with OsTB1 reduced OsMADS57 inhibition of D14 transcription. Therefore, OsMIR444a-regulated OsMADS57, together with OsTB1, target D14 to control tillering. This regulation mechanism could have important application in rice molecular breeding programs focused on high grain yield.	HTD2|D88|D14,OsMADS57,OsTB1|FC1
d14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers	2009	Plant Cell Physiol	Ishikawa Prefectural University, Nonoichi, Ishikawa 921-8836, Japan.	Recent studies using highly branched mutants of pea, Arabidopsis and rice have demonstrated that strigolactones, a group of terpenoid lactones, act as a new hormone class, or its biosynthetic precursors, in inhibiting shoot branching. Here, we provide evidence that DWARF14 (D14) inhibits rice tillering and may act as a new compo-nent of the strigolactone-dependent branching inhibition pathway. The d14 mutant exhibits increased shoot branch-ing with reduced plant height like the previously characterized strigolactone-deficient and -insensitive mutants d10 and d3, respectively. The d10-1 d14-1 double mutant is phenotypically indistinguishable from the d10-1 and d14-1 single mutants, consistent with the idea that D10 and D14 function in the same pathway. However, unlike with d10, the d14 branching phenotype could not be rescued by exogenous strigolactones. In addition, the d14 mutant contained a higher level of 2'-epi-5-deoxystrigol than the wild type. Positional cloning revealed that D14 encodes a protein of the alpha/beta-fold hydrolase superfamily, some members of which play a role in metabolism or signaling of plant hormones. We propose that D14 functions downstream of strigolactone synthesis, as a component of hormone signaling or as an enzyme that participates in the conversion of strigolactones to the bioactive form.	HTD2|D88|D14,D10|OsCCD8|OsCCD8b
Genetic and physiological analysis of a novel type of interspecific hybrid weakness in rice	2013	Mol Plant	National Key Laboratory of Plant Molecular Genetics and National Center for Plant Gene Research Shanghai, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.	Hybrid weakness is an important reproductive barrier that hinders genetic exchange between different species at the post-zygotic stage. However, our understanding of the molecular mechanisms underlying hybrid weakness is limited. In this study, we report discovery of a novel interspecific hybrid weakness in a rice chromosome segment substitution line (CSSL) library derived from a cross between the indica variety Teqing (Oryza sativa) and common wild rice (O. rufipogon). The dominant Hybrid weakness i1 (Hwi1) gene from wild rice is genetically incompatible with Teqing and induced a set of weakness symptoms, including growth suppression, yield decrease, impaired nutrient absorption, and the retardation of crown root initiation. Phytohormone treatment showed that salicylic acid (SA) could restore the height of plants expressing hybrid weakness, while other phytohormones appear to have little effect. Fine mapping indicated that Hwi1 is located in a tandem leucine-rich repeat receptor-like kinase (LRR-RLK) gene cluster. Within the 13.2-kb candidate region on the short arm of chromosome 11, there are two annotated LRR-RLK genes, LOC_Os11g07230 and LOC_Os11g07240. The Teqing allele of LOC_Os11g07230 and the wild rice allele of LOC_Os11g07240 encode predicted functional proteins. Based on the genetic inheritance of hybrid weakness, LOC_Os11g07240 is implicated as the candidate gene for Hwi1. Functional analysis of Hwi1 will expand our knowledge of the regulation of hybrid weakness in rice.	Hwi1
Structural, biochemical, and phylogenetic analyses suggest that indole-3-acetic acid methyltransferase is an evolutionarily ancient member of the SABATH family	2008	Plant Physiol	Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee 37996, USA.	The plant SABATH protein family encompasses a group of related small-molecule methyltransferases (MTs) that catalyze the S-adenosyl-L-methionine-dependent methylation of natural chemicals encompassing widely divergent structures. Indole-3-acetic acid (IAA) methyltransferase (IAMT) is a member of the SABATH family that modulates IAA homeostasis in plant tissues through methylation of IAA's free carboxyl group. The crystal structure of Arabidopsis (Arabidopsis thaliana) IAMT (AtIAMT1) was determined and refined to 2.75 A resolution. The overall tertiary and quaternary structures closely resemble the two-domain bilobed monomer and the dimeric arrangement, respectively, previously observed for the related salicylic acid carboxyl methyltransferase from Clarkia breweri (CbSAMT). To further our understanding of the biological function and evolution of SABATHs, especially of IAMT, we analyzed the SABATH gene family in the rice (Oryza sativa) genome. Forty-one OsSABATH genes were identified. Expression analysis showed that more than one-half of the OsSABATH genes were transcribed in one or multiple organs. The OsSABATH gene most similar to AtIAMT1 is OsSABATH4. Escherichia coli-expressed OsSABATH4 protein displayed the highest level of catalytic activity toward IAA and was therefore named OsIAMT1. OsIAMT1 exhibited kinetic properties similar to AtIAMT1 and poplar IAMT (PtIAMT1). Structural modeling of OsIAMT1 and PtIAMT1 using the experimentally determined structure of AtIAMT1 reported here as a template revealed conserved structural features of IAMTs within the active-site cavity that are divergent from functionally distinct members of the SABATH family, such as CbSAMT. Phylogenetic analysis revealed that IAMTs from Arabidopsis, rice, and poplar (Populus spp.) form a monophyletic group. Thus, structural, biochemical, and phylogenetic evidence supports the hypothesis that IAMT is an evolutionarily ancient member of the SABATH family likely to play a critical role in IAA homeostasis across a wide range of plants.	IAMT1
A novel gene IBF1 is required for the inhibition of brown pigment deposition in rice hull furrows	2012	Theor Appl Genet	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	The role of flavonoids as the major red, blue, purple and brown pigments in plants has gained these secondary products a great deal of attention over the years. In this study, we characterized a rice inhibitor for brown furrows1 (ibf1) mutant. In the ibf1 mutant, brown pigments specifically accumulate in hull furrows during seed maturation and reach a maximum level in dry seeds. Higher amounts of total flavonoids and anthocyanin in hull may be responsible for the brown pigmentation of ibf1. The IBF1 gene, which encodes a similar kelch repeat-containing F-box protein, was isolated by map-based cloning approach. Real-time RT-PCR and GUS activity assays revealed that IBF1 specifically expressed in reproductive tissues. GFP-IBF1 fusion protein mainly localized in cytoplasm. The expression of some major structural enzymatic genes involved in flavonoids biosynthesis could be up- or down-regulated to some different extent in ibf1 mutant. Our data suggested that IBF1 as a suppressor could inhibit the brown pigmentation of rice hull furrows.	IBF1
The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes	2009	Plant J	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Higher plants maintain iron homeostasis by regulating the expression of iron (Fe)-related genes in accordance with Fe availability. The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa (rice) by recognizing CATGC sequences within the Fe deficiency-responsive cis-acting element IDE1. To investigate the function of IDEF1 in detail, we analyzed the response to Fe deficiency in transgenic rice plants exhibiting induced or repressed IDEF1 expression. Fe-deficiency treatment in hydroponic culture revealed that IDEF1 knock-down plants are susceptible to early-stage Fe deficiency, in contrast to IDEF1-induced plants. Time-course expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation. However, this overall transactivation mediated by IDEF1 became less evident in subsequent stages. Microarray and in-silico analyses revealed that genes positively regulated by IDEF1, especially at the early stage, exhibit over-representation of CATGC and IDE1-like elements within the proximal promoter regions. These results indicate the existence of early and subsequent responses to Fe deficiency, with the former requiring IDEF1 more specifically. Proximal regions of IDEF1-regulated gene promoters also showed enrichment of RY elements (CATGCA), which regulate gene expression during seed maturation. The expression of several genes encoding late embryogenesis abundant proteins, including Osem, was induced in Fe-deficient roots and/or leaves in an IDEF1-dependent manner, suggesting a possible function of seed maturation-related genes in Fe-deficient vegetative organs.	IDEF1,OsIRO2,OsIRT1,OsNAS1,OsNAS2,OsNAS3,OsYSL15,OsYSL2
The rice transcription factor IDEF1 directly binds to iron and other divalent metals for sensing cellular iron status	2012	Plant J	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Iron is essential for most living organisms and its availability often determines survival and proliferation. The Oryza sativa (rice) transcription factor IDEF1 plays a crucial role in regulating iron deficiency-induced genes involved in iron homeostasis. In the present report, we found characteristic histidine-asparagine repeat and proline-rich regions in IDEF1 and its homolog in Hordeum vulgare (barley), HvIDEF1. An immobilized metal ion affinity chromatography assay revealed that IDEF1 and HvIDEF1 bind to various divalent metals, including Fe(2+) and Ni(2+) . Recombinant IDEF1 protein expressed in Escherichia coli contained mainly Fe and Zn. This metal-binding activity of IDEF1 was almost abolished by deletion of the histidine-asparagine and proline-rich regions, but DNA-binding and trans-activation functions were not impaired by the deletion. Transgenic rice plants constitutively overexpressing IDEF1 without these metal-binding domains failed to cause pleiotropic effects conferred by overexpression of full-length IDEF1, including a low germination rate, impaired seedling growth, tolerance to iron deficiency in hydroponic culture, and enhanced expression of various iron deficiency-inducible genes. Impairment of the transcriptional regulation of IDEF1 by deletion of the metal-binding domains occurred primarily at an early stage of iron deficiency. These results suggest that the histidine-asparagine and proline-rich regions in rice IDEF1 directly bind to divalent metals and sense the cellular metal ion balance caused by changes in iron availability.	IDEF1
The spatial expression and regulation of transcription factors IDEF1 and IDEF2	2010	Ann Bot	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	BACKGROUND AND AIMS: Under conditions of low iron availability, rice plants induce genes involved in iron uptake and utilization. The iron deficiency-responsive cis-acting element binding factors 1 and 2 (IDEF1 and IDEF2) regulate transcriptional response to iron deficiency in rice roots. Clarification of the functions of IDEF1 and IDEF2 could uncover the gene regulation mechanism. METHODS: Spatial patterns of IDEF1 and IDEF2 expression were analysed by histochemical staining of IDEF1 and IDEF2 promoter-GUS transgenic rice lines. Expression patterns of the target genes of IDEF1 and IDEF2 were analysed using transformants with induced or repressed expression of IDEF1 or IDEF2 grown in iron-rich or in iron-deficient solutions for 1 d. KEY RESULTS: IDEF1 and IDEF2 were highly expressed in the basal parts of the lateral roots and vascular bundles. IDEF1 and IDEF2 expression was dominant in leaf mesophyll and vascular cells, respectively. These expression patterns were similar under both iron-deficient and iron-sufficient conditions. IDEF1 was strongly expressed in pollen, ovaries, the aleurone layer and embryo. IDEF2 was expressed in pollen, ovaries and the dorsal vascular region of the endosperm. During seed germination, IDEF1 and IDEF2 were expressed in the endosperm and embryo. Expression of IDEF1 target genes was regulated in iron-rich roots similar to early iron-deficiency stages. In addition, the expression patterns of IDEF2 target genes were similar between iron-rich conditions and early or subsequent iron deficiency. CONCLUSIONS: IDEF1 and IDEF2 are constitutively expressed during both vegetative and reproductive stages. The spatial expression patterns of IDEF1 and IDEF2 overlap with their target genes in restricted cell types, but not in all cells. The spatial expression patterns and gene regulation of IDEF1 and IDEF2 in roots are generally conserved under conditions of iron sufficiency and deficiency, suggesting complicated interactions with unknown factors for sensing and transmitting iron-deficiency signals.	IDEF1,IDEF2
The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants	2007	Proc Natl Acad Sci U S A	Laboratory of Plant Biotechnology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Iron is essential for most living organisms and is often the major limiting nutrient for normal growth. Plants induce iron utilization systems under conditions of low iron availability, but the molecular mechanisms of gene regulation under iron deficiency remain largely unknown. We identified the rice transcription factor IDEF1, which specifically binds the iron deficiency-responsive cis-acting element IDE1. IDEF1 belongs to an uncharacterized branch of the plant-specific transcription factor family ABI3/VP1 and exhibits the sequence recognition property of efficiently binding to the CATGC sequence within IDE1. IDEF1 transcripts are constitutively present in rice roots and leaves. Transgenic tobacco plants expressing IDEF1 under the control of the constitutive cauliflower mosaic virus 35S promoter transactivate IDE1-mediated expression only in iron-deficient roots. Transgenic rice plants expressing an introduced IDEF1 exhibit substantial tolerance to iron deficiency in both hydroponic culture and calcareous soil. IDEF1 overexpression leads to the enhanced expression of the iron deficiency-induced transcription factor gene OsIRO2, suggesting the presence of a sequential gene regulatory network. These findings reveal cis element/trans factor interactions that are functionally linked to the iron deficiency response. Manipulation of IDEF1 also provides another approach for producing crops tolerant of iron deficiency to enhance food and biomass production in calcareous soils.	IDEF1
A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants	2008	J Biol Chem	Graduate School of Agricultural and Life Sciences, the University of Tokyo, 1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Iron is essential for most living organisms, and thus iron deficiency poses a major abiotic stress in crop production. Plants induce iron utilization systems under conditions of low iron availability, but the molecular mechanisms of gene regulation under iron deficiency remain largely unknown. We identified a novel transcription factor of rice and barley, IDEF2, which specifically binds to the iron deficiency-responsive cis-acting element 2 (IDE2) by yeast one-hybrid screening. IDEF2 belongs to an uncharacterized branch of the NAC transcription factor family and exhibits novel properties of sequence recognition. An electrophoretic mobility shift assay and cyclic amplification and selection of targets experiment revealed that IDEF2 predominantly recognized CA(A/C)G(T/C)(T/C/A)(T/C/A) within IDE2 as the core-binding site. IDEF2 transcripts are constitutively present in rice roots and leaves. Repression of the function of IDEF2 by the RNA interference (RNAi) technique and chimeric repressor gene-silencing technology (CRES-T) caused aberrant iron homeostasis in rice. Several genes up-regulated by iron deficiency, including the Fe(II)-nicotianamine transporter gene OsYSL2, were less induced by iron deficiency in the RNAi rice of IDEF2, suggesting that IDEF2 is involved in the regulation of these genes. Many genes with repressed expression in IDEF2 RNAi rice possessed the IDEF2-binding core sites in their promoters, and the flanking sequences were also highly homologous to IDE2. IDEF2 bound to OsYSL2 promoter region containing the binding core site, suggesting direct regulation of OsYSL2 expression. These results reveal novel cis-element/trans-factor interactions functionally associated with iron homeostasis.	IDEF2,OsYSL2
Increased leaf angle1, a Raf-like MAPKKK that interacts with a nuclear protein family, regulates mechanical tissue formation in the Lamina joint of rice	2011	Plant Cell	National Key Laboratory of Crop Genetic Improvement and National Center for Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.	Mitogen-activated protein kinase kinase kinases (MAPKKKs), which function at the top level of mitogen-activated protein kinase cascades, are clustered into three groups. However, no Group C Raf-like MAPKKKs have yet been functionally identified. We report here the characterization of a rice (Oryza sativa) mutant, increased leaf angle1 (ila1), resulting from a T-DNA insertion in a Group C MAPKKK gene. The increased leaf angle in ila1 is caused by abnormal vascular bundle formation and cell wall composition in the leaf lamina joint, as distinct from the mechanism observed in brassinosteroid-related mutants. Phosphorylation assays revealed that ILA1 is a functional kinase with Ser/Thr kinase activity. ILA1 is predominantly resident in the nucleus and expressed in the vascular bundles of leaf lamina joints. Yeast two-hybrid screening identified six closely related ILA1 interacting proteins (IIPs) of unknown function. Using representative IIPs, the interaction of ILA1 and IIPs was confirmed in vivo. IIPs were localized in the nucleus and showed transactivation activity. Furthermore, ILA1 could phosphorylate IIP4, indicating that IIPs may be the downstream substrates of ILA1. Microarray analyses of leaf lamina joints provided additional evidence for alterations in mechanical strength in ila1. ILA1 is thus a key factor regulating mechanical tissue formation at the leaf lamina joint.	ILA1
Dynamics of brassinosteroid response modulated by negative regulator LIC in rice	2012	PLoS Genet	Key Laboratory of Plant Molecular Physiology/Photosynthesis and Environmental Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, China.	Brassinosteroids (BRs) regulate rice plant architecture, including leaf bending, which affects grain yield. Although BR signaling has been investigated in Arabidopsis thaliana, the components negatively regulating this pathway are less well understood. Here, we demonstrate that Oryza sativa LEAF and TILLER ANGLE INCREASED CONTROLLER (LIC) acts as an antagonistic transcription factor of BRASSINAZOLE-RESISTANT 1 (BZR1) to attenuate the BR signaling pathway. The gain-of-function mutant lic-1 and LIC-overexpressing lines showed erect leaves, similar to BZR1-depleted lines, which indicates the opposite roles of LIC and BZR1 in regulating leaf bending. Quantitative PCR revealed LIC transcription rapidly induced by BR treatment. Image analysis and immunoblotting showed that upon BR treatment LIC proteins translocate from the cytoplasm to the nucleus in a phosphorylation-dependent fashion. Phosphorylation assay in vitro revealed LIC phosphorylated by GSK3-like kinases. For negative feedback, LIC bound to the core element CTCGC in the BZR1 promoter on gel-shift and chromatin immunoprecipitation assay and repressed its transcription on transient transformation assay. LIC directly regulated target genes such as INCREASED LEAF INCLINATION 1 (ILI1) to oppose the action of BZR1. Repression of LIC in ILI1 transcription in protoplasts was partially rescued by BZR1. Phenotypic analysis of the crossed lines depleted in both LIC and BZR1 suggested that BZR1 functionally depends on LIC. Molecular and physiology assays revealed that LIC plays a dominant role at high BR levels, whereas BZR1 is dominant at low levels. Thus, LIC regulates rice leaf bending as an antagonistic transcription factor of BZR1. The phenotypes of lic-1 and LIC-overexpressing lines in erect leaves contribute to ideal plant architecture. Improving this phenotype may be a potential approach to molecular breeding for high yield in rice.	ILI1,OsBZR1,OsIBH1|IBH1,LIC|OsLIC1,OsGSK4
Antagonistic HLH/bHLH transcription factors mediate brassinosteroid regulation of cell elongation and plant development in rice and Arabidopsis	2009	Plant Cell	Key Laboratory of Photosynthesis and Environmental Molecular Biology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.	In rice (Oryza sativa), brassinosteroids (BRs) induce cell elongation at the adaxial side of the lamina joint to promote leaf bending. We identified a rice mutant (ili1-D) showing an increased lamina inclination phenotype similar to that caused by BR treatment. The ili1-D mutant overexpresses an HLH protein homologous to Arabidopsis thaliana Paclobutrazol Resistance1 (PRE1) and the human Inhibitor of DNA binding proteins. Overexpression and RNA interference suppression of ILI1 increase and reduce, respectively, rice laminar inclination, confirming a positive role of ILI1 in leaf bending. ILI1 and PRE1 interact with basic helix-loop-helix (bHLH) protein IBH1 (ILI1 binding bHLH), whose overexpression causes erect leaf in rice and dwarfism in Arabidopsis. Overexpression of ILI1 or PRE1 increases cell elongation and suppresses dwarf phenotypes caused by overexpression of IBH1 in Arabidopsis. Thus, ILI1 and PRE1 may inactivate inhibitory bHLH transcription factors through heterodimerization. BR increases the RNA levels of ILI1 and PRE1 but represses IBH1 through the transcription factor BZR1. The spatial and temporal expression patterns support roles of ILI1 in laminar joint bending and PRE1/At IBH1 in the transition from growth of young organs to growth arrest. These results demonstrate a conserved mechanism of BR regulation of plant development through a pair of antagonizing HLH/bHLH transcription factors that act downstream of BZR1 in Arabidopsis and rice.	ILI1,OsIBH1|IBH1
Development of low phytate rice by RNAi mediated seed-specific silencing of inositol 1,3,4,5,6-pentakisphosphate 2-kinase gene (IPK1)	2013	PLoS One	Plant Molecular Biology and Biotechnology Laboratory, Department of Botany, University of Calcutta, Kolkata, West Bengal, India.	Phytic acid (InsP(6)) is considered to be the major source of phosphorus and inositol phosphates in most cereal grains. However, InsP(6) is not utilized efficiently by monogastric animals due to lack of phytase enzyme. Furthermore, due to its ability to chelate mineral cations, phytic acid is considered to be an antinutrient that renders these minerals unavailable for absorption. In view of these facts, reducing the phytic acid content in cereal grains is a desired goal for the genetic improvement of several crops. In the present study, we report the RNAi-mediated seed-specific silencing (using the Oleosin18 promoter) of the IPK1 gene, which catalyzes the last step of phytic acid biosynthesis in rice. The presence of the transgene cassette in the resulting transgenic plants was confirmed by molecular analysis, indicating the stable integration of the transgene. The subsequent T4 transgenic seeds revealed 3.85-fold down-regulation in IPK1 transcripts, which correlated to a significant reduction in phytate levels and a concomitant increase in the amount of inorganic phosphate (Pi). The low-phytate rice seeds also accumulated 1.8-fold more iron in the endosperm due to the decreased phytic acid levels. No negative effects were observed on seed germination or in any of the agronomic traits examined. The results provide evidence that silencing of IPK1 gene can mediate a substantial reduction in seed phytate levels without hampering the growth and development of transgenic rice plants.	IPK1
Rice debranching enzyme isoamylase3 facilitates starch metabolism and affects plastid morphogenesis	2011	Plant Cell Physiol	Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Japan.	Debranching enzymes, which hydrolyze alpha-1 and 6-glucosidic linkages in alpha-polyglucans, play a dual role in the synthesis and degradation of starch in plants. A transposon-inserted rice mutant of isoamylase3 (isa3) contained an increased amount of starch in the leaf blade at the end of the night, indicating that ISA3 plays a role in the degradation of transitory starch during the night. An epitope-tagged ISA3 expressed in Escherichia coli exhibited hydrolytic activity on beta-limit dextrin and amylopectin. We investigated whether ISA3 plays a role in amyloplast development and starch metabolism in the developing endosperm. ISA3-green fluorescent protein (GFP) fusion protein expressed under the control of the rice ISA3 promoter was targeted to the amyloplast stroma in the endosperm. Overexpression of ISA3 in the sugary1 mutant, which is deficient in ISA1 activity, did not convert water-soluble phytoglycogen to starch granules, indicating that ISA1 and ISA3 are not functionally redundant. Both overexpression and loss of function of ISA3 in the endosperm generated pleomorphic amyloplasts and starch granules. Furthermore, chloroplasts in the leaf blade of isa3 seedlings were large and pleomorphic. These results suggest that ISA3 facilitates starch metabolism and affects morphological characteristics of plastids in rice.	ISA3,OsISA1,OsPUL,FtsZ1,FtsZ2-1
Role of the rice transcription factor JAmyb in abiotic stress response	2013	J Plant Res	Research Institute for Biological Sciences, Okayama Prefectural Technology Center for Agriculture, Forestry, and Fisheries, 7549-1 Yoshikawa, Kibichuo, Okayama 716-1241, Japan.	Plants have developed certain adaptive responses to environmental stresses that cause adverse effects on growth. To identify genes involved in the adaptive mechanisms, we constructed a large population of transgenic Arabidopsis expressing rice full-length cDNAs, and performed gain-of-function screening under high-salinity stress. In this study, we identified a rice R2R3-type MYB transcription factor gene, JAmyb, as a gene whose overexpression causes tolerance to high salinity. JAmyb overexpression in transgenic Arabidopsis improved tolerance to high-salinity stress during seed germination, seedling growth, and root elongation. In rice seedlings, JAmyb expression was induced by high-salinity and high-osmotic stresses and reactive oxygen species (ROS), suggesting that JAmyb is responsible for abiotic stress response. Microarray analysis showed that the overexpression of JAmyb stimulates the expression of several defense-associated genes, some of which have been predicted to be involved in osmotic adjustment, ROS removal, and ion homeostasis. Several transcription factors involved in the jasmonate (JA)-mediated stress response are also regulated by JAmyb. JAmyb has been reported to be associated with disease response. Our observations suggest that JAmyb plays a role in JA-mediated abiotic stress response in addition to biotic stress response in rice.	JAmyb
Molecular cloning and characterization of a novel Jasmonate inducible pathogenesis-related class 10 protein gene, JIOsPR10, from rice (Oryza sativa L.) seedling leaves	2001	Biochem Biophys Res Commun	Department of Molecular Biology, Sejong University, Seoul, 143-747, Korea.	A novel rice (Oryza sativa L.) gene, homologous to a sorghum pathogenesis-related class 10 protein gene, was cloned from a cDNA library prepared from 2-week-old jasmonic acid-treated rice seedling leaves, and named as JIOsPR10 (jasmonate inducible). JIOsPR10 encoded a 160-amino-acid polypeptide with a predicted molecular mass of 17,173.23 Da and a pI of 5.84. JIOsPR10 was highly similar (77%) to the sorghum PR10 protein, but showed less than 55% similarity with other identified PR10s at the amino acid level. Genomic Southern analyses indicated the presence of related genes in the rice genome. The JIOsPR10 transcript was not detected in the healthy leaves, and was not induced after cut. Further expression analysis revealed that the signaling components of defense/stress pathways, jasmonate, salicylate, and H(2)O(2) significantly up-regulated the JIOsPR10 mRNA over the cut control, whereas two other stress regulators, ethylene and abscisic acid, failed to induce its expression. Interestingly the protein phosphatase (PP) inhibitors, cantharidin, endothall, and okadaic acid, rapidly and potently up-regulated the JIOsPR10 expression, suggesting involvement of the phosphorylation/dephosphorylation events. Additionally, the inducible expression of the JIOsPR10 gene was influenced by light signal(s). Finally, the blast pathogen (Magnaporthe grisea) also specifically elicited the accumulation of JIOsPR10 mRNA in leaves. Induction of the JIOsPR10 gene expression by signaling molecules, PP inhibitors and pathogen attack, strongly indicate a role for this novel gene in rice self-defense/stress response(s).	JIOsPR10|OsPR10
The rice pathogen-related protein 10 (JIOsPR10) is induced by abiotic and biotic stresses and exhibits ribonuclease activity	2008	Plant Cell Rep	Environmental Biotechnology National Core Research Center, Gyeongsang National University, Jinju, Korea.	We previously reported that rice blast fungus or jasmonic acid induced the expression of rice pathogenesis-related class 10 (JIOsPR10) proteins (Kim et al. 2003, 2004). However, no further studies have been carried out to examine the expression, localization, and enzymatic activity of this protein in either developmental tissues or in tissues under abiotic stress conditions. In this study, rice JIOsPR10 was examined by Western blot analysis, immunolocalization, and biochemical assays. Western blots revealed that the JIOsPR10 protein was expressed in developmental tissues, including in flower and root. The protein was also expressed under abiotic stresses, such as occurs during senescence and wounding. Using immunohistochemical techniques, we determined that expression of JIOsPR10 was localized to the palea of flower, in the exodermis, and inner part of the endodermis of the root. In senescencing tissues of leaf and coleoptiles, its expression was localized in vascular bundles. The RNase activity using JIOsPR10 recombinant protein was determined and abolished after treatment with DTT in a native in-gel assay. To test this, we created JIOsPR10 mutant proteins containing serine substitutions of amino acids C81S, C83S, or both and examined their RNase activities. The activity of the C83S mutant was decreased in the agarose gel assay compared to the wild type. Taken together, we hypothesize that the JIOsPR10 protein possesses RNase activity that is sensitive to DTT, suggesting the importance of the disulfide bonding between cysteine residues and that it might play a role in constitutive self-defense mechanisms in plants against biotic and abiotic stresses.	JIOsPR10|OsPR10
Control of transposon activity by a histone H3K4 demethylase in rice	2013	Proc Natl Acad Sci U S A	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Transposable elements (TEs) are ubiquitously present in plant genomes and often account for significant fractions of the nuclear DNA. For example, roughly 40% of the rice genome consists of TEs, many of which are retrotransposons, including 14% LTR- and approximately 1% non-LTR retrotransposons. Despite their wide distribution and abundance, very few TEs have been found to be transpositional, indicating that TE activities may be tightly controlled by the host genome to minimize the potentially mutagenic effects associated with active transposition. Consistent with this notion, a growing body of evidence suggests that epigenetic silencing pathways such as DNA methylation, RNA interference, and H3K9me2 function collectively to repress TE activity at the transcriptional and posttranscriptional levels. It is not yet clear, however, whether the removal of histone modifications associated with active transcription is also involved in TE silencing. Here, we show that the rice protein JMJ703 is an active H3K4-specific demethylase required for TEs silencing. Impaired JMJ703 activity led to elevated levels of H3K4me3, the misregulation of numerous endogenous genes, and the transpositional reactivation of two families of non-LTR retrotransposons. Interestingly, loss of JMJ703 did not affect TEs (such as Tos17) previously found to be silenced by other epigenetic pathways. These results indicate that the removal of active histone modifications is involved in TE silencing and that different subsets of TEs may be regulated by distinct epigenetic pathways.	JMJ703
Jumonji C domain protein JMJ705-mediated removal of histone H3 lysine 27 trimethylation is involved in defense-related gene activation in rice	2013	Plant Cell	National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.	Histone methylation is an important epigenetic modification in chromatin function, genome activity, and gene regulation. Dimethylated or trimethylated histone H3 lysine 27 (H3K27me2/3) marks silent or repressed genes involved in developmental processes and stress responses in plants. However, the role and the mechanism of the dynamic removal of H3K27me2/3 during gene activation remain unclear. Here, we show that the rice (Oryza sativa) Jumonji C (jmjC) protein gene JMJ705 encodes a histone lysine demethylase that specifically reverses H3K27me2/3. The expression of JMJ705 is induced by stress signals and during pathogen infection. Overexpression of the gene reduces the resting level of H3K27me2/3 resulting in preferential activation of H3K27me3-marked biotic stress-responsive genes and enhances rice resistance to the bacterial blight disease pathogen Xanthomonas oryzae pathovar oryzae. Mutation of the gene reduces plant resistance to the pathogen. Further analysis revealed that JMJ705 is involved in methyl jasmonate-induced dynamic removal of H3K27me3 and gene activation. The results suggest that JMJ705 is a biotic stress-responsive H3K27me2/3 demethylase that may remove H3K27me3 from marked defense-related genes and increase their basal and induced expression during pathogen infection.	JMJ705
Rice jmjC domain-containing gene JMJ706 encodes H3K9 demethylase required for floral organ development	2008	Proc Natl Acad Sci U S A	National Key Laboratory for Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.	Histone lysine methylation is an important epigenetic modification with both activating and repressive roles in gene expression. Jumonji C (jmjC) domain-containing proteins have been shown to reverse histone methylation in nonplant model systems. Here, we show that plant Jumonji C proteins have both conserved and specific features compared with mammalian homologues. In particular, the rice JMJD2 family jmjC gene JMJ706 is shown to encode a heterochromatin-enriched protein. The JMJ706 protein specifically reverses di- and trimethylations of lysine 9 of histone H3 (H3K9) in vitro. Loss-of-function mutations of the gene lead to increased di- and trimethylations of H3K9 and affect the spikelet development, including altered floral morphology and organ number. Gene expression and histone modification analysis indicates that JMJ706 regulates a subset of flower development regulatory genes. Taken together, our data suggest that rice JMJ706 encodes a heterochromatin-associated H3K9 demethylase involved in the regulation of flower development in rice.	JMJ706
Crystallographic analysis reveals a unique conformation of the ADP-bound novel rice kinesin K16	2010	Biochem Biophys Res Commun	Division of Bioinformatics, Graduate School of Engineering, Soka University, Hachioji, Tokyo 192-8577, Japan.	Biochemical studies revealed that the novel rice plant-specific kinesin K16 has several unique enzymatic characteristics as compared to conventional kinesins. The ADP-free form of K16 is very stable, whereas the ADP-free form of conventional kinesins is labile. In the present study, the crystal structure of the novel rice kinesin motor domain (K16MD) complexed with Mg-ADP was determined at 2.4 A resolutions. The overall structure of K16MD is similar to that of conventional kinesin motor domains, as expected from the high amino acid sequence similarity (43.2%). However, several unique structures in K16 were observed. The position and length of the L5, L11, and L12 loops, which are key functional regions, were different from those observed in conventional kinesins. Moreover, the neck-linker region of the ADP-bound K16MD showed an ordered conformation at a position quite different from that previously observed in conventional kinesins. These structural differences may reflect the unique enzymatic characteristics of rice kinesin K16.	K16
Preparation and characterization of a novel rice plant-specific kinesin	2006	J Biochem	Laboratories of Plant and Microbial Genome Control, Graduate School of Science and Technology, Niigata University, Niigata 950-2181.	Kinesin is an ATP-driven motor protein that plays important physiological roles in intracellular transport, mitosis and meiosis, control of microtubule dynamics, and signal transduction. The kinesin family is classified into subfamilies. Kinesin species derived from vertebrates have been well characterized. In contrast, plant kinesins have yet to be adequately characterized. In this study, we expressed the motor domain of a novel rice plant-specific kinesin, K16, in Escherichia coli, and then determined its enzymatic characteristics and compared them with those of kinesin 1. Our findings demonstrated that the rice kinesin motor domain has different enzymatic properties from those of well known kinesin 1.	K16
Conformational change of the loop L5 in rice kinesin motor domain induced by nucleotide binding	2006	J Biochem	Laboratories of Plant and Microbial Genome Control, Graduate School of Science and Technology, Niigata University, Niigata 950-2181.	Loop L5 of kinesin is located near the ATPase site, in common with kinesins of various animal species. The rice plant-specific kinesin K16 also has a corresponding loop that is slightly shorter than that of mouse brain kinesin. The present study was designed to monitor conformational changes in loop L5 during ATP hydrolysis. For this purpose, we introduced one reactive cysteine into the L5 of rice kinesin and modified it with fluorescent probes. The cysteine in L5 was labeled with a fluorescent probe 2-(4'(iodoacetamide) anilino-naphthalene-6-sulfonic acid sodium salt) [IAANS]. IAANS was incorporated into L5 at an almost equimolar ratio in the absence of nucleotides. In contrast, the incorporated amount was reduced to 0.62 and 0.32 mol IAANS/mol motor domain in the presence of ATP and ADP, respectively. Upon nucleotide addition, the fluorescent intensity of IAANS incorporated into L5 was significantly reduced to 63% and 51% for ATP and ADP, respectively. These results suggest that L5 of rice kinesin significantly changes its conformation during ATP hydrolysis.	K16
Ectopic expression of the K+ channel beta subunits from Puccinellia tenuiflora (KPutB1) and rice (KOB1) alters K+ homeostasis of yeast and Arabidopsis	2011	Mol Biotechnol	Asian Natural Environmental Science Center (ANESC), The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo-shi, Tokyo 188-0002, Japan.	In this study, we cloned a cDNA for the K+ channel beta subunit from the halophyte Puccinellia tenuiflora and named it KPutB1. KPutB1 was preferentially expressed in the roots and was transiently induced by K+-starvation, salt stress, or the combination of both stresses. By yeast two-hybrid assay, we demonstrated that KPutB1 interacts with PutAKT1, alpha subunit of an AKT1-type K+ channel of P. tenuiflora. The functional relevance of this interaction on K+-nutrition was investigated by co-expression experiments in yeast under various ionic conditions, and K+ channel alpha and beta subunit homologues from rice (OsAKT1 and KOB1, respectively) were included for comparison. Yeast co-expressing PutAKT1 and the beta subunits (KPutB1 and KOB1) had better growth and higher K+-uptake ability than yeast expressing PutAKT1 alone. In contrast, yeast co-expressing the beta subunits (KPutB1 and KOB1) with OsAKT1 had slower growth and lower K+ uptake than yeast expressing OsAKT1 alone. Arabidopsis plants over-expressing the K+ channel beta subunit of P. tenuiflora or rice showed increased shoot K+ content and decreased root Na+ content under control, 75 mM NaCl, and K+-starvation stress conditions. These results suggest that ectopic expression of the K+ channel beta subunit could alter K+ and Na+ homeostasis in plants.	KOB1
Molecular cloning and expression characterization of a rice K+ channel beta subunit	1998	Plant Mol Biol	Plant Science Department, College of Agriculture and Natural Resources, University of Connecticut, Storrs 06269-4067, USA.	K+ channel proteins native to animal membranes have been shown to be composed of two different types of polypeptides: the pore-forming alpha subunit and the beta subunit which may be involved in either modulation of conductance through the channel, or stabilization and surface expression of the channel complex. Several cDNAs encoding animal K+ channel beta subunits have been recently cloned and sequenced. We report the molecular cloning of a rice plant homolog of these animal beta subunits. The rice cDNA (KOB1) described in this report encodes a 36 kDa polypeptide which shares 45% sequence identity with these animal K+ channel beta subunits. and 72% identity with the only other cloned plant (Arabidopsis thaliana) K+ channel beta subunit (KAB1). The KOB1 translation product was demonstrated to form a tight physical association with a plant K+ channel alpha subunit. These results are consistent with the conclusion that the KOB1 cDNA encodes a K+ channel beta subunit. Expression studies indicated that KOB1 protein is more abundant in leaves than in either reproductive structures or roots. Later-developing leaves on a rice plant were found to contain increasing levels of the protein with the flag leaf having the highest titer of KOB1. Leaf sheaths are known to accumulate excess K+ and act as reserve sources of this cation when new growth requires remobilization of K+. Leaf sheaths were found to contain higher levels of KOB1 protein than the blade portions of leaves. It was further determined that when K+ was lost from older leaves of plants grown on K+-deficient fertilizer, the loss of cellular K+ was associated with a decline in both KOB1 mRNA and protein. This finding represents the first demonstration (in either plants or animals) that changes in cellular K+ status may specifically alter expression of a gene encoding a K+ channel subunit.	KOB1
Phytochrome B control of total leaf area and stomatal density affects drought tolerance in rice	2012	Plant Mol Biol	College of Life Sciences, Shandong Normal University, 250014 Jinan, People's Republic of China.	We report that phytochrome B (phyB) mutants exhibit improved drought tolerance compared to wild type (WT) rice (Oryza sativa L. cv. Nipponbare). To understand the underlying mechanism by which phyB regulates drought tolerance, we analyzed root growth and water loss from the leaves of phyB mutants. The root system showed no significant difference between the phyB mutants and WT, suggesting that improved drought tolerance has little relation to root growth. However, phyB mutants exhibited reduced total leaf area per plant, which was probably due to a reduction in the total number of cells per leaf caused by enhanced expression of Orysa;KRP1 and Orysa;KRP4 (encoding inhibitors of cyclin-dependent kinase complex activity) in the phyB mutants. In addition, the developed leaves of phyB mutants displayed larger epidermal cells than WT leaves, resulting in reduced stomatal density. phyB deficiency promoted the expression of both putative ERECTA family genes and EXPANSIN family genes involved in cell expansion in leaves, thus causing greater epidermal cell expansion in the phyB mutants. Reduced stomatal density resulted in reduced transpiration per unit leaf area in the phyB mutants. Considering all these findings, we propose that phyB deficiency causes both reduced total leaf area and reduced transpiration per unit leaf area, which explains the reduced water loss and improved drought tolerance of phyB mutants.	KRP1,PHYB|OsphyB
The cyclin-dependent kinase inhibitor Orysa;KRP1 plays an important role in seed development of rice	2006	Plant Physiol	Department of Plant Systems Biology, Flanders Interuniversity Institute for Biotechnology, Ghent University, B-9052 Ghent, Belgium.	Kip-related proteins (KRPs) play a major role in the regulation of the plant cell cycle. We report the identification of five putative rice (Oryza sativa) proteins that share characteristic motifs with previously described plant KRPs. To investigate the function of KRPs in rice development, we generated transgenic plants overexpressing the Orysa;KRP1 gene. Phenotypic analysis revealed that overexpressed KRP1 reduced cell production during leaf development. The reduced cell production in the leaf meristem was partly compensated by an increased cell size, demonstrating the existence of a compensatory mechanism in monocot species by which growth rate is less reduced than cell production, through cell expansion. Furthermore, Orysa;KRP1 overexpression dramatically reduced seed filling. Sectioning through the overexpressed KRP1 seeds showed that KRP overproduction disturbed the production of endosperm cells. The decrease in the number of fully formed seeds was accompanied by a drop in the endoreduplication of endosperm cells, pointing toward a role of KRP1 in connecting endocycle with endosperm development. Also, spatial and temporal transcript detection in developing seeds suggests that Orysa;KRP1 plays an important role in the exit from the mitotic cell cycle during rice grain formation.	KRP1
Isolation and characterisation of a dwarf rice mutant exhibiting defective gibberellins biosynthesis	2014	Plant Biol (Stuttg)	Department of Molecular Biotechnology, Konkuk University, Seoul, Korea.	We have isolated a severe dwarf mutant derived from a Ds (Dissociation) insertion mutant rice (Oryza sativa var. japonica c.v. Dongjin). This severe dwarf phenotype, has short and dark green leaves, reduced shoot growth early in the seedling stage, and later severe dwarfism with failure to initiate flowering. When treated with bioactive GA3 , mutants are restored to the normal wild-type phenotype. Reverse transcription PCR analyses of 22 candidate genes related to the gibberellin (GA) biosynthesis pathway revealed that among 22 candidate genes tested, a dwarf mutant transcript was not expressed only in one OsKS2 gene. Genetic analysis revealed that the severe dwarf phenotype was controlled by recessive mutation of a single nuclear gene. The putative OsKS2 gene was a chromosome 4-located ent-kaurene synthase (KS), encoding the enzyme that catalyses an early step of the GA biosynthesis pathway. Sequence analysis revealed that osks2 carried a 1-bp deletion in the ORF region of OsKS2, which led to a loss-of-function mutation. The expression pattern of OsKS2 in wild-type cv Dongjin, showed that it is expressed in all organs, most prominently in the stem and floral organs. Morphological characteristics of the dwarf mutant showed dramatic modifications in internal structure and external morphology. We propose that dwarfism in this mutant is caused by a point mutation in OsKS2, which plays a significant role in growth and development of higher plants. Further investigation on OsKS2 and other OsKS-like proteins is underway and may yield better understanding of the putative role of OsKS in severe dwarf mutants.	KS2
cDNA cloning of rice lipoxygenase L-2 and characterization using an active enzyme expressed from the cDNA in Escherichia coli	1992	European Journal of Biochemistry	Mitsui Plant Biotechnology Research Institute, Tsukuba, Japan	A full-length cDNA of rice lipoxygenase L-2 was cloned from 3-day old seedlings. The identity of the clone was determined by amino acid sequencing of selected peptides of the purified enzyme and immunological characterization of an active enzyme that was produced from the cDNA in Escherichia coli by cultivation at 15°C. The nucleotide sequence showed a strong bias toward G and C in the selection of nucleotides, especially at the third position of the codons(93%G/C). The complete amino acid sequence of the enzyme was deduced from the nucleotide sequence. The molecular mass of the enzyme was calculated to be 96657 Da based on 865 amino acids. The amino acid sequence shares similarity with those of dicot lipoxygenases throughout the enzyme at a level of 50%. A hydropathy profile calculated from the amino acid sequence resembled those of dicot lipoxygenases, suggesting conservation of the secondary structure of these enzymes. The active enzyme, expressed in Escherichia coli, was charaterized for pH dependence of the enzyme activity, intramolecular specificity, heat stability and Km. The enzyme had the same properties as the L-2 enzyme that was isolated from seedlings, but differed from the lipoxygenase L-3 isolated from mature plants.	L-2
LAZY1 controls rice shoot gravitropism through regulating polar auxin transport	2007	Cell Res	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Tiller angle of rice (Oryza sativa L.) is an important agronomic trait that contributes to grain production, and has long attracted attentions of breeders for achieving ideal plant architecture to improve grain yield. Although enormous efforts have been made over the past decades to study mutants with extremely spreading or compact tillers, the molecular mechanism underlying the control of tiller angle of cereal crops remains unknown. Here we report the cloning of the LAZY1 (LA1) gene that regulates shoot gravitropism by which the rice tiller angle is controlled. We show that LA1, a novel grass-specific gene, is temporally and spatially expressed, and plays a negative role in polar auxin transport (PAT). Loss-of-function of LA1 enhances PAT greatly and thus alters the endogenous IAA distribution in shoots, leading to the reduced gravitropism, and therefore the tiller-spreading phenotype of rice plants.	LA1
Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1	2012	Plant Biotechnol J	State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.	Crop architecture parameters such as tiller number, angle and plant height are important agronomic traits that have been considered for breeding programmes. Auxin distribution within the plant has long been recognized to alter architecture. The rice (Oryza sativa L.) genome contains 12 putative PIN genes encoding auxin efflux transporters, including four PIN1 and one PIN2 genes. Here, we report that over-expression of OsPIN2 through a transgenic approach in rice (Japonica cv. Nipponbare) led to a shorter plant height, more tillers and a larger tiller angle when compared with wild type (WT). The expression patterns of the auxin reporter DR5::GUS and quantification of auxin distribution showed that OsPIN2 over-expression increased auxin transport from the shoot to the root-shoot junction, resulting in a non-tissue-specific accumulation of more free auxin at the root-shoot junction relative to WT. Over-expression of OsPIN2 enhanced auxin transport from shoots to roots, but did not alter the polar auxin pattern in the roots. Transgenic plants were less sensitive to N-1-naphthylphthalamic acid, an auxin transport inhibitor, than WT in their root growth. OsPIN2-over-expressing plants had suppressed the expression of a gravitropism-related gene OsLazy1 in the shoots, but unaltered expression of OsPIN1b and OsTAC1, which were reported as tiller angle controllers in rice. The data suggest that OsPIN2 has a distinct auxin-dependent regulation pathway together with OsPIN1b and OsTAC1 controlling rice shoot architecture. Altering OsPIN2 expression by genetic transformation can be directly used for modifying rice architecture.	LA1,OsPIN2,TAC1
Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and -independent gravity signaling pathways	2007	Plant Cell Physiol	Botanical Gardens, Graduate School of Science, Osaka City University, Kisaichi, Katano-shi, Osaka, 576-0004 Japan.	We identified the gene responsible for three allelic lazy1 mutations of Japonica rice (Oryza sativa L.) by map-based cloning, complementation and RNA interference. Sequence analysis and database searches indicated that the wild-type gene (LAZY1) encodes a novel and unique protein (LAZY1) and that rice has no homologous gene. Two lazy1 mutants were LAZY1 null. Confirming and advancing the previously reported results on lazy1 mutants, we found the following. (i) Gravitropism is impaired, but only partially, in lazy1 coleoptiles. (ii) Circumnutation, observed in dark-grown coleoptiles, is totally absent from lazy1 coleoptiles. (iii) Primary roots of lazy1 mutants show normal gravitropism and circumnutation. (iv) LAZY1 is expressed in a tissue-specific manner in gravity-sensitive shoot tissues (i.e. coleoptiles, leaf sheath pulvini and lamina joints) and is little expressed in roots. (v) The gravitropic response of lazy1 coleoptiles is kinetically separable from that absent from lazy1 coleoptiles. (vi) Gravity-induced lateral translocation of auxin, found in wild-type coleoptiles, does not occur in lazy1 coleoptiles. Based on the genetic and physiological evidence obtained, it is concluded that LAZY1 is specifically involved in shoot gravitropism and that LAZY1-dependent and -independent signaling pathways occur in coleoptiles. It is further concluded that, in coleoptiles, only the LAZY1-dependent gravity signaling involves asymmetric distribution of auxin between the two lateral halves and is required for circumnutation.	LA1
Loose Plant Architecture1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism, regulates plant architecture in rice	2013	Plant Physiol	State Key Laboratory of Plant Genomics and Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Tiller angle and leaf angle are two important components of rice (Oryza sativa) plant architecture that play a crucial role in determining grain yield. Here, we report the cloning and characterization of the Loose Plant Architecture1 (LPA1) gene in rice, the functional ortholog of the AtIDD15/SHOOT GRAVITROPISM5 (SGR5) gene in Arabidopsis (Arabidopsis thaliana). LPA1 regulates tiller angle and leaf angle by controlling the adaxial growth of tiller node and lamina joint. LPA1 was also found to affect shoot gravitropism. Expression pattern analysis suggested that LPA1 influences plant architecture by affecting the gravitropism of leaf sheath pulvinus and lamina joint. However, LPA1 only influences gravity perception or signal transduction in coleoptile gravitropism by regulating the sedimentation rate of amyloplasts, distinct from the actions of LAZY1. LPA1 encodes a plant-specific INDETERMINATE DOMAIN protein and defines a novel subfamily of 28 INDETERMINATE DOMAIN proteins with several unique conserved features. LPA1 is localized in the nucleus and functions as an active transcriptional repressor, an activity mainly conferred by a conserved ethylene response factor-associated amphiphilic repression-like motif. Further analysis suggests that LPA1 participates in a complicated transcriptional and protein interaction network and has evolved novel functions distinct from SGR5. This study not only facilitates the understanding of gravitropism mechanisms but also generates a useful genetic material for rice breeding.	LA1,LPA1
The LAX1 and FRIZZY PANICLE 2 genes determine the inflorescence architecture of rice by controlling rachis-branch and spikelet development	2001	Dev Biol	Laboratory of Plant Molecular Genetics, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, 630-0101, Japan	We have analyzed two mutants that exhibit altered panicle architecture in rice (Oryza sativa L.). In lax1-2, which is a new and stronger allele of the previously reported lax mutant, initiation and/or maintenance of rachis-branches, lateral spikelets, and terminal spikelets was severely prevented. In situ hybridization analysis using OSH1, a rice knotted1 (kn1) ortholog, confirmed the absence of lateral meristems in lax1-2 panicles. These defects indicate that the LAX1 gene is required for the initiation/maintenance of axillary meristems in the rice panicle. In addition to its role in forming lateral meristems, the wild-type LAX1 gene acts as a floral meristem identity gene which specifies the terminal spikelet meristem. A comparison of the defects in lax1-1 and lax1-2 plants suggested that the sensitivities to reduced LAX1 activity were not uniform among different types of meristems. In the fzp2 mutant panicle, the basic branching pattern of the panicle was indistinguishable from that of the wild type; however, specification of both terminal and lateral spikelet meristems was blocked, and sequential rounds of branching occurred at the point where the spikelet meristems are initiated in the wild-type panicle. This resulted in the generation of a panicle composed of excessive ramification of rachis-branches. The lax1-1 fzp2 double mutants exhibited a novel, basically additive, phenotype, which suggests that LAX1 and FZP2 function in genetically independent pathways.	LAX1
Two-Step Regulation of LAX PANICLE1 Protein Accumulation in Axillary Meristem Formation in Rice	2009	Plant Cell	Graduate School of Agriculture and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8657, Japan.	Axillary meristem (AM) formation is an important determinant of plant architecture. In rice (Oryza sativa), LAX PANICLE1 (LAX1) function is required for the generation of AM throughout the plant's lifespan. Here, we show a close relationship between AM initiation and leaf development; specifically, the plastochron 4 (P4) stage of leaf development is crucial for the proliferation of meristematic cells. Coincident with this, LAX1 expression starts in the axils of leaves at P4 stage. LAX1 mRNA accumulates in two to three layers of cells in the boundary region between the initiating AM and the shoot apical meristem. In lax1 mutants, the proliferation of meristematic cells is initiated but fails to progress into the formation of AM. The difference in sites of LAX1 mRNA expression and its action suggests non-cell-autonomous characteristics of LAX1 function. We found that LAX1 protein is trafficked to AM in a stage- and direction-specific manner. Furthermore, we present evidence that LAX1 protein movement is required for the full function of LAX1. Thus, we propose that LAX1 protein accumulates transiently in the initiating AM at P4 stage by a strict regulation of mRNA expression and a subsequent control of protein trafficking. This two-step regulation is crucial to the establishment of the new AM.	LAX1
LAX PANICLE2 of rice encodes a novel nuclear protein and regulates the formation of axillary meristems	2011	Plant Cell	Crop Development Division, National Agriculture and Food Research Organization Agricultural Research Center, Niigata 943-0193, Japan.	Aerial architecture in higher plants is dependent on the activity of the shoot apical meristem (SAM) and axillary meristems (AMs). The SAM produces a main shoot and leaf primordia, while AMs are generated at the axils of leaf primordia and give rise to branches and flowers. Therefore, the formation of AMs is a critical step in the construction of plant architecture. Here, we characterized the rice (Oryza sativa) lax panicle2 (lax2) mutant, which has altered AM formation. LAX2 regulates the branching of the aboveground parts of a rice plant throughout plant development, except for the primary branch in the panicle. The lax2 mutant is similar to lax panicle1 (lax1) in that it lacks an AM in most of the lateral branching of the panicle and has a reduced number of AMs at the vegetative stage. The lax1 lax2 double mutant synergistically enhances the reduced-branching phenotype, indicating the presence of multiple pathways for branching. LAX2 encodes a nuclear protein that contains a plant-specific conserved domain and physically interacts with LAX1. We propose that LAX2 is a novel factor that acts together with LAX1 in rice to regulate the process of AM formation.	LAX1,Gnp4|LAX2
LAX and SPA: major regulators of shoot branching in rice	2003	Proc Natl Acad Sci U S A	Graduate School of Agriculture and Life Science, University of Tokyo, Yayoi 1-1-1, Bunkyo, Tokyo 113-8657, Japan.	The aerial architecture of plants is determined primarily by the pattern of shoot branching. Although shoot apical meristem initiation during embryogenesis has been extensively studied by molecular genetic approaches using Arabidopsis, little is known about the genetic mechanisms controlling axillary meristem initiation, mainly because of the insufficient number of mutants that specifically alter it. We identified the LAX PANICLE (LAX) and SMALL PANICLE (SPA) genes as the main regulators of axillary meristem formation in rice. LAX encodes a basic helix-loop-helix transcription factor and is expressed in the boundary between the shoot apical meristem and the region of new meristem formation. This pattern of LAX expression was repeatedly observed in every axillary meristem, consistent with our observation that LAX is involved in the formation of all types of axillary meristems throughout the ontogeny of a rice plant. Ectopic LAX expression in rice caused pleiotropic effects, including dwarfing, an altered pattern of stem elongation, darker color, bending of the lamina joint, absence of the midribs of leaves, and severe sterility.	LAX1
Fine Mapping and Cloning of the Grain Number Per-Panicle Gene (Gnp4) on Chromosome 4 in Rice (Oryza sativa L.)	2011	Agricultural Sciences in China	Key Laboratory of Crop Heterosis and Utilization, Ministry of Agriculture/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, P.R.China	Grain number per-panicle is one of the most important components for rice yield. Spikelets on the primary and secondary branches determine the grain number per-panicle in rice. In this study, we identified a natural mutant, gnp4, lack of lateral spikelet on the secondary branches in the field condition. In addition, the Gnp4 and Lax1-1 double mutant showed dramatically reduced secondary branches and spikelets in panicle at reproductive stage, and tillers at vegetative stage. By map-based cloning approach, and using four F2 segregating populations, the Gnp4 gene was finally mapped to a 10.7-kb region on the long arm of chromosome 4 in rice. In this region, only one gene was predicted, and genomic DNA sequencing of the 10.7-kb region showed no nucleotide differences between the mutant and wild type. Interestingly, we found that the methylation level of several cytosines in the promoter CpG islands region of the predicted gene in gnp4 were different from the wild type. Thus, we propose that the DNA methylation changes at these sites may induce to decrease expression level of Gnp4, consequently, resulting in phenotypic variation.	Gnp4|LAX2
Rice leaf inclination2, a VIN3-like protein, regulates leaf angle through modulating cell division of the collar	2010	Cell Res	Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.	As an important agronomic trait, inclination of leaves is crucial for crop architecture and grain yields. To understand the molecular mechanism controlling rice leaf angles, one rice leaf inclination2 (lc2, three alleles) mutant was identified and functionally characterized. Compared to wild-type plants, lc2 mutants have enlarged leaf angles due to increased cell division in the adaxial epidermis of lamina joint. The LC2 gene was isolated through positional cloning, and encodes a vernalization insensitive 3-like protein. Complementary expression of LC2 reversed the enlarged leaf angles of lc2 plants, confirming its role in controlling leaf inclination. LC2 is mainly expressed in the lamina joint during leaf development, and particularly, is induced by the phytohormones abscisic acid, gibberellic acid, auxin, and brassinosteroids. LC2 is localized in the nucleus and defects of LC2 result in altered expression of cell division and hormone-responsive genes, indicating an important role of LC2 in regulating leaf inclination and mediating hormone effects.	LC2|OsVIL3,OsVIL4
LC2 and OsVIL2 promote rice flowering by photoperoid-induced epigenetic silencing of OsLF	2013	Mol Plant	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese academy of Sciences, Shanghai 200032, PR China.	Proper flowering time is essential for plant reproduction. Winter annual Arabidopsis thaliana needs vernalization before flowering, during which AtVILs (VIN3 and VRN5, components of PRC2 complex) mediate the H3K27 tri-methylation at the FLC locus (a floral repressor) to repress the FLC expression and hence to induce flowering. However, how VILs (VIL, VERNALIZATION INSENSITIVE 3-LIKE) function in rice is unknown. Here we demonstrated that rice LC2 (OsVIL3) and OsVIL2 (two OsVILs, possible components of PRC2 complex) promote rice flowering. Our results showed that expressions of LC2 and OsVIL2 are induced by SD (short-day) conditions and both lc2 mutant and OsVIL2-RNAi lines display delayed heading date, consistent with the reduced expression levels of Hd1 and Hd3a. Interestingly, LC2 binds to the promoter region of a floral repressor OsLF and represses the OsLF expression via H3K27 tri-methylation modification. In addition, OsLF directly regulates the Hd1 expression through binding to Hd1 promoter. These results first demonstrated that the putative PRC2 in rice is involved in photoperiod flowering regulation, which is different from that of Arabidopsis, and revealed that LC2 binds the promoter region of target gene, presenting a possible mechanism of the recruitment process of PRC2 complex to its target genes. The studies provide informative clues on the epigenetic control of rice flowering.	LC2|OsVIL3,OsLF,OsVIL1,OsVIL2,OsVIL4
Rice LGD1 containing RNA binding activity affects growth and development through alternative promoters	2012	Plant J	Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan.	Tiller initiation and panicle development are important agronomical traits for grain production in Oryza sativa L. (rice), but their regulatory mechanisms are not yet fully understood. In this study, T-DNA mutant and RNAi transgenic approaches were used to functionally characterize a unique rice gene, LAGGING GROWTH AND DEVELOPMENT 1 (LGD1). The lgd1 mutant showed slow growth, reduced tiller number and plant height, altered panicle architecture and reduced grain yield. The fewer unelongated internodes and cells in lgd1 led to respective reductions in tiller number and to semi-dwarfism. Several independent LGD1-RNAi lines exhibited defective phenotypes similar to those observed in lgd1. Interestingly, LGD1 encodes multiple transcripts with different transcription start sites (TSSs), which were validated by RNA ligase-mediated rapid amplification of 5' and 3' cDNA ends (RLM-RACE). Additionally, GUS assays and a luciferase promoter assay confirmed the promoter activities of LGD1.1 and LGD1.5. LGD1 encoding a von Willebrand factor type A (vWA) domain containing protein is a single gene in rice that is seemingly specific to grasses. GFP-tagged LGD1 isoforms were predominantly detected in the nucleus, and weakly in the cytoplasm. In vitro northwestern analysis showed the RNA-binding activity of the recombinant C-terminal LGD1 protein. Our results demonstrated that LGD1 pleiotropically regulated rice vegetative growth and development through both the distinct spatiotemporal expression patterns of its multiple transcripts and RNA binding activity. Hence, the study of LGD1 will strengthen our understanding of the molecular basis of the multiple transcripts, and their corresponding polypeptides with RNA binding activity, that regulate pleiotropic effects in rice.	LGD1
Low-temperature-dependent expression of a rice gene encoding a protein with a leucine-zipper motif	1993	Mol Gen Genet	Laboratory of Plant Genetic Engineering, Akita Prefectural College of Agriculture, Japan.	We have isolated from rice suspension cells three non-sequence-related cDNAs the expression of which is markedly induced by low, non-freezing temperature. Here we further characterize one of the cDNA clones, lip19. Expression of lip19 is positively regulated by low temperature, but not affected by high (40 degrees C) temperature. Sequencing and primer extension analyses showed that lip19 has a long (552 bp) 5' non-coding sequence followed by a single open reading frame specifying a protein of 148 amino acids. The deduced amino acid sequence of the protein, Lip19, shows at its amino-terminus a conserved basic region followed by a "leucine-zipper" domain. The reported sequence most similar to Lip19 is maize OCSBF-1, which is a bZip-type DNA binding protein. The possibility is suggested that Lip19 is a transcriptional factor that is positively controlled by low temperature.	LIP19|OsbZIP38
Genome-wide analysis of basic leucine zipper transcription factor families in Arabidopsis thaliana, Oryza sativa and Populus trichocarpa	2009	Journal of Shanghai University (English Edition)	School of Life Sciences, Shanghai University, Shanghai, 200444, P. R. China	The basic leucine zipper (bZIP) transcription factors form a large gene family that is important in pathogen defense, light and stress signaling, etc. The Completed whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa) and poplar (Populus trichocarpa) constitute a valuable resource for genome-wide analysis and genomic comparative analysis, as they are representatives of the two major evolutionary lineages within the angiosperms: the monocotyledons and the dicotyledons. In this study, bioinformatics analysis identified 74, 89 and 88 bZIP genes respectively in Arabidopsis, rice and poplar. Moreover, a comprehensive overview of this gene family is presented, including the gene structure, phylogeny, chromosome distribution, conserved motifs. As a result, the plant bZIPs were organized into 10 subfamilies on basis of phylogenetic relationship. Gene duplication events during the family evolution history were also investigated. And it was further concluded that chromosomal/segmental duplication might have played a key role in gene expansion of bZIP gene family.	LIP19|OsbZIP38,OsABF1|OsABI5|OREB1|OsbZIP10,OsbZIP01,OsbZIP16,OsbZIP23,OsbZIP28|OsbZIP1,OsbZIP39,OsbZIP50|OsbZIP74,OsbZIP52|RISBZ5,OsbZIP60,OsbZIP71,OsbZIP72,OsOBF1|OsbZIP87,OsTGAP1|OsbZIP37,OsZIP-1a|OsbZIP86,OsZIP-2a|OsbZIP80,RF2a|OsbZIP75,RF2b|OsbZIP30
Genomic survey and gene expression analysis of the basic leucine zipper transcription factor family in rice	2008	Plant Physiol	Interdisciplinary Centre for Plant Genomics and Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.	The basic leucine (Leu) zipper (bZIP) proteins compose a family of transcriptional regulators present exclusively in eukaryotes. The bZIP proteins characteristically harbor a bZIP domain composed of two structural features: a DNA-binding basic region and the Leu zipper dimerization region. They have been shown to regulate diverse plant-specific phenomena, including seed maturation and germination, floral induction and development, and photomorphogenesis, and are also involved in stress and hormone signaling. We have identified 89 bZIP transcription factor-encoding genes in the rice (Oryza sativa) genome. Their chromosomal distribution and sequence analyses suggest that the bZIP transcription factor family has evolved via gene duplication. The phylogenetic relationship among rice bZIP domains as well as with bZIP domains from other plant bZIP factors suggests that homologous bZIP domains exist in plants. Similar intron/exon structural patterns were observed in the basic and hinge regions of their bZIP domains. Detailed sequence analysis has been done to identify additional conserved motifs outside the bZIP domain and to predict their DNA-binding site specificity as well as dimerization properties, which has helped classify them into different groups and subfamilies, respectively. Expression of bZIP transcription factor-encoding genes has been analyzed by full-length cDNA and expressed sequence tag-based expression profiling. This expression profiling was complemented by microarray analysis. The results indicate specific or coexpression patterns of rice bZIP transcription factors starting from floral transition to various stages of panicle and seed development. bZIP transcription factor-encoding genes in rice also displayed differential expression patterns in rice seedlings in response to abiotic stress and light irradiation. An effort has been made to link the structure and expression pattern of bZIP transcription factor-encoding genes in rice to their function, based on the information obtained from our analyses and earlier known results. This information will be important for functional characterization of bZIP transcription factors in rice.	LIP19|OsbZIP38,OsAREB8|OsAREB1|OsbZIP46|OsABF2|ABL1,OSBZ8|OsbZIP05,OsbZIP01,OsbZIP16,OsbZIP23,OsbZIP28|OsbZIP1,OsbZIP39,OsbZIP50|OsbZIP74,OsbZIP52|RISBZ5,OsbZIP60,OsbZIP71,OsbZIP72,OsOBF1|OsbZIP87,OsTGAP1|OsbZIP37,OsZIP-1a|OsbZIP86,OsZIP-2a|OsbZIP80,REB,RF2a|OsbZIP75,RF2b|OsbZIP30,RISBZ1|OsbZIP58,RSG,rTGA2.1|OsbZIP63|OsNIF1,TRAB1|OsbZIP66,RITA1
LIP19, a basic region leucine zipper protein, is a Fos-like molecular switch in the cold signaling of rice plants	2005	Plant Cell Physiol	Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi, Japan.	The rice low-temperature-induced lip19 gene encodes a 148-amino-acid basic region/leucine zipper (bZIP) protein, termed LIP19. In this study we characterized LIP19 and showed that it lacks the usual ability of bZIP proteins to homodimerize and to bind DNA, as does the Fos protein in mammals. Using a yeast two-hybrid system, the cDNA clones whose products interact with LIP19 were screened. This search revealed a clone termed OsOBF1 (Oryza sativa OBF1) that encodes a new bZIP protein (OsOBF1). This protein forms a homodimer and binds to the hexamer motif sequence (5'-ACGTCA-3'). The protein-protein interaction in homo- and hetero-combinations between LIP19 and OsOBF1 was confirmed in vitro and in planta. LIP19 and OsOBF1 most likely interact with each other more strongly than OsOBF1 interacts with itself, and the resulting heterodimer binds to the C/G hybrid sequence but not to the hexamer sequence. Whereas the expression patterns of lip19 and OsOBF1 in response to low temperatures were totally opposite, the locations of their expression were almost identical. Based upon the presented data, we propose a model describing the low-temperature signal switching mediated by LIP19 in rice.	LIP19|OsbZIP38,OsOBF1|OsbZIP87
Circadian rhythmicity in the expression of a novel light-regulated rice gene	1993	Plant Mol Biol	Institute of Plant Biology, University of Zurich, Switzerland.	We have identified and analyzed cDNAs corresponding to a single-copy gene from rice, designated lir1, whose expression exhibits dramatic diurnal fluctuations. The cDNAs encode a putative protein of 128 amino acids with no homology to known proteins. Lir1 mRNA accumulates in the light, reaching maximum and minimum steady-state levels at the end of the light and dark period, respectively. The oscillations of lir1 mRNA abundance persist after the plants have been transferred to continuous light or darkness. Plants germinated in the dark have very low levels of lir1 mRNA, whereas plants germinated in continuous light express lir1 at an intermediate but constant level. These results indicate that lir1 expression is controlled by light and a circadian clock.	Lir1
Direct control of shoot meristem activity by a cytokinin-activating enzyme	2007	Nature	Graduate School of Agricultural and Life Sciences, University of Tokyo, Yayoi, Bunkyo, Tokyo 113-8652, Japan.	The growth of plants depends on continuous function of the meristems. Shoot meristems are responsible for all the post-embryonic aerial organs, such as leaves, stems and flowers. It has been assumed that the phytohormone cytokinin has a positive role in shoot meristem function. A severe reduction in the size of meristems in a mutant that is defective in all of its cytokinin receptors has provided compelling evidence that cytokinin is required for meristem activity. Here, we report a novel regulation of meristem activity, which is executed by the meristem-specific activation of cytokinins. The LONELY GUY (LOG) gene of rice is required to maintain meristem activity and its loss of function causes premature termination of the shoot meristem. LOG encodes a novel cytokinin-activating enzyme that works in the final step of bioactive cytokinin synthesis. Revising the long-held idea of multistep reactions, LOG directly converts inactive cytokinin nucleotides to the free-base forms, which are biologically active, by its cytokinin-specific phosphoribohydrolase activity. LOG messenger RNA is specifically localized in shoot meristem tips, indicating the activation of cytokinins in a specific developmental domain. We propose the fine-tuning of concentrations and the spatial distribution of bioactive cytokinins by a cytokinin-activating enzyme as a mechanism that regulates meristem activity.	LOG
LOX genes in blast fungus (Magnaporthe grisea) resistance in rice	2012	Funct Integr Genomics	Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and Technology, Pantnagar, India. soma.marla@nbpgr.ernet.in	Plant Lipoxygenases (LOX) are known to play major role in plant immunity by providing front-line defense against pathogen-induced injury. To verify this, we isolated a full-length OsLOX3 gene and also 12 OsLOX cDNA clones from Oryza sativa indica (cultivar Pusa Basmati 1). We have examined the role played by LOXs in plant development and during attack by blast pathogen Magnaporthe grisea. Gene expression, promoter region analysis, and biochemical and protein structure analysis of isolated OsLOX3 revealed significant homology with LOX super family. Protein sequence comparison of OsLOXs revealed high levels of homology when compared with japonica rice (up to100%) and Arabidopsis (up to 64%). Isolated LOX3 gene and 12 OsLOX cDNAs contained the catalytic LOX domains much required for oxygen binding and synthesis of oxylipins. Amino acid composition, protein secondary structure, and promoter region analysis (with abundance of motifs CGTCA and TGACG) support the role of OsLOX3 gene in providing resistance to diseases in rice plants. OsLOX3 gene expression analysis of root, shoot, flag leaf, and developing and mature seed revealed organ specific patterns during rice plant development and gave evidence to association between tissue location and physiological roles played by individual OsLOXs. Increased defense activity of oxylipins was observed as demonstrated by PCR amplification of OsLOX3 gene and upon inoculation with virulent strains of M. grisea and ectopic application of methyl jasmonate in the injured leaf tissue in adult rice plants.	OsLOX3
Map-based cloning of the ERECT PANICLE 3 gene in rice	2009	Theor Appl Genet	Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea.	Panicle architecture in rice can have a strong influence on yield. Using N-methyl-N-nitrosourea mutagenesis, we isolated an erect panicle mutant, Hep, from Hwasunchalbyeo, a glutinous japonica rice cultivar. Genetic analysis revealed that the erect panicle phenotype was controlled by a single recessive mutation designated erect panicle 3 (ep3). Genetic mapping revealed that the ep3 mutation was located on the short arm of chromosome 2 in a 0.1 cM region delimited by the STS markers STS5803-5 and STS5803-7. The ep3 locus corresponded to 46.8 kb region and contained six candidate genes. Comparison of the DNA sequences of the candidate genes from wild-type and erect panicle plants revealed a single base-pair change in the second exon of LOC_Os02g15950, which is predicted to result in a nonsense mutation. LOC_Os02g15950 encodes a putative F-box protein containing 515 amino acids and is expressed throughout the plant during all growth stages. A line carrying a T-DNA insertion in LOC_ Os02g15950 was obtained and shown to have the same phenotype as the ep3 mutant, thus confirming the identification of LOC_Os02g15950 as the ERECT PANICLE 3 (EP3) gene. The ep3 mutation causes a significant increase in the number of small vascular bundles as well as the thickness of parenchyma in the peduncle, which results in the erect panicle phenotype.	EP3|LP
The LP2 leucine-rich repeat receptor kinase gene promoter directs organ-specific, light-responsive expression in transgenic rice	2009	Plant Biotechnol J	USDA-ARS, Western Regional Research Center, Crop Improvement and Utilization Research Unit, Albany, CA, USA. roger.thilmony@ars.usda.gov	Biotechnologists seeking to limit gene expression to nonseed tissues of genetically engineered cereal crops have only a few choices of well characterized organ-specific promoters. We have isolated and characterized the promoter of the rice Leaf Panicle 2 gene (LP2, Os02g40240). The LP2 gene encodes a leucine-rich repeat-receptor kinase-like protein that is strongly expressed in leaves and other photosynthetic tissues. Transgenic rice plants containing an LP2 promoter-GUS::GFP bifunctional reporter gene displayed an organ-specific pattern of expression. This expression corresponded to transcript levels observed on RNA blots of various rice organs and microarray gene expression data. The strongest beta-glucuronidase activity was observed in histochemically stained mesophyll cells, but other green tissues and leaf cell types including epidermal cells also exhibited expression. Low or undetectable levels of LP2 transcript and LP2-mediated reporter gene expression were observed in roots, mature seeds, and reproductive tissues. The LP2 promoter is highly responsive to light and only weak expression was detected in etiolated rice seedlings. The specificity and strength of the LP2 promoter suggests that this promoter will be a useful control element for green tissue-specific expression in rice and potentially other plants. Organ-specific promoters like LP2 will enable precise, localized expression of transgenes in biotechnology-derived crops and limit the potential of unintended impacts on plant physiology and the environment.	LP2
Over-expression of the rice LRK1 gene improves quantitative yield components	2009	Plant Biotechnol J	State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai 200433, China.	In rice (Oryza sativa L.), the number of panicles, spikelets per panicle and grain weight are important components of grain yield. These characteristics are controlled by quantitative trait loci (QTLs) and are derived from variation inherent in crops. As a result of the complex genetic basis of these traits, only a few genes involved in their control have been cloned and characterized. We have previously map-cloned a gene cluster including eight leucine-rich repeat receptor-like kinase (LRK) genes in Dongxiang wild rice (Oryza rufipogon Griff.), which increased the grain yield by 16%. In the present study, we characterized the LRK1 gene, which was contained in the donor parent (Dongxiang wild rice) genome and absent from the recurrent parent genome (Guichao2, Oryza sativa L. ssp. indica). Our data showed that rice LRK1 is a plasma membrane protein expressed constitutively in leaves, young panicles, roots and culms. The over-expression of rice LRK1 results in increased panicles, spikelets per panicle, weight per grain and enhanced cellular proliferation, leading to a 27.09% increase in total grain yield per plant. The increased number of panicles and spikelets per panicle are associated with increased branch number. Our data suggest that rice LRK1 regulates rice branch number by enhancing cellular proliferation. The functional characterization of rice LRK1 facilitates an understanding of the mechanisms involved in cereal crop yield, and may have utility in improving grain yield in cereal crops.	LRK1
Overexpression of rice LRK1 restricts internode elongation by down-regulating OsKO2	2013	Biotechnol Lett	State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, China. banmatus@gmail.com	Rice (Oryza sativa) has the potential to undergo rapid internodal elongation which determines plant height. Gibberellin is involved in internode elongation. Leucine-rich repeat receptor-like kinases (LRR-RLKs) are the largest subfamily of transmembrane receptor-like kinases in plants. LRR-RLKs play important functions in mediating a variety of cellular processes and regulating responses to environmental signals. LRK1, a PSK receptor homolog, is a member of the LRR-RLK family. In the present study, differences in ectopic expression of LRK1 were consistent with extent of rice internode elongation. Analyses of gene expression demonstrated that LRK1 restricts gibberellin biosynthesis during the internode elongation process by down-regulation of the gibberellin biosynthetic gene coding for ent-kaurene oxidase.	LRK1,D35|OsKOS3|OsKO2
The role of the rice aquaporin Lsi1 in arsenite efflux from roots	2010	New Phytol	Rothamsted Research, Harpenden, Herts AL5 2JQ, UK.	*When supplied with arsenate (As(V)), plant roots extrude a substantial amount of arsenite (As(III)) to the external medium through as yet unidentified pathways. The rice (Oryza sativa) silicon transporter Lsi1 (OsNIP2;1, an aquaporin channel) is the major entry route of arsenite into rice roots. Whether Lsi1 also mediates arsenite efflux was investigated. *Expression of Lsi1 in Xenopus laevis oocytes enhanced arsenite efflux, indicating that Lsi1 facilitates arsenite transport bidirectionally. *Arsenite was the predominant arsenic species in arsenate-exposed rice plants. During 24-h exposure to 5 mum arsenate, rice roots extruded arsenite to the external medium rapidly, accounting for 60-90% of the arsenate uptake. A rice mutant defective in Lsi1 (lsi1) extruded significantly less arsenite than the wild-type rice and, as a result, accumulated more arsenite in the roots. By contrast, Lsi2 mutation had little effect on arsenite efflux to the external medium. *We conclude that Lsi1 plays a role in arsenite efflux in rice roots exposed to arsenate. However, this pathway accounts for only 15-20% of the total efflux, suggesting the existence of other efflux transporters.	Lsi1|OsNIP2;1,Lsi2
A silicon transporter in rice	2006	Nature	Research Institute for Bioresources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan. maj@rib.okayama-u.ac.jp	Silicon is beneficial to plant growth and helps plants to overcome abiotic and biotic stresses by preventing lodging (falling over) and increasing resistance to pests and diseases, as well as other stresses. Silicon is essential for high and sustainable production of rice, but the molecular mechanism responsible for the uptake of silicon is unknown. Here we describe the Low silicon rice 1 (Lsi1) gene, which controls silicon accumulation in rice, a typical silicon-accumulating plant. This gene belongs to the aquaporin family and is constitutively expressed in the roots. Lsi1 is localized on the plasma membrane of the distal side of both exodermis and endodermis cells, where casparian strips are located. Suppression of Lsi1 expression resulted in reduced silicon uptake. Furthermore, expression of Lsi1 in Xenopus oocytes showed transport activity for silicon only. The identification of a silicon transporter provides both an insight into the silicon uptake system in plants, and a new strategy for producing crops with high resistance to multiple stresses by genetic modification of the root's silicon uptake capacity.	Lsi1|OsNIP2;1
An efflux transporter of silicon in rice	2007	Nature	Research Institute for Bioresources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan. maj@rib.okayama-u.ac.jp	Silicon is an important nutrient for the optimal growth and sustainable production of rice. Rice accumulates up to 10% silicon in the shoot, and this high accumulation is required to protect the plant from multiple abiotic and biotic stresses. A gene, Lsi1, that encodes a silicon influx transporter has been identified in rice. Here we describe a previously uncharacterized gene, low silicon rice 2 (Lsi2), which has no similarity to Lsi1. This gene is constitutively expressed in the roots. The protein encoded by this gene is localized, like Lsi1, on the plasma membrane of cells in both the exodermis and the endodermis, but in contrast to Lsi1, which is localized on the distal side, Lsi2 is localized on the proximal side of the same cells. Expression of Lsi2 in Xenopus oocytes did not result in influx transport activity for silicon, but preloading of the oocytes with silicon resulted in a release of silicon, indicating that Lsi2 is a silicon efflux transporter. The identification of this silicon transporter revealed a unique mechanism of nutrient transport in plants: having an influx transporter on one side and an efflux transporter on the other side of the cell to permit the effective transcellular transport of the nutrients.	Lsi1|OsNIP2;1,Lsi2
Genotypic difference in silicon uptake and expression of silicon transporter genes in rice	2007	Plant Physiol	Research Institute for Bioresources, Okayama University, Kurashiki 710-0046, Japan. maj@rib.okayama-u.ac.jp	Rice (Oryza sativa) is a highly silicon (Si)-accumulating species that shows genotypic differences in Si accumulation. We investigated the physiological and molecular mechanisms involved in the genotypic difference in Si uptake between the japonica var. Nipponbare and the indica var. Kasalath. Both the Si concentration in the shoot and the Si uptake per root dry weight were higher in Nipponbare than in Kasalath grown in either soil or nutrient solution. The Si uptake by a single root was also higher in Nipponbare than in Kasalath. A kinetics study showed that Nipponbare and Kasalath had a similar K(m) value, whereas the V(max) was higher in Nipponbare. The expression of two Si transporter genes (Low silicon rice 1 [Lsi1] and Lsi2) investigated using real-time reverse transcription polymerase chain reaction revealed higher expression of both genes in Nipponbare than in Kasalath. Immunostaining with Lsi1 and Lsi2 antibodies revealed a similar pattern of subcellular localization of these two Si transporters in both varieties; Lsi1 and Lsi2 were localized at the distal and proximal sides, respectively, of both exodermis and endodermis of the roots. These results revealed that the genotypic difference in the Si accumulation results from the difference in abundance of Si transporters in rice roots.	Lsi1|OsNIP2;1,Lsi2
Spatial distribution and temporal variation of the rice silicon transporter Lsi1	2007	Plant Physiol	Research Institute for Bioresources, Okayama University, Kurashiki 710-0046, Japan.	Rice (Oryza sativa) is a typical silicon (Si) accumulator and requires a large amount of Si for high-yield production. Recently, a gene (Low silicon rice1 [Lsi1]) encoding a Si transporter was identified in rice roots. Here, we characterized Lsi1 in terms of spatial distribution and temporal variation using both physiological and molecular approaches. Results from a multicompartment transport box experiment showed that the major site for Si uptake was located at the basal zone (>10 mm from the root tip) of the roots rather than at the root tips (<10 mm from the root tip). Consistent with the Si uptake pattern, Lsi1 expression and distribution of the Lsi1 protein were found only in the basal zone of roots. In the basal zones of the seminal, crown, and lateral roots, the Lsi1 protein showed a polar localization at the distal side of both the exodermis and endodermis, where the Casparian bands are formed. This indicates that Lsi1 is required for the transport of Si through the cells of the exodermis and endodermis. Expression of Lsi1 displayed a distinct diurnal pattern. Furthermore, expression was transiently enhanced around the heading stage, which coincides with a high Si requirement during this growth stage. Expression was down-regulated by dehydration stress and abscisic acid, suggesting that expression of Lsi1 may be regulated by abscisic acid.	Lsi1|OsNIP2;1
The rice aquaporin Lsi1 mediates uptake of methylated arsenic species	2009	Plant Physiol	Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, United Kingdom.	Pentavalent methylated arsenic (As) species such as monomethylarsonic acid [MMA(V)] and dimethylarsinic acid [DMA(V)] are used as herbicides or pesticides, and can also be synthesized by soil microorganisms or algae through As methylation. The mechanism of MMA(V) and DMA(V) uptake remains unknown. Recent studies have shown that arsenite is taken up by rice (Oryza sativa) roots through two silicon transporters, Lsi1 (the aquaporin NIP2;1) and Lsi2 (an efflux carrier). Here we investigated whether these two transporters also mediate the uptake of MMA(V) and DMA(V). MMA(V) was partly reduced to trivalent MMA(III) in rice roots, but only MMA(V) was translocated to shoots. DMA(V) was stable in plants. The rice lsi1 mutant lost about 80% and 50% of the uptake capacity for MMA(V) and DMA(V), respectively, compared with the wild-type rice, whereas Lsi2 mutation had little effect. The short-term uptake kinetics of MMA(V) can be described by a Michaelis-Menten plus linear model, with the wild type having 3.5-fold higher V(max) than the lsi1 mutant. The uptake kinetics of DMA(V) were linear with the slope being 2.8-fold higher in the wild type than the lsi1 mutant. Heterologous expression of Lsi1 in Xenopus laevis oocytes significantly increased the uptake of MMA(V) but not DMA(V), possibly because of a very limited uptake of the latter. Uptake of MMA(V) and DMA(V) by wild-type rice was increased as the pH of the medium decreased, consistent with an increasing proportion of the undissociated species. The results demonstrate that Lsi1 mediates the uptake of undissociated methylated As in rice roots.	Lsi1|OsNIP2;1,Lsi2
Involvement of silicon influx transporter OsNIP2;1 in selenite uptake in rice	2010	Plant Physiol	State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, 210008 Nanjing, China.	Rice (Oryza sativa) as a staple food, provides a major source of dietary selenium (Se) for humans, which essentially requires Se, however, the molecular mechanism for Se uptake is still poorly understood. Herein, we show evidence that the uptake of selenite, a main bioavailable form of Se in paddy soils, is mediated by a silicon (Si) influx transporter Lsi1 (OsNIP2;1) in rice. Defect of OsNIP2;1 resulted in a significant decrease in the Se concentration of the shoots and xylem sap when selenite was given. However, there was no difference in the Se concentration between the wild-type rice and mutant of OsNIP2;1 when selenate was supplied. A short-term uptake experiment showed that selenite uptake greatly increased with decreasing pH in the external solution. Si as silicic acid did not inhibit the Se uptake from selenite in both rice and yeast (Saccharomyces cerevisiae) at low pHs. Expression of OsNIP2;1 in yeast enhanced the selenite uptake at pH 3.5 and 5.5 but not at pH 7.5. On the other hand, defect of Si efflux transporter Lsi2 did not affect the uptake of Se either from selenite or selenate. Taken together, our results indicate that Si influx transporter OsNIP2;1 is permeable to selenite.	Lsi1|OsNIP2;1
Transporters of arsenite in rice and their role in arsenic accumulation in rice grain	2008	Proc Natl Acad Sci U S A	Research Institute for Bioresources, Okayama University, Chuo 2-20-1, Kurashiki 710-0046, Japan. maj@rib.okayama-u.ac.jp	Arsenic poisoning affects millions of people worldwide. Human arsenic intake from rice consumption can be substantial because rice is particularly efficient in assimilating arsenic from paddy soils, although the mechanism has not been elucidated. Here we report that two different types of transporters mediate transport of arsenite, the predominant form of arsenic in paddy soil, from the external medium to the xylem. Transporters belonging to the NIP subfamily of aquaporins in rice are permeable to arsenite but not to arsenate. Mutation in OsNIP2;1 (Lsi1, a silicon influx transporter) significantly decreases arsenite uptake. Furthermore, in the rice mutants defective in the silicon efflux transporter Lsi2, arsenite transport to the xylem and accumulation in shoots and grain decreased greatly. Mutation in Lsi2 had a much greater impact on arsenic accumulation in shoots and grain in field-grown rice than Lsi1. Arsenite transport in rice roots therefore shares the same highly efficient pathway as silicon, which explains why rice is efficient in arsenic accumulation. Our results provide insight into the uptake mechanism of arsenite in rice and strategies for reducing arsenic accumulation in grain for enhanced food safety.	Lsi1|OsNIP2;1,Lsi2
A transporter regulating silicon distribution in rice shoots	2008	Plant Cell	Research Institute for Bioresources, Okayama University, Kurashiki 710-0046, Japan.	Rice (Oryza sativa) accumulates very high concentrations of silicon (Si) in the shoots, and the deposition of Si as amorphous silica helps plants to overcome biotic and abiotic stresses. Here, we describe a transporter, Lsi6, which is involved in the distribution of Si in the shoots. Lsi6 belongs to the nodulin-26 intrinsic protein III subgroup of aquaporins and is permeable to silicic acid. Lsi6 is expressed in the leaf sheath and leaf blades as well as in the root tips. Cellular localization studies revealed that Lsi6 is found in the xylem parenchyma cells of the leaf sheath and leaf blades. Moreover, Lsi6 showed polar localization at the side facing toward the vessel. Knockdown of Lsi6 did not affect the uptake of Si by the roots but resulted in disordered deposition of silica in the shoots and increased excretion of Si in the guttation fluid. These results indicate that Lsi6 is a transporter responsible for the transport of Si out of the xylem and subsequently affects the distribution of Si in the leaf.	Lsi6
A transporter at the node responsible for intervascular transfer of silicon in rice	2009	Plant Cell	Research Institute for Bioresources, Okayama University, Kurashiki, Japan.	The concentration of essential mineral nutrients in the edible portion of plants such as grains may affect the nutritional value of these foods, while concentrations of toxic minerals in the plant are matter of food safety. Minerals taken up by the roots from soils are normally redirected at plant nodes before they are finally transported into developing seeds. However, the molecular mechanisms involved in this process have not been identified so far. Herein, we report on a transporter (Lsi6) responsible for the redirection of a plant nutrient at the node. Lsi6 is a silicon transporter in rice (Oryza sativa), and its expression in node I below the panicles is greatly enhanced when the panicle is completely emerged. Lsi6 is mainly localized at the xylem transfer cells located at the outer boundary region of the enlarged large vascular bundles in node I. Knockout of Lsi6 decreased Si accumulation in the panicles but increased Si accumulation in the flag leaf. These results suggest that Lsi6 is a transporter involved in intervascular transfer (i.e., transfer of silicon from the large vascular bundles coming from the roots to the diffuse vascular bundles connected to the panicles). These findings will be useful for selectively enhancing the accumulation of essential nutrients and reducing toxic minerals in the edible portion of cereals.	Lsi6
Inducibility by pathogen attack and developmental regulation of the rice Ltp1 gene	2002	Plant Mol Biol	BIOTROP and CALIM programmes, Cirad, Centre International de Recherches Agronomiques en cooperation pour le Developpement, Montpellier, France. Guiderdoni@cirad.fr	Using a genomic clone encoding a rice lipid transfer protein, LTP1, we analysed the activity of the 5' region of the Ltp1 gene in transgenic rice (Oryza sativa L.) during plant development and under pathogen attack. The -1176/+13, -556/+13 and -284/+13 regions of the promoter were fused upstream from the uidA reporter gene and nos 3' polyadenylation signal, resulting in the pdelta1176Gus, pdelta556Gus and pdelta284Gus constructs which were transferred to rice by microprojectile bombardment. Histochemical and fluorometric GUS assays and in situ detection of uidA transcripts in transgenic homozygous lines harbouring the pdelta1176Gus construct demonstrated that the Ltp1 promoter is preferentially active in aerial vegetative and reproductive organs and that both specificity and level of expression are regulated during organ development. In leaf sheath, GUS activity which is initially strictly localized in the epidermis of growing tissue, becomes restricted to the vascular system in mature tissues. In expanded leaf blade, expression of the uidA gene was restricted to the cutting level suggesting inducibility by wounding. Strong activity was detected in lemma and palea, sterile glumes, and immature anther walls and microspores but not in female reproductive organs. No GUS activity was detected during seed embryo maturation whereas the uidA gene was strongly expressed at early stages of somatic embryogenesis in scutellum tissue. The Ltp1 transcripts were found to strongly accumulate in response to inoculation with the fungal agent of the blast disease, Magnaporthe grisea, in two rice cultivars exhibiting compatible or incompatible host-pathogen interactions. Analysis of pdelta1176Gus leaf samples inoculated with the blast fungus demonstrated that the Ltp1 promoter is induced in all cell types of tissues surrounding the lesion and notably in stomata guard cells. In plants harbouring the Ltp1 promoter deletion construct pdelta556Gus, activity was solely detected in the vascular system of mature leaves whereas no uidA gene expression was observed in pdelta284Gus plants. These observations are consistent with the proposed role of LTP1 in strenghtening of structural barriers and organ protection against mechanical disruption and pathogen attack.	Ltp1
Evolutionary history of the non-specific lipid transfer proteins	2011	Mol Plant	IFM Molecular Genetics, Linkoping University, 581 83 Linkoping, Sweden.	The non-specific lipid transfer proteins (nsLTPs) are small, basic proteins characterized by a tunnel-like hydrophobic cavity, capable of transferring various lipid molecules between lipid bilayers. Most nsLTPs are synthesized with an N-terminal signal peptide that localizes the protein to the apoplastic space. The nsLTPs have only been identified in seed plants, where they are encoded by large gene families. We have initiated an analysis of the evolutionary history of the nsLTP family using genomic and EST information from non-seed land plants and green algae to determine: (1) when the nsLTP family arose, (2) how often new nsLTP subfamilies have been created, and (3) how subfamilies differ in their patterns of expansion and loss in different plant lineages. In this study, we searched sequence databases and found that genes and transcripts encoding nsLTPs are abundant in liverworts, mosses, and all other investigated land plants, but not present in any algae. The tertiary structures of representative liverwort and moss nsLTPs were further studied with homology modeling. The results indicate that the nsLTP family has evolved after plants conquered land. Only two of the four major subfamilies of nsLTPs found in flowering plants are present in mosses and liverworts. The additional subfamilies have arisen later, during land plant evolution. In this report, we also introduce a modified nsLTP classification system.	LTP2,YY1|OsLTPc2|LTPL45,OsLTPx1
Characterization of a gene encoding an abscisic acid-inducible type-2 lipid transfer protein from rice	1998	FEBS Lett	Laboratoire de Physiologie et Biologie Moleculaire Vegetales, UMR 5545 CNRS Universite de Perpignan, France.	The cloning and sequence analysis of a novel gene that encodes a type 2 non-specific lipid transfer-like protein (LTP) from rice is reported. Sequence analysis revealed an ORF encoding a protein showing characteristics of the LTP proteins. However, rice LTP2 is more similar to heterologous LTPs than to rice LTP1, supporting the existence of two distinct families of plant LTPs. Ltp2 mRNA is accumulated only in mature seeds. In vegetative tissues, mRNA was only detected after treatment with abscisic acid (ABA), mannitol or NaCl. Transient expression experiments that the 61 nucleotides upstream of the TATA box, containing two ACGT boxes and the motif I, are sufficient for ABA responsiveness of the Ltp gene.	LTP2
OsC6, encoding a lipid transfer protein, is required for postmeiotic anther development in rice	2010	Plant Physiol	School of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.	Synthesis of lipidic components in anthers, including of the pollen exine, is essential for plant male reproductive development. Plant lipid transfer proteins (LTPs) are small, abundant lipid-binding proteins that have the ability to exchange lipids between membranes in vitro. However, their biological role in male reproductive development remains less understood. Here, we report the crucial role of OsC6 in regulating postmeiotic anther development in rice (Oryza sativa). Found in monocots, OsC6 belongs to a distinct clade from previously identified LTP1 and LTP2 family members found in both dicots and monocots. OsC6 expression is mainly detectable in tapetal cells and weakly in microspores from stage 9 to stage 11 of anther development. Immunological assays indicated that OsC6 is widely distributed in anther tissues such as the tapetal cytoplasm, the extracellular space between the tapetum and middle layer, and the anther locule and anther cuticle. Biochemical assays indicated that recombinant OsC6 has lipid binding activity. Moreover, plants in which OsC6 was silenced had defective development of orbicules (i.e. Ubisch bodies) and pollen exine and had reduced pollen fertility. Furthermore, additional evidence is provided that the expression of OsC6 is positively regulated by a basic helix-loop-helix transcription factor, Tapetum Degeneration Retardation (TDR). Extra granule-like structures were observed on the inner surface of the tdr tapetal layer when the expression of OsC6 was driven by the TDR promoter compared with the tdr mutant. These data suggest that OsC6 plays a crucial role in the development of lipidic orbicules and pollen exine during anther development in rice.	LTP2,OSC4,OsC6,TDR,YY1|OsLTPc2|LTPL45
Solution structure of plant nonspecific lipid transfer protein-2 from rice (Oryza sativa)	2002	J Biol Chem	Department of Life Sciences, National Tsing Hua University, Taiwan 300, China.	The three-dimensional structure of rice nonspecific lipid transfer protein (nsLTP2) has been solved for the first time. The structure of nsLTP2 was obtained using 813 distance constraints, 30 hydrogen bond constraints, and 19 dihedral angle constraints. Fifteen of the 50 random simulated annealing structures satisfied all of the constraints and possessed good nonbonded contacts. The novel three-dimensional fold of rice nsLTP2 contains a triangular hydrophobic cavity formed by three prominent helices. The four disulfide bonds required for stabilization of the nsLTP2 structure show a different pattern of cysteine pairing compared with nsLTP1. The C terminus of the protein is very flexible and forms a cap over the hydrophobic cavity. Molecular modeling studies suggested that the hydrophobic cavity could accommodate large molecules with rigid structures, such as sterols. The positively charged residues on the molecular surface of nsLTP2 are structurally similar to other plant defense proteins.	LTP2
Mutation of the light-induced yellow leaf 1 gene, which encodes a geranylgeranyl reductase, affects chlorophyll biosynthesis and light sensitivity in rice	2013	PLoS One	Jiangsu Key Laboratory of Crop Genetics and Physiology/Key Laboratory of the Ministry of Education for Plant Functional Genomics, Yangzhou University, Yangzhou, Jiangsu, China.	Chlorophylls (Chls) are crucial for capturing light energy for photosynthesis. Although several genes responsible for Chl biosynthesis were characterized in rice (Oryza sativa), the genetic properties of the hydrogenating enzyme involved in the final step of Chl synthesis remain unknown. In this study, we characterized a rice light-induced yellow leaf 1-1 (lyl1-1) mutant that is hypersensitive to high-light and defective in the Chl synthesis. Light-shading experiment suggested that the yellowing of lyl1-1 is light-induced. Map-based cloning of LYL1 revealed that it encodes a geranylgeranyl reductase. The mutation of LYL1 led to the majority of Chl molecules are conjugated with an unsaturated geranylgeraniol side chain. LYL1 is the firstly defined gene involved in the reduction step from Chl-geranylgeranylated (Chl(GG)) and geranylgeranyl pyrophosphate (GGPP) to Chl-phytol (Chl(Phy)) and phytyl pyrophosphate (PPP) in rice. LYL1 can be induced by light and suppressed by darkness which is consistent with its potential biological functions. Additionally, the lyl1-1 mutant suffered from severe photooxidative damage and displayed a drastic reduction in the levels of alpha-tocopherol and photosynthetic proteins. We concluded that LYL1 also plays an important role in response to high-light in rice.	LYL1
Overexpression of an F-box protein gene reduces abiotic stress tolerance and promotes root growth in rice	2011	Mol Plant	State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.	As one of the largest gene families, F-box domain proteins have important roles in regulating various developmental processes and stress responses. In this study, we have investigated a rice F-box domain gene, MAIF1. The MAIF1 protein is mainly localized in the plasma membrane and nucleus. MAIF1 expression is induced rapidly and strongly by abscisic acid (ABA) and abiotic stresses. MAIF1 expression is also induced in root tips by sucrose, independent of its hydrolytic hexose products, glucose and fructose, and the plant hormones auxin and cytokinin. Overexpression of MAIF1 reduces rice ABA sensitivity and abiotic stress tolerance and promotes rice root growth. These results suggest that MAIF1 is involved in multiple signaling pathways in regulating root growth. Growth restraint in plants is an acclimatization strategy against abiotic stress. Our results also suggest that MAIF1 plays the negative role in response to abiotic stress possibly by regulating root growth.	MAIF1
Identification of a biosynthetic gene cluster in rice for momilactones	2007	J Biol Chem	Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, Japan.	Rice diterpenoid phytoalexins such as momilactones and phytocassanes are produced in suspension-cultured rice cells treated with a chitin oligosaccharide elicitor and in rice leaves irradiated with UV light. The common substrate geranylgeranyl diphosphate is converted into diterpene hydrocarbon precursors via a two-step sequential cyclization and then into the bioactive phytoalexins via several oxidation steps. It has been suggested that microsomal cytochrome P-450 monooxygenases (P-450s) are involved in the downstream oxidation of the diterpene hydrocarbons leading to the phytoalexins and that a dehydrogenase is involved in momilactone biosynthesis. However, none of the enzymes involved in the downstream oxidation of the diterpene hydrocarbons have been identified. In this study, we found that a putative dehydrogenase gene (AK103462) and two functionally unknown P-450 genes (CYP99A2 and CYP99A3) form a chitin oligosaccharide elicitor- and UV-inducible gene cluster, together with OsKS4 and OsCyc1, the diterpene cyclase genes involved in momilactone biosynthesis. Functional analysis by heterologous expression in Escherichia coli followed by enzyme assays demonstrated that the AK103462 protein catalyzes the conversion of 3beta-hydroxy-9betaH-pimara-7,15-dien-19,6beta-olide into momilactone A. The double knockdown of CYP99A2 and CYP99A3 specifically suppressed the elicitor-inducible production of momilactones, strongly suggesting that CYP99A2, CYP99A3, or both are involved in momilactone biosynthesis. These results provide strong evidence for the presence on chromosome 4 of a gene cluster involved in momilactone biosynthesis.	MAS
A germ cell specific gene of the ARGONAUTE family is essential for the progression of premeiotic mitosis and meiosis during sporogenesis in rice	2007	Plant Cell	Experimental Farm, National Institute of Genetics, Mishima, Shizuoka 411-8540, Japan. knonomur@lab.nig.ac.jp	The rice (Oryza sativa) genome contains 18 copies of genes of the ARGONAUTE (AGO) family. Although AGO members play important roles in RNA-mediated silencing during plant development, a family member that is specifically involved in sexual reproduction has not been identified in plants. We identified the rice AGO gene MEIOSIS ARRESTED AT LEPTOTENE1 (MEL1) from the analysis of seed-sterile mutants. In the mel1 mutant, chromosome condensation was arrested at early meiotic stages and irregularly sized, multinucleated, and vacuolated pollen mother cells (PMCs) frequently appeared in developing anthers. In addition, histone H3 lysine-9 dimethylation of pericentromeres was rarely reduced and modification of the nucleolar-organizing region was altered in mel1 mutant PMCs. The mutation also affected female germ cell development. These results indicate that the germ cell-specific rice MEL1 gene regulates the cell division of premeiotic germ cells, the proper modification of meiotic chromosomes, and the faithful progression of meiosis, probably via small RNA-mediated gene silencing, but not the initiation and establishment of germ cells themselves.	MEL1
A recurrent general RNA binding domain appended to plant methionyl-tRNA synthetase acts as a cis-acting cofactor for aminoacylation	2000	EMBO J	Laboratoire d'Enzymologie et Biochimie Structurales, CNRS, 1 Avenue de la Terrasse, 91190 Gif-sur-Yvette, France.	The cDNA encoding rice methionyl-tRNA synthetase was isolated. The protein exhibited a C-terminal polypeptide appended to a classical MetRS domain. This supplementary domain is related to endothelial monocyte activating polypeptide II (EMAPII), a cytokine produced in mammals after cleavage of p43, a component of the multisynthetase complex. It is also related to Arc1p and Trbp111, two tRNA binding proteins. We expressed rice MetRS and a derivative with a deletion of its EMAPII-like domain. Band-shift analysis showed that this extra-domain provides MetRS with non-specific tRNA binding properties. The EMAPII-like domain contributed a 10-fold decrease in K:(M) for tRNA in the aminoacylation reaction catalyzed by the native enzyme, as compared with the C-terminally truncated MetRS. Consequently, the EMAPII domain provides MetRS with a better catalytic efficiency at the free tRNA concentration prevailing in vivo. This domain binds the acceptor minihelix of tRNA(Met) and facilitates its aminoacylation. These results suggest that the EMAPII module could be a relic of an ancient tRNA binding domain that was incorporated into primordial synthetases for aminoacylation of RNA minihelices taken as the ancestor of modern tRNA.	MetRS|MRS
Identification of a rice RNA- and microtubule-binding protein as the multifunctional protein, a peroxisomal enzyme involved in the beta -oxidation of fatty acids	2002	J Biol Chem	Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.	The control of subcellular mRNA localization and translation is often mediated by protein factors that are directly or indirectly associated with the cytoskeleton. We report the identification and characterization of a rice seed protein that possesses both RNA and microtubule binding activities. In vitro UV cross-linking assays indicated that this protein binds to all mRNA sequences tested, although there was evidence for preferential binding to RNAs that contained A-C nucleotide sequence motifs. The protein was purified to homogeneity using a two-step procedure, and amino acid sequencing identified it as the multifunctional protein (MFP), a peroxisomal enzyme known to possess a number of activities involved in the beta-oxidation of fatty acids. The recombinant version of this rice MFP binds to RNA in UV cross-linking and gel mobility shift experiments, co-sediments specifically with microtubules, and possesses at least two enzymatic activities involved in peroxisomal fatty acid beta-oxidation. Taken together these data suggest that MFP has an important role in mRNA physiology in the cytoplasm, perhaps in regulating the localization or translation of mRNAs through an interaction with microtubules, in addition to its peroxisomal function.	MFP
MULTI-FLORET SPIKELET1, which encodes an AP2/ERF protein, determines spikelet meristem fate and sterile lemma identity in rice	2013	Plant Physiol	Rice Research Institute, Southwest University, Chongqing 400715, China.	The spikelet is a unique inflorescence structure of grass. The molecular mechanism that controls the development of the spikelet remains unclear. In this study, we identified a rice (Oryza sativa) spikelet mutant, multi-floret spikelet1 (mfs1), that showed delayed transformation of spikelet meristems to floral meristems, which resulted in an extra hull-like organ and an elongated rachilla. In addition, the sterile lemma was homeotically converted to the rudimentary glume and the body of the palea was degenerated in mfs1. These results suggest that the MULTI-FLORET SPIKELET1 (MFS1) gene plays an important role in the regulation of spikelet meristem determinacy and floral organ identity. MFS1 belongs to an unknown function clade in the APETALA2/ethylene-responsive factor (AP2/ERF) family. The MFS1-green fluorescent protein fusion protein is localized in the nucleus. MFS1 messenger RNA is expressed in various tissues, especially in the spikelet and floral meristems. Furthermore, our findings suggest that MFS1 positively regulates the expression of LONG STERILE LEMMA and the INDETERMINATE SPIKELET1 (IDS1)-like genes SUPERNUMERARY BRACT and OsIDS1.	MFS1
Ethylene-Induced Inhibition of Root Growth Requires Abscisic Acid Function in Rice (Oryza sativa L.) Seedlings	2014	PLoS Genet	State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.	Ethylene and abscisic acid (ABA) have a complicated interplay in many developmental processes. Their interaction in rice is largely unclear. Here, we characterized a rice ethylene-response mutant mhz4, which exhibited reduced ethylene-response in roots but enhanced ethylene-response in coleoptiles of etiolated seedlings. MHZ4 was identified through map-based cloning and encoded a chloroplast-localized membrane protein homologous to Arabidopsis thaliana (Arabidopsis) ABA4, which is responsible for a branch of ABA biosynthesis. MHZ4 mutation reduced ABA level, but promoted ethylene production. Ethylene induced MHZ4 expression and promoted ABA accumulation in roots. MHZ4 overexpression resulted in enhanced and reduced ethylene response in roots and coleoptiles, respectively. In root, MHZ4-dependent ABA pathway acts at or downstream of ethylene receptors and positively regulates root ethylene response. This ethylene-ABA interaction mode is different from that reported in Arabidopsis, where ethylene-mediated root inhibition is independent of ABA function. In coleoptile, MHZ4-dependent ABA pathway acts at or upstream of OsEIN2 to negatively regulate coleoptile ethylene response, possibly by affecting OsEIN2 expression. At mature stage, mhz4 mutation affects branching and adventitious root formation on stem nodes of higher positions, as well as yield-related traits. Together, our findings reveal a novel mode of interplay between ethylene and ABA in control of rice growth and development.	MHZ4
Identification and functional analysis of the MOC1 interacting protein 1	2010	Journal of Genetics and Genomics	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Rice tillering is one of the most important agronomic traits that determine grain yields. Our previous study has demonstrated that the MONOCULM1 (MOC1) gene is a key component that controls the formation of rice tiller buds. To further elucidate the molecular mechanism of MOC1 involved in the regulation of rice tillering, we performed a yeast-two-hybrid screening to identify MOC1 interacting proteins (MIPs). Here we reported that MIP1 interacted with MOC1 both in vitro and in vivo. The overexpression of MIP1 resulted in enhanced tillering and reduced plant height. In-depth characterization of the context of MIP1 and MOC1 would further our understanding of molecular regulatory mechanisms of rice tillering.	MIP1,MOC1
Rice-specific mitochondrial iron-regulated gene (MIR) plays an important role in iron homeostasis	2009	Mol Plant	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-Ku, Tokyo 113-8657, Japan.	Mitochondria utilize iron (Fe), but the proteins involved in mitochondrial Fe regulation are not characterized in plants. We cloned and characterized a mitochondrial iron-regulated (MIR) gene in rice involved in Fe homeostasis. MIR, when expressed in tobacco BY-2 cells, was localized to the mitochondria. MIR transcripts were greatly increased in response to Fe deficiency in roots and shoot tissue. MIR is not homologous to any known protein, as homologs were not found in the rice or Arabidopsis genome databases, or in the EST database for other organisms. Growth in the MIR T-DNA knockout rice mutant (mir) was significantly impaired compared to wild-type (WT) plants when grown under Fe-deficient or -sufficient conditions. Furthermore, mir plants accumulated more than twice the amount of Fe in shoot and root tissue compared to WT plants when grown under either Fe-sufficient or -deficient conditions. Despite the high accumulation of Fe in roots and shoots, mir plants triggered the expression of Fe-deficiency-inducible genes, indicating that mir may not be able to utilize Fe for physiological functions. These results clearly suggest that MIR is a rice-specific mitochondrial protein, recently evolved, and plays a significant role in Fe homeostasis.	MIR
The knockdown of OsVIT2 and MIT affects iron localization in rice seed	2013	Rice (N Y)	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan. annaoko@mail.ecc.u-tokyo.ac.jp.	BACKGROUND: The mechanism of iron (Fe) uptake in plants has been extensively characterized, but little is known about how Fe transport to different subcellular compartments affects Fe localization in rice seed. Here, we discuss the characterization of a rice vacuolar Fe transporter 2 (OsVIT2) T-DNA insertion line (osvit2) and report that the knockdown of OsVIT2 and mitochondrial Fe transporter (MIT) expression affects seed Fe localization. FINDINGS: osvit2 plants accumulated less Fe in their shoots when grown under normal or excess Fe conditions, while the accumulation of Fe was comparable to that in wild-type (WT) plants under Fe-deficient conditions. The accumulation of zinc, copper, and manganese also changed significantly in the shoots of osvit2 plants. The growth of osvit2 plants was also slow compared to that of WT plants. The concentration of Fe increased in osvit2 polished seeds. Previously, we reported that the expression of OsVIT2 was higher in MIT knockdown (mit-2) plants, and in this study, the accumulation of Fe in mit-2 seeds decreased significantly. CONCLUSIONS: These results suggest that vacuolar Fe trafficking is important for plant Fe homeostasis and distribution, especially in plants grown in the presence of excess Fe. Moreover, changes in the expression of OsVIT2 and MIT affect the concentration and localization of metals in brown rice as well as in polished rice seeds.	MIT,OsVIT2
The rice mitochondrial iron transporter is essential for plant growth	2011	Nat Commun	Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Tokyo 113-8657, Japan.	In plants, iron (Fe) is essential for mitochondrial electron transport, heme, and Fe-Sulphur (Fe-S) cluster synthesis; however, plant mitochondrial Fe transporters have not been identified. Here we show, identify and characterize the rice mitochondrial Fe transporter (MIT). Based on a transfer DNA library screen, we identified a rice line showing symptoms of Fe deficiency while accumulating high shoot levels of Fe. Homozygous knockout of MIT in this line resulted in a lethal phenotype. MIT localized to the mitochondria and complemented the growth of Deltamrs3Deltamrs4 yeast defective in mitochondrial Fe transport. The growth of MIT-knockdown (mit-2) plants was also significantly impaired despite abundant Fe accumulation. Further, the decrease in the activity of the mitochondrial and cytosolic Fe-S enzyme, aconitase, indicated that Fe-S cluster synthesis is affected in mit-2 plants. These results indicate that MIT is a mitochondrial Fe transporter essential for rice growth and development.	MIT
Identification and characterization of the major mitochondrial Fe transporter in rice	2011	Plant Signal Behav	Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-Ku, Tokyo, Japan.	The uptake, translocation, and compartmentalization of Fe are essential for plant cell function and life cycle. Despite rapid progress in our understanding of Fe homeostasis in plants, Fe transport from the cytoplasm to mitochondria was, until recently, poorly understood. The screening of 3,993 mutant lines for symptoms of Fe deficiency resulted in the identification and characterization of a major mitochondrial Fe transporter (MIT) in rice. MIT was found to localize to mitochondria and to complement the growth of a yeast strain defective in mitochondrial Fe transport. The knock-out of MIT resulted in a lethal phenotype, and in knock-down plants, several agronomic characteristics were compromised, such as plant height, average number of tillers, days to flower, fertility, and yield. Changes in the expression of genes involved in Fe transport suggested a disturbance of cellular Fe transport. Furthermore, the mitochondrial Fe concentration and the activity of the mitochondrial Fe-S enzyme aconitase were significantly reduced compared with wild-type plants. The identification of MIT is a significant advance in the field of plant Fe nutrition and should facilitate the cloning of paralogs from other plant species.	MIT
Sequence, expression and tissue localization of a gene encoding a makorin RING zinc-finger protein in germinating rice (Oryza sativa L. ssp. Japonica) seeds	2007	Plant Physiol Biochem	Laboratory of Molecular Cell Physiology, Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama 790-8566, Japan. thangs@mcb.agr.ehime-u.ac.jp	The makorin (MKRN) RING finger protein gene family encodes proteins (makorins) with a characteristic array of zinc-finger motifs and which are present in a wide array of eukaryotes. In the present study, we analyzed the structure and expression of a putative makorin RING finger protein gene in rice (Oryza sativa L. ssp. Japonica cv. Nipponbare). From the analysis of the genomic (AP003543), mRNA (AK120250) and deduced protein (BAD61603) sequences of the putative MKRN gene of rice, obtained from GenBank, we found that it was indeed a bona fide member of the MKRN gene family. The rice MKRN cDNA encoded a protein with four C3H zinc-finger-motifs, one putative Cys-His zinc-finger motif, and one RING zinc-finger motif. The presence of this distinct motif organization and overall amino acid identity clearly indicate that this gene is indeed a true MKRN ortholog. We isolated RNA from embryonic axes of rice seeds at various stages of imbibition and germination and studied the temporal expression profile of MKRN by RT-PCR. This analysis revealed that MKRN transcripts were present at all the time points studied. It was at very low levels in dry seeds, increased slowly during imbibition and germination, and slightly declined in the seedling growth stage. After 6days of germination, an organ-dependent expression pattern of MKRN was observed: highest in roots and moderate in leaves. Similarly to MKRN transcripts, transcripts of cytoskeletal actin and tubulin were also detected in dry embryos, steadily increased during imbibition and germination and leveled off after 24h of germination. We studied the spatial expression profile of MKRN in rice tissues, by using a relatively fast, simple and effective non-radioactive mRNA in situ hybridization (NRISH) technique, which provided the first spatial experimental data that hints at the function of a plant makorin. This analysis revealed that MKRN transcripts were expressed in young plumules, lateral root primordia, leaf primordia, leaves and root tissues at many different stages of germination. The presence of MKRN transcripts in dry seeds, its early induction during germination and its continued spatiotemporal expression during early vegetative growth suggest that MKRN has an important role in germination, leaf and lateral root morphogenesis and overall development in rice.	MKRN
MKRN expression pattern during embryonic and post-embryonic organogenesis in rice (Oryza sativa L. var. Nipponbare)	2013	Planta	Laboratory of Molecular Cell Physiology, Faculty of Agriculture, Ehime University, 3-5-7 Tarumi, Matsuyama, 790-8566, Japan. 	Rice MKRN is a member of the makorin RING finger protein gene (MKRN) family, which encodes a protein with a characteristic array of zinc-finger motifs conserved in various eukaryotes. Using non-radioactive in situ hybridization, we investigated the spatio-temporal gene expression pattern of rice MKRN during embryogenesis, imbibition, seminal and lateral root development of Oryza sativa L. var. Nipponbare. MKRN expression was ubiquitous during early organogenesis in the embryo along the apical-basal and radial axes. The expression of MKRN decreased during embryonic organ elongation and maturation compared to early embryogenesis, but increased again during imbibition. Tissue-specific and position-dependent MKRN expression was found during embryonic and post-embryonic root and shoot development. Meristematic cells ubiquitously expressed MKRN transcripts, while differentiating cells showed a gradual reduction and termination of MKRN expression. Interestingly, during post-germination MKRN expression was prominent and continued in the metabolically active, differentiated companion cells of the phloem. The differential expression pattern was observed both in the differentiating and differentiated cells. Also, MKRN was expressed in the various developmental stages of the lateral root primordia and the cells surrounding them. Expression of MKRN was also observed after periclinal division of the presumptive pericycle founder cells. The MKRN expression pattern during development of various growth stages suggests an important role of makorin RING finger protein gene (MKRN) in embryonic and post-embryonic organogenesis in both apical-basal and radial developmental axes of rice.	MKRN
OsCERK1 and OsRLCK176 play important roles in peptidoglycan and chitin signaling in rice innate immunity	2014	Plant J	State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, 510275, Guangzhou, People's Republic of China.	Microbe-associated molecular pattern (MAMP)-triggered immunity plays critical roles in the basal resistance defense response in plants. Chitin and peptidoglycan (PGN) are major molecular patterns for fungi and bacteria, respectively. Two rice (Oryza sativa) lysin motif-containing proteins, OsLYP4 and OsLYP6, function as receptors that sense bacterial PGN and fungal chitin. These membrane receptors, which lack intracellular kinase domains, likely contain another component for transmembrane immune signal transduction. Here, we demonstrate that the rice LysM receptor-like kinase OsCERK1, a key component of the chitin elicitor signaling pathway, also plays an important role in PGN-triggered immunity in rice. Silencing of OsCERK1 suppressed PGN-induced (and chitin-induced) immunity responses, including reactive oxygen species generation, defense gene expression, and callose deposition, indicating that OsCERK1 is essential for both PGN and chitin signaling initiated by OsLYP4 and OsLYP6. OsLYP4 associated with OsLYP6 and the rice chitin receptor CEBiP in the absence of PGN or chitin, and treatment with PGN or chitin led to their disassociation in vivo. OsCERK1 associated with OsLYP4 or OsLYP6 when induced by PGN but it associated with OsLYP4, OsLYP6, or CEBiP under chitin treatment, suggesting the presence of different patterns of ligand-induced heterooligomeric receptor complexes. Furthermore, the receptor-like cytoplasmic kinase OsRLCK176 functions downstream of OsCERK1 in the PGN and chitin signaling pathways, suggesting that these MAMPs share overlapping intracellular signaling components. Therefore, OsCERK1 plays dual roles in PGN and chitin signaling in rice innate immunity and as an adaptor involved in signal transduction at the plasma membrane in conjunction with OsLYP4 and OsLYP6.	MLO,OsRLCK176,PAL
Methylmalonate-semialdehyde dehydrogenase is induced in auxin-stimulated and zinc-stimulated root formation in rice	2004	Plant Cell Rep	Faculty of Agriculture, Miyazaki University, Miyazaki, 889-2192, Japan.	Proteins induced in rice by auxin and zinc were determined by proteome analysis. Cultured suspension cells of rice were treated with 2,4-dichlorophenoxyacetic acid and ZnSO4 and then proteins were separated by two-dimensional polyacrylamide gel electrophoresis; seven proteins were found to be induced by auxin and zinc. Of these seven, methylmalonate-semialdehyde dehydrogenase (MMSDH) was elevated by treatment with auxin alone. MMSDH was detected in cultured suspension cells, root and leaf sheath, but not in leaf blades. MMSDH responded to auxin and gibberellin, but did not respond to brassinolide and cytokinin. Furthermore, the amount of MMSDH in slr1, a constitutive gibberellin response mutant, was 2-fold that of wild type. MMSDH mRNA and protein were stimulated in root formation induced by auxin and/or zinc over a 4-week period. These results suggest that MMSDH may be necessary for root formation in rice induced by auxin and/or zinc.	MMSDH
Control of tillering in rice	2003	Nature	Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Tillering in rice (Oryza sativa L.) is an important agronomic trait for grain production, and also a model system for the study of branching in monocotyledonous plants. Rice tiller is a specialized grain-bearing branch that is formed on the unelongated basal internode and grows independently of the mother stem (culm) by means of its own adventitious roots. Rice tillering occurs in a two-stage process: the formation of an axillary bud at each leaf axil and its subsequent outgrowth. Although the morphology and histology and some mutants of rice tillering have been well described, the molecular mechanism of rice tillering remains to be elucidated. Here we report the isolation and characterization of MONOCULM 1 (MOC1), a gene that is important in the control of rice tillering. The moc1 mutant plants have only a main culm without any tillers owing to a defect in the formation of tiller buds. MOC1 encodes a putative GRAS family nuclear protein that is expressed mainly in the axillary buds and functions to initiate axillary buds and to promote their outgrowth.	MOC1
Rice APC/C(TE) controls tillering by mediating the degradation of MONOCULM 1	2012	Nat Commun	National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.	Rice MONOCULM 1 (MOC1) and its orthologues LS/LAS (lateral suppressor in tomato and Arabidopsis) are key promoting factors of shoot branching and tillering in higher plants. However, the molecular mechanisms regulating MOC1/LS/LAS have remained elusive. Here we show that the rice tiller enhancer (te) mutant displays a drastically increased tiller number. We demonstrate that TE encodes a rice homologue of Cdh1, and that TE acts as an activator of the anaphase promoting complex/cyclosome (APC/C) complex. We show that TE coexpresses with MOC1 in the axil of leaves, where the APC/C(TE) complex mediates the degradation of MOC1 by the ubiquitin-26S proteasome pathway, and consequently downregulates the expression of the meristem identity gene Oryza sativa homeobox 1, thus repressing axillary meristem initiation and formation. We conclude that besides having a conserved role in regulating cell cycle, APC/C(TE) has a unique function in regulating the plant-specific postembryonic shoot branching and tillering, which are major determinants of plant architecture and grain yield.	MOC1,OsCCS52A|TAD|TE
Degradation of MONOCULM 1 by APC/C(TAD1) regulates rice tillering	2012	Nat Commun	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	A rice tiller is a specialized grain-bearing branch that contributes greatly to grain yield. The MONOCULM 1 (MOC1) gene is the first identified key regulator controlling rice tiller number; however, the underlying mechanism remains to be elucidated. Here we report a novel rice gene, Tillering and Dwarf 1 (TAD1), which encodes a co-activator of the anaphase-promoting complex (APC/C), a multi-subunit E3 ligase. Although the elucidation of co-activators and individual subunits of plant APC/C involved in regulating plant development have emerged recently, the understanding of whether and how this large cell-cycle machinery controls plant development is still very limited. Our study demonstrates that TAD1 interacts with MOC1, forms a complex with OsAPC10 and functions as a co-activator of APC/C to target MOC1 for degradation in a cell-cycle-dependent manner. Our findings uncovered a new mechanism underlying shoot branching and shed light on the understanding of how the cell-cycle machinery regulates plant architecture.	MOC1,OsCCS52A|TAD|TE
Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes	2009	Proc Natl Acad Sci U S A	State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	Comparative genomics is a powerful tool to decipher gene and genome evolution. Placing multiple genome comparisons in a phylogenetic context improves the sensitivity of evolutionary inferences. In the genus Oryza, this comparative approach can be used to investigate gene function, genome evolution, domestication, polyploidy, and ecological adaptation. A large genomic region surrounding the MONOCULM1 (MOC1) locus was chosen for study in 14 Oryza species, including 10 diploids and 4 allotetraploids. Sequencing and annotation of 18 bacterial artificial chromosome clones for these species revealed highly conserved gene colinearity and structure in the MOC1 region. Since the Oryza radiation about 14 Mya, differences in transposon amplification appear to be responsible for the different current sizes of the Oryza genomes. In the MOC1 region, transposons were only conserved between genomes of the same type (e.g., AA or BB). In addition to the conserved gene content, several apparent genes have been generated de novo or uniquely retained in the AA lineage. Two different 3-gene segments have been inserted into the MOC1 region of O. coarctata (KK) or O. sativa by unknown mechanism(s). Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection. The allotetraploids Oryza alta and Oryza minuta were found to be products of recent polyploidization, less than 1.6 and 0.4 Mya, respectively. In allotetraploids, pseudogenization of duplicated genes was common, caused by large deletions, small frame-shifting insertions/deletions, or nonsense mutations.	MOC1
Rice monoculm mutation moc2, which inhibits outgrowth of the second tillers, is ascribed to lack of a fructose-1,6-bisphosphatase	2013	Plant Biotechnology	Department of Biological Science and Technology, Tokyo University of Science	We characterized a rice monoculm mutant moc2, which showed significantly reduced tiller numbers, pale-green leaves, a reduced growth rate, and a consequent dwarf phenotype. The monoculm feature was attributed to a deficiency in the efficient outgrowth of tiller buds, although the moc2 mutant produced tiller buds. Inconsistent change was observed in the expression of genes involved in tiller bud outgrowth, suggesting that the moc2 mutant has a defective function necessary for the tiller bud outgrowth. The gene responsible for the moc2 mutant was mapped to a locus encoding cytosolic fructose-1,6-bisphosphatase 1 (FBP1), in which a Tos17 retrotransposon was inserted in exon 4. Reverse-transcription PCR for the FBP1 gene amplified a shorter transcript from the moc2 mutant than from the wild-type plant. The sequence of the shorter transcript revealed a deletion of exon 4 by abnormal splicing, and the resulting frameshift generated a new translation termination signal. The moc2 mutant showed a very low level of FBPase activity, suggesting that it involves a loss-of-function mutation of FBP1. Cytosolic FBPase is considered a key enzyme in the sucrose biosynthesis pathway. Defective FBPase activity is anticipated to lead a shortage of sucrose supply, which probably causes the inhibition of tiller bud outgrowth in the moc2 mutant. The monoculm phenotype of the moc2 mutant supports the idea that sucrose supply may be an important cue to outgrow tiller buds.	MOC2|FBP1
Rice MPR25 encodes a pentatricopeptide repeat protein and is essential for RNA editing of nad5 transcripts in mitochondria	2012	Plant J	Laboratory of Environmental Plant Biotechnology, Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Sendai 981-8555, Japan.	Pentatricopeptide repeat (PPR) proteins are involved in the modification of organelle transcripts. In this study, we investigated the molecular function in rice of the mitochondrial PPR-encoding gene MITOCHONDRIAL PPR25 (MPR25), which belongs to the E subgroup of the PPR family. A Tos17 knockout mutant of MPR25 exhibited growth retardation and pale-green leaves with reduced chlorophyll content during the early stages of plant development. The photosynthetic rate in the mpr25 mutant was significantly decreased, especially under strong light conditions, although the respiration rate did not differ from that of wild-type plants. MPR25 was preferentially expressed in leaves. FLAG-tagged MPR25 accumulated in mitochondria but not in chloroplasts. Direct sequencing revealed that the mpr25 mutant fails to edit a C-U RNA editing site at nucleotide 1580 of nad5, which encodes a subunit of complex I (NADH dehydrogenase) of the respiratory chain in mitochondria. RNA editing of this site is responsible for a change in amino acid from serine to leucine. Recombinant MPR25 directly interacted with the proximal region of the editing site of nad5 transcripts. However, the NADH dehydrogenase activity of complex I was not affected in the mutant. By contrast, genes encoding alternative NADH dehydrogenases and alternative oxidase were up-regulated. The mpr25 mutant may therefore provide new information on the coordinated interaction between mitochondria and chloroplasts.	MPR25
Mutation of a rice gene encoding a phenylalanine biosynthetic enzyme results in accumulation of phenylalanine and tryptophan	2008	Plant Cell	CREST, Japan Science and Technology Agency, Tokyo 103-0027, Japan.	Two distinct biosynthetic pathways for Phe in plants have been proposed: conversion of prephenate to Phe via phenylpyruvate or arogenate. The reactions catalyzed by prephenate dehydratase (PDT) and arogenate dehydratase (ADT) contribute to these respective pathways. The Mtr1 mutant of rice (Oryza sativa) manifests accumulation of Phe, Trp, and several phenylpropanoids, suggesting a link between the synthesis of Phe and Trp. Here, we show that the Mtr1 mutant gene (mtr1-D) encodes a form of rice PDT with a point mutation in the putative allosteric regulatory region of the protein. Transformed callus lines expressing mtr1-D exhibited all the characteristics of Mtr1 callus tissue. Biochemical analysis revealed that rice PDT possesses both PDT and ADT activities, with a preference for arogenate as substrate, suggesting that it functions primarily as an ADT. The wild-type enzyme is feedback regulated by Phe, whereas the mutant enzyme showed a reduced feedback sensitivity, resulting in Phe accumulation. In addition, these observations indicate that rice PDT is critical for regulating the size of the Phe pool in plant cells. Feeding external Phe to wild-type callus tissue and seedlings resulted in Trp accumulation, demonstrating a connection between Phe accumulation and Trp pool size.	Mtr1
Expression of an NADP-malic enzyme gene in rice (Oryza sativa. L) is induced by environmental stresses; over-expression of the gene in Arabidopsis confers salt and osmotic stress tolerance	2007	Plant Mol Biol	Alkali Soil Natural Environmental Science Center (ASNESC), Stress Molecular Biology Laboratory, Northeast Forestry University, Harbin 150040, P. R. China.	NADP-malic enzyme (NADP-ME, EC 1.1.1.40) functions in many different pathways in plants, and has recently been implicated in plant defense such as in responses to wounding and UV-B radiation. In this study, we isolated a complementary DNA (cDNA) clone by using the differential display method and screening of a root cDNA library of rice (Oryza sativa. L) under carbonate (NaHCO3) stress, and identified it as one of the rice NADP-ME genes (we named it NADP-ME2, GenBank accession no. AB053295). The 5' end of NADP-ME2 was obtained by the 5'-RACE method, and the full-length cDNA had a length of 2217 bp encoding 593 amino acids. Expression of NADP-ME2 mRNA in roots was induced by stress from carbonates (NaHCO3 and Na2CO3, NaCl, and environmental pH changes. NADP-ME2 transcripts increased during 72-h exposures to NaHCO3, NaCl, and PEG stresses. Furthermore, NADP-ME activities in leaves and roots of rice seedlings increased by more than 50% in the presence of carbonates (NaHCO3 and Na2CO3), NaCl, and PEG. These results indicate that rice NADP-ME2 responds to salts and osmotic stresses. Transgenic Arabidopsis plants over-expressing NADP-ME2 were obtained through transformation, screening, Northern analysis and in situ NADP-ME activity assay. Transgenic Arabidopsis plants over-expressing NADP-ME2 grew well in 1/2 x MS medium with 100 mM NaCl or 4% mannitol, whereas growth of wild-type (WT) Arabidopsis seedlings was strongly inhibited. In addition, under 125 mM NaCl stress, the root lengths of transgenic lines were about twice as long as those of the WT. These results suggest that NADP-ME2 has a role in enhancing tolerance of plants to salt and osmotic stress.	NADP-ME2
Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1	2012	Plant Cell Rep	State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China.	Leaf width is an important agricultural trait in rice. QTL mapping in a recombinant inbred line population derived from the cross between the javanica cultivar D50 (narrow-leaved) and the indica cultivar HB277 (wide-leaved) identified five QTLs controlling flag leaf width. Fine mapping of the major QTL qFLW4 narrowed its location to a 74.8 kb interval between the SSR loci RM17483 and RM17486, a region which also contains the gene NAL1 (Narrow leaf 1). There was no difference in the level of NAL1 expression between cvs. D50 and HB277, but an analysis of the NAL1 transcripts showed that while most (if not all) of those produced in cv. D50 were full-length, two-thirds of those in HB277 were non-functional due to either loss or gain of sequence. The inference was that NAL1 is probably synonymous with qFLW4, and that the functional difference between the two alleles was due to alternative splicing. The analysis of expression of other known genes involved in the determination of leaf width provided no evidence of their having any clear functional association with qFLW4/NAL1.	NAL1|qFLW4
Mutation of the rice Narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport	2008	Plant Physiol	State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	The size and shape of the plant leaf is an important agronomic trait. To understand the molecular mechanism governing plant leaf shape, we characterized a classic rice (Oryza sativa) dwarf mutant named narrow leaf1 (nal1), which exhibits a characteristic phenotype of narrow leaves. In accordance with reduced leaf blade width, leaves of nal1 contain a decreased number of longitudinal veins. Anatomical investigations revealed that the culms of nal1 also show a defective vascular system, in which the number and distribution pattern of vascular bundles are altered. Map-based cloning and genetic complementation analyses demonstrated that Nal1 encodes a plant-specific protein with unknown biochemical function. We provide evidence showing that Nal1 is richly expressed in vascular tissues and that mutation of this gene leads to significantly reduced polar auxin transport capacity. These results indicate that Nal1 affects polar auxin transport as well as the vascular patterns of rice plants and plays an important role in the control of lateral leaf growth.	NAL1|qFLW4
NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars	2013	Proc Natl Acad Sci U S A	Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, Metro Manila, Philippines.	Increasing crop production is essential for securing the future food supply in developing countries in Asia and Africa as economies and populations grow. However, although the Green Revolution led to increased grain production in the 1960s, no major advances have been made in increasing yield potential in rice since then. In this study, we identified a gene, SPIKELET NUMBER (SPIKE), from a tropical japonica rice landrace that enhances the grain productivity of indica cultivars through pleiotropic effects on plant architecture. Map-based cloning revealed that SPIKE was identical to NARROW LEAF1 (NAL1), which has been reported to control vein pattern in leaf. Phenotypic analyses of a near-isogenic line of a popular indica cultivar, IR64, and overexpressor lines revealed increases in spikelet number, leaf size, root system, and the number of vascular bundles, indicating the enhancement of source size and translocation capacity as well as sink size. The near-isogenic line achieved 13-36% yield increase without any negative effect on grain appearance. Expression analysis revealed that the gene was expressed in all cell types: panicles, leaves, roots, and culms supporting the pleiotropic effects on plant architecture. Furthermore, SPIKE increased grain yield by 18% in the recently released indica cultivar IRRI146, and increased spikelet number in the genetic background of other popular indica cultivars. The use of SPIKE in rice breeding could contribute to food security in indica-growing regions such as South and Southeast Asia.	NAL1|qFLW4
The rice narrow leaf2 and narrow leaf3 loci encode WUSCHEL-related homeobox 3A (OsWOX3A) and function in leaf, spikelet, tiller and lateral root development	2013	New Phytol	Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Korea.	. In order to understand the molecular genetic mechanisms of rice (Oryza sativa) organ development, we studied the narrow leaf2 narrow leaf3 (nal2 nal3; hereafter nal2/3) double mutant, which produces narrow-curly leaves, more tillers, fewer lateral roots, opened spikelets and narrow-thin grains. . We found that narrow-curly leaves resulted mainly from reduced lateral-axis outgrowth with fewer longitudinal veins and more, larger bulliform cells. Opened spikelets, possibly caused by marginal deformity in the lemma, gave rise to narrow-thin grains. . Map-based cloning revealed that NAL2 and NAL3 are paralogs that encode an identical OsWOX3A (OsNS) transcriptional activator, homologous to NARROW SHEATH1 (NS1) and NS2 in maize and PRESSED FLOWER in Arabidopsis. . OsWOX3A is expressed in the vascular tissues of various organs, where nal2/3 mutant phenotypes were displayed. Expression levels of several leaf development-associated genes were altered in nal2/3, and auxin transport-related genes were significantly changed, leading to pin mutant-like phenotypes such as more tillers and fewer lateral roots. OsWOX3A is involved in organ development in rice, lateral-axis outgrowth and vascular patterning in leaves, lemma and palea morphogenesis in spikelets, and development of tillers and lateral roots.	NAL3,NAL2|OsWOX3A|WOX3
Two WUSCHEL-related homeobox genes, narrow leaf2 and narrow leaf3, control leaf width in rice	2013	Plant Cell Physiol	Department of Biological Mechanisms and Functions, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601 Japan.	Leaf shape is one of the key determinants of plant architecture. Leaf shape also affects the amount of sunlight captured and influences photosynthetic efficiency; thus, it is an important agronomic trait in crop plants. Understanding the molecular mechanisms governing leaf shape is a central issue of plant developmental biology and agrobiotechnology. Here, we characterized the narrow-leaf phenotype of FL90, a linkage tester line of rice (Oryza sativa). Light and scanning electron microscopic analyses of FL90 leaves revealed defects in the development of marginal regions and a reduction in the number of longitudinal veins. The narrow-leaf phenotype of FL90 shows a two-factor recessive inheritance and is caused by the loss of function of two WUSCHEL-related homeobox genes, NAL2 and NAL3 (NAL2/3), which are duplicate genes orthologous to maize NS1 and NS2 and to Arabidopsis PRS. The overexpression of NAL2/3 in transgenic rice plants results in wider leaves containing increased numbers of veins, suggesting that NAL2/3 expression regulates leaf width. Thus, NAL2/3 can be used to modulate leaf shape and improve agronomic yield in crop plants.	NAL3,NAL2|OsWOX3A|WOX3
Overexpression of a Rice NPR1 Homolog Leads to Constitutive Activation of Defense Response and Hypersensitivity to Light	2005	Molecular Plant-Microbe Interactions	Department of Plant Pathology, University of California, Davis 95616, USA.	Arabidopsis NPR1/NIM1 is a key regulator of systemic acquired resistance (SAR), which confers lasting broad-spectrum resistance. Previous reports indicate that rice has a disease-resistance pathway similar to the Arabidopsis SAR pathway. Here we report the isolation and characterization of a rice NPR1 homologue (NH1). Transgenic rice plants overexpressing NH1 (NH1ox) acquire high levels of resistance to Xanthomonas oryzae pv. oryzae. The resistance phenotype is heritable and correlates with the presence of the transgene and reduced bacterial growth. Northern analysis shows that NH1ox rice spontaneously activates defense genes, contrasting with NPR1-overexpressing Arabidopsis, where defense genes are not activated until induction. Wild-type NH1, but not a point mutant corresponding to npr1-1, interacts strongly with the rice transcription factor rTGA2.2 in yeast two-hybrid. Greenhouse-grown NH1ox plants develop lesion-mimic spots on leaves at preflowering stage although no other developmental effects are observed. However, when grown in growth chambers (GCs) under low light, NH1ox plants are dwarfed, indicating elevated sensitivity to light. The GC-grown NH1ox plants show much higher salicylic acid (SA) levels than the wild type, whereas greenhouse-grown NH1ox plants contain lower SA. These results indicate that NH1 may be involved in the regulation of SA in response to environmental changes.	NH2
Functional analysis of rice NPR1-like genes reveals that OsNPR1/NH1 is the rice orthologue conferring disease resistance with enhanced herbivore susceptibility	2007	Plant Biotechnol J	National Key Laboratory of Plant Molecular Genetics, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China.	The key regulator of salicylic acid (SA)-mediated resistance, NPR1, is functionally conserved in diverse plant species, including rice (Oryza sativa L.). Investigation in depth is needed to provide an understanding of NPR1-mediated resistance and a practical strategy for the improvement of disease resistance in the model crop rice. The rice genome contains five NPR1-like genes. In our study, three rice homologous genes, OsNPR1/NH1, OsNPR2/NH2 and OsNPR3, were found to be induced by rice bacterial blight Xanthomonas oryzae pv. oryzae and rice blast Magnaporthe grisea, and the defence molecules benzothiadiazole, methyl jasmonate and ethylene. We confirmed that OsNPR1 is the rice orthologue by complementing the Arabidopsis npr1 mutant. Over-expression of OsNPR1 conferred disease resistance to bacterial blight, but also enhanced herbivore susceptibility in transgenic plants. The OsNPR1-green fluorescent protein (GFP) fusion protein was localized in the cytoplasm and moved into the nucleus after redox change. Mutations in its conserved cysteine residues led to the constitutive localization of OsNPR1(2CA)-GFP in the nucleus and also abolished herbivore hypersensitivity in transgenic rice. Different subcellular localizations of OsNPR1 antagonistically regulated SA- and jasmonic acid (JA)-responsive genes, but not SA and JA levels, indicating that OsNPR1 might mediate antagonistic cross-talk between the SA- and JA-dependent pathways in rice. This study demonstrates that rice has evolved an SA-mediated systemic acquired resistance similar to that in Arabidopsis, and also provides a practical approach for the improvement of disease resistance without the penalty of decreased herbivore resistance in rice.	NH2,OsNPR1|NH1
Enhanced disease resistance and hypersensitivity to BTH by introduction of an NH1/OsNPR1 paralog	2011	Plant Biotechnol J	Department of Plant Pathology, University of California, Davis, CA, USA.	Non-expresser of pathogenesis-related genes 1 (NPR1) is the master regulator of salicylic acid-mediated systemic acquired resistance. Over-expression of Arabidopsis NPR1 and rice NH1 (NPR1 homolog1)/OsNPR1 in rice results in enhanced resistance. While there are four rice NPR1 paralogs in the rice genome, none have been demonstrated to function in disease resistance. To study rice NPR1 paralog 3, we introduced constructs into rice and tested for effects on resistance to infection by Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial blight. While over-expression of NH3 using the maize ubiquitin-1 promoter failed to enhance resistance, introduction of an extra copy of NH3 driven by its own promoter (nNT-NH3) resulted in clear, enhanced resistance. Progeny analysis confirms that the enhanced resistance phenotype, measured by Xoo-induced lesion length, is associated with the NH3 transgene. Bacterial growth curve analysis indicates that bacterial population levels are reduced 10-fold in nNT-NH3 lines compared to control rice lines. The transgenic plants exhibit higher sensitivity to benzothiadiazole (BTH) and 2,6-dichloroisonicotinic acid (INA) treatment as measured by increased cell death. Expression analysis of pathogenesis-related (PR) genes showed that nNT-NH3 plants display greatly enhanced induction of PR genes only after treatment with BTH. Our study demonstrates an alternative method to employ a regulatory protein to enhance plant defence. This approach avoids using undesirable constitutive, high-level expression and may prove to be more practical for engineering resistance.	NH3
A nitrate-inducible GARP family gene encodes an auto-repressible transcriptional repressor in rice	2013	Plant Cell Physiol	Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657 Japan.	Nitrogen is the most important macronutrient in plants and its supply induces responses in gene expression, metabolism and developmental processes. However, the molecular mechanisms underlying the nitrogen responses remain poorly understood. Here we show that the supply of nitrate but not ammonium immediately induces the expression of a transcriptional repressor gene in rice, designated NIGT1 (Nitrate-Inducible, GARP-type Transcriptional Repressor 1). The results of DNA-binding site selection experiments and electrophoretic mobility shift assays indicated that NIGT1 binds to DNA containing either of two consensus sequences, GAATC or GAATATTC. In transient reporter assays, NIGT1 was found to repress transcription from the promoters containing the identified NIGT1-binding sequences in vivo. Furthermore, NIGT1 repressed the activity of its own promoter, suggesting an autorepression mechanism. Consistently, nitrate-induced NIGT1 expression was found to be down-regulated after a transient peak during nitrate treatment, and the nitrate-induced expression of NIGT1 decreased in transgenic rice plants in which this gene was constitutively overexpressed. Furthermore, the chlorophyll content that could be a marker of nitrogen utilization was found to be decreased in NIGT1 overexpressors of rice grown with nitrate medium but not with ammonium medium. Thus, we propose NIGT1 as a nitrate-inducible and autorepressible transcriptional repressor that may play a role in the nitrogen response in rice. Taken together with the fact that the NIGT1-binding sites are conserved in promoter sequences of Arabidopsis NIGT1 homologs, our findings imply the presence of a time-dependent complex system for nitrate-responsive transcriptional regulation that is conserved in both monocots and dicots.	NIGT1
Semi-dominant mutations in the CC-NB-LRR-type R gene, NLS1, lead to constitutive activation of defense responses in rice	2011	Plant J	State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China.	In this study, we characterized the semi-dominant mutant nls1-1D (necrotic leaf sheath 1) of rice, which displays spontaneous lesions, specifically on leaf sheaths, with a developmental pattern. nls1-1D plants also exhibited constitutively activated defense responses, including extensive cell death, excess hydrogen peroxide and salicylic acid (SA) accumulation, up-regulated expressions of pathogenesis-related genes, and enhanced resistance to bacterial pathogens. Map-based cloning revealed that NLS1 encodes a typical CC-NB-LRR-type protein in rice. The nls1-1D mutation causes a S367N substitution in the non-conserved region close to the GLPL motif of the NB domain. An adjacent S366T substitution was found in another semi-dominant mutant, nls1-2D, which exhibited the same phenotypes as nls1-1D. Combined analyses of wild-type plants transformed with the mutant NLS1 gene (nls1-1D), NLS1 RNAi and over-expression transgenic lines showed that nls1-2D is allelic to nls1-1D, and both mutations may cause constitutive auto-activation of the NLS1 R protein. Further real-time PCR analysis revealed that NLS1 is expressed constitutively in an age-dependent manner. In addition, because the morphology and constitutive defense responses of nls1-1D were not suppressed by blocking SA or NPR1 transcript accumulation, we suggest that NLS1 mediates both SA and NPR1-independent defense signaling pathways in rice.	NLS1,OsNPR1|NH1
Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice	2007	Plant Physiol	Department of Plant Biology , North Carolina State University, Raleigh, North Carolina 27695, USA.	Core DNA replication proteins mediate the initiation, elongation, and Okazaki fragment maturation functions of DNA replication. Although this process is generally conserved in eukaryotes, important differences in the molecular architecture of the DNA replication machine and the function of individual subunits have been reported in various model systems. We have combined genome-wide bioinformatic analyses of Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) with published experimental data to provide a comprehensive view of the core DNA replication machinery in plants. Many components identified in this analysis have not been studied previously in plant systems, including the GINS (go ichi ni san) complex (PSF1, PSF2, PSF3, and SLD5), MCM8, MCM9, MCM10, NOC3, POLA2, POLA3, POLA4, POLD3, POLD4, and RNASEH2. Our results indicate that the core DNA replication machinery from plants is more similar to vertebrates than single-celled yeasts (Saccharomyces cerevisiae), suggesting that animal models may be more relevant to plant systems. However, we also uncovered some important differences between plants and vertebrate machinery. For example, we did not identify geminin or RNASEH1 genes in plants. Our analyses also indicate that plants may be unique among eukaryotes in that they have multiple copies of numerous core DNA replication genes. This finding raises the question of whether specialized functions have evolved in some cases. This analysis establishes that the core DNA replication machinery is highly conserved across plant species and displays many features in common with other eukaryotes and some characteristics that are unique to plants.	NOC3,OsORC4,OsORC5,OsORC6
Two short-chain dehydrogenase/reductases, NON-YELLOW COLORING 1 and NYC1-LIKE, are required for chlorophyll b and light-harvesting complex II degradation during senescence in rice	2009	Plant J	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan.	Yellowing, which is related to the degradation of chlorophyll and chlorophyll-protein complexes, is a notable phenomenon during leaf senescence. NON-YELLOW COLORING 1 (NYC1) in rice encodes a membrane-localized short-chain dehydrogenase/reductase (SDR) that is thought to represent a chlorophyll b reductase necessary for catalyzing the first step of chlorophyll b degradation. Analysis of the nyc1 mutant, which shows the stay-green phenotype, revealed that chlorophyll b degradation is required for the degradation of light-harvesting complex II and thylakoid grana in leaf senescence. Phylogenetic analysis further revealed the existence of NYC1-LIKE (NOL) as the most closely related protein to NYC1. In the present paper, the nol mutant in rice was also found to show a stay-green phenotype very similar to that of the nyc1 mutant, i.e. the degradation of chlorophyll b was severely inhibited and light-harvesting complex II was selectively retained during senescence, resulting in the retention of thylakoid grana even at a late stage of senescence. The nyc1 nol double mutant did not show prominent enhancement of inhibition of chlorophyll degradation. NOL was localized on the stromal side of the thylakoid membrane despite the lack of a transmembrane domain. Immunoprecipitation analysis revealed that NOL and NYC1 interact physically in vitro. These observations suggest that NOL and NYC1 are co-localized in the thylakoid membrane and act in the form of a complex as a chlorophyll b reductase in rice.	NOL,NYC1
Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II and grana degradation during leaf senescence	2007	Plant Cell	Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan. akusaba@mail.ecc.u-tokyo.ac.jp	Chlorophyll degradation is an aspect of leaf senescence, which is an active process to salvage nutrients from old tissues. non-yellow coloring1 (nyc1) is a rice (Oryza sativa) stay-green mutant in which chlorophyll degradation during senescence is impaired. Pigment analysis revealed that degradation of not only chlorophylls but also light-harvesting complex II (LHCII)-bound carotenoids was repressed in nyc1, in which most LHCII isoforms were selectively retained during senescence. Ultrastructural analysis of nyc1 chloroplasts revealed that large and thick grana were present even in the late stage of senescence, suggesting that degradation of LHCII is required for the proper degeneration of thylakoid membranes. Map-based cloning of NYC1 revealed that it encodes a chloroplast-localized short-chain dehydrogenase/reductase (SDR) with three transmembrane domains. The predicted structure of the NYC1 protein and the phenotype of the nyc1 mutant suggest the possibility that NYC1 is a chlorophyll b reductase. Although we were unable to detect the chlorophyll b reductase activity of NYC1, NOL (for NYC1-like), a protein closely related to NYC1 in rice, showed chlorophyll b reductase activity in vitro. We suggest that NYC1 and NOL encode chlorophyll b reductases with divergent functions. Our data collectively suggest that the identified SDR protein NYC1 plays essential roles in the regulation of LHCII and thylakoid membrane degradation during senescence.	NOL,NYC1
Rice plastidial N-glycosylated nucleotide pyrophosphatase/phosphodiesterase is transported from the ER-golgi to the chloroplast through the secretory pathway	2006	Plant Cell	Laboratory of Plant and Microbial Genome Control, Department of Applied Biological Chemistry, Niigata University, Niigata 950-2181, Japan.	A nucleotide pyrophosphatase/phosphodiesterase (NPP) activity that catalyzes the hydrolytic breakdown of ADP-glucose (ADPG) has been shown to occur in the plastidial compartment of both mono- and dicotyledonous plants. To learn more about this enzyme, we purified two NPPs from rice (Oryza sativa) and barley (Hordeum vulgare) seedlings. Both enzymes are glycosylated, since they bind to concanavalin A, stain with periodic acid-Schiff reagent, and are digested by Endo-H. A complete rice NPP cDNA, designated as NPP1, was isolated, characterized, and overexpressed in transgenic plants displaying high ADPG hydrolytic activity. Databank searches revealed that NPP1 belongs to a functionally divergent group of plant nucleotide hydrolases. NPP1 contains numerous N-glycosylation sites and a cleavable hydrophobic signal sequence that does not match with the N-terminal part of the mature protein. Both immunocytochemical analyses and confocal fluorescence microscopy of rice cells expressing NPP1 fused with green fluorescent protein (GFP) revealed that NPP1-GFP occurs in the plastidial compartment. Brefeldin A treatment of NPP1-GFP-expressing cells prevented NPP1-GFP accumulation in the chloroplasts. Endo-H digestibility studies revealed that both NPP1 and NPP1-GFP in the chloroplast are glycosylated. Collectively, these data demonstrate the trafficking of glycosylated proteins from the endoplasmic reticulum-Golgi system to the chloroplast in higher plants.	NPP1|OsPAP27b
Identification of rice purple acid phosphatases related to phosphate starvation signalling	2011	Plant Biol (Stuttg)	State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou, China.	Purple acid phosphatases (PAPs) are a family of metallo-phosphoesterases involved in a variety of physiological functions, especially phosphate deficiency adaptations in plants. We identified 26 putative PAP genes by a genome-wide analysis of rice (Oryza sativa), 24 of which have isolated EST sequences in the dbEST database. Amino acid sequence analysis revealed that 25 of these genes possess sets of metal-ligating residues typical of known PAPs. Phylogenetic analysis classified the 26 rice and 29 Arabidopsis PAPs into three main groups and seven subgroups. We detected transcripts of 21 PAP genes in roots or leaves of rice seedlings. The expression levels of ten PAP genes were up-regulated by both phosphate deprivation and over-expression of the transcription factor OsPHR2. These PAP genes all contained one or two OsPHR2 binding elements in their promoter regions, implying that they are directly regulated by OsPHR2. Both acid phosphatase (AP) and surface secretory acid phosphatase (SAP) activity assays showed that the up-regulation of PAPs by Pi starvation, OsPHR2 over-expression, PHO2 knockout or OsSPX1 RNA interference led to an increase in AP and SAP activity in rice roots. This study reveals the potential for developing technologies for crop improvement in phosphorus use efficiency.	NPP1|OsPAP27b
A novel rice gene, NRR responds to macronutrient deficiency and regulates root growth	2012	Mol Plant	State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.	To better understand the response of rice to nutrient stress, we have taken a systematic approach to identify rice genes that respond to deficiency of macronutrients and affect rice growth. We report here the expression and biological functions of a previously uncharacterized rice gene that we have named NRR (nutrition response and root growth). NRR is alternatively spliced, producing two 5'-coterminal transcripts, NRRa and NRRb, encoding two proteins of 308 and 223 aa, respectively. Compared to NRRb, NRRa possesses an additional CCT domain at the C-terminus. Expression of NRR in rice seedling roots was significantly influenced by deficiency of macronutrients. Knock-down of expression of NRRa or NRRb by RNA interference resulted in enhanced rice root growth. By contrast, overexpression of NRRa in rice exhibited significantly retarded root growth. These results revealed that both NRRa and NRRb played negative regulatory roles in rice root growth. Our findings suggest that NRRa and NRRb, acting as the key components, modulate the rice root architecture with the availability of macronutrients.	NRR
A rice transient assay system identifies a novel domain in NRR required for interaction with NH1/OsNPR1 and inhibition of NH1-mediated transcriptional activation	2012	Plant Methods	Department of Plant Pathology, University of California, Davis, Davis, CA 95616, USA. pcronald@ucdavis.edu.	BACKGROUND: Arabidopsis NPR1 is a master regulator of systemic acquired resistance. NPR1 binds to TGA transcription factors and functions as a transcriptional co-activator. In rice, NH1/OsNPR1 functions to enhance innate immunity. NRR disrupts NH1 function, when over-expressed. RESULTS: We have established a rice transient protoplast assay to demonstrate that NH1 is a transcriptional co-activator and that NRR represses NH1-mediated activation. We identified three NRR homologues (RH1, RH2, and RH3). RH1 and RH3, but not RH2, also effectively repress NH1-mediated transcriptional activation. NRR, RH1, RH2, and RH3 share sequence similarity in a region beyond the previously identified NPR1-interacting domain. This region is required for strong interaction with NH1. A double point mutation, W66A/F70A, in this novel NH1-interacting domain severely reduces interaction with NH1. Mutation W66A/F70A also greatly reduces the ability of NRR to repress NH1-mediated activation. RH2 carries a deviation (amino acids AV) in this region as compared to consensus sequences (amino acids ED) among NRR, RH1, and RH3. A substitution (AV to ED) in RH2 results in strong binding of mutant RH2ED to NH1 and effective repression of NH1-mediated activation. CONCLUSIONS: The protoplast-based transient system can be used to dissect protein domains associated with their functions. Our results demonstrate that the ability of NRR and its homologues to repress NH1-mediated transcriptional activation is tightly correlated with their ability to bind to NH1. Furthermore, a sequence is identified as a novel NH1-interacting domain. Importantly, this novel sequence is widely present in plant species, from cereals to castor bean plants, to poplar trees, to Arabidopsis, indicating its significance in plants.	NRR,OsNPR1|NH1,RH1,RH2,RH3
Rice NRR, a negative regulator of disease resistance, interacts with Arabidopsis NPR1 and rice NH1	2005	Plant J	Department of Plant Pathology, University of California, Davis, CA 95616, USA.	Arabidopsis NPR1/NIM1 is a key regulator of systemic acquired resistance (SAR), which confers lasting broad-spectrum resistance. Over-expression of Arabidopsis NPR1 or the NPR1 homolog 1 (NH1) in rice results in enhanced resistance to the pathogen Xanthomonasoryzae pv. oryzae (Xoo), suggesting the presence of a related defense pathway in rice. We investigated this pathway in rice by identifying proteins that interact with NH1. Here we report the isolation and characterization of a rice cDNA encoding a novel protein, named NRR (for negative regulator of resistance). NRR interacts with NPR1 in the NPR1-interacting domain (NI25) consisting of 25 amino acids. NRR also interacts with NH1; however, NI25 was not sufficient for a strong interaction, indicating a difference between the rice and the Arabidopsis proteins. Silencing of NRR in rice had little effect on resistance to Xoo. When constitutively over-expressed in rice, NRR affected basal resistance, age-related resistance and Xa21-mediated resistance, causing enhanced susceptibility to Xoo. This phenotype was correlated with elevated NRR mRNA and protein levels and increased Xoo growth. Over-expression of NRR suppressed the induction of defense-related genes. NRR:GFP (green fluorescent protein) protein was localized to the nucleus, indicating that NRR may act directly to suppress the activation of defense genes. The fact that NRR compromises Xa21-mediated resistance indicates cross-talk or overlap between NH1- and Xa21-mediated pathways.	NRR,OsNPR1|NH1
Suppression of expression of the putative receptor-like kinase gene NRRB enhances resistance to bacterial leaf streak in rice	2014	Mol Biol Rep	Xiamen Key Laboratory for Plant Genetics, School of Life Sciences, Xiamen University, Xiamen, 361005, People's Republic of China, heartone@126.com.	Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is an important disease of rice, which is responsible for the economic losses worldwide. Functional investigation of differentially expressed protein genes (DEPGs) from rice (Oryza sativa L.) upon Xoc infection provides insight into the molecular mechanism of rice-Xoc interactions. Here, we show that one of DEPGs designated NRRB plays a role in rice-Xoc interactions. NRRB, a receptor-like cytoplasmic kinase gene was preferentially expressed in leaf blades and leaf sheaths where the pathogen colonized. Its transcription was depressed by two defense-signal compounds salicylic acid and 1-aminocyclopropane-1-carboxylic-acid, but was activated by wounding and abscisic acid. Additionally, a plenty of cis-elements associated with stress responses were discovered in the promoter region of NRRB. These data suggest that NRRB is involved in stress responses. More importantly, the NRRB-suppressing rice plants exhibited enhanced resistance against BLS, with the markedly shorter average lesion length than that of the wild type. Furthermore, transcription of some salicylic acid synthesis-related and pathogenesis-related genes including PAD4, PR1a and WRKY13 in transgenic plants was activated, implying that enhanced resistance to BLS might be mediated by the activation of the SA signaling pathway. In conclusion, NRRB gene is involved in various stress responses and regulating resistance to BLS, therefore it might be one of useful genes for rice improvement in future.	NRRB,OsPR1a,OsWRKY13
Rice OsNAR2.1 interacts with OsNRT2.1, OsNRT2.2 and OsNRT2.3a nitrate transporters to provide uptake over high and low concentration ranges	2011	Plant Cell Environ	State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, China.	Plants take up both nitrate and ammonium as main nitrogen (N) sources. Although ammonium is the predominant form in anaerobic-flooded paddy soil, it has been proposed that rice and other wetland plants may take up significant amounts of nitrate formed by nitrification of ammonium in the rhizosphere. A two-component system for nitrate transport including NRT2s with a partner protein (NAR2 or NRT3.1) has been identified in Arabidopsis. We report the physiological function of another member of the NAR2 family, OsNAR2.1 in rice (Oryza sativa, ssp. Japonica, cv. Nipponbare). OsNAR2.1 was mainly expressed in roots and induced by nitrate and suppressed by ammonium and some amino acids. Knockdown of OsNAR2.1 by RNA interference synchronously suppressed expression of OsNRT2.1, OsNRT2.2 and OsNRT2.3a in the osnar2.1mutants. Both high- and low-affinity nitrate transports were greatly impaired by OsNAR2.1 knockdown. Yeast two hybridization showed that OsNAR2.1 not only interacted with OsNRT2.1/OsNRT2.2, but also with OsNRT2.3a. Taken together, the data demonstrate that OsNAR2.1 plays a key role in enabling the plant to cope with variable nitrate supply.	NRT1,OsNRT2.2,OsNAR2.1,OsNRT2.3a|OsNRT2.3b,OsNAR2.2
Cloning and functional characterization of a constitutively expressed nitrate transporter gene, OsNRT1, from rice	2000	Plant Physiol	Department of Life Science, School of Life Science, National Tsing Hua University, 30043, Hsin-Chu, Taiwan.	Elucidating how rice (Oryza sativa) takes up nitrate at the molecular level could help improve the low recovery rate (<50%) of nitrogen fertilizer in rice paddies. As a first step toward that goal, we have cloned a nitrate transporter gene from rice called OsNRT1. OsNRT1 is a new member of a growing transporter family called PTR, which consists not only of nitrate transporters from higher plants that are homologs of the Arabidopsis CHL1 (AtNRT1) protein, but also peptide transporters from a wide variety of genera including animals, plants, fungi, and bacteria. However, despite the fact that OsNRT1 shares a higher degree of sequence identity with the two peptide transporters from plants (approximately 50%) than with the nitrate transporters (approximately 40%) of the PTR family, no peptide transport activity was observed when OsNRT1 was expressed in either Xenopus oocytes or yeast. Furthermore, contrasting the dual-affinity nitrate transport activity of CHL1, OsNRT1 displayed only low-affinity nitrate transport activity in Xenopus oocytes, with a K(m) value of approximately 9 mM. Northern-blot and in situ hybridization analysis indicated that OsNRT1 is constitutively expressed in the most external layer of the root, epidermis and root hair. These data strongly indicate that OsNRT1 encodes a constitutive component of a low-affinity nitrate uptake system for rice.	NRT1
Knockdown of a rice stelar nitrate transporter alters long-distance translocation but not root influx	2012	Plant Physiol	State Key Laboratory of Crop Genetics and Germplasm Enhancement and Key Laboratory of Plant Nutrition and Fertilization in Low-Middle Reaches of the Yangtze River, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.	Root nitrate uptake is well known to adjust to the plant's nitrogen demand for growth. Long-distance transport and/or root storage pools are thought to provide negative feedback signals regulating root uptake. We have characterized a vascular specific nitrate transporter belonging to the high-affinity Nitrate Transporter2 (NRT2) family, OsNRT2.3a, in rice (Oryza sativa ssp. japonica 'Nipponbare'). Localization analyses using protoplast expression, in planta promoter-beta-glucuronidase assay, and in situ hybridization showed that OsNRT2.3a was located in the plasma membrane and mainly expressed in xylem parenchyma cells of the stele of nitrate-supplied roots. Knockdown expression of OsNRT2.3a by RNA interference (RNAi) had impaired xylem loading of nitrate and decreased plant growth at low (0.5 mm) nitrate supply. In comparison with the wild type, the RNAi lines contained both nitrate and total nitrogen significantly higher in the roots and lower in the shoots. The short-term [(15)N]NO(3)(-) influx (5 min) in entire roots and NO(3)(-) fluxes in root surfaces showed that the knockdown of OsNRT2.3a in comparison with the wild type did not affect nitrate uptake by roots. The RNAi plants showed no significant changes in the expression of some root nitrate transporters (OsNRT2.3b, OsNRT2.4, and OsNAR2.1), but transcripts for nia1 (nitrate reductase) had increased and OsNRT2.1 and OsNRT2.2 had decreased when the plants were supplied with nitrate. Taken together, the data demonstrate that OsNRT2.3a plays a key role in long-distance nitrate transport from root to shoot at low nitrate supply level in rice.	OsNRT2.2,OsNRT2.4,OsNRT2.3a|OsNRT2.3b,OsNIA1|OsNia1
Spatial expression and regulation of rice high-affinity nitrate transporters by nitrogen and carbon status	2011	J Exp Bot	State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing 210095, PR China. ghxu@njau.edu.cn	The high affinity nitrate transport system (HATS) plays an important role in rice nitrogen acquisition because, even under flooded anaerobic cultivation when NH(4)(+) dominates, significant nitrification occurs on the root surface. In the rice genome, four NRT2 and two NAR2 genes encoding HATS components have been identified. One gene OsNRT2.3 was mRNA spliced into OsNRT2.3a and OsNRT2.3b and OsNAR2.1 interacts with OsNRT2.1/2.2 and OsNRT2.3a to provide nitrate uptake. Using promoter-GUS reporter plants and semi-quantitative RT-PCR analyses, it was observed that OsNAR2.1 was expressed mainly in the root epidermal cells, differently from the five OsNRT2 genes. OsNAR2.1, OsNRT2.1, OsNRT2.2, and OsNRT2.3a were up-regulated by nitrate and suppressed by NH(4)(+) and high root temperature (37 degrees C). Expression of all these genes was increased by light or external sugar supply. Root transcripts of OsNRT2.3b and OsNRT2.4 were much less abundant and not affected by temperature. Expression of OsNRT2.3b was insensitive to the form of N supply. Expression of OsNRT2.4 responded to changes in auxin supply unlike all the other NRT2 genes. A region from position -311 to -1, relative to the translation start site in the promoter region of OsNAR2.1, was found to contain the cis-element(s) necessary for the nitrate-, but not light- and sugar-dependent activation. However, it was difficult to define a conserved cis-element in the promoters of the nitrate-regulated OsNRT2/OsNAR2 genes. The results imply distinct physiological functions for each OsNRT2 transporter, and differential regulation pathways by N and C status.	OsNRT2.2,OsNRT2.4,OsNAR2.1,OsNRT2.3a|OsNRT2.3b,OsNAR2.2
High-affinity nitrate uptake by rice (Oryza sativa) coleoptiles	2011	J Plant Res	Graduate School of Environmental Science, University of Shiga Prefecture, 2500 Hassaka-cho, Hikone, Shiga 522-8533, Japan.	Nitrate uptake by rice coleoptiles was evaluated using (1)(5)N-nitrate in relation to the expression of high-affinity nitrate uptake-related genes, OsNRT2s (OsNRT2.1-2.4) and OsNAR2s (OsNAR2.1 and 2.2). Apparent nitrate uptake by coleoptiles was about one-sixth of that by hydroponically cultured seedling roots. Real-time RT-PCR analysis revealed that OsNRT2.1, a root-specific key gene of inducible high-affinity transport system for nitrate, was most strongly induced in coleoptiles following nitrate supply initiation, while other OsNRT2s and OsNAR2s showed modest induction. These results suggest that rice coleoptiles may have high-affinity transport systems for nitrate similar to roots, and can be model organs for nutrient uptake by submerged plant shoots.	OsNRT2.2,OsNRT2.4,OsNAR2.2
Rice NTRC is a high-efficiency redox system for chloroplast protection against oxidative damage	2006	Plant Cell	Instituto de Bioquimica Vegetal y Fotosintesis, Centro de Investigaciones Cientificas Isla de la Cartuja, 41092 Seville, Spain.	One of the mechanisms plants have developed for chloroplast protection against oxidative damage involves a 2-Cys peroxiredoxin, which has been proposed to be reduced by ferredoxin and plastid thioredoxins, Trx x and CDSP32, the FTR/Trx pathway. We show that rice (Oryza sativa) chloroplast NADPH THIOREDOXIN REDUCTASE (NTRC), with a thioredoxin domain, uses NADPH to reduce the chloroplast 2-Cys peroxiredoxin BAS1, which then reduces hydrogen peroxide. The presence of both NTR and Trx-like domains in a single polypeptide is absolutely required for the high catalytic efficiency of NTRC. An Arabidopsis thaliana knockout mutant for NTRC shows irregular mesophyll cell shape, abnormal chloroplast structure, and unbalanced BAS1 redox state, resulting in impaired photosynthesis rate under low light. Constitutive expression of wild-type NTRC in mutant transgenic lines rescued this phenotype. Moreover, prolonged darkness followed by light/dark incubation produced an increase in hydrogen peroxide and lipid peroxidation in leaves and accelerated senescence of NTRC-deficient plants. We propose that NTRC constitutes an alternative system for chloroplast protection against oxidative damage, using NADPH as the source of reducing power. Since no light-driven reduced ferredoxin is produced at night, the NTRC-BAS1 pathway may be a key detoxification system during darkness, with NADPH produced by the oxidative pentose phosphate pathway as the source of reducing power.	NTRC,CDSP32
Defect in non-yellow coloring 3, an alpha/beta hydrolase-fold family protein, causes a stay-green phenotype during leaf senescence in rice	2009	Plant J	Institute of Radiation Breeding, National Institute of Agrobiological Sciences, Hitachi-ohmiya 219-2293, Japan.	Chlorophyll degradation is an important phenomenon in the senescence process. It is necessary for the degradation of certain chlorophyll-protein complexes and thylakoid membranes during leaf senescence. Mutants retaining greenness during leaf senescence are known as 'stay-green' mutants. Non-functional type stay-green mutants, which possess defects in chlorophyll degradation, retain greenness but not leaf functionality during senescence. Here, we report a new stay-green mutant in rice, nyc3. nyc3 retained a higher chlorophyll a and chlorophyll b content than the wild-type but showed a decrease in other senescence parameters during dark incubation, suggesting that it is a non-functional stay-green mutant. In addition, a small amount of pheophytin a, a chlorophyll a-derivative without Mg(2+) ions in its tetrapyrrole ring, accumulated in the senescent leaves of nyc3. nyc3 shows a similar but weaker phenotype to stay green (sgr), another non-functional stay-green mutant in rice. The chlorophyll content of nyc3 sgr double mutants at the late stage of leaf senescence was also similar to that of sgr. Linkage analysis revealed that NYC3 is located near the centromere region of chromosome 6. Map-based cloning of genes near the centromere is very difficult because of the low recombination rate; however, we overcame this problem by using ionizing radiation-induced mutant alleles harboring deletions of hundreds of kilobases. Thus, it was revealed that NYC3 encodes a plastid-localizing alpha/beta hydrolase-fold family protein with an esterase/lipase motif. The possible function of NYC3 in the regulation of chlorophyll degradation is discussed.	NYC3
NYC4, the rice ortholog of Arabidopsis THF1, is involved in the degradation of chlorophyll - protein complexes during leaf senescence	2013	Plant J	Graduate School of Science, Hiroshima University, Higashi-Hiroshima, 739-8526, Japan.	Yellowing/chlorophyll breakdown is a prominent phenomenon in leaf senescence, and is associated with the degradation of chlorophyll - protein complexes. From a rice mutant population generated by ionizing radiation, we isolated nyc4-1, a stay-green mutant with a defect in chlorophyll breakdown during leaf senescence. Using gene mapping, nyc4-1 was found to be linked to two chromosomal regions. We extracted Os07g0558500 as a candidate for NYC4 via gene expression microarray analysis, and concluded from further evidence that disruption of the gene by a translocation-related event causes the nyc4 phenotype. Os07g0558500 is thought to be the ortholog of THF1 in Arabidopsis thaliana. The thf1 mutant leaves show variegation in a light intensity-dependent manner. Surprisingly, the Fv /Fm value remained high in nyc4-1 during the dark incubation, suggesting that photosystem II retained its function. Western blot analysis revealed that, in nyc4-1, the PSII core subunits D1 and D2 were significantly retained during leaf senescence in comparison with wild-type and other non-functional stay-green mutants, including sgr-2, a mutant of the key regulator of chlorophyll degradation SGR. The role of NYC4 in degradation of chlorophyll and chlorophyll - protein complexes during leaf senescence is discussed.	NYC4
The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm	2010	J Exp Bot	United Graduate School of Agricultural Sciences, Iwate University, 3-18-8, Ueda, Morioka, Iwate 020-8550, Japan.	During rice (Oryza sativa L.) seed development, the primary endosperm nucleus undergoes a series of divisions without cytokinesis, producing a multinucleate cell, known as a syncytium. After several rounds of rapid nuclear proliferation, the syncytium ceases to undergo mitosis; thereafter, the syncytium is partitioned into individual cells by a specific type of cytokinesis called cellularization. The transition between syncytium and cellularization is important in determining the final seed size and is a model for studying the cell cycle and cytokinesis. The involvement of cyclin-dependent kinase (CDK) inhibitors (CKIs) in cell cycle control was investigated here during the transition between syncytium and cellularization. It was found that one of the rice CKIs, Orysa;KRP3, is strongly expressed in the caryopsis at 2 d after flowering (DAF), and its expression is significantly reduced at 3 DAF. The other CKI transcripts did not show such a shift at 2 DAF. In situ hybridization analysis revealed that Orysa;KRP3 is expressed in multinucleate syncytial endosperm at 2 DAF, but not in cellularized endosperm at 3 DAF. Two-hybrid assays showed that Orysa;KRP3 binds Orysa;CDKA;1, Orysa;CDKA;2, Orysa;CycA1;1, and Orysa;CycD2;2. By contrast, Orysa;CDKB2;1 and Orysa;CycB2;2 do not show binding to Orysa;KRP3. Orysa;KRP3 was able to rescue yeast premature cell division due to the dominant positive expression of mutant rice CDKA;1 indicating that Orysa;KRP3 inhibited rice CDK. These data suggest that Orysa;KRP3 is involved in cell cycle control of syncytial endosperm.	KRP3
Characterization of rice anthranilate synthase alpha-subunit genes OASA1 and OASA2. Tryptophan accumulation in transgenic rice expressing a feedback-insensitive mutant of OASA1	2001	Plant Physiol	National Agriculture Research Center, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666, Japan.	Anthranilate synthase (AS) is a key enzyme in the synthesis of tryptophan (Trp), indole-3-acetic acid, and indole alkaloids. Two genes, OASA1 and OASA2, encoding AS alpha-subunits were isolated from a monocotyledonous plant, rice (Oryza sativa cv Nipponbare), and were characterized. A phylogenetic tree of AS alpha-subunits from various species revealed a close evolutionary relationship among OASA1 and Arabidopsis ASA2, Ruta graveolens AS alpha 2, and tobacco ASA2, whereas OASA2, Arabidopsis ASA1, and R. graveolens AS alpha 1 were more distantly related. OASA1 is expressed in all tissues tested, but the amount of its mRNA was greater in panicles than in leaves and roots. The abundance of OASA2 transcripts is similar among tissues and greater than that of OASA1 transcripts; furthermore, OASA2 expression was induced by a chitin heptamer, a potent elicitor, suggesting that OASA2 participates in secondary metabolism. Expression of wild-type OASA1 or OASA2 transgenes did not affect the Trp content of rice calli or plants. However, transformed calli and plants expressing a mutated OASA1 gene, OASA1(D323N), that encodes a protein in which aspartate-323 is replaced with asparagine manifested up to 180- and 35-fold increases, respectively, in Trp accumulation. These transgenic calli and plants were resistant to 300 microM 5-methyl-Trp, and AS activity of the calli showed a markedly reduced sensitivity to Trp. These results show that OASA1 is important in the regulation of free Trp concentration, and that mutation of OASA1 to render the encoded protein insensitive to feedback inhibition results in accumulation of Trp at high levels. The OASA1(D323N) transgene may prove useful for the generation of crops with an increased Trp content.	OASA1,OASA2
Functional characterization of ObgC in ribosome biogenesis during chloroplast development	2012	Plant J	Swine Science and Technology Center, Gyeongnam National University of Science and Technology-GNTECH, Jinju 660-758, Korea.	The Spo0B-associated GTP-binding protein (Obg) GTPase, essential for bacterial viability, is also conserved in eukaryotes, but its primary role in eukaryotes remains unknown. Here, our functional characterization of Arabidopsis and rice obgc mutants strongly underlines the evolutionarily conserved role of eukaryotic Obgs in organellar ribosome biogenesis. The mutants exhibited a chlorotic phenotype, caused by retarded chloroplast development. A plastid DNA macroarray revealed a plastid-encoded RNA polymerase (PEP) deficiency in an obgc mutant, caused by incompleteness of the PEP complex, as its western blot exhibited reduced levels of RpoA protein, a component of PEP. Plastid rRNA profiling indicated that plastid rRNA processing is defective in obgc mutants, probably resulting in impaired ribosome biogenesis and, in turn, in reduced levels of RpoA protein. RNA co-immunoprecipitation revealed that ObgC specifically co-precipitates with 23S rRNA in vivo. These findings indicate that ObgC functions primarily in plastid ribosome biogenesis during chloroplast development. Furthermore, complementation analysis can provide new insights into the functional modes of three ObgC domains, including the Obg fold, G domain and OCT.	OsObgC1
Characterization of a stress responsive proteinase inhibitor gene with positive effect in improving drought resistance in rice	2007	Planta	National Center of Plant Gene Research (Wuhan), National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China.	A full-length cDNA gene, designated Oryza sativa chymotrypsin inhibitor-like 1 (OCPI1), was characterized in rice. The predicted protein of OCPI1 shows very high sequence identity to reported chymotrypsin inhibitors from various plant species. Northern-blot analysis showed that the expression of OCPI1 was strongly induced by dehydration stresses and abscisic acid (ABA). The expression of beta-glucuronidase (GUS) reporter gene under the control of OCPI1 promoter transformed into rice was strongly induced by drought and salt stresses. Interestingly, strong dehydration stress-induced GUS activity was also detected in the transgenic rice containing the reverse sequence of OCPI1 promoter fused to GUS gene, suggesting of a bidirectional transcriptional activity in the OCPI1 promoter. OCPI1 gene was over-expressed in japonica cv. Zhonghua 11 and transgenic plants containing single copy of transgene were tested for drought resistance at reproductive stage. The positive transgenic plants (OCPI1 was over-expressed) had significantly higher grain yield and seed setting rate than the wild type and the negative transgenic control (no over-expression of the transgene) under the severe drought stress conditions, whereas the potential yield of transgenic plants under normal growth conditions was not affected. Chymotrypsin-inhibitor activity assay showed that the crude protein of the positive transgenic plants had stronger inhibitory activity than the negative control. Transgenic plants had less decrease of total proteins than the wild type under drought stress. Taken together, these data indicate that OCPI1 might potentially be useful in the genetic improvement of drought resistance in rice.	OCPI1
Rice OGR1 encodes a pentatricopeptide repeat-DYW protein and is essential for RNA editing in mitochondria	2009	Plant J	Department of Integrative Bioscience and Biotechnology, National Research Laboratory of Plant Functional Genomics and Functional Genomic Center, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea.	RNA editing is the alteration of RNA sequences via insertion, deletion and conversion of nucleotides. In flowering plants, specific cytidine residues of RNA transcribed from organellar genomes are converted into uridines. Approximately 35 editing sites are present in the chloroplasts of higher plants; six pentatricopeptide repeat genes involved in RNA editing have been identified in Arabidopsis. However, although approximately 500 editing sites are found in mitochondrial RNAs of flowering plants, only one gene in Arabidopsis has been reported to be involved in such editing. Here, we identified rice mutants that are defective in seven specific RNA editing sites on five mitochondrial transcripts. Their various phenotypes include delayed seed germination, retarded growth, dwarfism and sterility. Mutant seeds from heterozygous plants are opaque. This mutation, named opaque and growth retardation 1 (ogr1), was generated by T-DNA insertion into a gene that encodes a pentatricopeptide repeat protein containing the DYW motif. The OGR1-sGFP fusion protein is localized to mitochondria. Ectopic expression of OGR1 in the mutant complements the altered phenotypes. We conclude that OGR1 is essential for RNA editing in rice mitochondria and is required for normal growth and development.	OGR1
Identification and characterization of cytokinin-signalling gene families in rice	2006	Gene	Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan.	We identified four histidine kinase (HK) genes of a cytokinin receptor family, two histidine-containing phosphotransmitter (HPt) genes, thirteen A-type response regulator (RR) genes and six B-type RR genes in the rice genome. The HK genes (OHK2, OHK3, OHK4 and OHK5 for Oryza sativa HK), the HPt genes (OHP1 and OHP2 for O. sativa HPt) and the B-type RR genes (ORR1, ORR2, ORR3, ORR4 and ORR6 for O. sativa RR) except one (ORR5) showed expression in various organs. ORR5 was expressed in callus and flower. Three A-type RR genes (OsRR4, OsRR9 and OsRR10 for O. sativa RR) showed cytokinin-induced expression, and three (OsRR8, OsRR12 and OsRR13) showed expression in flower. We also identified two other genes named OHK1 and CHARK (CHASE domain Receptor-like serine/threonine Kinase). OHK1 encodes an HK similar to Arabidopsis CKI1, which is involved in female gametophyte development. CHARK encodes a protein with an extracellular cytokinin-perceiving CHASE domain and a cytoplasmic serine/threonine kinase domain which are connected with a single transmembrane domain. The presence of all four gene families and CHARK in the rice genome suggests that a cytokinin signal is transduced by the phosphotransfer mechanism as is the case in Arabidopsis, and that rice may have an additional novel signalling pathway involving serine/threonine phosphorylation.	OHK1,OHK2|OsHk3,OHK3|OsHk5,OHK4,OHK5|OsHk6,OHP1,OHP2,OsRR1,OsRR2,OsRR3,OsRR4,OsRR5,OsRR6,OsRR7,OsRR8,OsRR9
Functional identification of OsHk6 as a homotypic cytokinin receptor in rice with preferential affinity for iP	2012	Plant Cell Physiol	Department of Life Sciences and Functional Genomics Center, Pohang University of Science and Technology, Pohang 790-784, Korea.	Cytokinins are involved in key developmental processes in rice (Oryza sativa), including the regulation of cell proliferation and grain yield. However, the in vivo action of histidine kinases (OsHks), putative cytokinin receptors, in rice cytokinin signaling remains elusive. This study examined the function and characteristics of OsHk3, 4 and 6 in rice. OsHk6 was highly sensitive to isopentenyladenine (iP) and was capable of restoring cytokinin-dependent ARR6 reporter expression in the ahk2 ahk3 Arabidopsis mutant upon treatment with 1 nM iP. OsHk4 recognized trans-zeatin (tZ) and iP, while OsHk3 scarcely induced cytokinin signaling activity. OsHk4 and OsHk6 mediated the canonical two-component signaling cascade of Arabidopsis to induce phosphorylation of ARR2. OsHk4 and OsHk6 were highly expressed in spikelets, suggesting that tZ and iP might play key roles in grain development. OsHk6 formed a self-interacting homomer in rice protoplasts, although the trans-phosphorylation activity between subunits was much lower than the intra-molecular trans-phosphorylation activity. This indicates that the action mechanism of OsHks is evolutionarily diverged from bacterial histidine kinases. Ectopic expression of OsHk6 in rice calli promoted green pigmentation and subsequent shoot induction, further supporting an OsHk6 in planta function as a cytokinin receptor. From the results of this study, OsHks are homomeric cytokinin receptors with distinctive cytokinin preferences in rice.	OHK2|OsHk3,OHK3|OsHk5,OHK4,OHK5|OsHk6
OIP30, a RuvB-like DNA helicase 2, is a potential substrate for the pollen-predominant OsCPK25/26 in rice	2011	Plant Cell Physiol	Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan, 40227 ROC.	Calcium ions are a well-known essential component for pollen germination and tube elongation. Several calcium-dependent protein kinases (CDPKs) are expressed predominantly in mature pollen grains and play a critical role in pollen. However, none of their interacting proteins or downstream substrates has been identified. Using yeast two-hybrid screening, we isolated OsCPK25/26-interacting protein 30 (OIP30), which is also predominantly expressed in pollen. OIP30 encodes a RuvB-like DNA helicase 2 (RuvBL2) that is well conserved in eukaryotic species from yeast to human. Yeast and Drosophila defective in RuvBL2 are non-viable. The interaction between OsCPK26 and OIP30 was confirmed by far-Western blot and pull-down experiments. OIP30 was phosphorylated in a calcium-dependent manner by OsCPK26 but not OsCPK2, which is highly similar to OsCPK26 in sequence and expression profile. OIP30 unwound partial duplex DNA with a 3' to 5' directionality by ATP hydrolysis. Concurrently, the ATPase activity of OIP30 depended on single-stranded DNA. OsCPK26 phosphorylated OIP30 and enhanced both its helicase and ATPase activity about 3-fold. OIP30 may be the potential downstream substrate for OsCPK25/26 in pollen. This report characterizes a RuvBL in plants and links its activities with its upstream regulator.	OIP30,OsCPK25,OsCPK26
Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice	2014	J Exp Bot	National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	MicroRNAs constitute a large group of endogenous small RNAs of ~22 nt that emerge as vital regulators, mainly by targeting mRNAs for post-transcriptional repression. Previous studies have revealed that the miR164 family in Arabidopsis is comprised of three members which guide the cleavage of the mRNAs of five NAC genes to modulate developmental processes. However, the functions of the miR164-targeted NAC genes in crops are poorly deciphered. In this study, the conserved features of six miR164-targeted NAC genes (OMTN1-OMTN6) in rice are described, and evidence is provided that four of them confer a negative regulatory role in drought resistance. OMTN proteins have the characteristics of typical NAC transcriptional factors. The miR164 recognition sites of the OMTN genes are highly conserved in rice germplasms. Deletion of the recognition sites impaired the transactivation activity, indicating that the conserved recognition sites play a crucial role in maintaining the function of the OMTN proteins. The OMTN genes were responsive to abiotic stresses, and showed diverse spatio-temporal expression patterns in rice. Overexpression of OMTN2, OMTN3, OMTN4, and OMTN6 in rice led to negative effects on drought resistance at the reproductive stage. The expression of numerous genes related to stress response, development, and metabolism was altered in OMTN2-, OMTN3-, OMTN4-, and OMTN6-overexpressing plants. Most of the up-regulated genes in the OMTN-overexpressing plants were down-regulated by drought stress. The results suggest that the conserved miR164-targeted NAC genes may be negative regulators of drought tolerance in rice, in addition to their reported roles in development.	OMTN1,OMTN3,OMTN4,OMTN6
Overexpression of a NAC transcription factor enhances rice drought and salt tolerance	2009	Biochem Biophys Res Commun	National Center for Gene Research & Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China.	The plant-specific NAC (NAM, ATAF1/2, CUC2) transcription factors play diverse roles in plant development and stress responses. In this study, a rice NAC gene, ONAC045, was functionally characterized, especially with regard to its role in abiotic stress resistance. Expression analysis revealed that ONAC045 was induced by drought, high salt, and low temperature stresses, and abscisic acid (ABA) treatment in leaves and roots. Transcriptional activation assay in yeast indicated that ONAC045 functioned as a transcriptional activator. Transient expression of GFP-ONAC045 in onion epidermal cells revealed that ONAC045 protein was localized in the nucleus. Transgenic rice plants overexpressing ONAC045 showed enhanced tolerance to drought and salt treatments. Two stress-responsive genes were upregulated in transgenic rice. Together, these results suggest that ONAC045 encodes a novel stress-responsive NAC transcription factor and is potential useful for engineering drought and salt tolerant rice.	ONAC045
Tolerance to various environmental stresses conferred by the salt-responsive rice gene ONAC063 in transgenic Arabidopsis	2009	Planta	Research Institute for Biological Sciences, Okayama, 7549-1 Yoshikawa, Kibichuo-cho, Okayama 716-1241, Japan.	Environmental stresses limit plant growth and crop production worldwide. We attempted to isolate rice genes involved in conferring tolerance to environmental stresses by using a transgenic Arabidopsis population expressing full-length cDNAs of rice. Among these lines, a thermotolerant line, R08946, was detected. The rice cDNA inserted in R08946 encoded a NAC transcription factor, ONAC063. This protein was localized in the nucleus and showed transactivation activity at the C-terminus. ONAC063 expression was not induced by high-temperature but highly induced by high-salinity in rice roots. High-osmotic pressure and reactive oxygen species levels also induced ONAC063 expression. The seeds of ONAC063-expressing transgenic Arabidopsis showed enhanced tolerance to high-salinity and osmotic pressure. Microarray and real-time reverse transcription-polymerase chain reaction analyses showed upregulated expression of some salinity-inducible genes, including the amylase gene AMY1, in ONAC063-expressing transgenic Arabidopsis. Thus, ONAC063 may play an important role in eliciting responses to high-salinity stress.	ONAC063
Functions of rice NAC transcriptional factors, ONAC122 and ONAC131, in defense responses against Magnaporthe grisea	2013	Plant Mol Biol	National Key Laboratory for Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, Zhejiang, China.	NAC (NAM/ATAF/CUC) transcription factors have important functions in regulating plant growth, development, and abiotic and biotic stress responses. Here, we characterized two rice pathogen-responsive NAC transcription factors, ONAC122 and ONAC131. We determined that these proteins localized to the nucleus when expressed ectopically and had transcriptional activation activities. ONAC122 and ONAC131 expression was induced after infection by Magnaporthe grisea, the causal agent of rice blast disease, and the M. grisea-induced expression of both genes was faster and higher in the incompatible interaction compared with the compatible interaction during early stages of infection. ONAC122 and ONAC131 were also induced by treatment with salicylic acid, methyl jasmonate or 1-aminocyclopropane-1-carboxylic acid (a precursor of ethylene). Silencing ONAC122 or ONAC131 expression using a newly modified Brome mosaic virus (BMV)-based silencing vector resulted in an enhanced susceptibility to M. grisea. Furthermore, expression levels of several other defense- and signaling-related genes (i.e. OsLOX, OsPR1a, OsWRKY45 and OsNH1) were down-regulated in plants silenced for ONAC122 or ONAC131 expression via the BMV-based silencing system. Our results suggest that both ONAC122 and ONAC131 have important roles in rice disease resistance responses through the regulated expression of other defense- and signaling-related genes.	ONAC131,ONAC122|OsNAC10,OsNPR1|NH1,OsPR1a,OsWRKY45
Molecular characterization of ONAC300, a novel NAC gene specifically expressed at early stages in various developing tissues of rice	2005	Mol Genet Genomics	Genetic Diversity Department, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.	Members of the plant-specific gene family referred to as the NAC family (for NAM-ATAF-CUC-related) are involved in various functions including the regulation of plant development. However, no detailed molecular characterization of any member of the NAC family has yet been reported from monocots. Here, we report such a characterization of ONAC300, a novel NAC-family gene identified using a cDNA cloned from microdissected phloem cells of rice. The predicted ONAC300 protein sequence falls into the NAM subgroup, which also contains the proteins CUC1 and CUC2 from Arabidopsis, CUP from snapdragon, CmNACP from pumpkin and NAM from petunia. High levels of ONAC300 mRNA were detected by in situ hybridization in developing shoot apical meristem (SAM) and in the associated young leaves. The use of an ONAC300:: GUS reporter gene revealed that the ONAC300 promoter was expressed predominantly in developing vascular tissues of the leaves and roots. The construct was also expressed in anther filaments, rachis and carpel styles. RT-PCR analysis further revealed that the levels of ONAC300 transcripts were higher in leaves, roots and culms than in panicles. The observed expression pattern of ONAC300 is quite different from those of the dicot NAC genes previously reported. Thus, ONAC300 is a novel member of the NAC family which is expressed at very early developmental stages in the shoot, root and flower, as well as in the mature phloem of vascular tissues in rice.	ONAC300
Fatty acid elongase is required for shoot development in rice	2011	Plant J	Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan. yukito@bios.tohoku.ac.jp	Organisms are covered extracellularly with cuticular waxes that consist of various fatty acids. In higher plants, extracellular waxes act as indispensable barriers to protect the plants from physical and biological stresses such as drought and pathogen attacks. However, the effect of fatty acid composition on plant development under normal growth conditions is not well understood. Here we show that the ONION1 (ONI1) gene, which encodes a fatty acid elongase (beta-ketoacyl CoA synthase) involved in the synthesis of very-long-chain fatty acids, is required for correct fatty acid composition and normal shoot development in rice. oni1 mutants containing a reduced amount of very-long-chain fatty acids produced very small shoots, with an aberrant outermost epidermal cell layer, and ceased to grow soon after germination. These mutants also showed abnormal expression of a KNOX family homeobox gene. ONI1 was specifically expressed in the outermost cell layer of the shoot apical meristem and developing lateral organs. These results show that fatty acid elongase is required for formation of the outermost cell layer, and this layer is indispensable for entire shoot development in rice.	ONI1
ONION2 fatty acid elongase is required for shoot development in rice	2013	Plant Cell Physiol	Plant Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka-ken, Japan.	A plant's surface is covered with epicuticular wax, which protects plants from inappropriate environmental conditions such as drought and pathogen attack. Very-long-chain fatty acids (VLCFAs) are the main component of epicuticular wax on the surface of above-ground organs. Here we show that a fatty acid elongase catalyzing an elongation reaction of VLCFAs is required for shoot development in rice. onion2 (oni2) mutants produced very small shoots in which leaves were fused to each other, and ceased growing after germination. The midrib of oni2 leaf blades was not developed correctly. Molecular cloning showed that ONI2 encodes a fatty acid elongase, which catalyzes the first step of elongation reactions of a carbon chain of VLCFAs, and oni2 had a reduced amount of VLCFAs. Expression analysis showed that ONI2 is specifically expressed in the outermost cell layer of young lateral organs. These results suggest that ONI2 is a layer 1-specific gene required for development of the entire shoot and that VLCFAs play an essential role in normal shoot development in rice.	ONI2
Organ fusion and defective shoot development in oni3 mutants of rice	2014	Plant Cell Physiol	Graduate School of Agricultural Science, Tohoku University, Sendai, 981-8555 Japan.	Maintenance of organ separation is one of the essential phenomena for normal plant development. We have identified and analyzed ONION3 (ONI3), which is required for avoiding organ fusions in rice. Loss-of-function mutations of ONI3, which were identified as mutants with ectopic expression of KNOX genes in leaves and morphologically resembling KNOX overexpressors, showed abnormal organ fusions in developing shoots. The mutant seedlings showed fusions between neighboring organs and also within an organ; they stopped growing soon after germination and subsequently died. ONI3 was shown to encode an enzyme that is most similar to Arabidopsis HOTHEAD and is involved in biosynthesis of long-chain fatty acids. Expression analyses showed that ONI3 was specifically expressed in the outermost cell layer in the shoot apex throughout life cycle, and the oni3 mutants had an aberrant outermost cell layer. Our results together with previous studies suggest that long-chain fatty acids are required for avoiding organ fusions and promoting normal shoot development in rice.	ONI3
Rice Rab11 is required for JA-mediated defense signaling	2013	Biochem Biophys Res Commun	Department of Molecular Biotechnology, Dong-A University, Busan 604-714, South Korea.	Rab proteins play an essential role in regulating vesicular transport in eukaryotic cells. Previously, we characterized OsRab11, which in concert with OsGAP1 and OsGDI3 regulates vesicular trafficking from the trans-Golgi network (TGN) to the plasma membrane or vacuole. To further elucidate the physiological function of OsRab11 in plants, we performed yeast two-hybrid screens using OsRab11 as bait. OsOPR8 was isolated and shown to interact with OsRab11. A co-immunoprecipitation assay confirmed this interaction. The green fluorescent protein-OsOPR8 fusion product was targeted to the cytoplasm and peroxisomes of protoplasts from Arabidopsis thaliana. OsOPR8 exhibited NADPH-dependent reduction activity when 2-cyclohexen-1-one (CyHE) and 12-oxo-phytodienoic acid (OPDA) were supplied as possible substrates. Interestingly, NADPH oxidation by OsOPR8 was increased when wild-type OsRab11 or the constitutively active form of OsRab11 (Q78L) were included in the reaction mix, but not when the dominant negative form of OsRab11 (S28N) was included. OsRab11 was expressed broadly in plants and both OsRab11 and OsOPR8 were induced by jasmonic acid (JA) and elicitor treatments. Overexpressed OsRab11 transgenic plants showed resistance to pathogens through induced expression of JA-responsive genes. In conclusion, OsRab11 may be required for JA-mediated defense signaling by activating the reducing activity of OsOPR8.	OPR8,OsRab11
Comparative characterization, expression pattern and function analysis of the 12-oxo-phytodienoic acid reductase gene family in rice	2011	Plant Cell Rep	State Key Laboratory for Biocontrol and Key Laboratory of Gene Engineering of Ministry of Education, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, People's Republic of China.	The 12-oxo-phytodienoic acid reductases (OPRs) belong to the old yellow enzyme family of flavoenzymes and form multiple subfamilies in angiosperm plants. In our previous study, a comparative genomic analysis showed that five OPR subfamilies (subs. I-V) occur in monocots, and two subfamilies (subs. I and II) in dicots. Here, a comparative study of five OsOPR genes, representing five subfamilies (I-V) in rice, was performed to provide insights into OPR biochemical properties and physiological importance. Comparative analysis of the three-dimensional structure by homology modeling indicated all five OsOPR proteins contained a highly conserved backbone with (alpha/beta)(8)-barrels, while two middle variable regions (MVR i and ii) were also detected and defined. Analysis of enzymatic characteristics revealed that all five OsOPR fusion proteins exhibit distinct substrate specificity. Different catalytic activity was observed using racemic OPDA and trans-2-hexen-1-al as substrates, suggesting OsOPR family genes participate in two main branches of the octadecanoid pathway, including the allene oxide synthase and hydroperoxide lyase pathways which regulate various developmental processes and/or defense responses. The transcript profiles of five OsOPR genes exhibited strong tissue-specific and inducible expression patterns under abiotic stress, hormones and plant wounding treatments. Furthermore, the transcriptions of OsOPR04-1 (OsOPR11) and OsOPR08-1 (OsOPR7), representing subs. I and II, respectively, were observed in all six selected tissues and with all above-stress treatments. This suggests that these two subfamilies play an important role during different developmental stages and in response to stresses; while the expressions of OsOPR06-1 (OsOPR6), OsOPR01-1 (OsOPR10) and OsOPR02-1 (OsOPR8), representing subs. III, IV and V respectively, were strongly up-regulated with abscisic acid (ABA) and indoleacetic acid (IAA) treatments in roots, suggesting these three subfamilies play an important role in responding to hormones especially ABA and IAA signals in roots.	OPR8
Identification of the OsOPR7 gene encoding 12-oxophytodienoate reductase involved in the biosynthesis of jasmonic acid in rice	2007	Planta	Biotechnology Research Center, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan.	Enzyme 12-oxophytodienoate (OPDA) reductase (EC1.3.1.42), which is involved in the biosynthesis of jasmonic acid (JA), catalyses the reduction of 10, 11-double bonds of OPDA to yield 3-oxo-2-(2'-pentenyl)-cyclopentane-1-octanoic acid (OPC-8:0). The rice OsOPR1 gene encodes OPDA reductase (OPR) converting (-)-cis-OPDA preferentially, rather than (+)-cis-OPDA, a natural precursor of JA. Here, we provide evidence that an OPR family gene in rice chromosome 8, designated OsOPR7, encodes the enzyme involved in the JA biosynthesis. Recombinant OsOPR7-His protein efficiently catalysed the reduction of both enantiomers of cis-OPDA, similar to the OPR3 protein in Arabidopsis thaliana (L.) Heynh. The expression of OsOPR7 mRNA was induced and reached maximum levels within 0.5 h of mechanical wounding and drought stress, and the endogenous JA level started to increase in accordance with the increase in OsOPR7 expression. The GFP-OsOPR7 fusion protein was detected exclusively in peroxisomes in onion epidermal cells. Furthermore, complementation analysis using an Arabidopsis opr3 mutant indicated that the OsOPR7 gene, but not OsOPR1, was able to complement the phenotypes of male sterility in the mutant caused by JA deficiency, and that JA production in the opr3 mutant was also restored by the expression of the OsOPR7 gene. We conclude that the OsOPR7 gene encodes the enzyme catalysing the reduction of natural (+)-cis-OPDA for the JA biosynthesis in rice.	OPR8
OsTZF1, a CCCH-tandem zinc finger protein, confers delayed senescence and stress tolerance in rice by regulating stress-related genes	2013	Plant Physiol	Biological Resources and Post-harvest Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Ibaraki 305-8686, Japan.	OsTZF1 is a member of the CCCH-type zinc finger gene family in rice (Oryza sativa). Expression of OsTZF1 was induced by drought, high-salt stress, and hydrogen peroxide. OsTZF1 gene expression was also induced by abscisic acid, methyl jasmonate, and salicylic acid. Histochemical activity of beta-glucuronidase in transgenic rice plants containing the promoter of OsTZF1 fused with beta-glucuronidase was observed in callus, coleoptile, young leaf, and panicle tissues. Upon stress, OsTZF1-green fluorescent protein localization was observed in the cytoplasm and cytoplasmic foci. Transgenic rice plants overexpressing OsTZF1 driven by a maize (Zea mays) ubiquitin promoter (Ubi:OsTZF1-OX [for overexpression]) exhibited delayed seed germination, growth retardation at the seedling stage, and delayed leaf senescence. RNA interference (RNAi) knocked-down plants (OsTZF1-RNAi) showed early seed germination, enhanced seedling growth, and early leaf senescence compared with controls. Ubi:OsTZF1-OX plants showed improved tolerance to high-salt and drought stresses and vice versa for OsTZF1-RNAi plants. Microarray analysis revealed that genes related to stress, reactive oxygen species homeostasis, and metal homeostasis were regulated in the Ubi:OsTZF1-OX plants. RNA-binding assays indicated that OsTZF1 binds to U-rich regions in the 3' untranslated region of messenger RNAs, suggesting that OsTZF1 might be associated with RNA metabolism of stress-responsive genes. OsTZF1 may serve as a useful biotechnological tool for the improvement of stress tolerance in various plants through the control of RNA metabolism of stress-responsive genes.	OPT|OsOPT7,OsTZF1,akin-b|akin-beta
Characterization of the origin recognition complex (ORC) from a higher plant, rice (Oryza sativa L.)	2005	Gene	Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo, 2641 Yamazaki, Noda-shi, Chiba-ken 278-8510, Japan.	The origin recognition complex (ORC) protein plays a critical role in DNA replication through binding to sites (origins) where replication commences. The protein is composed of six subunits (ORC1 to 6) in animals and yeasts. Our knowledge of the ORC protein in plants is, however, much less complete. We have performed cDNA cloning and characterization of ORC subunits in rice (Oryza sativa L. cv. Nipponbare) in order to facilitate study of plant DNA replication mechanisms. Our previous report provided a description of a gene, ORC1 (OsORC1), that encodes one of the protein subunits. The present report extends this initial analysis to include the genes that encode four other rice ORC subunits, OsORC2, 3, 4 and 5. Northern hybridization analyses demonstrated the presence of abundant transcripts for all OsORC subunits in shoot apical meristems (SAM) and cultured cells, but not in mature leaves. Interestingly, only OsORC5 showed high levels of expression in organs in which cell proliferation is not active, such as flag leaves, the ears and the non-tip roots. The pattern of expression of OsORC2 also differed from other OsORC subunits. When cell proliferation was temporarily halted for 6-10 days by removal of sucrose from the growth medium, expression of OsORC1, OsORC3, OsORC4 and OsORC5 was substantially reduced. However, the level of expression of OsORC2 remained constant. We suggest from these results that expression of OsORC1, 3, 4 and 5 are correlated with cell proliferation, but the expression of OsORC2 is not.	OsORC4,OsORC5
Cloning, expression and immunological characterization of Ory s 1, the major allergen of rice pollen	1995	Gene	School of Botany, University of Melbourne, Parkville, Victoria, Australia.	We have isolated and characterized a cDNA clone, Ory s 1, encoding a group-1 allergen of rice pollen. The Ory s 1 protein shows significant sequence identity to the major allergen of rye-grass pollen, Lol p 1. RNA gel blot analysis shows that the Ory s 1 gene is expressed in mature anthers, but not in vegetative or other floral tissues tested. Southern blot analysis indicates that this clone represents a member of a small gene family in rice. Western blot analyses of total rice pollen proteins with the group-1 allergen-specific monoclonal 3A2 and IgE antibodies from grass pollen-allergic patients, revealed the presence of cross-reactive antigenic and allergenic epitopes in Ory s 1.	Orys1
Agrobacterium-mediated transformation of Australian rice varieties and promoter analysis of major pollen allergen gene, Ory s 1	2011	Plant Cell Rep	Plant Molecular Biology and Biotechnology Laboratory, Melbourne School of Land and Environment, The University of Melbourne, Parkville, VIC 3010, Australia.	A simple protocol for Agrobacterium-mediated transformation of Australian rice using mature embryos is described. Transgenic plants of two commercial genotypes of Australian rice, Amaroo and Millin, were produced. Transgenic plants were obtained by applying selection pressure to callus and to the regenerated shoots. Exclusion of the selective agent (hygromycin) during plant regeneration was found to be critical for recovery of transgenic plants from these commercial varieties. Transgenic plants were produced after 3 months. The developed system was also used to study spatial and temporal expression of a rice pollen-specific gene, Ory s 1. Expression of pOry s 1::uidA in transgenic rice demonstrated GUS expression in mature pollen, hence indicating potential use of this promoter to direct pollen-specific gene expression. Further Ory s 1 5' deletion study indicated that the pollen-specificity element may reside within -405 bp to the start of the transcription, while the region upstream of -405 contained a cis-acting regulatory element(s) responsible for quantitative expression of this gene.	Orys1
Interacting proteins and differences in nuclear transport reveal specific functions for the NAP1 family proteins in plants	2005	Plant Physiol	State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433, People's Republic of China. awdong001@yahoo.com.cn	Nucleosome assembly protein 1 (NAP1) is conserved from yeast to human and facilitates the in vitro assembly of nucleosomes as a histone chaperone. Inconsistent with their proposed function in the nucleus, however, many NAP1 proteins had been reported to localize in the cytoplasm. We investigated the subcellular localization of tobacco (Nicotiana tabacum) and rice (Oryza sativa) NAP1 family proteins first by identification of interacting partners and by direct examination of the localization of green fluorescent protein-tagged proteins. Through treatment of tobacco cells with leptomycin B and mutagenesis of nuclear export signal, we demonstrated that Nicta;NAP1;1 and Orysa;NAP1;1 shuttle between the cytoplasm and the nucleus. Together with the demonstration that tobacco NAP1 proteins bind histone H2A and H2B, our results support the current model and provide additional evidence that function of NAP1 as histone chaperones appears to be conserved in plants. In addition, we show that tobacco NAP1 proteins interact with tubulin and the mitotic cyclin Nicta;CYCB1;1, suggesting a role for NAP1 in microtubule dynamics. Interestingly, in spite of their high homology with the above NAP1 proteins, the other three tobacco proteins and Orysa;NAP1;2 did not show nucleocytoplasmic shuttling and were localized only in the cytoplasm. Moreover, Orysa;NAP1;3 that lacks a typical nuclear localization signal sequence was localized in both the cytoplasm and the nucleus. Finally, we show that only Orysa;NAP1;3 could be phosphorylated by casein kinase 2alpha in vitro. However, this phosphorylation was not responsible for nuclear import of Orysa;NAP1;3 as being demonstrated through mutagenesis studies. Together, our results provide an important step toward elucidating the molecular mechanism of function of the NAP1 family proteins in plants.	Orysa;NAP1;1|OsNAP1_L1,Orysa;NAP1;2|OsNAP1_L2,Orysa;NAP1;3|OsNAP1_L3
Rice Aspartic Proteinase, Oryzasin, Expressed During Seed Ripening and Germination, has a Gene Organization Distinct from Those of Animal and Microbial Aspartic Proteinases	1995	European Journal of Biochemistry	Laboratory for Food Science, Atomi Junior College, Tokyo, Japan.	The gene organization and nucleotide sequence of an aspartic proteinase (AP) of plant origin were first disclosed by cDNA and genomic DNA cloning of a rice AP (oryzasin). The deduced amino acid sequence of oryzasin 1 was significantly similar to those of other APs (34-85%), with highest similarity (85%) to barley AP (HvAP). Oryzasin 1, as well as HvAP, is distinct from animal and microbial APs in that the plant APs contain a unique 104-amino-acid insertion in the C-terminal region. The oryzasin 1 gene spans approximately 6.6 kbp and is composed of 14 exons and 13 introns. The exon-intron organization of the oryzasin 1 gene is totally different from those of genes for animal and microbial APs such as human cathepsin D, rat renin, bovine chymosin, aspergillopepsin A of Aspergillus awamori, proteinase A of Saccharomyces cerevisiae and rhizopuspepsin of Rhizopus niveus, despite the fact that oryzasin 1 shows overall sequence similarity to these APs.	Oryzasin
OsAP65, a rice aspartic protease, is essential for male fertility and plays a role in pollen germination and pollen tube growth	2013	J Exp Bot	National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.	Aspartic proteases (APs) comprise a large proteolytic enzyme family widely distributed in animals, microbes, viruses, and plants. The rice genome encodes 96 APs, of which only a few have been functionally characterized. Here, the identification and characterization of a novel AP gene, OsAP65, which plays an indispensable role in pollen tube growth in rice, is reported. The T-DNA insertion line of OsAP65 caused severe segregation distortion. In the progeny derived from an individual heterozygous for the T-DNA insertion, the wild type and T-DNA-carrying heterozygote segregated at a ratio close to 1:1, while homozygotes of disrupted OsAP65 (OsAP65-/-) were not recovered. Reciprocal crosses between heterozygotes and wild-type plants demonstrated that the mutant alleles could not be transmitted through the male gamete. Examination of the anthers from heterozygous plants revealed that the mutant pollen matured normally, but did not germinate or elongate. OsAP65 was expressed in various tissues and the transcript level in heterozygous plants was about half of the amount measured in the wild-type plants. The subcellular localization showed that OsAP65 is a pre-vacuolar compartment (PVC) protein. These results indicated that OsAP65 was essential for rice pollen germination and tube growth.	Oryzasin,OsAP65
OVP1, a vacuolar H+-translocating inorganic pyrophosphatase (V-PPase), overexpression improved rice cold tolerance	2011	Plant Physiol Biochem	State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100094, China.	Vacuolar H(+)-translocating inorganic pyrophosphatase (V-PPase, EC 3.6.1.1) is an electrogenic proton pump and has been studied in many plants. Here we report characterization of the OVP1 gene from rice (Oryza sativa L.). Quantitative reverse transcriptase-polymerase chain reaction analysis (RT-qPCR) showed that OVP1 was induced by cold stress. OVP1 overexpression resulted in enhanced cold tolerance in transgenic rice, which was related to an increased integrity of cell membrane, decreased MDA content and accumulation of proline to higher level as compared with wild type rice seedlings. These results indicated that V-PPase was an important element in the survival strategies of plants under cold stress.	OVP1
Isolation and characterization of cDNAs encoding vacuolar H+-pyrophosphatase isoforms from rice (Oryza sativa L.)	1996	Plant Mol Biol	Molecular Function Laboratory, National Food Research Institute, 2-1-2 Kannondai, 305, Tsukuba, Ibaraki, Japan	The vacuolar H(+)-pyrophosphatase (V-PPase) is an electrogenic H+ pump, which was found in the plant vacuolar membrane. Two cDNA clones (OVP1 and OVP2) encoding the V-PPase were isolated from cultured rice (Oryza sativa L.) cells and subsequently sequenced. The sequence analysis has revealed that OVP1 contains 2316 nucleotides of open reading frame (ORF) and 362 nucleotides of the 3'-untranslated region, whereas OVP2 comprises 2304 nucleotides of ORF and 312 nucleotides of the 3'-untranslated region. The nucleotide sequences of ORF of OVP1 and OVP2 are 80.7% identical, and their 5'- and 3'-untranslated regions have 39.4% and 48.4% identity, respectively. The polypeptides encoded by the ORF of OVP1 and OVP2 contain 771 and 767 amino acids, respectively, and the sequences of the OVP proteins are very similar to those of other V-PPases, which are shown to have 85-91% homology. Chromosomal mapping by RFLP techniques demonstrates that OVP1 and OVP2 are isoforms encoded by different genes. Both OVP1 and OVP2 are mapped on the same chromosome (chromosome 6) to a distance of ca.90 cM. Northern analysis indicates that the OVP1 and OVP2 are also expressed in intact rice plants and OVP2 shows higher expression in the calli than the roots and shoots, compared to OVP1. These results show that at least two genes encoding the V-PPases are present in rice genome and their expressions are probably regulated in a different manner.	OVP2
Expression of vacuolar H+-pyrophosphatase (OVP3) is under control of an anoxia-inducible promoter in rice	2010	Plant Mol Biol	Department of Biological Sciences, Macquarie University, Sydney, NSW, 2109, Australia.	Vacuolar H(+)-pyrophosphatase (V-PPase) expression increases in a number of abiotic stresses and is thought to play a role in adaptation to abiotic stresses. This paper reports on the regulation of six V-PPase genes in rice (Oryza sativa L.) coleoptiles under anoxia, using flood tolerant and intolerant cultivars to test our hypothesis. Quantitative PCR analysis showed that one vacuolar H(+)-pyrophosphatase (OVP3) was induced by anoxia, particularly in flood-tolerant rice. Regulation of OVP3 expression under anoxia was investigated by analysing putative OVP promoters. The putative OVP3 promoter contained more previously identified anoxia-inducible motifs than the putative promoters of the other five OVP genes. GUS activity in transgenic rice plants containing the OVP3 promoter region linked to the GUS reporter gene was induced only by anoxia. Salt and cold treatments had little effect on OVP3 promoter-driven GUS expression when compared to the anoxic treatment.	OVP3
Os11Gsk gene from a wild rice, Oryza rufipogon improves yield in rice	2012	Funct Integr Genomics	Biotechnology Unit, Directorate of Rice Research, Rajendranagar, Hyderabad 500 030, India.	Chromosomal segments from wild rice species Oryza rufipogon, introgressed into an elite indica rice restorer line (KMR3) using molecular markers, resulted in significant increase in yield. Here we report the transcriptome analysis of flag leaves and fully emerged young panicles of one of the high yielding introgression lines IL50-7 in comparison to KMR3. A 66-fold upregulated gene Os11Gsk, which showed no transcript in KMR3 was highly expressed in O. rufipogon and IL50-7. A 5-kb genomic region including Os11Gsk and its flanking regions could be PCR amplified only from IL50-7, O. rufipogon, japonica varieties of rice-Nipponbare and Kitaake but not from the indica varieties, KMR3 and Taichung Native-1. Three sister lines of IL50-7 yielding higher than KMR3 showed presence of Os11Gsk, whereas the gene was absent in three other ILs from the same cross having lower yield than KMR3, indicating an association of the presence of Os11Gsk with high yield. Southern analysis showed additional bands in the genomic DNA of O. rufipogon and IL50-7 with Os11Gsk probe. Genomic sequence analysis of ten highly co-expressed differentially regulated genes revealed that two upregulated genes in IL50-7 were derived from O. rufipogon and most of the downregulated genes were either from KMR3 or common to KMR3, IL50-7, and O. rufipogon. Thus, we show that Os11Gsk is a wild rice-derived gene introduced in KMR3 background and increases yield either by regulating expression of functional genes sharing homology with it or by causing epigenetic modifications in the introgression line.	Os11Gsk
Transcription activator-like (TAL) effectors targeting OsSWEET genes enhance virulence on diverse rice (Oryza sativa) varieties when expressed individually in a TAL effector-deficient strain of Xanthomonas oryzae	2012	New Phytol	Department of Bioagricultural Sciences and Pest Management, Colorado State University, Fort Collins, CO 80523-1177, USA.	Genomes of the rice (Oryza sativa) xylem and mesophyll pathogens Xanthomonas oryzae pv. oryzae (Xoo) and pv. oryzicola (Xoc) encode numerous secreted transcription factors called transcription activator-like (TAL) effectors. In a few studied rice varieties, some of these contribute to virulence by activating corresponding host susceptibility genes. Some activate disease resistance genes. The roles of X. oryzae TAL effectors in diverse rice backgrounds, however, are poorly understood. Xoo TAL effectors that promote infection by activating SWEET sucrose transporter genes were expressed in TAL effector-deficient X. oryzae strain X11-5A, and assessed in 21 rice varieties. Some were also tested in Xoc on variety Nipponbare. Several Xoc TAL effectors were tested in X11-5A on four rice varieties. Xoo TAL effectors enhanced X11-5A virulence on most varieties, but to varying extents depending on the effector and variety. SWEET genes were activated in all tested varieties, but increased virulence did not correlate with activation level. SWEET activators also enhanced Xoc virulence on Nipponbare. Xoc TAL effectors did not alter X11-5A virulence. SWEET-targeting TAL effectors contribute broadly and non-tissue-specifically to virulence in rice, and their function is affected by host differences besides target sequences. Further, the utility of X11-5A for characterizing individual TAL effectors in rice was established.	Os11N3,Os8N3|xa13
Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3	2010	Plant Cell	Department of Plant Pathology, Kansas State University, Manhattan, Kansas 66506, USA.	The rice (Oryza sativa) gene xa13 is a recessive resistance allele of Os-8N3, a member of the NODULIN3 (N3) gene family, located on rice chromosome 8. Os-8N3 is a susceptibility (S) gene for Xanthomonas oryzae pv oryzae, the causal agent of bacterial blight, and the recessive allele is defeated by strains of the pathogen producing any one of the type III effectors AvrXa7, PthXo2, or PthXo3, which are all members of the transcription activator-like (TAL) effector family. Both AvrXa7 and PthXo3 induce the expression of a second member of the N3 gene family, here named Os-11N3. Insertional mutagenesis or RNA-mediated silencing of Os-11N3 resulted in plants with loss of susceptibility specifically to strains of X. oryzae pv oryzae dependent on AvrXa7 or PthXo3 for virulence. We further show that AvrXa7 drives expression of Os-11N3 and that AvrXa7 interacts and binds specifically to an effector binding element within the Os-11N3 promoter, lending support to the predictive models for TAL effector binding specificity. The result indicates that variations in the TAL effector repetitive domains are driven by selection to overcome both dominant and recessive forms of resistance to bacterial blight in rice. The finding that Os-8N3 and Os-11N3 encode closely related proteins also provides evidence that N3 proteins have a specific function in facilitating bacterial blight disease.	Os11N3,Os8N3|xa13
Structural and enzymatic characterization of Os3BGlu6, a rice beta-glucosidase hydrolyzing hydrophobic glycosides and (1->3)- and (1->2)-linked disaccharides	2009	Plant Physiol	School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.	Glycoside hydrolase family 1 (GH1) beta-glucosidases play roles in many processes in plants, such as chemical defense, alkaloid metabolism, hydrolysis of cell wall-derived oligosaccharides, phytohormone regulation, and lignification. However, the functions of most of the 34 GH1 gene products in rice (Oryza sativa) are unknown. Os3BGlu6, a rice beta-glucosidase representing a previously uncharacterized phylogenetic cluster of GH1, was produced in recombinant Escherichia coli. Os3BGlu6 hydrolyzed p-nitrophenyl (pNP)-beta-d-fucoside (k(cat)/K(m) = 67 mm(-1) s(-1)), pNP-beta-d-glucoside (k(cat)/K(m) = 6.2 mm(-1) s(-1)), and pNP-beta-d-galactoside (k(cat)/K(m) = 1.6 mm(-1)s(-1)) efficiently but had little activity toward other pNP glycosides. It also had high activity toward n-octyl-beta-d-glucoside and beta-(1-->3)- and beta-(1-->2)-linked disaccharides and was able to hydrolyze apigenin beta-glucoside and several other natural glycosides. Crystal structures of Os3BGlu6 and its complexes with a covalent intermediate, 2-deoxy-2-fluoroglucoside, and a nonhydrolyzable substrate analog, n-octyl-beta-d-thioglucopyranoside, were solved at 1.83, 1.81, and 1.80 A resolution, respectively. The position of the covalently trapped 2-F-glucosyl residue in the enzyme was similar to that in a 2-F-glucosyl intermediate complex of Os3BGlu7 (rice BGlu1). The side chain of methionine-251 in the mouth of the active site appeared to block the binding of extended beta-(1-->4)-linked oligosaccharides and interact with the hydrophobic aglycone of n-octyl-beta-d-thioglucopyranoside. This correlates with the preference of Os3BGlu6 for short oligosaccharides and hydrophobic glycosides.	Os3BGlu6,Os3BGlu7
Rice family GH1 glycoside hydrolases with beta-D-glucosidase and beta-D-mannosidase activities	2009	Arch Biochem Biophys	School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand.	Plant beta-D-mannosidases and a rice beta-D-glucosidase, Os3BGlu7, with weak beta-D-mannosidase activity, cluster together in phylogenetic analysis. To investigate the relationship between substrate specificity and amino acid sequence similarity in family GH1 glycoside hydrolases, Os3BGlu8 and Os7BGlu26, putative rice beta-D-glucosidases from this cluster, and a beta-D-mannosidase from barley (rHvBII), were expressed in Escherichia coli and characterized. Os3BGlu8, the amino acid sequence and molecular model of which are most similar to Os3BGlu7, hydrolysed 4-nitrophenyl-beta-D-glucopyranoside (4NPGlc) faster than 4-nitrophenyl-beta-D-mannopyranoside (4NPMan), while Os7BGlu26, which is most similar to rHvBII by these criteria, hydrolysed 4NPMan faster than 4NPGlc. All the enzymes hydrolyzed cellooligosaccharides with increased hydrolytic rates as the degree of polymerization increased from 3-6, but only rHvBII hydrolyzed cellobiose with a higher k(cat)/K(m) value than cellotriose. This was primarily due to strong binding of glucosyl residues at the+2 subsite for the rice enzymes, and unfavorable interactions at this subsite with rHvBII.	Os3BGlu7,Os3BGlu8,Os7BGlu26
The crystal structure of rice (Oryza sativa L.) Os4BGlu12, an oligosaccharide and tuberonic acid glucoside-hydrolyzing beta-glucosidase with significant thioglucohydrolase activity	2011	Arch Biochem Biophys	Institute of Science, Schools of Biochemistry and Chemistry, Suranaree University of Technology, Nakhon Ratchasima, Thailand.	Rice Os4BGlu12, a glycoside hydrolase family 1 (GH1) beta-glucosidase, hydrolyzes beta-(1,4)-linked oligosaccharides of 3-6 glucosyl residues and the beta-(1,3)-linked disaccharide laminaribiose, as well as certain glycosides. The crystal structures of apo Os4BGlu12, and its complexes with 2,4-dinitrophenyl-2-deoxyl-2-fluoroglucoside (DNP2FG) and 2-deoxy-2-fluoroglucose (G2F) were solved at 2.50, 2.45 and 2.40A resolution, respectively. The overall structure of rice Os4BGlu12 is typical of GH1 enzymes, but it contains an extra disulfide bridge in the loop B region. The glucose ring of the G2F in the covalent intermediate was found in a (4)C(1) chair conformation, while that of the noncovalently bound DNP2FG had a (1)S(3) skew boat, consistent with hydrolysis via a (4)H(3) half-chair transition state. The position of the catalytic nucleophile (Glu393) in the G2F structure was more similar to that of the Sinapsis alba myrosinase G2F complex than to that in covalent intermediates of other O-glucosidases, such as rice Os3BGlu6 and Os3BGlu7 beta-glucosidases. This correlated with a significant thioglucosidase activity for Os4BGlu12, although with 200- to 1200-fold lower k(cat)/K(m) values for S-glucosides than the comparable O-glucosides, while hydrolysis of S-glucosides was undetectable for Os3BGlu6 and Os3BGlu7.	Os4BGlu12
Rice Os4BGlu12 is a wound-induced beta-glucosidase that hydrolyzes cell wall-beta-glucan-derived oligosaccharides and glycosides	2010	Plant Science	School of Biochemistry, Institute of Science, Suranaree University of Technology, Muang District, Nakhon Ratchasima 30000, Thailand	Rice Os4BGlu12 beta-glucosidase is a family 1 glycoside hydrolase, the transcript levels of which have previously been found to be induced in response to herbivore attack and salinity stress. Here, high levels of Os4bglu12 transcripts were also detected in the shoot during germination, in the leaf sheath and stem of mature rice plants under normal growth conditions. The transcripts of this gene were up-regulated in response to wounding, methyl jasmonate and ethephon in 10-day-old rice seedlings. Os4BGlu12 expressed in recombinant Escherichia coli hydrolyzed beta-(1,3;1,4)-glucooligosaccharides generated by the wounding-induced rice endo-(1,3;1,4)-beta-glucanase OsEGL1, suggesting that both enzymes may act in concert in remodeling of damaged cell wall. Among oligosaccharides tested, Os4BGlu12 hydrolyzed beta-(1,4)-linked glucooligosaccharides with highest catalytic efficiency (kcat/Km = 2.7–4.9 s−1 mM−1) when the degree of polymerization ranged from 3 to 6. It also hydrolyzed the beta-(1,3)-linked disaccharide laminaribiose with high catalytic efficiency (kcat/Km = 4.5 s−1 mM−1). Among the natural glycosides tested, Os4BGlu12 efficiently hydrolyzed deoxycorticosterone 21-glucoside (kcat/Km = 20 s−1 mM−1) and apigenin 7-O-beta-d-glucoside (kcat/Km = 6.7 s−1 mM−1). The amino acid residues predicted to line the active site of Os4BGlu12 are more similar to those of cyanogenic and flavonoid beta-glucosidases than oligosaccharide hydrolases, and it may function in defense, as well as in cell wall-derived oligosaccharide break-down.	Os4BGlu12
Analysis of rice glycosyl hydrolase family 1 and expression of Os4bglu12 beta-glucosidase	2006	BMC Plant Biol	Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand. opassiri@hotmail.com <opassiri@hotmail.com>	BACKGROUND: Glycosyl hydrolase family 1 (GH1) beta-glucosidases have been implicated in physiologically important processes in plants, such as response to biotic and abiotic stresses, defense against herbivores, activation of phytohormones, lignification, and cell wall remodeling. Plant GH1 beta-glucosidases are encoded by a multigene family, so we predicted the structures of the genes and the properties of their protein products, and characterized their phylogenetic relationship to other plant GH1 members, their expression and the activity of one of them, to begin to decipher their roles in rice. RESULTS: Forty GH1 genes could be identified in rice databases, including 2 possible endophyte genes, 2 likely pseudogenes, 2 gene fragments, and 34 apparently competent rice glycosidase genes. Phylogenetic analysis revealed that GH1 members with closely related sequences have similar gene structures and are often clustered together on the same chromosome. Most of the genes appear to have been derived from duplications that occurred after the divergence of rice and Arabidopsis thaliana lineages from their common ancestor, and the two plants share only 8 common gene lineages. At least 31 GH1 genes are expressed in a range of organs and stages of rice, based on the cDNA and EST sequences in public databases. The cDNA of the Os4bglu12 gene, which encodes a protein identical at 40 of 44 amino acid residues with the N-terminal sequence of a cell wall-bound enzyme previously purified from germinating rice, was isolated by RT-PCR from rice seedlings. A thioredoxin-Os4bglu12 fusion protein expressed in Escherichia coli efficiently hydrolyzed beta-(1,4)-linked oligosaccharides of 3-6 glucose residues and laminaribiose. CONCLUSION: Careful analysis of the database sequences produced more reliable rice GH1 gene structure and protein product predictions. Since most of these genes diverged after the divergence of the ancestors of rice and Arabidopsis thaliana, only a few of their functions could be implied from those of GH1 enzymes from Arabidopsis and other dicots. This implies that analysis of GH1 enzymes in monocots is necessary to understand their function in the major grain crops. To begin this analysis, Os4bglu12 beta-glucosidase was characterized and found to have high exoglucanase activity, consistent with a role in cell wall metabolism.	Os4BGlu12
Expression, purification, crystallization and preliminary X-ray analysis of rice (Oryza sativa L.) Os4BGlu12 beta-glucosidase	2010	Acta Crystallogr Sect F Struct Biol Cryst Commun	School of Biochemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.	Rice (Oryza sativa L.) Os4BGlu12, a glycoside hydrolase family 1 beta-glucosidase (EC 3.2.1.21), was expressed as a fusion protein with an N-terminal thioredoxin/His(6) tag in Escherichia coli strain Origami B (DE3) and purified with subsequent removal of the N-terminal tag. Native Os4BGlu12 and its complex with 2,4-dinitrophenyl-2-deoxy-2-fluoro-beta-D-glucopyranoside (DNP2FG) were crystallized using 19% polyethylene glycol (3350 or 2000, respectively) in 0.1 M Tris-HCl pH 8.5, 0.16 M NaCl at 288 K. Diffraction data sets for the apo and inhibitor-bound forms were collected to 2.50 and 2.45 A resolution, respectively. The space group and the unit-cell parameters of the crystal indicated the presence of two molecules per asymmetric unit, with a solvent content of 50%. The structure of Os4BGlu12 was successfully solved in space group P4(3)2(1)2 by molecular replacement using the white clover cyanogenic beta-glucosidase structure (PDB code 1cbg) as a search model.	Os4BGlu12
Functional characterization of evolutionarily