Citations

Please cite our paper if you use the funRiceGenes database in your study!

Publications that cite the funRiceGenes database:

• Cai et al. Revisiting regulatory coherence: accounting for temporal bias in plant gene co-expression analyses, 2023, New Phytologist.
• Nguyen et al. Genome-Wide Transcriptome Analysis of Rice Transporters and Its Application to Elucidate the Uncharacterized Functions of OsABCC7 Gene Using the CRISPR/Cas9 System, 2023, Journal of Plant Biology.
• Sun et al. Dissecting the genetic basis of heterosis in elite super-hybrid rice, 2023, Plant Physiology.
• Guo et al. The translational landscape of bread wheat during grain development, 2023, The Plant Cell.
• Mahto et al. Cytological, transcriptome and miRNome temporal landscapes decode enhancement of rice grain size, 2023, BMC Biology.
• Lee et al. Identifying QTLs Related to Grain Filling Using a Doubled Haploid Rice (Oryza sativa L.) Population, 2023, Agronomy.
• Zhang et al. Rice3K56 is a high-quality SNP array for genome-based genetic studies and breeding in rice (Oryza sativa L.), 2023, The Crop Journal.
• Pang et al. Genome-wide differences of alternative splicing between Oryza sativa ssp. indica and Oryza sativa ssp. japonica, 2023, Acta Physiologiae Plantarum.
• Zhang et al. Genome-wide association and epistasis studies reveal the genetic basis of saline-alkali tolerance at the germination stage in rice, 2023, Frontiers in Plant Science.
• Adam et al. African rice (Oryza glaberrima) genomic introgressions impacting upon panicle architecture in Asian rice (O. sativa) lead to the identification of key QTLs, 2023, Research Square.
• Li et al. Integrating GWAS and transcriptomics to identify candidate genes conferring heat tolerance in rice, 2023, Frontiers in Plant Science.
• Beye et al. Traces of introgression from cAus into tropical Japonica observed in African upland rice varieties, 2023, Rice.
• Rahimi et al. Genome-wide association study to identify genomic loci associated with early vigor in bread wheat under simulated water deficit complemented with quantitative trait loci meta-analysis, 2023, G3: Genes|Genomes|Genetics.
• Liu et al. 作物种业发展态势分析, 2022, 科技导报.
• Beye et al. Traces of introgression from cAus into tropical Japonica observed in African upland rice varieties, 2022, Research Square.
• Ahmad et al. Genomics and transcriptomics to protect rice (Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger, 2022, Frontiers in Plant Science.
• Muvunyi et al. Identification of Potential Zinc Deficiency Responsive Genes and Regulatory Pathways in Rice by Weighted Gene Co-expression Network Analysis, 2022, Rice Science.
• Hackauf et al. Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding, 2022, Plants.
• Zhang et al. The genetic basis for panicle trait variation in switchgrass (Panicum virgatum), 2022, Theoretical and Applied Genetics.
• Kingsley et al. Genetic Improvement of Minor Crop Legumes: Prospects of De Novo Domestication, 2022, Legumes Research - Volume 1.
• Aglyamova et al. Growing Maize Root: Lectins Involved in Consecutive Stages of Cell Development, 2022, Plants.
• Fu et al. Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis, 2022, BMC Plant Biology.
• Chen et al. The T. ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1, 2022, Theoretical and Applied Genetics.
• Huang et al. Genetic Analysis of a Collection of Rice Germplasm (Oryza sativa L.) through High-Density SNP Array Provides Useful Information for Further Breeding Practices, 2022, Genes.
• Hong et al. Comparative transcriptome analysis of pollen and anther wall reveals novel insights into the regulatory mechanisms underlying anther wall development and its dehiscence in rice, 2022, Plant Cell Reports.
• Pinit et al. Hyperspectral and genome-wide association analyses of leaf phosphorus status in local Thai indica rice, 2022, PLoS ONE.
• Mei et al. Combining Genome-Wide Association Study and Gene-Based Haplotype Analysis to Identify Candidate Genes for Alkali Tolerance at the Germination Stage in Rice, 2022, Frontiers in Plant Science.
• Yu et al. Genome-wide Association Study and Genomic Prediction for Yield and Grain Quality Traits of Hybrid Rice, 2022, Molecular Breeding.
• Rana et al. Deciphering Haplotypic Variation and Gene Expression Dynamics Associated with Nutritional and Cooking Quality in Rice, 2022, Cells.
• Waseem et al. Advances in Integrated High-Throughput and Phenomics Application in Plants and Agriculture, 2022, Principles and Practices of OMICS and Genome Editing for Crop Improvement.
• Wittern et al. Overexpression of the WAPO-A1 gene increases the number of spikelets per spike in bread wheat, 2022, bioRxiv.
• Liu et al. CG and CHG Methylation Contribute to the Transcriptional Control of OsPRR37-Output Genes in Rice, 2022, Frontiers in Plant Science.
• Soto et al. Rice agronomic traits and variability induced by mutagenesis, 2022, Research Square.
• Wang et al. Sympatric genetic divergence between early- and late-season weedy rice populations, 2022, New Phytologist.
• Yang et al. Coordinating High Yield and Superior Eating Quality of Rice: A Case Study of Hybrid Varieties Derived from Longke638S and Jing4155S, 2022, Agronomy.
• Abdirad et al. Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation, 2022, Frontiers in Plant Science.
• Taagen et al. Counting on Crossovers: Insights into Gene Mapping and Controlled Recombination for Allopolyploid Plant Breeding, 2022, Cornell University.
• Vasumathy et al. SSR Marker Based Genetic Diversity Analysis and SNP Haplotyping of Genes Associating Abiotic and Biotic Stress Tolerance, Rice Growth and Development and Yield Across 93 Rice Landraces, 2021, Molecular Biology Reports.
• Zhang et al. A Graph-based Approach for Integrating Biological Heterogeneous Data Based on Connecting Ontology, 2021, 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM).
• Cai et al. Revisiting regulatory decoherence and phenotypic integration: accounting for temporal bias in co-expression analyses, 2022, bioRxiv.
• Cross et al. Grain dispersal mechanism in cereals arose from a genome duplication followed by changes in spatial expression of genes involved in pollen development, 2022, Theoretical and Applied Genetics.
• Chen et al. The T. ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1, 2022, bioRxiv.
• Yu et al. Genome-wide Association Study and Genomic Prediction for Yield and Grain Quality Traits of Hybrid Rice, 2022, Research Square.
• Zhou et al. Identification and Validation of Quantitative Trait Loci Mapping for Spike-Layer Uniformity in Wheat, 2022, International Journal of Molecular Sciences.
• Tan et al. An Efficient Marker Gene Excision Strategy Based on CRISPR/Cas9-Mediated Homology-Directed Repair in Rice, 2022, International Journal of Molecular Sciences.
• Yang et al. The genome of the rice variety LTH provides insight into its universal susceptibility mechanism to worldwide rice blast fungal strains, 2022, Computational and Structural Biotechnology Journal.
• Habila et al. Salt stress responses and SNP-based phylogenetic analysis of Thai rice cultivars, 2022, The Plant Genome.
• Shen et al. Assembly of yield heterosis of an elite rice hybrid is promising by manipulating dominant QTLs, 2022, Journal of Integrative Plant Biology.
• Yu et al. From Green Super Rice to green agriculture: Reaping the promise of functional genomics research, 2022, Molecular Plant.
• Kim et al. Transcriptome Analysis of Triple Mutant for OsMADS62, OsMADS63, and OsMADS68 Reveals the Downstream Regulatory Mechanism for Pollen Germination in Rice (Oryza sativa), 2022, International Journal of Molecular Sciences.
• Yang et al. Integration of Genomics with Crop Modeling for Predicting Rice Days to Flowering: A Multi-Model Analysis, 2022, Field Crops Research.
• Cai et al. Revisiting regulatory decoherence: Accounting for temporal bias in a co-expression analysis reveals novel candidates controlling environmental response, 2022, Research Square.
• Hong et al. Transcriptome Analysis of Anther Wall Reveals Novel Insights Into the Regulatory Mechanisms Underlying Anther Wall Development in Rice, 2021, Research Square.
• Daryani et al. Identification and classification of the WRKY transcription factors family in Japonica rice, 2021, Crop Biotech.
• Jing et al. Phenotype and Genome Variation Analysis of Ion-beam Induced Mutant Rice JD-1, 2021, Journal of Plant Genetic Resources.
• Cross et al. Grain Dispersal Mechanism In Cereals Arose From a Genome Duplication Followed By Changes in Spatial Expression of Genes Involved In Pollen Development, 2021, Research Square.
• Kumari et al. Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice, 2021, Frontiers in plant science.
• Achary et al. CRISPR-Cas9 mediated mutation in GRAIN WIDTH and WEIGHT2 (GW2) locus improves aleurone layer and grain nutritional quality in rice, 2021, Scientific Reports.
• Chen et al. A FLASH pipeline for arrayed CRISPR library construction and the gene function discovery of rice receptor-like kinases, 2021, Molecular Plant.
• Siekmann et al. A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Secale cereale L.), 2021, Frontiers in plant science.
• Phan et al. Low Temperature Antioxidant Activity QTL Associate with Genomic Regions Involved in Physiological Cold Stress Tolerance Responses in Rice (Oryza sativa L.), 2021, Genes.
• Jia et al. Rice bioinformatics in the genomic era: Status and perspectives, 2021, The Crop Journal.
• Gottin et al. A new comprehensive annotation of leucine-rich repeat-containing receptors in rice, 2021, The Plant Journal.
• Hosni et al. Redox-related gene expression and sugar accumulation patterns are altered in the edible inflorescence produced by the cultivated form of pacaya palm (Chamaedorea tepejilote), 2021, Annals of Botany.
• Abbas et al. Isolation and evaluation of the biocontrol potential of Talaromyces spp. against rice sheath blight guided by soil microbiome, 2021, Environmental Microbiology.
• Ouyang et al. Decoding the plant genome: From epigenome to 3D organization, 2021, Journal of Genetics and Genomics.
• Hong et al. CAFRI-Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice, 2021, The Plant Journal.
• Chen et al. Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice, 2020, Journal of Genetics and Genomics.
• Wittern et al. Wheat EARLY FLOWERING3 is a dawn-expressed circadian oscillator component that regulates heading date, 2021, bioRxiv.
• Bohra et al. Integrating Phenomics with Breeding for Climate-Smart Agriculture, 2021, Omics Technologies for Sustainable Agriculture and Global Food Security (Vol II).
• Dash et al. Perspectives and Challenges of Phenotyping in Rice Research, 2021, Applications of Bioinformatics in Rice Research.
• Yang et al. High-Throughput Phenotyping (HTP) and Genetic Analysis Technologies Reveal the Genetic Architecture of Grain Crops, 2021, High-Throughput Crop Phenotyping.
• Gouda et al. Introduction of the Databases of Rice, 2021, Bioinformatics in Rice Research.
• Do et al. PyRice: a Python package for querying Oryza sativa databases, 2021, Bioinformatics.
• P.Panibe et al. Chromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution, 2021, Genomics.
• Hernández-Soto et al. Rice breeding in the new era: Comparison of useful agronomic traits, 2021, Current Plant Biology.
• Zhang et al. High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan, 2021, Science China Life Sciences.
• Qin et al. Comparative population genomic analysis provides insights into breeding of modern indica rice in China, 2020, Gene.
• Gupta et al. Using Network-Based Machine Learning to Predict Transcription Factors Involved in Drought Resistance, 2021, Frontiers in Genetics.
• Taagen et al. Positional-based cloning ‘fail-safe’ approach is overpowered by wheat chromosome structural variation, 2021, The Plant Genome.
• Sandhu et al. Endoplasmic reticulum stress pathway mediates the early heat stress response of developing rice seeds, 2021, Plant, Cell & Environment.
• Feng et al. Mapping causal genes and genetic interactions for agronomic traits using a large F2 population in rice, 2021, G3 Genes Genomes Genetics.
• Zhang et al. Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics, 2021, Plant Cell.
• Qin et al. Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations, 2021, Cell.
• Vasumathy et al. SSR Marker Based Genetic Diversity Analysis and SNP Haplotyping of Genes Associating Abiotic and Biotic Stress Tolerance, Rice Growth and Development and Yield Across 93 Rice Landraces, 2021, Research Square.
• Muvunyi et al. Identification of potential Zinc deficiency responsive genes and regulatory pathways in rice genotypes by Weighted Gene Co-expression Network Analysis, 2021, Research Square.
• Singh et al. Rice Adaptation to Climate Change: Opportunities and Priorities in Molecular Breeding, 2021, John Wiley & Sons, Ltd.
• Khahani et al. Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions, 2021, Scientific Reports.
• Wang et al. Identification of QTL for barley grain size, 2021, PeerJ.
• Li et al. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes, 2021, Nature Genetics.
• Jiang et al. Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice, 2021, Planta.
• Frontini et al. Genome-wide association of rice response to blast fungus identifies loci for robust resistance under high nitrogen, 2021, BMC Plant Biology.
• Hua et al. The bundle sheath of rice is conditioned to play an active role in water transport as well as sulfur assimilation and jasmonic acid synthesis, 2021, Plant Journal.
• Zhang et al. The landscape of gene–CDS–haplotype diversity in rice: Properties, population organization, footprints of domestication and breeding, and implications for genetic improvement, 2021, Molecular Plant.
• Cai et al. Temporal correlations robustly reveal regulatory coherence upon environmental perturbation, 2021, bioRxiv.
• Bheemanahalli et al. Genome-wide association study and gene network analyses reveal potential candidate genes for high night temperature tolerance in rice, 2021, Scientific Reports.
• Song et al. High-throughput phenotyping: breaking through the bottleneck in future crop breeding, 2021, The Crop Journal.
• Warraich et al. Rice GWAS reveals key genomic regions essential for salinity tolerance at reproductive stage, 2020, Acta Physiologiae Plantarum.
• Deveshwar et al. Analysis of rice nuclear-localized seed-expressed proteins and their database (RSNP-DB), 2020, Scientific Reports.
• Chandran et al. Rice Male Gamete Expression Database (RMEDB): A Web Resource for Functional Genomic Studies of Rice Male Organ Development, 2020, Journal of Plant Biology.
• Bhati et al. Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation, 2020, G3: Genes Genomes Genetics.
• Ren et al. Transcriptome and genome sequencing elucidates the molecular basis for the high yield and good quality of the hybrid rice variety Chuanyou6203, 2020, Scientific Reports.
• Kim et al. Two nuclear effectors of the rice blast fungus modulate host immunity via transcriptional reprogramming, 2020, Nature Communications.
• Hong et al. CAFRI‐Rice: CRISPR applicable functional redundancy inspector to accelerate functional genomics in rice, 2020, Plant Journal.
• Pang et al. High-Resolution Genome-wide Association Study Identifies Genomic Regions and Candidate Genes for Important Agronomic Traits in Wheat, 2020, Molecular Plant.
• Ye et al. Orphan Crops and their Wild Relatives in the Genomic Era, 2020, Molecular Plant.
• Mathew et al. SUPER STARCHY1/ONAC025 participates in rice grain filling, 2020, Plant Direct.
• Paul et al. Sequencing the Rice Genome: Gateway to Agricultural Development, 2020, Springer.
• Kandpal et al. Gene Expression Dynamics in Rice Peduncles at the Heading Stage, 2020, Frontiers in Genetics.
• Gupta et al. Prediction and characterization of transcription factors involved in drought stress response, 2020, BioRxiv.
• Kumar et al. CRISPR-Cas9 mediated genome editing of drought and salt tolerance (OsDST) gene in indica mega rice cultivar MTU1010, 2020, Physiology and Molecular Biology of Plants.
• Yang et al. A lamin‐like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice, 2020, New Phytologist.
• Khahani et al. Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice, 2020, BMC Genomics.
• Do et al. PyRice: a Python package for querying Oryza Sativa functional databases, 2020, BioRxiv.
• Mohammed Abdullah Abdulraheem Ghaleb et al. Heterosis analysis and underlying molecular regulatory mechanism in a wide-compatible neo-tetraploid rice line with long panicles, 2020, BMC Plant Biology.
• Dhaka et al. Transcriptional trajectories of anther development provide candidates for engineering male fertility in sorghum, 2020, Scientific Reports.
• Yoo et al. Fast Track to Discover Novel Promoters in Rice, 2020, Plants.
• Yang et al. Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives, 2020, Molecular Plant.
• DO et al. Candidate gene prioritization using graph embedding, 2020, BioRxiv.
• Jia et al. Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice, 2020, Journal of Plant Physiology.
• Lu et al. A direct PCR–based SNP marker–assisted selection system (D-MAS) for different crops, 2020, Molecular Breeding.
• Cubry et al. Genome wide association study pinpoints key agronomic QTLs in African rice Oryza glaberrima, 2020, BioRxiv.
• Rice, A. D. QTL Mapping of Panicle Architecture and Yield-Related Traits Between Two U.S. Rice Cultivars ‘LaGrue’ and ‘Lemont’, 2019, Theses and Dissertations Retrieved from University of Arkansas, Fayetteville.
• Hong et al. Infrastructures of systems biology that facilitate functional genomic study in rice, 2019, Rice.
• Borrill et al. Identification of transcription factors regulating senescence in wheat through gene regulatory network modelling, 2019, Plant physiology.
• Yoo et al. A Systematic View Exploring the Role of Chloroplasts in Plant Abiotic Stress Responses, 2019, BioMed Research International.
• Ram et al. Insertional Mutagenesis Approaches and Their Use in Rice for Functional Genomics, 2019, Plants.
• Dhaka et al. Small RNA profiling from meiotic and post-meiotic anthers reveals prospective miRNA-target modules for engineering male fertility in sorghum, 2019, Genomics.
• Chandran et al. A web-based tool for the prediction of rice transcription factor function, 2019, Database.
• Peng et al. MBKbase for rice: an integrated omics knowledgebase for molecular breeding in rice, 2019, Nucleic Acids Research.
• Liu et al. Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study, 2019, Rice.
• Yuan et al. Rice Protocol eBook facilitates rice research, 2018, Plant Physiology Journal.
• Golicz et al. MCRiceRepGP: a framework for identification of sexual reproduction associated coding and lincRNA genes in rice, 2018, Plant Journal.
• Gianinetti et al. Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition, 2018, Plants.
• Liao et al. A comprehensive review of web-based resources of non-coding RNAs for plant science research, 2018, Int J Biol Sci.
• Wing et al. The rice genome revolution: from an ancient grain to Green Super Rice, 2018, Nature Reviews Genetics.
• Kim Nhung TA et al. A genome-wide association study using a Vietnamese landrace panel of rice (Oryza sativa) reveals new QTLs controlling panicle morphological traits, 2018, BMC Plant Biology.
• Das et al. Revisiting the decoded genomes to promptly reveal their genomic perspectives, 2017, Current Science.
• Dingkuhn et al. Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility, 2017, Journal of Experimental Botany.
• Zong et al. Feedback Regulation of ABA Signaling and Biosynthesis by a bZIP Transcription Factor Targets Drought-Resistance-Related Genes, 2016, Plant physiology.
• Daware et al. An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice, 2016, Frontiers in plant science.
• Badoni et al. Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice, 2016, Scientific reports.