ArticleRice (New York, N.Y.)2012
OGRO: The Overview of functionally characterized Genes in Rice online database.
Article in Rice (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers, 1 of them a synthesis that pooled it.
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74 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Genetic bases of resistance to the rice hoja blanca disease deciphered by a quantitative trait locus approach.G3 (Bethesda, Md.) · 2023Pooled it
- Rice Annotation Project Database (RAP-DB): Literature-Curated Gene Annotation and Integrated Omics Resources for Rice Functional Genomics and Molecular Breeding.Rice (New York, N.Y.) · 2026Article
- Genome-wide analysis of Udai21: Unraveling the genetic basis of superior eating quality in rice.PloS one · 2025Article
- Allelic combinations of Hd1, Hd16, and Ghd7 exhibit pleiotropic effects on agronomic traits in rice.G3 (Bethesda, Md.) · 2024Article
- Integration of genome-wide association studies reveal loci associated with salt tolerance score of rice at the seedling stage.Journal of applied genetics · 2023Article
- Genome-Wide Identification and Analysis of Collar Region-Preferential Genes in Rice.Plants (Basel, Switzerland) · 2023Article
- Multiple domestications of Asian rice.Nature plants · 2023Article
- Gene based markers improve precision of genome-wide association studies and accuracy of genomic predictions in rice breeding.Heredity · 2023Article
- An open source plant kinase chemogenomics set.Plant direct · 2022Article
- Patterns of genetic variation and QTLs controlling grain traits in a collection of global wheat germplasm revealed by high-quality SNP markers.BMC plant biology · 2022Article
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- Scripting Analyses of Genomes in Ensembl Plants.Methods in molecular biology (Clifton, N.J.) · 2022Article
- A Systemic View of Carbohydrate Metabolism in Rice to Facilitate Productivity.Plants (Basel, Switzerland) · 2021Article
- Development of anPlants (Basel, Switzerland) · 2021Article
- Genetic differentiation and restricted gene flow in rice landraces from Yunnan, China: effects of isolation-by-distance and isolation-by-environment.Rice (New York, N.Y.) · 2021Article
- Genome-wide association mapping for resistance to bacterial blight and bacterial leaf streak in rice.Planta · 2021Article
- Meta-Analysis of Yield-Related and N-Responsive Genes Reveals Chromosomal Hotspots, Key Processes and Candidate Genes for Nitrogen-Use Efficiency in Rice.Frontiers in plant science · 2021Article
- A Genome-Wide Association Study Pinpoints Quantitative Trait Genes for Plant Height, Heading Date, Grain Quality, and Yield in Rye (Frontiers in plant science · 2021Article
- Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes.International journal of molecular sciences · 2020Article
- Identification of Novel QTL Conferring Sheath Blight Resistance in Two Weedy Rice Mapping Populations.Rice (New York, N.Y.) · 2020Article
14 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
backgroundThe high-quality sequence information and rich bioinformatics tools available for rice have contributed to remarkable advances in functional genomics. To facilitate the application of gene function information to the study of natural variation in rice, we comprehensively searched for articles related to rice functional genomics and extracted information on functionally characterized genes.
resultsAs of 31 March 2012, 702 functionally characterized genes were annotated. This number represents about 1.6% of the predicted loci in the Rice Annotation Project Database. The compiled gene information is organized to facilitate direct comparisons with quantitative trait locus (QTL) information in the Q-TARO database. Comparison of genomic locations between functionally characterized genes and the QTLs revealed that QTL clusters were often co-localized with high-density gene regions, and that the genes associated with the QTLs in these clusters were different genes, suggesting that these QTL clusters are likely to be explained by tightly linked but distinct genes. Information on the functionally characterized genes compiled during this study is now available in the O verview of Functionally Characterized G enes in R ice O nline database (OGRO) on the Q-TARO website ( http://qtaro.abr.affrc.go.jp/ogro ). The database has two interfaces: a table containing gene information, and a genome viewer that allows users to compare the locations of QTLs and functionally characterized genes.
conclusionsOGRO on Q-TARO will facilitate a candidate-gene approach to identifying the genes responsible for QTLs. Because the QTL descriptions in Q-TARO contain information on agronomic traits, such comparisons will also facilitate the annotation of functionally characterized genes in terms of their effects on traits important for rice breeding. The increasing amount of information on rice gene function being generated from mutant panels and other types of studies will make the OGRO database even more valuable in the future.
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