OGRO

The overview of functionally characterized genes in rice online database

Eiji Yamamoto, Jun ichi Yonemaru, Toshio Yamamoto, Masahiro Yano

Research output: Contribution to journalArticle

85 Citations (Scopus)

Abstract

Background: The 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. Results: As 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 Overview of Functionally Characterized Genes in Rice Online 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. Conclusions: OGRO 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.

Original languageEnglish
Pages (from-to)1-10
Number of pages10
JournalRice
Volume5
Issue number1
DOIs
Publication statusPublished - Dec 25 2012
Externally publishedYes

Fingerprint

rice
gene
quantitative trait loci
genes
genomics
type of study
bioinformatics
agronomic traits
genome
breeding

Keywords

  • Database
  • Functionally characterized genes
  • QTL
  • Rice (Oryza sativa L)

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Soil Science
  • Plant Science

Cite this

OGRO : The overview of functionally characterized genes in rice online database. / Yamamoto, Eiji; Yonemaru, Jun ichi; Yamamoto, Toshio; Yano, Masahiro.

In: Rice, Vol. 5, No. 1, 25.12.2012, p. 1-10.

Research output: Contribution to journalArticle

Yamamoto, Eiji ; Yonemaru, Jun ichi ; Yamamoto, Toshio ; Yano, Masahiro. / OGRO : The overview of functionally characterized genes in rice online database. In: Rice. 2012 ; Vol. 5, No. 1. pp. 1-10.
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abstract = "Background: The 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. Results: As 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 Overview of Functionally Characterized Genes in Rice Online 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. Conclusions: OGRO 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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