Oryzabase. An integrated biological and genome information database for rice

Abstract

The aim of Oryzabase is to create a comprehensive view of rice (Oryza sativa) as a model monocot plant by integrating biological data with molecular genomic information (http://www.shigen.nig.ac.jp/rice/oryzabase/top/top.jsp). The database contains information about rice development and anatomy, rice mutants, and genetic resources, especially for wild varieties of rice. The anatomical description of rice development is unique and is the first known representation for rice. Developmental and anatomical descriptions include in situ gene expression data serving as stage and tissue markers. The systematic presentation of a large number of rice mutant and mutant trait genes is indispensable, as is description of research in wild strains, core collections, and their detailed characterization. Several genetic, physical, and expression maps with full genome and cDNA sequences are also combined with biological data in Oryzabase. These datasets, when pooled together, could provide a useful tool for gaining greater knowledge about the life cycle of rice, the relationship between phenotype and gene function, and rice genetic diversity. For exchanging community information, Oryzabase publishes the Rice Genetics Newsletter organized by the Rice Genetics Cooperative and provides a mailing service, rice-e-net/rice-net.

Figure 1.

An example of the shootless 1 mutant as described in the sections Trait Genes and Mutants. For this mutant the gene symbol is shown along with a short description of the mutant phenotype, photographs comparing the mutant with a wild-type plant, and references used for the analyses.

Figure 2.

Indica IR24 genome (red block) substitution lines with a japonica Asominori (white block) background. Eighty-seven lines almost cover all the regions of the indica genome. The purple blocks indicate regions needed for discriminating between homozygosity and heterozygosity of indica genome. These lines revealed to show high performance in quantitative trait analysis of many characters.