Rice Genetics IV - IRRI books - International Rice Research Institute

Equally important as the genomic information are the germplasm resourcesthat will provide the basis for direct application of molecular tools. These resourcesrange from tester lines and mutant lines to cultivated varieties, landraces, and wildspecies maintained in various crop germplasm centers worldwide. The databaseservers provide information on acquisition, preservation, evaluation, and distributionof all available rice strains. The literature on different aspects of rice researchhas also been catalogued for searching on the Web for the user community.Informatics for the rice communityMore than 20 databases and Web sites are currently available online for ricegenomics (Table 2). Most of these databases focus on specialized and detailedinformation covering a broad range of research on rice genomics or rice biology,whereas some are designed for ordinary users and offer general information onrice. An overview of these databases is briefly given here.Rice genome databasesOne of the earliest databases that have been serving the rice community since 1993is RiceGenes (http://genome.cornell.edu/rice/). Supported by the USDA-ARS Centerfor Bioinformatics in partnership with Cornell University, this database focuseson comparative genetic maps, molecular markers, morphological markers, quantitativetrait loci (QTLs), and germplasm data. Newly added features includemicrosatellite marker data and microsatellite maps of the 12 rice chromosomes.RiceGenes is currently being converted to a relational database management systemto allow for increased data integration and greater flexibility.Table 2. Major rice genome and germplasm databases.Database/ URL Information categoriesorganization aINE http://rgp.dna.affrc.go.jp/ Genetic map, YAC physical map, ESTmap, PAC contigs, chr. 1 and 6 PAC/BAC clone sequence/annotation,IRGSP sequencing statusRiceGenes http://genome.cornell. Genetic maps, molecular markers,edu/rice/morphological markers, QTLs,comparative maps, rice varietyreleases, referencesOryzabase http://www.shigen.nig. Genetic maps, integrated maps,ac.jp/rice/oryzabase/genetic stocks, gene dictionary,mutant images, general information,referencescontinued on next page296 Antonio et al