Plant & Animal Genomes XIII Conference

January 15-19, 2005
Town & Country Convention Center
San Diego, CA

GrainGenes 2.0: An Integrated Resource For The Triticeae

David E. Matthews¹ , David Hummel² , Nancy Lui³ , David Hane³ , Victoria L. Carollo³ , Gerard R. Lazo³ , Olin D. Anderson³

¹  USDA-ARS, Cornell University, Department of Plant Breeding and Genetics, Ithaca, NY 14853 USA

²  Children's Hospital Informatics Program, Children's Hospital Boston, 320 Longwood Avenue, Boston, MA 02115 USA

³  USDA-ARS, Western Regional Research Center, 800 Buchanan Street, Albany, CA 94710 USA

GrainGenes (http://wheat.pw.usda.gov), the international database for genetic and genomic data about Triticeae species (e.g. wheat, barley, and rye) and Avena sativa (oat), was updated and extensively redesigned in 2004. The underlying database is now built on the MySQL relational database platform, and is fully integrated with the GrainGenes website into one resource. The new architecture provides marked improvements in data delivery with respect to speed, query power and user-friendliness. Pre-formatted "Quick Queries" from the traditional GrainGenes have been updated to interface with the new database, and additional advanced SQL and Batch Queries have been added. Over 1,100 chromosome maps from over 120 map studies can now be viewed via CMap, a comparative map display to identify and highlight common loci among multiple genetic and physical maps. The GrainGenes CMap server includes all maps in the GrainGenes collection, plus a separate database with Rudi Appels' Wheat Composite map compared to its component maps. A BLAST server offers custom databases such as mapped wheat ESTs, EST-SSRs, Barley1 GeneChip exemplars, and Triticeae repeat sequences. Other improvements include extended report pages, such as a new "marker" page that combines locus and probe data. Many of the improvements in GrainGenes 2.0 have been guided by comments and suggestions from our users, and we welcome further feedback as we continue to enhance its value as a resource for the grains research community. GrainGenes is a product of the USDA Agricultural Research Service (ARS).