Plant & Animal Genomes XIX Conference

January 15-19, 2011
Town & Country Convention Center
San Diego, CA

CottonDB: An Integrated Repository Resource For Cotton

Jing Yu¹ , Russell Kohel² , Lori Hinze² , James Frelichowski² , John Yu² , Richard Percy²

¹  Texas A&M University/USDA-ARS, 2881 F&B Road, College Station, TX 77845

²  USDA-ARS, 2881 F&B Road, College Station, TX 77845

CottonDB (http://cottondb.org), the first and the most comprehensive cotton genome database established by USDA-ARS, has being updated and extensively redesigned since 2006. The CottonDB project includes both a website and database creating a repository of information for over 480,000 gene, EST and contig sequences, many with genetic and physical maps, DNA primer or probes, germplasm, pathology, and other accessions. Over 1,100 chromosome or linkage maps of AD, A, D, and G genomes (containing over 20,000 loci and over 1,000 QTLs) from over 40 map studies can now be viewed, compared, and downloaded via CMap Viewer (http://cottondb.org/wwwroot/cmap.php). A BLAST server (http://cottondb.org/wwwroot/webblast.php) offers custom databases such as cotton ESTs, EST-SSRs, contigs, repeat sequences, and proteins. Through CottonDB Genome Browser Viewer (http://cottondb.org/wwwroot/gbrowse.php), comparisons among genetic and physical maps, or between cotton and Arabidopsis genomes can be viewed and downloaded at the nucleotide or peptide level. The Quick Queries (http://cottondb.org/wwwroot/cdbqq.php) provides the query results dynamically for the most frequently asked queries. Other improvements include extended special queries to the cotton breeders via Cotton Breeder’s Tool Box. CottonDB has 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 cotton research community. CottonDB is a product of the USDA Agricultural Research Service (ARS).