Plant & Animal Genomes XV Conference

January 13-17, 2007
Town & Country Convention Center
San Diego, CA

Cotton Microsatellite Database: A Centralized Public Repository And Data Mining Resource For Gossypium SSRs

Anna Blenda¹ , Margaret Staton¹ , Michael Palmer¹ , Sook Jung¹ , Roy Cantrell² , Doreen Main³

¹  Department of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Str., Clemson, SC, 29634, USA

²  Agricultural Research Division, Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA

³  Department of Horticulture and Landscape Architecture, Washington State University, 45 Johnson Hall, Pullman, WA, 99164, USA

The Cotton Microsatellite Database (CMD) (http://www.cottonssr.org) is a curated repository providing centralized access to the largest collection of publicly available cotton simple sequence repeats (SSRs). CMD is orientated toward researchers involved in molecular marker development and their application to cotton breeding. It is being actively used by the international cotton community, and can be viewed as an important vehicle toward increased collaboration among academic, government and industry cotton scientists, both nationally and worldwide. The present collection of 5,484 SSRs in CMD was generated through collaboration with major cotton research groups from the USA, France and China. Currently, the cotton SSRs deposited in CMD is represented by 2,285 EST-SSRs and 3,199 genomic SSRs. CMD provides a suite of online tools for data mining and comparative analysis. Future development of the CMD will focus on the establishment of a standard nomenclature for cotton SSRs, adding new microsatellite data from the cotton genome sequence and other sources both public and private, enhanced SSR data mining and analysis capabilities such as full sequence processing facilities, and provision of a quarterly newsletter for the cotton community. Annotation of SSRs will include further classification using gene ontology terms with links to the KEGG and MetaCyc pathway databases.