Plant & Animal Genomes XIV Conference

January 14-18, 2006
Town & Country Convention Center
San Diego, CA

CMD: Cotton Microsatellite Database Resource For Gossypium Genomics

Anna Blenda¹ , Preetham Yellambalase¹ , Margaret Staton¹ , Stephen Ficklin¹ , Christopher Jesudurai¹ , Michael Palmer¹ , Roy Cantrell² , Doreen Main¹

¹  Department of Genetics and Biochemistry, Clemson University, 51 New Cherry str., Clemson, SC, 29634, USA

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

The Cotton Microsatellite Database (CMD) is a curated and integrated web-based relational database (http://www.cottonSSR.org). CMD has been initiated and funded by Cotton Incorporated to provide centralized access to all publicly available cotton SSRs and accelerate basic and applied research in molecular breeding and genetic mapping. A significant number of SSRs have been developed in the last few years in the public and private sector. The CMD will contain relevant sequence information, homology results, polymorphism, PIC values on a standard panel and chromosome and map information. At present it contains information on the publicly available cotton microsatellite projects: BNL, CIR, CM, JESPR, MGHES, MUSB, MUSS-MUCS, NAU, TMB. Microsatellite sequences and relevant information, primers and standardized panel screened data are available for download. Computational search against existing cotton SSRs using the BLAST or FASTA server tools, identification of SSRs in all other publicly available cotton sequences using the CMD SSR server, and assembly of sequences using Advanced CAP 3 server can be performed by users.