CMD: a Cotton Microsatellite Database resource for Gossypium genomics
1 Department of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USA
2 ARS Crop Genetics & Production Research Unit, Stoneville, MS, USA
3 ARS MSA Genomics Laboratory, Stoneville, MS, USA
4 Clemson University Genomics Institute, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USA
5 CIRAD, Centre International en Recherche Agronomique pour le Développement, 34398, Montpellier Cedex 5, France
6 USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USA
7 USDA-ARS, WICS Research Unit, Cotton Enhancement Program, Shafter, CA, 93263, USA
8 USDA-ARS, Crop Science Research Laboratory, P.O. Box 5367, Mississippi State, MS 39762, USA
9 Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
10 Monsanto, St. Louis, MO 63167, USA
11 National Key Laboratory of Crop Genetics & Germplasm Enhancement/Cotton Research Institute, Nanjing Agricultural University, Nanjing 210095, China
12 Delta and Pine Land Company, Winterville, MS 38782, USA
13 Dept of Biology, Texas A&M University, College Station, TX 77843, USA
14 Dow AgroSciences LLC, Indianapolis, IN, 46268, USA
15 Bayer BioScience N.V., Technologiepark 38, B-9052 Gent, Belgium
16 Cotton Incorporated, Cary, NC, 27513, USA
17 Department of Horticulture and Landscape Architecture, Washington State University, WA, 99164, USA
BMC Genomics 2006, 7:132 doi:10.1186/1471-2164-7-132Published: 31 May 2006
The Cotton Microsatellite Database (CMD) http://www.cottonssr.org webcite is a curated and integrated web-based relational database providing centralized access to publicly available cotton microsatellites, an invaluable resource for basic and applied research in cotton breeding.
At present CMD contains publication, sequence, primer, mapping and homology data for nine major cotton microsatellite projects, collectively representing 5,484 microsatellites. In addition, CMD displays data for three of the microsatellite projects that have been screened against a panel of core germplasm. The standardized panel consists of 12 diverse genotypes including genetic standards, mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and contemporary Upland cottons with significant acreage. A suite of online microsatellite data mining tools are accessible at CMD. These include an SSR server which identifies microsatellites, primers, open reading frames, and GC-content of uploaded sequences; BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and primers, a CAP3 server to assemble EST sequences into longer transcripts prior to mining for SSRs, and CMap, a viewer for comparing cotton SSR maps.
The collection of publicly available cotton SSR markers in a centralized, readily accessible and curated web-enabled database provides a more efficient utilization of microsatellite resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in Gossypium spp.