Open Access Database

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

Anna Blenda1*, Jodi Scheffler2, Brian Scheffler3, Michael Palmer4, Jean-Marc Lacape5, John Z Yu6, Christopher Jesudurai1, Sook Jung1, Sriram Muthukumar1, Preetham Yellambalase1, Stephen Ficklin4, Margaret Staton1, Robert Eshelman1, Mauricio Ulloa7, Sukumar Saha8, Ben Burr9, Shaolin Liu10, Tianzhen Zhang11, Deqiu Fang12, Alan Pepper13, Siva Kumpatla14, John Jacobs15, Jeff Tomkins4, Roy Cantrell16 and Dorrie Main17*

Author Affiliations

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

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BMC Genomics 2006, 7:132  doi:10.1186/1471-2164-7-132

Published: 31 May 2006

Abstract

Background

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.

Description

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.

Conclusion

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.