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CMD: a Cotton Microsatellite Database resource for Gossypium genomics

Anna V. BlendaDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC 29634, USA. [email protected]Jodi SchefflerARS Crop Genetics & Production Research Unit, Stoneville, MS, USABrian E. SchefflerARS MSA Genomics Laboratory, Stoneville, MS, USAMichael PalmerClemson University Genomics Institute, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USAJean-Marc LacapeCIRAD, Centre International en Recherche Agronomique pour le Développement, 34398, Montpellier Cedex 5, FranceJohn Z. YuUSDA-ARS, Southern Plains Agricultural Research Center, College Station, TX, 77845, USAChristopher JesuduraiDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USASook JungDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USASriram MuthukumarDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USAPreetham YellambalaseDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USAStephen FicklinClemson University Genomics Institute, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USAMargaret StatonDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USARobert EshelmanDepartment of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USAMauricio UlloaUSDA-ARS, WICS Research Unit, Cotton Enhancement Program, Shafter, CA, 93263, USASukumar SahaUSDA-ARS, Crop Science Research Laboratory, P.O. Box 5367, Mississippi State, MS, 39762, USAB BurrBiology Department, Brookhaven National Laboratory, Upton, NY, 11973, USAShaolin LiuMonsanto, St. Louis, MO, 63167, USATianzhen ZhangNational Key Laboratory of Crop Genetics & Germplasm Enhancement/Cotton Research Institute, Nanjing Agricultural University, Nanjing, 210095, ChinaDeqiu FangDelta and Pine Land Company, Winterville, MS, 38782, USAAlan E. PepperDept of Biology, Texas A&M University, College Station, TX, 77843, USASiva P. KumpatlaJohn JacobsBayer BioScience N.V., Technologiepark 38, B-9052, Gent, BelgiumJ. P. TomkinsClemson University Genomics Institute, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC, 29634, USAR. G. CantrellCotton Incorporated, Cary, NC, 27513, USADorrie MainDepartment of Horticulture and Landscape Architecture, Washington State University, WA, 99164, USA

2006en

ABI

Annotatsiya

BACKGROUND: The Cotton Microsatellite Database (CMD) http://www.cottonssr.org 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.

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DOI: 10.1186/1471-2164-7-132

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