title: CMD: a Cotton Microsatellite Database resource for Gossypium genomics.
abstract: 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.
  
  
  METHODS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC 29634, USA. blenda@clemson.edu
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authors.lastname: Blenda
authors.forename: Jodi
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authors.lastname: Scheffler
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authors.lastname: Scheffler
authors.forename: Michael
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authors.lastname: Palmer
authors.forename: Jean-Marc
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authors.lastname: Lacape
authors.forename: John Z
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authors.lastname: Yu
authors.forename: Christopher
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authors.lastname: Jesudurai
authors.forename: Sook
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authors.lastname: Jung
authors.forename: Sriram
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authors.lastname: Muthukumar
authors.forename: Preetham
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authors.lastname: Staton
authors.forename: Robert
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authors.lastname: Eshelman
authors.forename: Mauricio
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authors.lastname: Ulloa
authors.forename: Sukumar
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authors.lastname: Saha
authors.forename: Ben
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authors.forename: Shaolin
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authors.lastname: Liu
authors.forename: Tianzhen
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authors.lastname: Zhang
authors.forename: Deqiu
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authors.lastname: Fang
authors.forename: Alan
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authors.lastname: Pepper
authors.forename: Siva
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authors.lastname: Kumpatla
authors.forename: John
authors.initials: J
authors.lastname: Jacobs
authors.forename: Jeff
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authors.lastname: Tomkins
authors.forename: Roy
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authors.lastname: Cantrell
authors.forename: Dorrie
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authors.lastname: Main
mesh_terms: D002874:Chromosome Mapping; D030541:Databases, Genetic; D018745:Genome, Plant; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D020407:Internet; D018895:Microsatellite Repeats