BMC Genomics (May 2006)

CMD: a Cotton Microsatellite Database resource for <it>Gossypium </it>genomics

  • Liu Shaolin,
  • Burr Ben,
  • Saha Sukumar,
  • Ulloa Mauricio,
  • Eshelman Robert,
  • Staton Margaret,
  • Ficklin Stephen,
  • Yellambalase Preetham,
  • Muthukumar Sriram,
  • Jung Sook,
  • Jesudurai Christopher,
  • Yu John Z,
  • Lacape Jean-Marc,
  • Scheffler Brian,
  • Palmer Michael,
  • Scheffler Jodi,
  • Blenda Anna,
  • Zhang Tianzhen,
  • Fang Deqiu,
  • Pepper Alan,
  • Kumpatla Siva,
  • Jacobs John,
  • Tomkins Jeff,
  • Cantrell Roy,
  • Main Dorrie

DOI
https://doi.org/10.1186/1471-2164-7-132
Journal volume & issue
Vol. 7, no. 1
p. 132

Abstract

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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. 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.