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. 2006 May 31:7:132.
doi: 10.1186/1471-2164-7-132.

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

Anna Blenda  1 , Jodi Scheffler, Brian Scheffler, Michael Palmer, Jean-Marc Lacape, John Z Yu, Christopher Jesudurai, Sook Jung, Sriram Muthukumar, Preetham Yellambalase, Stephen Ficklin, Margaret Staton, Robert Eshelman, Mauricio Ulloa, Sukumar Saha, Ben Burr, Shaolin Liu, Tianzhen Zhang, Deqiu Fang, Alan Pepper, Siva Kumpatla, John Jacobs, Jeff Tomkins, Roy Cantrell, Dorrie Main
Affiliations

CMD: a Cotton Microsatellite Database resource for Gossypium genomics

Anna Blenda et al. BMC 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.

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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Figures

Figure 1
Figure 1
CMD home page and the representative search pages. This figure illustrates the CMD homepage (A) and the representative search pages; microsatellite projects (B), marker search and view, homology search (C-F).
Figure 2
Figure 2
Cotton CMap Viewer. A. The opening page of CMap Viewer with 4 major genetic maps of cotton. B. An example of individual linkage group pages with the associated markers.
See this image and copyright information in PMC

References

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    1. Cotton Microsatellite Database http://www.cottonssr.org
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