CMD: a Cotton Microsatellite Database resource for Gossypium genomics.
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.
Blenda
Anna
A
Department of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Street, Clemson, SC 29634, USA. blenda@clemson.edu
Scheffler
Jodi
J
Scheffler
Brian
B
Palmer
Michael
M
Lacape
Jean-Marc
JM
Yu
John Z
JZ
Jesudurai
Christopher
C
Jung
Sook
S
Muthukumar
Sriram
S
Yellambalase
Preetham
P
Ficklin
Stephen
S
Staton
Margaret
M
Eshelman
Robert
R
Ulloa
Mauricio
M
Saha
Sukumar
S
Burr
Ben
B
Liu
Shaolin
S
Zhang
Tianzhen
T
Fang
Deqiu
D
Pepper
Alan
A
Kumpatla
Siva
S
Jacobs
John
J
Tomkins
Jeff
J
Cantrell
Roy
R
Main
Dorrie
D
D002874:Chromosome Mapping; D030541:Databases, Genetic; D018745:Genome, Plant; D005838:Genotype; D003368:Gossypium / Q000235:genetics*; D020407:Internet; D018895:Microsatellite Repeats