Abstract
BackgroundThe Cotton Microsatellite Database (CMD) 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.DescriptionAt 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.ConclusionThe 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.
Highlights
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
Database and web interface development Currently, the database is composed of 14 tables which store all the data for the microsatellite projects including information on project collaborators, simple sequence repeats (SSRs)-containing clones, sequences, primers flanking the SSRs, repeat motif, open reading frame position, genetic markers and maps, standardized panel varieties, and data homology, and publications
The CMD serves the cotton community as a major repository of the publicly available cotton microsatellite data and a unique repository for the CMD standardized panel screened data, a key tool for systematic characterization of the SSR markers developed for cotton
Summary
The CMD has been initiated to provide researchers, engaged worldwide in cotton research, with centralized access to microsatellite markers, an invaluable resource for basic and applied research in cotton breeding. The CMD serves the cotton community as a major repository of the publicly available cotton microsatellite data and a unique repository for the CMD standardized panel screened data, a key tool for systematic characterization of the SSR markers developed for cotton. SJ implemented CMap, uploaded mapping data and was involved with the database schema design and implementation, SF managed the oracle system and was involved in database schema design and tool development, MS performed all homology searches and was involved with database design and construction, RE helped design and implement the SSR, FASTA, BLAST and CAP3 servers, JS and BS screened the cotton SSRs against the CMD standardized http://www.biomedcentral.com/1471-2164/7/132 panel.
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