Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 5/15/2006
Publication Date: 5/31/2006
Citation: Blenda, A.V., Scheffler, J.A., Scheffler, B.E., Palmer, M., Lacape, J., Yu, J., Jesudraui, C., Jung, S., Muthukumar, S., Yellambalase, P., Ficklin, S., Staton, M., Eschelman, R., Ulloa, M., Saha, S., Burr, B., Lui, S., Zhang, T., Fang, D., Pepper, A.E., Kumpatla, S.P., Jacobs, J., Tomkins, J.P., Cantrell, R.G., Main, D. 2006. CMD: A Cotton Microsatellite Database Resource for Gossypium Genomics. Biomed Central (BMC) Genomics. 7:132. Interpretive Summary: Unlike other major crops such as soybean and corn, cotton had no coordinated public DNA marker database. DNA markers are small pieces of DNA that can be different lengths depending on the genetic make-up of the plant. A marker can have a characteristic length unique for a particular crop variety and several of these markers together can create a “fingerprint” for identification of the variety. When a specific marker is associated with a gene governing resistance to a specific pest or disease, it can be used as a diagnostic tool to identify plants with potential resistance. This paper reports on the development of a curated Web accessible database (http://www.cottonssr.org) that resulted from a joint project with grower funded Cotton Incorporated (CI), Clemson University Genomics Institute (CUGI) and ARS scientists. The database contains information on DNA markers and chromosome maps. It also has a number of tools to identify markers within DNA sequences, and a computer software program for comparing different cotton marker maps. The collection of all publicly available cotton DNA markers into a centralized, readily accessible web-enabled database allows more efficient utilization of marker resources and will accelerate the development of DNA based tools needed to identify important agronomic traits and facilitate selection for these traits.
Technical Abstract: The Cotton Microsatellite Database (CMD) is a curated and integrated web-based database providing centralized access to all publicly available cotton microsatellite markers (SSRs) (http://www.cottonssr.org). At present it contains DNA sequence, SSR marker, mapping and similarity data for nine cotton marker projects. In addition, CMD displays data for three of the projects that have been screened against a standard panel of twelve cotton (Gossypium hirsutum) lines, including genetic stocks, wild species, and contemporary Upland cottons with significant acreage. A range of online marker data mining tools are accessible at CMD. These include an SSR server which identifies SSRs within DNA sequences, BLAST and FASTA servers providing sequence similarity searches against the existing cotton SSR sequences and markers, and CMap, a viewer for comparing different cotton marker maps. The collection of all publicly available cotton SSR markers into a centralized, readily accessible web-enabled database provides a more efficient utilization of marker resources and will help accelerate basic and applied research in molecular breeding and genetic mapping in cotton.