Plant & Animal Genomes XVI Conference

January 12-16, 2008
Town & Country Convention Center
San Diego, CA

Development Of A Cotton Marker Database (CMD) For Gossypium Genome And Genetic Research

Anna Blenda¹ , Taein Lee² , Randall Svancara² , Don Jones³ , Dorrie Main²

¹  Department of Genetics and Biochemistry, Clemson University, Biosystems Research Center, 51 New Cherry Str., Clemson, SC, 29634, USA

²  Department of Horticulture and Landscape Architecture, Washington State University, 45 Johnson Hall, Pullman, WA, 99164, USA

³  Agricultural Research Division, Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA

Over the last few years thousands of SSRs and more recently SNP markers have been discovered in cotton. Each of these markers provides a valuable molecular tool applying genetic and genomic research to cotton improvement. The primary objective of the project is to develop and maintain a comprehensive cotton DNA marker (SSR and SNP) database (CMD) resource for the cotton research community (http://www.cottonmarker.org). Important features that will be additionally incorporated in the CMD include extension of the SSR source sequence display of results of significant homology with public protein detabases to display protein domains or blocks. The addition of SNP markers will include displaying the SNP-containing consensus sequence with the SNP highlighted, as well as displaying the individual sequences that are part of the consensus sequence (where possible). The results of any significant homology between the consensus sequences with the public protein databases will be displayed as well. In addition, future development will focus on the establishment of a standard nomenclature for cotton SSRs and SNPs, collecting of all available genetic maps data, annotation of genetic traits/genes in cotton linked to the CMD SSRs/SNPs, improving the tools and functionality of the web interface, such as an advanced search site with options for search/display categories, as well as increased collaboration with CottonDB. When the cotton physical map is available, users also will be able to retrieve the anchored BAC clones containing the SSRs of interest through the anchored BACs page in the map viewer. With cotton genome sequencing in progress, the CMD also will focus on enhanced SSR and other markers’ data mining and analysis capabilities such as full sequence processing facilities. The cotton marker database developed at Clemson University has been well received and participation by the community has been significant. The continued expansion of this database will continue to serve the cotton research community and enhance efforts in cotton cultivar improvement, providing direct benefit to the cotton industry.