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Development of a Cotton Marker Database (CMD) for Gossypium genome and genetic research Anna Blenda1, Taein Lee2,Randall Svancara2, Don Jones3, Doreen Main2 1Department of Genetics and Biochemistry, Clemson University, 51 New Cherry St., Clemson, SC, 29634, USA 2Department of Horticulture and Landscape Architecture, Washington State University, WA,99164, USA 3Agricultural Research Division, Cotton Incorporated, 6399 Weston Parkway, Cary, NC, 27513, USA Summary 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 SNPcontaining 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. CMD Main Goals • Collect and integrate all the publicly available cotton SSR and SNP data in a centralized, curated, non-redundant online oracle database; http://www.cottonmarker.org Advisory Board Referencing CMD: Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J-M, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D. 2006. CMD: A Cotton Database Resourse for Gossypium Genomics. BMC Genomics. 7:132. CMD Tools & Resources Tools • Provide access to the CMD standardized panel screened data; • Provide a set of comprehensive interface tools for rapid data retrieval; • Provide a set of stand alone microsatellite and SNP data mining tools; • Provide a communication portal for the cotton research community collaboration. CMD SSR Projects Currently, CMD contains information on 8,915 annotated cotton microsatellites from 13 SSR projects (BNL, CIR, CM, DPL, Gh, HAU, JESPR, MGHES, MUSB, MUSS/MUCS, NAU, STV, TMB) which can be viewed and downloaded: Search engine The individual project pages access to public data currently available for each microsatellite project, all of which have been approved by the project principal investigator. The standardized project information includes: summary abstract, contact information, related publications, microsatellite information, including GenBank accession numbers, clone sequences, primer sequences, repeat motif, standardized panel screened data (if available), mapping data, and any homology with known proteins. New markers need to be characterized systematically prior to application. After consultation and discussion with many cotton researchers, a standardized panel of 12 diverse genotypes was selected from cultivated and exotic cottons. This panel represents a balanced diversity of the core Gossypium germplasm that includes genetic standards, base mapping parents, BAC donors, subgenome representatives, unique breeding lines, exotic introgression sources, and four contemporary Upland cottons each with significant acreage. Panel screened data is available for four SSR projects: BNL, CIR, JESPR, STV. CMD Standardized Panel Acknowledgments: Mapped SSRs CMap 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. We acknowledge with thanks Cotton Incorporated for funding this project and the cotton community for their support, data and feedback.