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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.