Development of a Cotton Marker Database (CMD) for Gossypium genome and genetic research

1
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
SummaryOver 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.
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. 7132.

• CMD Main Goals
• Collect and integrate all the publicly available
  cotton SSR and SNP data in a centralized,
• curated, non-redundant online oracle
  database
• 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 Tools Resources
Tools
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.
Mapped SSRs
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
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.
Acknowledgments We acknowledge with thanks
Cotton Incorporated for funding this project and
the cotton community for their support, data and
feedback.