Overview
The Cotton Marker Database is a community collaboration initiated and funded by Cotton Incorporated to provide centralized access to all 8,915 publicly available SSRs and 312 mapped cotton RFLP sequences containing SSRs. Currently, single nucleotide polymorphisms computationally mined in cotton ESTs (eSNPs) from the NCBI dbEST database have been included. The standardized panel screened data is available for many of the microsatellites. The standardized panel consists of 12 diverse genotypes selected from cultivated and exotic cottons.

Points of Interest
  The SSR project pages contain all available marker, primer, sequence, mapping, contact
    and publication information.
  The eSNP project pages contain summary information about CAP3 unigene
    asemblies and SNP data mining results.
  Download standardized panel screened marker data: 375 BNL, 127 JESPR, 204 CIR,
    150 STV, and 200 DPL.
  View mapped microsatellites for F2, BC1, BC2 and RIL (10 cotton genetic maps) in the
    comparative map viewer cMap.
  Mine sequences for SSRs using the CMD SSR server.
  Search new sequences against existing SSRs using the batch upload BLAST or FASTA
  server tools.
  Since 2008, 15 new publications are available.
  Since 2008, CMD has been accessed by users from 39 countries and 30 states in USA.
  CMD published in BMC Genomics 2006, 7: 132.

News
Cotton genome sequencing and assembly by the Joint Genome Institute is in progress.

Forthcoming Data
  Dr Allen Van Deynze provided data for the first cotton SNP project. Available soon.
  Dr. Ramesh Kantety will provide data for 200 new cotton genomic SSRs.
  Dr. Siva Kumpatla (Dow AgroSciences) will provide data for 100 new mapped genomic
    SSRs.