CMD - Cotton Marker Database

Overview
The Cotton Marker Database is a community collaboration initiated and funded by Cotton Incorporated to provide centralized access to all 17,448 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
-  DOW SSR project (100 mapped genomic SSRs from Dow AgroSciences) is available for view, search
   and download.
-  NBRI SSR project (263 genomic SSRs and 1970 EST-SSRs) from the National Botanical Research
   Institute (India) is available for view, search and download.
-  Data of 29 agriculturally important cotton traits linked to the CMD SSRs have been added to the
   new sections View Traits and Search Traits.
-  View mapped microsatellites for F2, BC1, BC2, DH, RIL and 4WC (26 cotton genetic maps) in the
   comparative map viewer cMap.
- MON SSR project (2,937 genomic SSRs provided by Monsanto) is available for view, search and
   download.
-  The SSR project pages contain all available marker, primer, sequence, mapping, contact and
   publication information.
-  The SNP 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.
-  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 2010, 24 new publications are available.
-  Since 2009, CMD has been accessed by users from 101 countries and 48 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. Ramesh Kantety will provide data for 200 new cotton genomic SSRs.