CMD - Cotton Microsatellite Database

Contributors
John Yu
Russell J. Kohel
Jianmin Dong

USDA-ARS, Southern Plains Research Center, College Station, TX, 77845. Phone : (979) 260-9237, Fax : (979) 260-9333
Project Description
Five large-insert BAC and BIBAC libraries were constructed from TM-1, the genetic standard of Upland cottons, and its nearly isogenic line (NIL) containing a major glandless gene. More than 2,000 BAC clones that contain a SSR locus with repeat motif of CA, GA, TA, or GAA were identified and sequences of the subclones were generated. Approximately 1,000 new SSR loci from positive BAC clones of the TM-1/HindIII and TM-1/BamHI BAC libraries were developed. Forward and reverse primers were designed from the flanking sequence of the SSR loci used to screen for polymorphism information content (PIC) values on a standardized cotton panel that consists of 12 diverse genotypes. The success rate of developing SSR markers from SSR subclones through amplification of SSR loci was about 50%. Analysis also revealed that about 60% of the SSRs were polymorphic in the interspecific TM-1 x 3-79 population. Sixty-one percent of these SSR primers amplified single-copy, co-dominant DNA fragments. Such SSR markers provide a valuable tool for identifying A- or D-specific subgenomes of the cultivated Upland cottons (AD genome). Collaboration with Cotton Inc. and other cotton researchers led to the establishment and distribution of a standardized set of 12 diverse cotton genotypes for a systematic evaluation of cotton DNA markers. Sequence analysis by BLAST search against the cotton SSR database showed that a majority of the SSR subclones were new, indicating that the cotton genome is abundant in SSR loci. Initial sets of 192 pairs of BAC-derived SSR primer sequences were distributed nationally and internationally for specific cotton genetic studies. "TM" stands for genetic standard TM-1 from which BAC/BIBAC libraries were constructed. "B" in the "TMB" stands for BAC/BIBAC libraries".