Projects

TMB Project : Development of Integrative Microsatellite Markers from TM-1 BAC Libraries

• 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".
  
  
    Download the TMB marker data (Excel format).
    Download the TMB primer sequences (Excel format).
    Download the TMB microsatellite sequences (fasta format).
    Search your sequences against the TMB microsatellites using the BLAST or FASTA server.
    References
  
  • Abdurakhmonov IY, Buriev ZT, Saha S, Pepper AE, Musaev JA, Almatov A, Shermatov SE, Kushanov FN, Mavlonov GT, Reddy UK, Yu JZ, Jenkins JN, Kohel RJ, Abdukarimov A. 2007. Microsatellite markers associated with lint percentage trait in cotton, Gossypium hirsutum. Euphytica. 156(1-2): 141-156..
  • Abdurakhmonov IY, Kushanov FN, Djaniqulov F, Buriev ZT, Pepper AE, Fayzieva N, Mavlonov GT, Saha S, Jenkins JN, Abdukarimov A. 2007. The Role of Induced Mutation in Conversion of Photoperiod Dependence in Cotton. Journal of Heredity. 98: 258 - 266.
  • Yu J, Kohel RJ, Dong RJ. 2002. Development of integrative ssr markers from TM-1 BACs. Proceedings of Beltwide Cotton Conference CD-Rom.