Projects

MUSB: Development of Microsatellite Markers for Cotton from Acala 'Maxxa' BAC-end Sequence Information

• Contributors
  Mauricio Ulloa, James E. Frelichowski (Cotton Inc Fellow)
  USDA-ARS, WCIS, Research Unit, Cotton Enhancement Program, 17053 N. Shafter Ave., Shafter, CA, 93263

  Michael Palmer (Cotton Inc Fellow), Dorrie Main *, Jeffrey Tomkins
  Genetics, Biochemistry & Life Science Studies, Clemson University Genomics Institute, Main Bioinformatics Laboratory, Clemson, SC 29634

• Project Description
  A new set of microsatellites or simple sequence repeat (SSR) markers with di-, tri-, tetra-, and pentanucleotide sequence repeats were developed from BAC-end sequence information. The large insert BAC library was constructed from Acala ‘Maxxa’, standard California cotton (Gossypium hirsutum L.) cultivar for fiber quality. Clones have an average insert size of nearly 140 kb. A total of 2603 SSR sequences were obtained from the Genomics Institute, Clemson University, SC. Microsatellite (MUSB) markers were designed and screened for PCR product polymorphisms on a four cotton panel (G. hirsutum ‘Maxxa’, G. hirsutum TM-1, G. barbadense 3-79 and G. raimondii D5-3). From a total of 1316 BAC-derived MUSB primer-pairs, 1,082 (82%) of the DNA markers successfully amplified PCR products from a survey panel of three Gossypium species, of which 285 (26.3%) were polymorphic between the species G. hirsutum and G. barbadense using electrophoretic separation on an agarose gel system. Genetic map position and chromosomal location on the tetraploid cotton were assigned for some polymorphic markers. These BAC-derived loci were mapped to 21 chromosomes and 11 linkage groups. New microsatellite loci were designated “MUSB”: M for microsatellite, U last name of principal investigator, S for simple, and B for BAC. The information provided here includes: description, primer sequences, map and chromosomal location, and polymorphic data for the 1316 MUSB markers from the panel of three Gossypium species, four cultivars.
  
  
    Download the MUSB marker data (Excel format).
    Download the MUSB primers (Excel format).
    Download the MUSB microsatellite sequences (fasta format).
    Search your sequences against the MUSB microsatellites using the BLAST or FASTA server.
    References
  • Frelichowski JEJr, Palmer MB, Main D, Tomkins JP, Cantrell RG, Stelly DM, Yu J, Kohel RJ, Ulloa M. 2006. Cotton genome mapping with new microsatellites from Acala 'Maxxa' BAC-ends. Molecular Genetics Genomics. 275(5): 479-491
  • Frelichowski JE, Ulloa M, Palmer M, Main D, Tomkins JP, Stelly DM, Cantrell RG, Kohel RJ, Yu J. 2005. Genetic, physical and QTL mapping assessments of BAC-end derived microsatellite markers developed from cotton (Gossypium. hirsutum L.) Acala ‘Maxxa’. Plant and Animal Genome XIII Conference, San Diego, CA, Jan 15-19, 2005.
  • Frelichowski JE, Ulloa M, Tomkins JP, Palmer M, Main D, Stelly DM, Cantrell RG. 2004. New BAC-end derived microsatellite markers in cotton (Gossypium. hirsutum L.) Acala ‘Maxxa’. The 49th ASA-CSSA-SSSA International Annual Meeting with the Canadian Society of Soil Science, Seattle, WA, Oct 31 - Nov 4.
  • Palmer M, Main D, Frelichowski JE, Tomkins JP, Ulloa M. 2004. High-throughput development of new molecular markers for cotton. National Cotton Council Beltwide Cotton Conference, San Antonio, January 5-9. P: 1131