Projects

BNL: Microsatellites Derived from Gossypium hirsutum cv. Delta Pine 90 Small Insert Enriched Genomic Libraries

• Contributors
  Ben Burr, Michael Blewitt and Eileen Matz
  Biology Department
  Brookhaven National Laboratory
  Upton, NY 11973 USA
  
  Phone 1-631-344-3396
  Fax 1-631-344-3407
  E-mail: burr@bnl.gov
  URL: http://ukcrop.net/perl/ace/search/CottonDB
  
  
• Project Description
  In cotton, the first SSR markers were developed at Brookhaven National Laboratory (prefix “BNL”). The BNL microsatellites was derived from G. hirsutum cv. Delta Pine 90 small insert genomic libraries enriched for (GA/CT)n and (CA/GT)n inserts. DNA from 4,046 colonies with positive hybridization signals was sequenced and primers were made for 766 unique flanking sequences with inserts containing at least 10 simple repeats. Primer pairs were tested against a panel of Gossypium hirsitum and Gossypium barbadense cultivars and those that that gave products for all cultivars and showed at least one polymorphism were selected for further work. Of these, 74 primer pairs failed, 303 were not polymorphic, and 389 were polymorphic. A total of 379 primer pairs are presented in the CMD.
  
  
  •   View / Download the standardized panel screened BNL marker data (375).
  •   Download the BNL primers (Excel format).
  •   Download the BNL microsatellite sequences (fasta format).
  •   Search your sequences against the BNL microsatellites using the BLAST or FASTA server.
  •   References
  • Konan ON, D'Hont A, Baudoin JP, Mergeai G. 2007. Cytogenetics of a new trispecies hybrid in cotton: [(Gossypium hirsutum L. x G. thurberi Tod.)2 x G. longicalyx Hutch. & Lee]. Plant Breeding.
    126(2): 176-181.
  • Lacape JM, Dessauw D, Rajab M, Noyer JL, Hau B. 2007. Microsatellite diversity in tetraploid Gossypium germplasm: assembling a highly informative genotyping set of cotton SSRs. Molecular Breeding.
    19(1): 45-58
  • Wang K, Guo W, Zhang T. 2007. Development of one set of chromosome-specific microsatellite-containing BACs and their physical mapping in Gossypium hirsutum L. Theoretical and Applied Genetics. DOI: 10.1007/s00122-007-0598-x.
  • Yang X, Zhang X, Jin S, Fu L, Wang L. 2007. Production and characterization of asymmetric hybrids between upland cotton Coker 201 (Gossypium hirsutum) and wild cotton (G. klozschianum Anderss). Plant Cell, Tissue and Organ Culture. DOI: 10.1007/s11240-007-9245-0.
  • Liu D, Guo X, Lin Z, Nie Y, Zhang X. 2006. Genetic diversity of Asian cotton (Gossypium arboreum L.) in China evaluated by microsatellite analysis. Genetic Resources and Crop Evolution. 53(6): 1145-1152.
  • Zhang J, Lu Y, Cantrell RG, Hughs E. 2005. Molecular marker diversity and field performance in commercial cotton cultivars evaluated in the Southwestern USA. Crop Science. 45: 1483-1490.
  • Guo W-Z, Fang D, Yu W-D, Zhang T-Z. 2005. Sequence divergence of microsatellites and phylogeny analysis in tetraploid cotton species and their putative diploid ancestors. Journal of Integrative Plant Biology. 47(12) : 1418-1430.
  • Gao W, Chen ZJ, Yu JZ, Raska D, Kohel RJ, Womack JE, Stelly DM. 2004. Wide-cross whole-genome radiation hybrid mapping of cotton (Gossypium hirsutum L.). Genetics. 167(3): 1317-29.
  • Lacape J-M, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B. 2003. A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum x Gossypium barbadense backcross population. Genome. 46(4): 612-26.
  • Gutierrez OA, Basu S, Saha S, Jenkins JN, Shoemaker DB, Cheatham CL, McCarty JC. 2002. Genetic distance among selected cotton genotypes and its relationship with F2 performance. Crop Science. 42: 1841-1847
  • Liu S, Saha S, Stelly D, Burr B, Cantrell RG. 2000. Chromosomal assignment of microsatellite loci in cotton. Journal of Heredity. 91(4): 326-32.
  • Liu S, Cantrell RG, McCarty JC, Stewart JMcD. 2000. Simple sequence repeat-based assesment of genetic diversity in cotton race stock accessions. Crop science. 40: 1459-1469.