BAC-derived SSR markers chromosome locations in cotton Academic Article uri icon


  • Bacterial artificial chromosome (BAC) libraries with large DNA fragment inserts have rapidly become the preferred choice for physical mapping. BAC-derived microsatellite or simple sequence repeats (SSRs) markers facilitate the integration of physical maps with genetic maps. The objective of this research was to identify chromosome locations of the BAC-derived SSR markers in tetraploid cotton. A total of 192 SSR primer pairs were derived from BAC clones of an Upland cotton genetic standard line TM-1 (Gossypium hirsutum L.). Metaphor agarose gel electrophoresis results revealed 76 and 59 polymorphic markers between TM-1 and 3-79 (G. barbadense) or G. tomentosum, respectively. Using deletion analysis method, we assigned 39 markers out of the 192 primer pairs to 17 different chromosomes or chromosome arms. Among them, 19 and 17 markers were localized to A-subgenomes (chromosome 1-13) and D-subgenomes (chromosome 14-26), respectively. The subgenome status for the remaining three markers remained unclear due to their two potential chromosome locations achieved by tertiary monosomic stocks deletion analysis. Chromosomal assignment of these BAC-derived SSR markers will help in integrating physical and cotton genetic linkage maps and thus facilitate positional candidate gene cloning, comparative genome analysis, and the coordination of chromosome-based genome sequencing project in cotton. 2007 GovernmentEmployee: U. S. Department of Agriculture, Agricultural Research Service.

published proceedings


author list (cited authors)

  • Guo, Y., Saha, S., Yu, J. Z., Jenkins, J. N., Kohel, R. J., Scheffler, B. E., & Stelly, D. M.

citation count

  • 18

complete list of authors

  • Guo, Yufang||Saha, Sukumar||Yu, John Z||Jenkins, Johnie N||Kohel, Russell J||Scheffler, Brian E||Stelly, David M

publication date

  • June 2008