Submitted to: Euphytica
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/1/2007
Publication Date: 5/1/2008
Citation: Guo, Y., Saha, S., Yu, J., Jenkins, J.N., Kohel, R.J., Scheffler, B.E., Stelly, D.M. 2008. BAC-derived SSR chromosome locations in cotton. Euphytica. 161:361-370. Interpretive Summary: DNA markers linked with important traits improves the efficacy of breeding programs. Simple sequence repeat (SSR) markers are considered as the marker of choice for marker-assisted selection and germplasm evaluation in cotton. Generation of SSR markers from a large-insert BAC library have rapidly become the preferred choice for physical mapping of important genes in may crop species. The genetic mapping of the BAC-derived SSR markers will also empower high-resolution mapping and positional cloning of genes of interest. The objective of this research was to identify chromosomal locations of the BAC derived SSR markers in tetraploid cotton. Chromosomal location of SSR markers will provide a platform in the future for chromosome based sequencing of the cotton genome. Using deletion analysis method with aneuploid chromosome substitution lines we identified chromosomal locations of 39 BAC-derived SSR primer pairs to 18 different chromosomes or chromosome arms. There has been no previous report on chromosomal location of BAC-derived SSR markers in cotton. These markers will be useful in developing integrated physical and genetic maps of the cotton genome.
Technical Abstract: Bacterial artificial chromosome (BAC) libraries with large DNA inserts have rapidly become the preferred choice for physical mapping. BAC-derived microsatellite or simple sequence repeats (SSRs) markers facilitate integration of physical maps with genetic maps. The objective of this research was to identify chromosomal locations of the BAC-derived SSR markers in tetraploid cotton. Using deletion analysis method with interspecific aneuploid chromosome substitution lines, we identified chromosomal locations of 39 SSR primer pairs out of totally 192 SSR primer pairs derived from BAC clones of an Upland cotton genetic standard TM-1 line. There were 76 (39%) polymorphic primer pairs between TM-1 (G. hirsutum) and 3-79 (G. barbadense) and 59 (31%) polymorphic primer pairs between TM-1 and G. tomentosum, respectively. The polymorphic primer pairs within G. hirsutum were 15% (29). In this study, we located 39 SSR markers to 18 different chromosomes or chromosome arms. The similarity was 25% between TM-1 and G. raimondii Ulbr. (D5), 23% between TM-1 and G. arboreum L.A2, 23% between 3-79 and G. raimondii Ulbr. D5, and 27% between 3-79 and G. arboreum L. There has been no previous report on chromosomal locations of BAC-derived SSR markers in cotton. Our work should provide a platform in the future for chromosome based sequencing of the cotton genome and results of this study will advance genomic research in cotton.