Chromosomal assignment of microsatellite loci in cotton

Microsatellite markers or simple sequence repeats (SSRs) represent a new cl ass of genetic markers for cotton (Gossypium sp,), Sixty-five SSR primer pa irs were used to amplify 71 marker loci and genotype 13 monosomic and 27 mo notelodisomic cotton cytogenetic stocks, Forty-two SSR loci were assigned t o cotton chromosomes or chromosome arms. Thirty SSRs were not located to sp ecific chromosomes in this study, Nineteen marker loci were shown to occur on the A subgenome and 11 on the D subgenome by screening accessions of G. herbaceum (2n = 2x = 26 = 2A(1)) and G. raimondii(2n = 2x = 26 = 2D(5)). Th e aneuploid stocks proved to be very powerful tools for localizing SSR mark ers to individual cotton chromosomes. Multiplex PCR bins of the SSR primers and semiautomated detection of the amplified products were optimized in th is experiment, Thirteen multiplex PCR bins were optimized to contain an ave rage of 4 SSR primer pairs per bin. This provides a protocol for high-throu ghput genotyping of cotton SSRs that improves the efficiency of genetic map ping and marker-assisted programs utilizing SSR markers.