Differentiation of Tetraploid Cotton Species with cpSSR Markers.

Differentiation of tetraploid cotton species with chloroplast SSR markers

M.V. Sharma, S.K. Kantartzi, A.Shi and J. McD Stewart
Microsatellites, i.e. tandem DNA repeats characterized by short (<6bp), repetitive motifs, have been identified in plant nuclear and mitochondrial genomes as well as in the chloroplast genome, where AT repeats are almost exclusively observed. While nuclear microsatellites are the marker system of choice for genetic diversity, genome mapping, DNA fingerprinting and parentage analysis, chloroplast microsatellites (cpSSRs) are of special value in studies of plant population geographic structure and differentiation. The chloroplast genome is a useful source of markers for genetic studies of plants because of synteny and the general lack of heteroplasmy and recombination. The possibility to use cpSSRs instead of nSSRs to differentiate tetraploid cotton species (Gossypium hirsutum, G. barbadense, G. tomentosum, G. mustelinum and G. darwinii) was tested at 20 loci. Overall, our results indicate that chloroplast microsatellites can be used for haplotype discrimination in many contexts including diversity studies and in distinguishing between the species cytoplasms.