The identification of simple sequence repeat (SSR) markers associated with salt tolerance in cotton contributes to molecular assisted selection (MAS), which can improve the efficiency of traditional breeding. In this study, 134 samples of upland cotton cultivars were selected. The seedling emergence rates were tested under 0.3% NaCl stress. A total of 74 SSR markers were used to scan the genomes of these samples.
The genetic diversity of 51 upland cotton cultivars with different parental origins and breeding periods that were developed in Hubei Province was studied on the basis of 237 mapped simple sequence repeat markers covering the cotton genome. A total of 108 polymorphic primer pairs amplified 196 loci; the polymorphism information content range was 0.04 to 0.83, with an average of 0.46. A model-based clustering analysis (STRUCTURE) of the genomic data identified 3 clear subpopulations, and the result was confirmed by principal components analysis.