Genetic dissection of upland cotton (Gossypium hirsutum) cultivars developed in Hubei Province by mapped SSRs.

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. The genetic similarity coefficient among 51 upland cotton cultivars was 0.598 on average, ranging from 0.378 to 0.817. The unweighted pair group method with arithmetic average cluster analysis revealed inconsistencies in other clustering patterns: "Tianmian1" was distinct from the rest of the materials and formed a separate cluster. This study will provide a guide for breeders to develop new cultivars efficiently and to choose parents, and it supports the need to introduce new alleles into the gene pool of the upland cotton breeding program in Hubei Province.