Molecular diversity, genomic constitution, and QTL mapping of fiber quality by mapped SSRs in introgression lines derived from Gossypium hirsutum × G. darwinii Watt.

Because the genetic basis of current upland cotton cultivars is narrow, exploring new germplasm resources and discovering novel alleles relevant to important agronomic traits have become two of the most important themes in the field of cotton research. In this study, G. darwinii Watt, a wild cotton species, was crossed with four upland cotton cultivars with desirable traits. A total of 105 introgression lines (ILs) were successfully obtained. By using 310 mapped SSRs evenly distributed across the interspecific linkage map of G. hirsutum × G. barbadense, these 105 ILs and their corresponding parents were analyzed. A total of 278 polymorphic loci were detected among the 105 ILs, and the average length of introgression segments accumulated to 333.5 cM, accounting for 6.7 % of the whole genome. These lines included many variations. However, high similarity coefficients existed between lines, even between those derived from different parents. Finally, all the ILs and their upland cotton parents were used for association mapping of fiber quality in three environments. A total of 40 SSRs were found to be associated with five fiber quality indexes (P < 0.05) with some being detected in multiple environments and traits. The contribution rate for trait variation was 6.31 % on average, ranging from 2.00 to 14.79 %. This study develops novel ILs for cotton genetics and breeding and provides the basis for future research into fine mapping of genes related to fiber quality, analyses of candidate gene association, and molecular marker-assisted breeding.