Association Mapping and Domestication Analysis to Dissect Genetic Improvement Process of Upland Cotton Yield-Related Traits in China

Background: Cotton fiber yield is a complex trait, which can be influenced by multiple agronomic traits. Unravelling the genetic basis of cotton fiber yield related traits contributes to genetic improvement of cotton fiber. ResultsIn this study, 503 upland cotton varieties covering the 4 breeding stages in China were used to for association mapping and domestication analysis of upland cotton yield-related traits in China. 140 quantitative trait loci (QTLs) significantly associated with ten fiber yield related traits were identified, among which, 29 QTLs showed an increasing trend contribution to cotton yield-related traits from BS1 to BS4, and 26 QTLs showed decreased trend effect. 4 favorable alleles of 9 major QTLs (R 2 ≥3) were strongly selected during the breeding stages, and the candidate genes of the 4 strongly selected alleles were predicated according to the gene function annotation and tissue expression data. ConclusionsThe study not only uncovers the genetic basis of 10 cotton yield related traits, but also provides genetic evidence for cotton improvement during the cotton breeding process in China.