Genetic Dissection of Allelic Loci Associated with Economic Traits of Upland Cottons in Xinjiang

Objective] We completed anassociation analysis of economic traits for upland cotton using simple sequence repeat (SSR) markers. We then explored the allelic variation sites to analyze the genetic basis of economically important traits, studied the genetic mechanism of Xinjiang upland cotton, and aimed to accelerate efficient breeding of upland cotton. Method] We carried out polymorphic scanning on 156 upland cotton varieties in Xinjiang by screening 73 pairs of SSR markers encompassing the whole cotton genome. We constructed boxplot maps using R statistical computing software and graphics language and used TASSEL software to correlate yield or fiber quality traits with significant allelic variation loci. Results] We obtained 10 allelic variation loci related to yield traits using the correlation analysis of Xinjiang upland cotton varieties from six different environments. The interpretation rate of phenotypic variation ranged from 6.69% to 9.88% with an average of 8.43%. Twenty-three allelic variation loci associated with fiber quality traits and phenotypic variation interpretation rates ranged from 3.73% to 13.22% with an average of 7.52%. The 22 detected quantitative trait loci were reported in previous studies and 10 showed the same associated traits as previously reported. Conclusion] The population genetic structure of Xinjiang upland cotton varieties is simple, the linkage disequilibrium level is low, and the phenotypic traits show a stable trend under six environments. Using association analysis, we discovered unique allelic variation genes related to yield and fiber quality and diverse allele loci.