Genome-wide association mapping of stress-tolerance traits in cotton

Environmental stresses severely impair cotton production worldwide. To identify the genetic basis of, and molecular markers associated with, environmental stresses such as salt, cold and Verticillium wilt, association mapping of salt-, cold-, and disease-tolerance traits was performed in a population of 503 upland cotton accessions using 179 polymorphic SSR markers and 11,975 array-derived SNP markers. Salt and cold tolerance was evaluated via the relative germination rate(RGR) of the seeds under seven and four environments, respectively. The disease index of Verticillium wilt was investigated for two years in the field in Xinjiang. These three traits showed large variation across environments. A genome-wide association study revealed that 31, 19, and 15 SSR markers were associated with RGR-Salt(the relative germination rates of seeds under salt stress),RGR-Cold(the relative germination rates of seeds under cold stress), and DIV(the disease index of Verticillium wilt), respectively. Six SNPs in seven environments and two SNPs in BLUP(best linear unbiased prediction) results were associated with RGR-Salt, and the phenotypic variance explained ranged from 3.96 to 5.00%. Two SNPs(i02237 Gh, i02243 Gh)on D01 were concluded to be stable genetic loci associated with RGR-Salt. A total of 223 genes were found in a candidate gene interval(D01, 37771–1942912). Of these four genes,GhPIP3A, GhSAG29, GhTZF4, and GhTZF4a, showed expression changes in sensitive and tolerant genotype accessions under salt stress, and were assigned as candidate genes associated with RGR-Salt. This study revealed the genetic basis of stress resistance in upland cotton and will facilitate stress-resistance breeding in cotton.