A genome-wide association study identifies novel QTL for wheat yield stability under drought stress

Global climate changes have led to severe and frequent drought stress in many areas, seriously threatening the stability of yield in wheat. Exploring the quantitative trait loci for yield stability under drought condition is needed for wheat molecular breeding. In this study, we collected a panel of 432 diverse wheat accessions from different regions around the world and evaluated the drought stress susceptibility index of wheat yield-related phenotypes under drought stress and genotyped the panel with the wheat660K SNP array. Genome-wide association analysis has identified 40 yield stability-related loci, which distribute on various chromosomes. Four loci on Chromosome 1 A, 2B, 3 A and 7B are associate with more than two phenotypic indicators, explaining 1.59% − 8.07% of the phenotypic variation. Among them, Qgns.cas-3A.2 is a novel QTL for wheat yield stability under drought stress. Venn diagram analysis on the drought-responsive expression patterns of Qtgw.cas-3A genes in drought-tolerant and sensitive cultivars, and linkage disequilibrium analysis of the 57Kb region flanking SNP marker AX-108784842 on chromosomes 3 A which displays the highest confidence identified the same candidate gene, which encodes a glycosyl hydrolases family 17 protein. Haplotype analysis indicated that GG allele of this gene is the favorable allele for wheat yield stability under drought. Taken together, these results provide new insights on understanding the genetic basis of wheat yield stability under drought stress and new tools for developing molecular markers to engineer drought-tolerant wheat cultivars.