Genome-wide association study and gene network analysis of drought tolerance in wheat during early growth

Introduction Drought is one of the most damaging abiotic stresses, reducing seed germination, impairing seedling establishment, and ultimately decreasing crop yield. The objectives of the present study were to identify associated SNP markers and genes associated with drought tolerance in wheat at early developmental stages and to explore gene networks that reveal gene–gene interactions under drought stress. Methods A total of 168 genotypes were tested for drought tolerance under 20% PEG (drought stress) and 0% PEG (control). Genome-wide association study, annotation analyses, gene network analysis were performed. Results High genetic variation was observed among genotypes for all traits scored under both conditions. The GWAS identified 130 and 128 significant SNPs under drought and control conditions, respectively. Gene annotation identified 98 genes responsive to drought stress, of which 54 have been previously reported to be associated with drought tolerance. Ten SNPs were common between control and drought treatments, nine of which were located within genes controlling variation in germination percentage. Gene network analysis of these nine gene models showed that they were organized into eight distinct pathways. Discussion These networks were regulated by master genes encoding proteins with diverse biological functions, including rRNA and tRNA methyltransferases, protein kinases, and potassium transmembrane transporters. These findings provide fundamental insights into the genetic basis of drought tolerance in wheat. These results indicate that GWAS is a robust and instrumental approach to identifying the associated genes. The network analysis explored the interactions among several genes, not the effect of each gene individually, which will help us to understand the drought tolerance during early stages in wheat. These findings are fundamental to better understand drought tolerance in wheat.