Exploring genomic loci and candidate genes associated with drought tolerance indices in spring wheat evaluated under two levels of drought

Wheat is a major global crop, and increasing its productivity is essential to meet the growing population demand. However limited water resources is the primary constraint. This study aimed to identify genetic factors associated with drought tolerance using a diverse panel of 287 wheat genotypes evaluated under well-watered and drought-stressed conditions. Water Use Efficiency (WUE) and Grain Yield (GY), along with drought tolerance indices, were assessed. A genome-wide association study (GWAS) using 26,814 high-density SNP markers identified loci linked to these traits, with 768 SNPs showing significant associations. Additionally, genomic selection (GS) was performed using the rrBLUP model to predict trait performance across environments.

Among the 768 significant SNPs associated with the measured traits at -log10 (P) ≥ 3, 81 SNPs were mapped with a higher threshold -log10 (P) ≥ 4, indicating pleiotropic and QTL-by-environment interaction effects. Several novel and known genes, previously reported to have functions related to biotic and abiotic stresses response were linked to significant SNPs. Among the drought indices evaluated, stress tolerance index (STI), geometric mean productivity (GMP), and tolerance index (TOL) were the most reliable indicators for selecting stable, high-yielding genotypes under drought and control conditions. The same three indices exhibited high prediction values under the severe drought stress (SS) condition. Five genotypes were identified as promising candidates for breeding programs based on their superior drought tolerance, high grain yield, and nutritional value.

This study provides valuable insights into the genetic basis of drought tolerance in wheat, highlighting key SNPs and genomic regions associated with improved water use efficiency and yield stability. The findings contribute to the development of drought-tolerant wheat varieties with optimized water utilization to achieve increased yield per unit of water at diverse water levels, ultimately contributing to sustainable agriculture and food security.