Email: zone4vijay@gmail.com

Multi-locus genome-wide association study (ML-GWAS) was undertaken using a set of 320 diverse spring wheat accessions, which were each genotyped for 9,626 SNPs. The association panel underwent replicated trials in four distinct environments, consisting of two irrigated (IR) and two rainfed (RF) conditions. We recorded phenotypic data for nine essential traits: days to heading, days to anthesis, days to maturity, plant height, grain filling duration, grain number per ear, grain weight per ear, thousand-grain weight, and grain yield, alongside seven stress-related indices.

Our analysis unveiled a total of 76 significant marker-trait associations (MTAs) across the nine traits, with 35 MTAs found in IR and 33 MTAs in RF environments. Additionally, eight MTAs were common to both environments. Furthermore, we identified 153 MTAs related to the seven stress-related indices. Among these, ten MTAs co-localized with previously known QTL/MTAs, while the remaining MTAs represented novel discoveries, contributing to the existing knowledge base.

In addition to MTAs, we identified three favourable haplotypes associated with agronomic traits: one for enhancing performance in RF conditions and two for improving performance in IR environments. We also pinpointed twenty promising candidate genes (CGs) associated with seven distinct biological activities using the wheat genome assembly IWGSC1.0.

Notably, the expression patterns of four out of the 20 genes, namely Trehalose-6-Phosphate, APETALA2/Ethylene-responsive factor, DNA-binding One Zinc Finger, and Gibberellin dioxygenases, demonstrated induction in response to drought stress in wheat seedlings. These MTAs, haplotypes, and CG-based markers hold significant potential for marker-assisted breeding to enhance wheat drought tolerance.