Multi-environment GWAS and Post-GWAS prioritization reveal stable genomic regions for Powdery Mildew and resistant donors in bread wheat through MGIDI analysis

Powdery Mildew (PM), caused by Blumeria graminis f. sp. tritici (Bgt), remains a recurrent constraint to wheat production in cool-humid wheat ecologies and can expand under susceptible cultivars, dense crops and high nitrogen inputs. In India, the disease is especially prominent in hilly regions and has been reported as a serious issue in epidemiologically important zones including the north-western plains under conducive seasons. This study evaluated 403 bread wheat germplasm accessions (predominantly landraces) across four Indian PM hot-spot locations over two seasons and quantified their adult-plant response to PM. Genome-wide association study (GWAS) was conducted using 15,845 polymorphic SNPs. Across the environments, genotypic effects were highly significant with broad-sense heritability ranging from 85 to 92%, indicating strong genetic control and favorable prospects for selection. Multi-model GWAS identified 11 significant marker-trait associations (MTAs), including a putatively novel and stable association on chromosome 5B ( Affx-92565503 at 663,523,422 bp; candidate gene id: TraesCS5B03G1205400 ) detected across all environments and GWAS models. Furthermore, Affx-92145634 (43,405,817 bp; gene id: LN999386 ) has been found in a close proximity of well-known characterized PM resistant gene, Pm2b on chromosome 5D . Post-GWAS analysis highlighted plausible defence-related candidate genes (NLR-type resistance, redox homeostasis, chromatin remodeling, secondary metabolism and folate pathway genes), and multi-trait selection using MGIDI prioritized elite resistant accessions combining low PM scores and high favorable-allele counts. These results can be potentially targeted for development of improved PM resistant wheat varieties.