MULTI-RUST RESISTANCE IN BREAD WHEAT (TRITICUM AESTIVUM L.): INSIGHTS FROM MULTI TRAIT GWAS, CANDIDATE GENES, HAPLOTYPES, MGIDI ANALYSIS AND KASP VALIDATION

Wheat (Triticum aestivum) is a major global staple but suffers severe yield losses from leaf rust (LR), stem rust (SR), and stripe rust (YR). Developing cultivars with resistance to all three rusts is crucial but remains challenging due to pathogen diversity and complex host–pathogen interactions. In this study, a diverse panel of 346 bread wheat accessions was evaluated at the seedling stage for two years against prevalent and virulent pathotypes. Phenotypic data, analyzed using Best Linear Unbiased Estimators (BLUEs), showed right-skewed distributions for LR and YR, while SR displayed a bimodal pattern. Genotyping with the 35K Axiom Wheat Breeders Array followed by stringent quality control yielded 11,910 high-quality SNPs. Population structure analysis identified five subpopulations, and whole-genome linkage disequilibrium decay was estimated at 3.49 Mb. Multi-trait genome-wide association analysis using the statgenQTL×T package detected 11 significant marker–trait associations (MTAs) located on chromosomes 3A, 3B, 3D, and 7B, with chromosome 3D harboring the maximum associations. These MTAs corresponded to 47 disease resistance genes, 22 of which showed high expression under at least one condition. Haplotype analysis revealed eight haplotypes, of which H006 and H007 exhibited superior multiple rust resistance (MRR). Multi-Trait Genotype-Ideotype Distance Index (MGIDI) analysis identified 17 elite accessions, including IC427824 and HGP1-359, as potential donors. Furthermore, three key KASP markers (AX94381808, AX94874313, and AX94807942) were developed and validated. This integrated genomic strategy provides valuable resources to accelerate the breeding of wheat cultivars with durable resistance to all three rusts.