Dissecting multi‐rust resistance in wheat through genome‐wide association study, haplotype analysis, and marker validation

Wheat is a major global staple food affected by three diseases: leaf rust (LR), stem rust (SR), and stripe rust (YR), all of which can cause substantial yield losses. Identifying genotypes with broad-spectrum resistance to diverse pathotypes of all three rusts remains a major challenge. In this study, we examined the genomic basis of resistance to three rust diseases LR, SR, and YR in a diverse panel of 346 bread wheat (Triticum aestivum) accessions. The seedling stage phenotypic evaluation was performed for 2 years using prevalent and virulent pathotypes. Based on best linear unbiased estimators, LR and YR displayed right-skewed distributions, whereas SR showed a bimodal pattern. Genotyping with the 35K Axiom Wheat Breeders Array, followed by quality control, yielded 11,910 high-quality single nucleotide polymorphisms (SNPs). Population structure analysis revealed five subpopulations and a whole genome linkage disequilibrium decay of 3.49 Mb. Multi-trait genome-wide association studies identified 11 significant SNPs distributed on chromosomes 3A, 3B, 3D, and 7B, which were associated with 47 disease resistance genes, 22 of which were highly expressed in at least one condition. The haplotype analysis revealed eight different haplotypes, where H006 and H007 were superior in terms of multiple rust resistance (MRR). Note that 17 elite accessions, including IC427824 and HGP1-359, were selected using multi-trait genotype ideotype distance index analysis. Three key Kompetitive allele specific polymerase chain reaction (KASP) markers, AX94381808, AX94874313, and AX94807942 were developed and validated. This integrated genomic approach advances the identification process and can accelerate the breeding of wheat cultivars with durable MRR.