Dissecting adult plant resistance to stripe and leaf rust in advanced Indian wheat breeding lines through a genome-wide association study

While several genome-wide association studies (GWAS) have examined rust resistance in diverse Indian wheat germplasm, none have specifically focused on indigenously bred advanced breeding lines. This study investigates the genetic basis of adult plant resistance to leaf rust and stripe rust in such lines, using a high-density single nucleotide polymorphism (SNP) array and the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) multi-locus GWAS model, complemented with haplotype-based linkage disequilibrium analysis. Multi-environment phenotyping was conducted across three seasons to capture the effects of environmental variation. The analysis identified 17 and 7 significant SNP-trait associations (Marker trait associations, MTAs) for leaf rust and stripe rust, respectively, including both known and novel loci located on chromosomes 3B, 5B, 7B, and 6 A. These MTAs were found in proximity to well-characterized rust resistance genes such as Lr12/Lr31, Yr27/Lr13, Lr18, Lr52/Yr47, and Yr66, confirming previous reports from gene postulation and marker-based studies. LD-block analysis identified the novel quantitative trait loci (QTLs) qLr.iari.3BL.1, qLr.iari.5BL.2, qLr.iari.7BL.3, and qSr.iari.6AL.1, which exhibited strong phenotypic effects and consistent performance across environments, making them promising candidates for marker-assisted selection. Among these, qLr.iari.3BL.1, flanked by SNP AX-94,715,535, emerged as a stable and widely distributed resistance locus in Indian wheat. The QTLs qLr.iari.5BL.2 and qLr.iari.7BL.3 were detected in two environments and appear to reside in genomic regions with no previously reported resistance genes. The findings underscore the continued breeding value of classical resistance genes (e.g., Lr13/Yr27) and the potential of novel loci for developing durable, rust-resistant wheat varieties adapted to Indian conditions.