Molecular Characterisation of Diverse Wheat Germplasm for Enhanced Resistance to Puccinia triticina

Leaf rust (LR) epidemics present a persistent threat to global wheat production, despite the presence of resistance (Lr) genes in wheat. The evolving pathogen Puccinia triticina continually challenges these resistance mechanisms. This study assessed 10 wheat lines for relative resistance index (RRI) and screened them for Lr genes or quantitative trait loci (QTLs) using microsatellite markers. The lines were classified into three groups: Ssusceptible (< 5; 4.32 ± 0.68), moderate (5–7; 6.05 ± 0.67) and resistant (> 7; 8.50 ± 0.22) (p < 0.001). Genetic analysis with 12 polymorphic markers revealed 186 alleles with varying allelic diversity. Markers Xbarc124 and Xgwm512 showed greater diversity, and resistance-related alleles were linked to markers Xgwm512 and Xgwm493, associated with the Lr34 gene. Moderate associations were found with Lr37 (Xbarc1138 and Xgwm400) and Lr24 (Xgwm273), while Lr26 (Xwmc407) was linked to susceptibility. Parental line crosses resulted in higher RRI, indicating beneficial recombination. Structure analysis revealed genetic diversity among resistance groups, with susceptible groups showing distinct clustering. Lines AN179 and PR127 clustered together, showing key resistance alleles, particularly in crosses with resistant PR123. The findings highlight novel pathogen races contributing to resistance breakdown and suggest combining all-stage resistance genes (Lr9, Lr24, Lr37) with adult plant resistance (APR) genes (Lr48, Lr22a, Lr34, Lr46) for durable LR resistance. The identified alleles offer valuable insights for marker-assisted breeding to enhance wheat resistance to LR.