Molecular mapping of quantitative trait loci controlling Karnal bunt resistance in wheat

Karnal bunt (KB) significantly challenges the grain industry due to quarantine regulations that restrict international movement and trade of affected grain stocks. It is an air-, soil- and seed-borne disease resistant to effective chemical control. Quantitative trait loci (QTLs) mapping can decipher the genetic control of complex traits within populations, offering valuable insights into the phenotypic trait–molecular marker associations. This study aimed to identify QTLs associated with KB resistance in a mapping population of 214 wheat recombinant inbred line (RILs) derived from a cross between highly resistant genotype (KBRL22) and susceptible cultivar (PBW343). The population was screened for phenotypic response against the virulent isolate of Tilletia indica during two growing seasons. Pearson correlation and principal component analysis were performed to study traits relationship, and QTL mapping was conducted to identify genomic regions associated with KB resistance. Significant differences in per cent disease severity were observed among the RILs (G), year (E) and G × E interaction. A positive correlation was found with flag leaf length and KB infection. Six consistent QTLs were detected on chromosomes 2B, 3A, 4B and 5B, explaining 13%–18.9% of phenotypic variance. Notably, two major QTLs were located on chromosome 4B and 5B, accounting for 18% and 18.9% of phenotypic variation, respectively, underscoring their significance in conferring resistance to KB. Additionally, two significant hitherto unreported putative QTLs, namely QKb.iiwbr-3A.1 and QKb.iiwbr-3A.2, were also identified on chromosome 3A using SSR markers. The best lines carrying resistance alleles at all identified loci can be utilized for inter-crossing and selection of improved germplasm in future breeding efforts.