Genome-Wide Association Study Reveals Novel QTNs and Candidate Genes Implicated in Resistance to Northern Corn Leaf Blight in Maize (Zea mays L.)

Northern corn leaf blight is a major fungal disease hindering maize production worldwide. Among the various strategies of disease management, the deployment of host plant resistance is the most economic means to mitigate the yield losses, as it is cost-effective and durable. In this study, we performed the genome-wide association study (GWAS) analysis in a set of 336 maize inbred lines. The experimental material was evaluated for northern corn leaf blight disease response across two seasons during the rainy seasons of 2023 and 2024. The ANOVA results and estimates of genetic variability parameters indicated the existence of a substantial amount of genetic variability. High heritability and high genetic advance as percent mean suggested the presence of additive genetic effects in controlling the disease response. GWAS analysis was performed employing GLM, MLM, CMLM, MLMM, FarmCPU and BLINK. The results from GWAS identified 74 marker associations from GLM and FarmCPU models. The QTN <i>S1_7356398</i>, located on chromosome 1, identified from the GLM model, explained 12.12 percent of phenotypic variation. Another QTN <i>S2_51098833</i> located on chromosome 2, identified from the FarmCPU model, explained 6.14 percent variation. Remaining associations explained lesser PVE, suggesting the quantitative inheritance of NCLB resistance. Candidate gene identification was performed by keeping B73 as a reference genome. The identified QTNs from the current study were found to be located in annotated genes with functional domains implicated in defence mechanisms in maize and other crops. Many candidate genes, including chitinase, putative serine/threonine protein kinase, and aldehyde oxygenase, were identified and found to play a crucial role in plant defence mechanisms against several biotic and abiotic stresses.