Genome-wide association study and transcriptome analysis of candidate resistance genes for northern corn leaf blight

Northern corn leaf blight (NCLB) is a leaf disease caused by <i>Setosphaeria turcica</i> that infects maize at multiple growth stages and severely impairs photosynthesis and grain yield. Breeding for resistance to northern corn leaf blight would be an effective strategy to mitigate the damage caused by this disease. Mapping of resistance genes provides an opportunity to understand the resistance mechanisms and to utilize the information in developing an introgression breeding strategy. The resistance of 421 maize inbred lines with extensive genetic variation to northern corn leaf blight was evaluated over three consecutive years in Xinzhou, Shanxi. The proportions of maize lines classified as HR, R, MR, S, and HS were 1.06%, 7.16%, 20.16%, 37.13%, and 34.48%, respectively. A total of 39,676 high-quality SNP markers were employed for genome-wide association study (GWAS). In the early and late stages, 85 SNPs associated with northern corn leaf blight resistance were identified, of which 11 stable SNPs were detected across the two environments. Through comparative transcriptome analysis, 4,758 and 3,779 differentially expressed genes (DEGs) were identified in the resistant inbred line Jing724 and the susceptible inbred line PH4CV after infection with <i>S. turcica</i>, respectively. GO and KEGG analyses indicated that more DEGs were enriched in plant defense pathways in the resistant line. Furthermore, two candidate genes were identified by integrating GWAS and transcriptome analyses. These findings could provide a foundation for cloning resistance genes and breeding resistant varieties.