Genome-wide association study identifies ZmMYB42 as a candidate gene for resistance to maize head smut

Background Maize head smut, a severe fungal disease, poses significant threats to production, particularly in spring maize regions in northern and eastern China. Mining head smut resistant genes and developing resistant varieties are one of the most effective strategies for mitigating this disease. Results This study evaluated the resistance to head smut in 292 maize inbred lines through artificial inoculation over two years at the same locations. Genome-wide association study (GWAS) identified three consistent loci— SNP230557995 , SNP220821587 , and SNP191418784 —linked to head smut resistance. Twelve candidate genes were identified across these loci, seven of which were functionally annotated. After 12 h and 6 d of inoculation with Sporisorium reilianum ( S.reilianum ), the expression of ZmMYB42 showed significant ( P  < 0.01) between resistant lines and susceptible lines to head smut. qRT-PCR validation revealed that ZmMYB42 ( Zm00001d053220 ) was a candidate regulatory gene for head smut resistance. In the development of dCAPS markers, SNP837 was an SNP significantly associated with head smut resistance ( P  < 0.01), contributing 18.11% to phenotypic variance. The SNP837 associated with head smut resistance was converted into a functional cleaved amplified polymorphic sequence (CAPS) marker and validated across 254 maize inbred lines. The results showed that the genotype (G/C) of the molecular marker DNdCAPS837 had a 77.78% concordance rate with the (resistant/susceptible) phenotype. Conclusion Overall, GWAS by integrating maize head smut incidence and genotype data, we were able to identify a total of three potential SNPs and twelve related candidate genes, including a head smut resistance candidate gene, ZmMYB42 . Further, the functional marker DNdCAPS837 developed provides a potential target and valuable information for improving head smut resistance in maize.