Abstract
BACKGROUND: Maize white spot (MWS) is a highly destructive leaf disease and has become a major threat to global maize production in recent years. This indicates that identifying new anti-MWS genes is of vital importance. In this study, two recombinant inbred line (RIL) subpopulations derived from Suwan germplasms with MWS resistance were used. RESULTS: By integrating quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) strategies, resistance-related loci were successfully identified. The analysis results consistently indicated that there was a major resistance region on chromosome 3, where the major QTL locus qMWS3-2, consistently identified across three environments and BLUP values, could explain up to 10.81% of the phenotypic variation and co-localized with two significant single nucleotide polymorphisms (SNPs). Within this region, two candidate genes were identified: Zm00001eb155730 encoding mitogen-activated protein kinase and Zm00001eb155910 involved in sulfur metabolism. Haplotype analysis showed that the favorable haplotypes of these two genes were both associated with significantly enhanced resistance to MWS and were only present in the subpopulation derived from the highly resistant parent D39. Expression analysis further revealed a unique defense mechanism of D39. This parent strongly suppressed the candidate gene Zm00001eb155730, which was significantly upregulated in the highly susceptible parent. As for the defense-related gene Zm00001eb155910, its expression pattern is different from the induced expression of the susceptible parents Ye107 and the parent YML32. CONCLUSIONS: The candidate genes and favorable haplotypes identified in this study provide valuable resources for molecular breeding of maize and will promote the breeding process of high-resistance MWS varieties. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-026-08403-2.