Integrating BSA-Seq and RNA-Seq to Identify Major QTLs and Candidate Genes Conferring Resistance to Fusarium Ear Rot in Maize

<i>Fusarium</i> ear rot (FER), caused by <i>Fusarium verticillioides</i>, is a devastating disease that substantially reduces maize yield and compromises kernel quality. To investigate the genetic and molecular basis of resistance, an F₂ population derived from a cross between the resistant inbred line 3IBZ2 and the susceptible inbred line KW5G321 was analysed. By integrating bulked segregant analysis sequencing (BSA-Seq) with RNA sequencing (RNA-Seq), a major quantitative trait locus (QTL), designated <i>qFER4</i>, was identified on chromosome 4. Genetic analysis further demonstrated that <i>qFER4</i> confers resistance through partial dominance. Transcriptome profiling of the resistant line revealed 7684 and 7906 differentially expressed genes (DEGs) at 36 and 72 h post inoculation (hpi), respectively. These DEGs were significantly enriched in defence-related biological processes and pathways, including phenylpropanoid biosynthesis, jasmonic acid signalling, MAPK cascades, and plant-pathogen interactions. By combining QTL mapping with transcriptome analyses, four candidate genes within the <i>qFER4</i> interval were screened. Sequence analysis identified extensive structural variations in the promoter and coding regions of <i>Zm00001d053393</i>, including a premature stop codon predicted to lead to a gain-of-function mutation. In contrast, the other three genes exhibited only minor promoter polymorphisms with identical coding sequences between the parental lines. Overall, this study identifies a novel major-effect QTL and candidate gene associated with FER resistance, providing a foundation for gene function and a valuable genetic resource for breeding FER-resistant maize varieties.