Identification of Maize Fusarium Ear Rot Resistance Genes via Integrated BSA-Seq and RNA-Seq Analysis

Maize ear rot, often caused by Fusarium graminearum ( F. graminearum ) and other fungi, is a widespread fungal disease that severely reduces grain yield and quality, while mycotoxins produced by these pathogens pose significant threats to human and animal health. However, the defense responses of maize to pathogen infection and the underlying genetic regulatory mechanisms remain largely unclear. To investigate the molecular basis of maize ear rot resistance, maize ears were artificially inoculated with F. graminearum at 7 days after pollination, and cytological, physiological, biochemical, and multi-omics analyses were performed between the maize resistant inbred line K0743 and susceptible inbred line K0742 at different time points after F. graminearum inoculation. The results showed that the resistant inbred line K0743 maintained more intact cellular structures than susceptible inbred line K0742 following inoculation and exhibited significantly higher activities of defense-related enzymes, including phenylalanine ammonia-lyase (PAL), polyphenol oxidase (PPO), and superoxide dismutase (SOD), as well as significantly increased accumulation of osmotic regulatory substances such as proline, soluble sugars, and soluble proteins ( P  < 0.05 or P  < 0.01). BSA-Seq identified 8 resistance-associated loci on Chr 5, 6, 7, 9, and 10, among which qGER5 and qGER6-2 were defined as major loci. Transcriptome analysis revealed that the resistant inbred line K0743 exhibited much higher numbers of differentially expressed genes (DEGs) than the susceptible inbred line K0742 across three time points (72 h, 96 h, and 7 d) relative to their respective 0 h controls. Specifically, after 72 h of inoculation, the resistant inbred line K0743 had 6,030 DEGs (compared to 805 in K0742); after 96 h, 4,929 DEGs (vs. 2,212 in K0742); and after 7 d, 10,254 DEGs (vs. 3,255 in K0742). Integrative analyses of BSA-Seq and RNA-Seq, combined with weighted gene co-expression network analysis (WGCNA), identified 6 high-confidence candidate genes. These genes were distributed across two key co-expression modules: MEfloralwhite, primarily involved in oxidative stress response and ubiquitin-mediated proteolysis; and MEblue4, enriched in plant hormone signal transduction, MAPK signaling, and cell wall modification pathways. These findings provide new insights into the molecular mechanisms underlying maize resistance to F. graminearum and offer valuable candidate genes for resistance breeding and functional characterization.