Screening and identification of candidate resistance genes to gibberella ear rot caused by Fusarium graminearum in maize

Gibberella ear rot (GER) of maize (<italic>Zea mays</italic> L.), caused by <italic>Fusarium graminearum</italic> (<italic>Fg</italic>), is a major factor contributing to yield losses in southwestern China. In this study, two highly resistant inbred lines (4019 and NMJT) and two highly susceptible lines (Huangzaosi and GEMS61) were selected. Kernels at 15 days after pollination were inoculated with <italic>Fg</italic>, and samples were collected at three post-infection time points for transcriptome sequencing. Candidate resistance genes were identified, cloned, and preliminarily validated through a combination of differentially expressed gene (DEG) analysis, previous genome-wide association study (GWAS) results, qRT-PCR validation, cloning and sequence alignment, and expression pattern analysis. The main findings were as follows: (1) Transcriptome analysis revealed a large number of DEGs between resistant and susceptible lines at all three infection stages. The two resistant lines shared common defense responses, with DEGs significantly enriched in pathways such as plant secondary metabolism, plant hormone signal transduction, calcium signaling, and the antioxidant system. In addition, each resistant line exhibited specific defense mechanisms by regulating unique gene expression patterns. (2) Integration of DEG and GWAS data identified 24 co-localized genes. Based on gene annotation and literature reports, 12 genes were predicted as potential candidates for GER resistance. Among these, two genes—<italic>Zm00001eb104020 </italic>and <italic>Zm00001eb195780</italic>—were successfully cloned and validated by qRT-PCR. (3) Protein sequence analysis revealed shared mutations and deletions between resistant and susceptible lines. The two candidate genes also showed distinct spatiotemporal expression patterns, with significantly higher expression levels in resistant lines. Both genes were strongly induced and upregulated in kernels following <italic>Fg</italic> inoculation. These results provide a theoretical foundation for further functional characterization of GER resistance mechanisms and the breeding of resistant maize germplasm.