Genome-Wide Association Study Identifies Loci and Candidate Genes for Fusarium Stalk Rot Resistance in Maize

Maize stalk rot, primarily caused by Fusarium spp., is a significant disease in many maize-growing areas worldwide, often leading to considerable yield losses under favorable conditions for infection. In this study, a genome-wide association study (GWAS) for Fusarium stalk rot resistance was carried out using 230,506 single nucleotide polymorphism (SNP) markers on phenotypic data from 178 maize inbred lines. Four SNPs were significantly associated with stalk rot resistance, with three located within previously reported QTL regions and one novel locus identified on chromosome 9 (9_149289012). Candidate genes within a 600-kb window around each SNP were retrieved from the MaizeGDB database, revealing 174 candidate genes in the B73_RefGen_v5 reference genome, including 8 R genes and 8 differentially expressed genes (DEGs). Notably, three potential candidate genes were identified around the novel SNP 9_149289012 on chromosome 9. Additionally, transcriptome analysis identified 1,597 genes related to disease resistance, associated with GO terms involved in resistance responses, nutrient metabolism, and toxin metabolism. Overall, this study provides valuable insights into the genetic basis of Fusarium stalk rot resistance in maize, highlighting both known and novel loci along with candidate genes for further functional characterization.