Combined genome-wide association study and transcriptome analysis reveal candidate genes for resistance to Fusarium ear rot in maize

Fusariumear rot, caused byFusarium verticillioides, is a devastating fungal disease in maize that reduces yield and quality; moreover,F. verticillioidesproduces fumonisin mycotoxins, which pose serious threats to human and animal health. Here, we performed a genome-wide association study (GWAS) under three environmental conditions and identified 34 single-nucleotide polymorphisms (SNPs) that were significantly associated withFusariumear rot resistance. With reference to the maize B73 genome, 69 genes that overlapped with or were adjacent to the significant SNPs were identified as potential resistance genes toFusariumear rot. Comparing transcriptomes of the most resistant and most susceptible lines during the very early response toFusariumear rot, we detected many differentially expressed genes enriched for pathways related to plant immune responses, such as plant hormone signal transduction, phenylpropanoid biosynthesis, and cytochrome P450 metabolism. More than one-fourth of the potential resistance genes detected in the GWAS were differentially expressed in the transcriptome analysis, which allowed us to predict numbers of candidate genes for maize resistance to ear rot, including genes related to plant hormones, a MAP kinase, a PR5-like receptor kinase, and heat shock proteins. We propose that maize plants initiate early immune responses toFusariumear rot mainly by regulating the growth-defense balance and promoting biosynthesis of defense compounds.