Aspergillus flavus is a facultative pathogen capable of producing aflatoxins (AF), potent carcinogens that accumulate in corn kernels, peanuts, cottonseed and tree nuts. To understand resistance mechanisms in corn to AF accumulation we performed a high-throughput genomics study using an in vitro kernel screening assay with A. flavus 3357, resistant corn hybrid TZAR102 and susceptible corn hybrid Va35. Furthermore, we incorporated gene expression data with genomic data to perform redundancy analysis (RDA). We determined that corn genotype, fungal treatment and duration of infection significantly co-vary to influence the overall gene expression patterns. We performed gene ontology enrichment analysis on highly significant genes and found enrichment of pathways linked to fungal and microbial responses such as Pathogenesis-related (PR) proteins. To determine additional genes of interest using field and gene expression data, we linked genome-wide association analysis results with gene expression data, allowing us to detect significant expression quantitative trait loci (eQTL). Our results showed that resistance to aflatoxin contamination is a polygenic trait and found significant association between specific flavonoid biosynthetic pathway genes and infection by A. flavus. Additional experiments including functional genomics analyses and fungal bioassays to identify the role of flavonoids and their contribution to corn resistance to A. flavus growth and AF production will also be presented.