AbstractBackgroundFungus infection in staple grains affects the food storage and threatens food security. TheAspergillus flavusis known to infect multiple grains and produce mycotoxin Aflatoxin B1, which is mutagenic, teratogenic and causes immunosuppression in animals. However, the molecular mechanism of maize resistance toA. flavusis largely unknown.ResultsHere we used corn kernels to investigate resistance genes toA. flavususing genome-wide association study (GWAS) of 313 inbred lines. We characterized the resistance levels of kernels after inoculating withA. flavus. The GWAS with 558,529 SNPs identified four associated loci involving 29 candidate genes that were linked to seed development, resistance or infection, and involved in signal pathways, seed development, germination, dormancy, epigenetic modification, and antimicrobial activity. In addition, a few candidate genes were also associated with several G-protein signaling and phytohormones that might involve in synergistic work conferring different resistance during seed development. Expression of 16 genes out of 29 during kernel development was also associated with resistance levels.ConclusionsWe characterized the resistance levels of 313 maize kernels after inoculating withA. flavus, and found four associated loci and 16 candidate maize genes. The expressed 16 genes involved in kernel structure and kernel composition most likely contribute to mature maize kernels’ resistance toA. flavus, and in particular, in the development of pericarp. The linked candidate genes could be experimentally transformed to validate and manipulate fungal resistance. Thus this result adds value to maize kernels in breeding programs.