Association mapping and pathway analysis of ear rot disease caused by Aspergillus flavus in a panel of tropical maize germplasm

Abstract

AbstractThe fungus Aspergillus flavus can produce high, unsafe levels of aflatoxin in maize (Zea mays L.) and other high‐oil seed crops under environmental conditions favoring fungal growth and sporulation. At high levels, aflatoxin can kill, and chronic exposure to lower levels causes liver cancer, stunted growth during childhood, and depressed immune systems in humans and animals. Aspergillus ear rot (AER) is especially problematic in tropical environments, but most gene identification studies have been done in temperate or subtropical maize. Thus, the objectives of this research include identifying and mapping chromosomal regions and genes associated with AER resistance in tropical maize inbred lines via genome‐wide association study (GWAS) and tying these genes to metabolic pathways and potential resistance mechanisms. A panel of 320 tropical field corn and popcorn inbred lines was analyzed with phenotypic data for AER collected in two environments after harvest, and a set of 291,633 high‐quality polymorphic single‐nucleotide polymorphisms (SNPs) generated via genotyping by sequencing. Seven SNPs significantly associated with AER were identified. Pathway analysis identified 56 associated pathways, yielding possible resistance mechanisms related to flavonoid and phytoalexin plant compounds, plant signaling via hormones, starch biosynthesis, and general plant growth and metabolism. Many of the same genes were identified by both analyses, but GWAS and pathway analysis jointly identified more candidate genes than either alone.