Analysis of Genome-Wide Association Data to Identify Candidate Metabolic Pathways for Aflatoxin Accumulation Resistance in Maize

Aflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus.  Resistance to aflatoxin accumulation in corn, however, is a complex trait with low heritability.  In our prior studies, genome-wide association analysis was used to find the SNPs (single nucleotide polymorphisms) and closest genes that showed the most significant associations with aflatoxin resistance.   The association mapping panel was composed of 300 inbred corn lines that exhibited varying degrees of aflatoxin accumulation after inoculation with A. flavus in replicated field trials.  In this analysis, we coupled our genome-wide association study with a gene-set enrichment analysis for a pathway-based approach.  The rationale was that the cumulative effects of genes in a pathway might give more insight into the biological processes that were contributing to aflatoxin resistance.  Of the 298 metabolic pathways analyzed, the most significant was jasmonic acid biosynthesis (FDR = 0.001).  Other notable pathways (0.1 < FDR < 0.2) were biosynthesis of (1) the branched amino acids (isoleucine, valine, and leucine) and L-glutamate by degradation of arginine, (2) 4-hydroxy-benzoate, tyrosine, chlorogenic acid, and divinyl ether, (3) inosine-5'-phosphate and tetrahydrofolate, and (4) acetyl-CoA, fatty acid β-oxidation, and the glyoxylate cycle.  Possible roles for these four groups, respectively, are:  (1) biosynthesis of jasmonic acid-isoleucine, (2) production of secondary metabolites involved in defense, (3) purine biosynthesis, and (4) generation of precursor metabolites and energy.