Abstract
BackgroundAflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus. However, resistance to aflatoxin accumulation in maize is a complex trait with low heritability. Here, two complementary analyses were performed to better understand the mechanisms involved. The first coupled results of a genome-wide association study (GWAS) that accounted for linkage disequilibrium among single nucleotide polymorphisms (SNPs) with gene-set enrichment for a pathway-based approach. The rationale was that the cumulative effects of genes in a pathway would give insight into genetic differences that distinguish resistant from susceptible lines of maize. The second involved finding non-pathway genes close to the most significant SNP-trait associations with the greatest effect on reducing aflatoxin in multiple environments. Unlike conventional GWAS, the latter analysis emphasized multiple aspects of SNP-trait associations rather than just significance and was performed because of the high genotype x environment variability exhibited by this trait.ResultsThe most significant metabolic pathway identified was jasmonic acid (JA) biosynthesis. Specifically, there was at least one allelic variant for each step in the JA biosynthesis pathway that conferred an incremental decrease to the level of aflatoxin observed among the inbred lines in the GWAS panel. Several non-pathway genes were also consistently associated with lowered aflatoxin levels. Those with predicted functions related to defense were: leucine-rich repeat protein kinase, expansin B3, reversion-to-ethylene sensitivity1, adaptor protein complex2, and a multidrug and toxic compound extrusion protein.ConclusionsOur genetic analysis provided strong evidence for several genes that were associated with aflatoxin resistance. Inbred lines that exhibited lower levels of aflatoxin accumulation tended to share similar haplotypes for genes specifically in the pathway of JA biosynthesis, along with several non-pathway genes with putative defense-related functions. Knowledge gained from these two complementary analyses has improved our understanding of population differences in aflatoxin resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1874-9) contains supplementary material, which is available to authorized users.
Highlights
Aflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus
The frequency of linkage types were: 46.3 % unlinked, 33.5 % reference single nucleotide polymorphisms (SNPs) linked to single SNP, 19.1 % reference SNP linked to a SNP block where the associations in the block had a majority effect sign, that is the majority of associations had either a positive or negative effect, and 1.1 % where the block had no majority effect sign (Additional file 2: Figure S2)
The SNP to gene algorithm was designed to account for all possibilities present
Summary
Aflatoxin is a potent carcinogen that can contaminate grain infected with the fungus Aspergillus flavus. Resistance to aflatoxin accumulation in maize is a complex trait with low heritability. The second involved finding non-pathway genes close to the most significant SNP-trait associations with the greatest effect on reducing aflatoxin in multiple environments. Unlike conventional GWAS, the latter analysis emphasized multiple aspects of SNP-trait associations rather than just significance and was performed because of the high genotype x environment variability exhibited by this trait. Infection does not typically reduce yield in temperate environments, the grain can become contaminated with aflatoxin, a polyketide secondary metabolite produced by the fungus that is highly toxic to humans and animals even in minute amounts [1]. Most of the known resistance to aflatoxin accumulation in maize has been found in tropical lines, typically with Tuxpan or Tuxpeño in their pedigree [4]. Host plant improvement by introgression of resistance into temperate lines adapted to the major corn production areas in the US, China, and Europe, has not been efficient
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