Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance.
BACKGROUND
Aflatoxin 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.


RESULTS
The 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.


CONCLUSIONS
Our 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.
USDA FS Forest Products Laboratory, Durability and Wood Protection, Starkville, MS, 39759, USA.
Juliet D
JD
Tang
Computer Science and Engineering, Mississippi State, MS, 39762, USA.
Andy
A
Perkins
USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS, 39762, USA.
W Paul
WP
Williams
USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, MS, 39762, USA. marilyn.warburton@ars.usda.gov.
Marilyn L
ML
Warburton
D000348:Aflatoxins / Q000378:metabolism*; D000465:Algorithms; D032461:Chromosomes, Plant / Q000235:genetics; D003663:Decision Trees; D017343:Genes, Plant; D055106:Genome-Wide Association Study; D015810:Linkage Disequilibrium / Q000235:genetics; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics; D015203:Reproducibility of Results; D003313:Zea mays / Q000235:genetics*
D000348:Aflatoxins