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ARS Home » Southeast Area » Mississippi State, Mississippi » Crop Science Research Laboratory » Corn Host Plant Resistance Research » Research » Publications at this Location » Publication #314976

Title: Using Genome-Wide Associations to Identify Metabolic Pathways Involved in Maize Aflatoxin Accumulation Resistance

item TANG, JULIET - Us Forest Service (FS)
item PERKINS, ANDY - Mississippi State University
item Williams, William
item Warburton, Marilyn

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/24/2015
Publication Date: 8/28/2015
Citation: Tang, J.D., Perkins, A., Williams, W.P., Warburton, M.L. 2015. Using genome-wide associations to identify metabolic pathways involved in maize aflatoxin accumulation resistance. BMC Genomics. 16:673. doi:10.1186/s12864-015-1874-9.

Interpretive Summary: Aflatoxin is a potent carcinogen that can contaminate corn grain infected with the fungus Aspergillus flavus. While creating new corn cultivars that resist infection by A. flavus is an efficient and attractive option for reducing aflatoxin contamination, it is difficult to breed for this trait. In order to breed more efficiently for reduced aflatoxin contamination, it is important to understand the mechanisms by which corn grain can resist infection by the fungus and subsequent production of aflatoxin. A previous study in this lab created mapping data where different parts of the maize chromosomes that had something to do with resistance were identified. This study identifies all the genes in these parts of the chromosomes previously identified and puts the genes together in a pathway analysis. This allowed us to identify metabolic pathways in the corn cells that create compounds that actively resist infection by the fungus or the production of aflatoxin. The most significant metabolic pathway we identified was jasmonic acid (JA) biosynthesis. Jasmonic acid is a plant hormone that is known to regulate plant responses to insects, bacterial, viral, and fungal pathogens. This analysis, along with the analysis of individual genes identified in this and previous studies, now give us a clearer picture of how resistant corn plants fight off infection by A. flavus, and this will aid in the rapid creation of new resistant cultivars.

Technical Abstract: 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. 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 defence were: leucine-rich repeat protein kinase, expansin B3, reversion-to-ethylene sensitivity1, adaptor protein complex2, and a multidrug and toxic compound extrusion protein. 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 defence-related functions. Knowledge gained from these two complementary analyses has improved our understanding of population differences in aflatoxin resistance and will provide markers for host plant improvement by introgression.