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

BMC Genomics
Juliet D TangMarilyn L Warburton

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 biosy...Continue Reading

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Jan 1, 2017·Molecular Plant·Yingjie XiaoJianbing Yan
Dec 6, 2016·Plants·Eli J Borrego, Michael V Kolomiets
Feb 12, 2019·The Plant Journal : for Cell and Molecular Biology·Hui LiMarilyn L Warburton
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Jun 26, 2020·Frontiers in Microbiology·Bryan MusunguMatt Geisler
May 11, 2021·3 Biotech·Kumari ShikhaB Sinha

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Methods Mentioned

BETA
genotyping

Software Mentioned

QVALUE
TASSEL
MaizeCyc
Perl
ARGASED
R

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