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Plant Cell. 2019 May;31(5):937-955. doi: 10.1105/tpc.18.00772. Epub 2019 Mar 28.

Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites.

Author information

1
Boyce Thompson Institute, Ithaca, New York 14853.
2
Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.
3
Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853.
4
Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853.
5
U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853.
6
Boyce Thompson Institute, Ithaca, New York 14853 gj32@cornell.edu.

Abstract

Cultivated maize (Zea mays) has retained much of the genetic diversity of its wild ancestors. Here, we performed nontargeted liquid chromatography-mass spectrometry metabolomics to analyze the metabolomes of the 282 maize inbred lines in the Goodman Diversity Panel. This analysis identified a bimodal distribution of foliar metabolites. Although 15% of the detected mass features were present in >90% of the inbred lines, the majority were found in <50% of the samples. Whereas leaf bases and tips were differentiated by flavonoid abundance, maize varieties (stiff-stalk, nonstiff-stalk, tropical, sweet maize, and popcorn) showed differential accumulation of benzoxazinoid metabolites. Genome-wide association studies (GWAS), performed for 3,991 mass features from the leaf tips and leaf bases, showed that 90% have multiple significantly associated loci scattered across the genome. Several quantitative trait locus hotspots in the maize genome regulate the abundance of multiple, often structurally related mass features. The utility of maize metabolite GWAS was demonstrated by confirming known benzoxazinoid biosynthesis genes, as well as by mapping isomeric variation in the accumulation of phenylpropanoid hydroxycitric acid esters to a single linkage block in a citrate synthase-like gene. Similar to gene expression databases, this metabolomic GWAS data set constitutes an important public resource for linking maize metabolites with biosynthetic and regulatory genes.

PMID:
30923231
PMCID:
PMC6533025
[Available on 2020-05-01]
DOI:
10.1105/tpc.18.00772

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