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

Zhou, Shaoqun; Kremling, Karl A.; Bandillo, Nonoy; Richter, Annett; Zhang, Ying K.; Ahern, Kevin R.; Artyukhin, Alexander B.; Hui, Joshua X.; Younkin, Gordon C.; Schroeder, Frank C.; Buckler, Edward S.; Jander, Georg

doi:10.1105/tpc.18.00772

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

Abstract

Cultivated maize (Zea mays) has retained much of the genetic diversity of its wild ancestors. In this work, 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. While 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 reflected 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 formore »« less

Authors:

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Boyce Thompson Institute, Ithaca, New York 14853; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
Boyce Thompson Institute, Ithaca, New York 14853
Boyce Thompson Institute, Ithaca, New York 14853; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853
Boyce Thompson Institute, Ithaca, New York 14853; Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853
Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, New York 14853; U.S. Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, New York 14853

Publication Date:: Thu Mar 28 00:00:00 EDT 2019

Research Org.:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Org.:: USDOE Advanced Research Projects Agency - Energy (ARPA-E); National Science Foundation (NSF)

OSTI Identifier:: 1503915

Alternate Identifier(s):: OSTI ID: 1547359

Grant/Contract Number:: AR0000598; DGE-1650441; CHE-1531632

Resource Type:: Published Article

Journal Name:: Plant Cell

Additional Journal Information:: Journal Name: Plant Cell Journal Volume: 31 Journal Issue: 5; Journal ID: ISSN 1040-4651

Publisher:: American Society of Plant Biologists

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Zhou, Shaoqun, Kremling, Karl A., Bandillo, Nonoy, Richter, Annett, Zhang, Ying K., Ahern, Kevin R., Artyukhin, Alexander B., Hui, Joshua X., Younkin, Gordon C., Schroeder, Frank C., Buckler, Edward S., and Jander, Georg. Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites.  United States: N. p., 2019. 
Web.  doi:10.1105/tpc.18.00772.

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                    Zhou, Shaoqun, Kremling, Karl A., Bandillo, Nonoy, Richter, Annett, Zhang, Ying K., Ahern, Kevin R., Artyukhin, Alexander B., Hui, Joshua X., Younkin, Gordon C., Schroeder, Frank C., Buckler, Edward S., & Jander, Georg. Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites.  United States.  https://doi.org/10.1105/tpc.18.00772

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                    Zhou, Shaoqun, Kremling, Karl A., Bandillo, Nonoy, Richter, Annett, Zhang, Ying K., Ahern, Kevin R., Artyukhin, Alexander B., Hui, Joshua X., Younkin, Gordon C., Schroeder, Frank C., Buckler, Edward S., and Jander, Georg. Thu .  
"Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites".  United States.  https://doi.org/10.1105/tpc.18.00772.

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@article{osti_1503915,

  title        = {Metabolome-Scale Genome-Wide Association Studies Reveal Chemical Diversity and Genetic Control of Maize Specialized Metabolites},

  author       = {Zhou, Shaoqun and Kremling, Karl A. and Bandillo, Nonoy and Richter, Annett and Zhang, Ying K. and Ahern, Kevin R. and Artyukhin, Alexander B. and Hui, Joshua X. and Younkin, Gordon C. and Schroeder, Frank C. and Buckler, Edward S. and Jander, Georg},

  abstractNote = {Cultivated maize (Zea mays) has retained much of the genetic diversity of its wild ancestors. In this work, 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. While 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 reflected 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.},

  doi          = {10.1105/tpc.18.00772},

  journal      = {Plant Cell},

  number       = 5,

  volume       = 31,

  place        = {United States},

  year         = {Thu Mar 28 00:00:00 EDT 2019},

  month        = {Thu Mar 28 00:00:00 EDT 2019}

}

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

Abstract

Citation Formats

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