Metabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plants
Autor: | Jeffrey P. Simpson, Cole G Wunderlich, Clint Chapple, Elizabeth Svedin, Xu Li, Brian P. Dilkes |
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Rok vydání: | 2020 |
Předmět: |
0106 biological sciences
0301 basic medicine Metabolite Large-Scale Biology Articles Arabidopsis Plant Science Computational biology Biology 01 natural sciences Mass Spectrometry Isotopic labeling 03 medical and health sciences chemistry.chemical_compound Metabolome Arabidopsis thaliana Metabolomics Gene Retrospective Studies Phenylpropanoid Cell Biology biology.organism_classification Metabolic pathway 030104 developmental biology chemistry Isotope Labeling 010606 plant biology & botany Genome-Wide Association Study |
Zdroj: | Plant Cell |
ISSN: | 1532-298X |
Popis: | The optimal extraction of information from untargeted metabolomics analyses is a continuing challenge. Here, we describe an approach that combines stable isotope labeling, liquid chromatography– mass spectrometry (LC–MS), and a computational pipeline to automatically identify metabolites produced from a selected metabolic precursor. We identified the subset of the soluble metabolome generated from phenylalanine (Phe) in Arabidopsis thaliana, which we refer to as the Phe-derived metabolome (FDM) In addition to identifying Phe-derived metabolites present in a single wild-type reference accession, the FDM was established in nine enzymatic and regulatory mutants in the phenylpropanoid pathway. To identify genes associated with variation in Phe-derived metabolites in Arabidopsis, MS features collected by untargeted metabolite profiling of an Arabidopsis diversity panel were retrospectively annotated to the FDM and natural genetic variants responsible for differences in accumulation of FDM features were identified by genome-wide association. Large differences in Phe-derived metabolite accumulation and presence/absence variation of abundant metabolites were observed in the nine mutants as well as between accessions from the diversity panel. Many Phe-derived metabolites that accumulated in mutants also accumulated in non-Col-0 accessions and was associated to genes with known or suspected functions in the phenylpropanoid pathway as well as genes with no known functions. Overall, we show that cataloguing a biochemical pathway’s products through isotopic labeling across genetic variants can substantially contribute to the identification of metabolites and genes associated with their biosynthesis. |
Databáze: | OpenAIRE |
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