Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map

  1. Joost J.B. Keurentjes1,3
  1. 1Laboratory of Genetics, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
  2. 2Laboratory of Biometris, Wageningen University and Research, 6708 PB Wageningen, The Netherlands;
  3. 3Centre for Biosystems Genomics, 6708 PB Wageningen, The Netherlands;
  4. 4Groningen Bioinformatics Centre, University of Groningen, 9747 AG Groningen, The Netherlands;
  5. 5Business Unit Bioscience, Wageningen Plant Research, 6708 PB Wageningen, The Netherlands;
  6. 6Institute for Advanced Study, Technical University of Munich, 85748 Garching, Germany;
  7. 7Tea Research Institute, Chinese Academy of Agricultural Sciences, 310008 Hangzhou, P.R. China;
  8. 8Netherlands Metabolomics Centre, 2333 CC Leiden, The Netherlands;
  9. 9Population Epigenetics and Epigenomics, Department of Plant Sciences, Technical University of Munich, 85354 Freising, Germany
  • Corresponding author: joost.keurentjes{at}wur.nl
  • Abstract

    Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions and their putative trans-targets, we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.

    Footnotes

    • [Supplemental material is available for this article.]

    • Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.232371.117.

    • Freely available online through the Genome Research Open Access option.

    • Received November 13, 2017.
    • Accepted November 27, 2018.

    This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.

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