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

R. Kooke, L.N. Morgado, F.F.M. Becker, H.D.L.M. van Eekelen, Rashmi Hazarika, Qunfeng Zhang, C.H. de Vos, Frank Johannes, J.J.B. Keurentjes

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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 or 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.
LanguageEnglish
Pages96-106
JournalGenome Research
Volume29
Issue number1
Early online date30 Nov 2018
DOIs
Publication statusPublished - 2019

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Metabolome
Arabidopsis
Epigenomics
Phenotype
RNA
Genes
Growth
Computer Simulation

Cite this

@article{1d88e9cb6af6473f9cd206509fd42bfc,
title = "Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map",
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 or 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.",
author = "R. Kooke and L.N. Morgado and F.F.M. Becker and {van Eekelen}, H.D.L.M. and Rashmi Hazarika and Qunfeng Zhang and {de Vos}, C.H. and Frank Johannes and J.J.B. Keurentjes",
year = "2019",
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journal = "Genome Research",
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Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. / Kooke, R.; Morgado, L.N.; Becker, F.F.M.; van Eekelen, H.D.L.M.; Hazarika, Rashmi; Zhang, Qunfeng; de Vos, C.H.; Johannes, Frank; Keurentjes, J.J.B.

In: Genome Research, Vol. 29, No. 1, 2019, p. 96-106.

Research output: Contribution to journalArticleAcademicpeer-review

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AU - Kooke, R.

AU - Morgado, L.N.

AU - Becker, F.F.M.

AU - van Eekelen, H.D.L.M.

AU - Hazarika, Rashmi

AU - Zhang, Qunfeng

AU - de Vos, C.H.

AU - Johannes, Frank

AU - Keurentjes, J.J.B.

PY - 2019

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N2 - 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 or 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.

AB - 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 or 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.

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