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Article

The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline

1
Plant Cell Biology, Department of Biology, University of Marburg, 35043 Marburg, Germany
2
ecSeq Bioinformatics GmbH, 04103 Leipzig, Germany
3
Bioinformatics Group, Department of Computer Science, University of Leipzig, 04107 Leipzig, Germany
4
Plant Evolutionary Ecology, Institute of Evolution and Ecology, University of Tübingen, Auf der Morgenstelle 5, 72076 Tübingen, Germany
5
Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences, Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria
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Genetics, Faculty of Biology, Ludwig-Maximilians-University München, 82152 Martinsried, Germany
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Department of Forest Genetic Resources, Nordwestdeutsche Forstliche Versuchsanstalt (NW-FVA), 37079 Göttingen, Germany
8
Conservation Biology, Department of Biology, University of Marburg, 35043 Marburg, Germany
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Plant Ecology and Geobotany, Department of Biology, University of Marburg, 35043 Marburg, Germany
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Centre for Biological Signaling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
11
SYNMIKRO Center for Synthetic Microbiology, University of Marburg, 35043 Marburg, Germany
*
Author to whom correspondence should be addressed.
Academic Editors: Cao Xuan Hieu and Vu Thi Ha Giang
Received: 15 March 2021 / Revised: 16 April 2021 / Accepted: 20 April 2021 / Published: 4 May 2021
(This article belongs to the Special Issue Advances in Plant Epigenetics and Epigenomics)
Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use. View Full-Text
Keywords: EWAS; GWAS; plant epigenetics; DNA methylation; non-model species; pipeline EWAS; GWAS; plant epigenetics; DNA methylation; non-model species; pipeline
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MDPI and ACS Style

Can, S.N.; Nunn, A.; Galanti, D.; Langenberger, D.; Becker, C.; Volmer, K.; Heer, K.; Opgenoorth, L.; Fernandez-Pozo, N.; Rensing, S.A. The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. Epigenomes 2021, 5, 12. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5020012

AMA Style

Can SN, Nunn A, Galanti D, Langenberger D, Becker C, Volmer K, Heer K, Opgenoorth L, Fernandez-Pozo N, Rensing SA. The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline. Epigenomes. 2021; 5(2):12. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5020012

Chicago/Turabian Style

Can, Sultan N.; Nunn, Adam; Galanti, Dario; Langenberger, David; Becker, Claude; Volmer, Katharina; Heer, Katrin; Opgenoorth, Lars; Fernandez-Pozo, Noe; Rensing, Stefan A. 2021. "The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline" Epigenomes 5, no. 2: 12. https://0-doi-org.brum.beds.ac.uk/10.3390/epigenomes5020012

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