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Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees

The vast majority of previous studies on epigenetics in plants have centered on the study of inheritance of DNA methylation patterns in annual plants. In contrast, perennial plants may have the ability to accumulate changes in DNA methylation patterns over numerous years. However, currently little i...

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Autores principales: Perrin, Adrien, Daccord, Nicolas, Roquis, David, Celton, Jean-Marc, Vergne, Emilie, Bucher, Etienne
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594697/
https://www.ncbi.nlm.nih.gov/pubmed/34968238
http://dx.doi.org/10.3390/epigenomes4010004
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author Perrin, Adrien
Daccord, Nicolas
Roquis, David
Celton, Jean-Marc
Vergne, Emilie
Bucher, Etienne
author_facet Perrin, Adrien
Daccord, Nicolas
Roquis, David
Celton, Jean-Marc
Vergne, Emilie
Bucher, Etienne
author_sort Perrin, Adrien
collection PubMed
description The vast majority of previous studies on epigenetics in plants have centered on the study of inheritance of DNA methylation patterns in annual plants. In contrast, perennial plants may have the ability to accumulate changes in DNA methylation patterns over numerous years. However, currently little is known about long-lived perennial and clonally reproducing plants that may have evolved different DNA methylation inheritance mechanisms as compared to annual plants. To study the transmission of DNA methylation patterns in a perennial plant, we used apple (Malus domestica) as a model plant. First, we investigated the inheritance of DNA methylation patterns during sexual reproduction in apple by comparing DNA methylation patterns of mature trees to juvenile seedlings resulting from selfing. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear variations in DNA methylation patterns localized in regions enriched for genes involved in photosynthesis. Using transcriptomics, we also observed that genes involved in this pathway were overexpressed in seedlings. To assess how DNA methylation patterns are transmitted during clonal propagation we then compared global DNA methylation of a newly grafted tree to its mature donor tree. We identified significant, albeit weak DNA methylation changes resulting from grafting. Overall, we found that a majority of DNA methylation patterns from the mature donor tree are transmitted to newly grafted plants, however with detectable specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their donor tree.
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spelling pubmed-85946972021-12-28 Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees Perrin, Adrien Daccord, Nicolas Roquis, David Celton, Jean-Marc Vergne, Emilie Bucher, Etienne Epigenomes Article The vast majority of previous studies on epigenetics in plants have centered on the study of inheritance of DNA methylation patterns in annual plants. In contrast, perennial plants may have the ability to accumulate changes in DNA methylation patterns over numerous years. However, currently little is known about long-lived perennial and clonally reproducing plants that may have evolved different DNA methylation inheritance mechanisms as compared to annual plants. To study the transmission of DNA methylation patterns in a perennial plant, we used apple (Malus domestica) as a model plant. First, we investigated the inheritance of DNA methylation patterns during sexual reproduction in apple by comparing DNA methylation patterns of mature trees to juvenile seedlings resulting from selfing. While we did not observe a drastic genome-wide change in DNA methylation levels, we found clear variations in DNA methylation patterns localized in regions enriched for genes involved in photosynthesis. Using transcriptomics, we also observed that genes involved in this pathway were overexpressed in seedlings. To assess how DNA methylation patterns are transmitted during clonal propagation we then compared global DNA methylation of a newly grafted tree to its mature donor tree. We identified significant, albeit weak DNA methylation changes resulting from grafting. Overall, we found that a majority of DNA methylation patterns from the mature donor tree are transmitted to newly grafted plants, however with detectable specific local differences. Both the epigenomic and transcriptomic data indicate that grafted plants are at an intermediate phase between an adult tree and seedling and inherit part of the epigenomic history of their donor tree. MDPI 2020-03-01 /pmc/articles/PMC8594697/ /pubmed/34968238 http://dx.doi.org/10.3390/epigenomes4010004 Text en © 2020 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) ).
spellingShingle Article
Perrin, Adrien
Daccord, Nicolas
Roquis, David
Celton, Jean-Marc
Vergne, Emilie
Bucher, Etienne
Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
title Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
title_full Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
title_fullStr Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
title_full_unstemmed Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
title_short Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees
title_sort divergent dna methylation signatures of juvenile seedlings, grafts and adult apple trees
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8594697/
https://www.ncbi.nlm.nih.gov/pubmed/34968238
http://dx.doi.org/10.3390/epigenomes4010004
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