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.<b> </b>In contrast,<b> </b>perennial plants may have the ability to accumulate changes in DNA methylation patterns over numer...
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| Format: | Article |
| Language: | English |
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MDPI AG
2020-03-01
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| Series: | Epigenomes |
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| Online Access: | https://www.mdpi.com/2075-4655/4/1/4 |
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| author | Adrien Perrin Nicolas Daccord David Roquis Jean-Marc Celton Emilie Vergne Etienne Bucher |
| author_facet | Adrien Perrin Nicolas Daccord David Roquis Jean-Marc Celton Emilie Vergne Etienne Bucher |
| author_sort | Adrien Perrin |
| collection | DOAJ |
| 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.<b> </b>In contrast,<b> </b>perennial plants may have the ability to accumulate changes in DNA methylation patterns over numerous years.<b> </b>However,<b> </b>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 (<i>Malus </i><i>domestica</i>) 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. |
| first_indexed | 2024-03-12T18:21:13Z |
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| institution | Directory Open Access Journal |
| issn | 2075-4655 |
| language | English |
| last_indexed | 2024-03-12T18:21:13Z |
| publishDate | 2020-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Epigenomes |
| spelling | doaj.art-721aae131c6242cfa08441bac154b85e2023-08-02T08:55:25ZengMDPI AGEpigenomes2075-46552020-03-0141410.3390/epigenomes4010004epigenomes4010004Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple TreesAdrien Perrin0Nicolas Daccord1David Roquis2Jean-Marc Celton3Emilie Vergne4Etienne Bucher5IRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé F-49071, FranceIRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé F-49071, FranceIRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé F-49071, FranceIRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé F-49071, FranceIRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé F-49071, FranceIRHS (Institut de Recherche en Horticulture et Semences), UMR 1345, INRA, Agrocampus-Ouest, Université d’Angers, SFR 4207 QuaSaV, Beaucouzé F-49071, FranceThe vast majority of previous studies on epigenetics in plants have centered on the study of inheritance of DNA methylation patterns in annual plants.<b> </b>In contrast,<b> </b>perennial plants may have the ability to accumulate changes in DNA methylation patterns over numerous years.<b> </b>However,<b> </b>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 (<i>Malus </i><i>domestica</i>) 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.https://www.mdpi.com/2075-4655/4/1/4epigeneticsperennial planttransmission of methylation signaturesmalus domesticasexual and asexual propagation |
| spellingShingle | Adrien Perrin Nicolas Daccord David Roquis Jean-Marc Celton Emilie Vergne Etienne Bucher Divergent DNA Methylation Signatures of Juvenile Seedlings, Grafts and Adult Apple Trees Epigenomes epigenetics perennial plant transmission of methylation signatures malus domestica sexual and asexual propagation |
| 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 | epigenetics perennial plant transmission of methylation signatures malus domestica sexual and asexual propagation |
| url | https://www.mdpi.com/2075-4655/4/1/4 |
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