Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach
Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and ‘Spinoso sardo’ is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant pla...
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ftunivtorino:oai:iris.unito.it:2318/1714172 2023-11-05T03:41:37+01:00 Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach Cerruti E. Comino C. Acquadro A. Marconi G. Repetto A. M. Pisanu A. B. Pilia R. Albertini E. Portis E. Cerruti E. Comino C. Acquadro A. Marconi G. Repetto A.M. Pisanu A.B. Pilia R. Albertini E. Portis E. 2019 http://hdl.handle.net/2318/1714172 https://doi.org/10.3390/genes10040263 https://www.mdpi.com/2073-4425/10/4/263/pdf eng eng info:eu-repo/semantics/altIdentifier/pmid/30939865 info:eu-repo/semantics/altIdentifier/wos/WOS:000467302800013 volume:10 issue:263 firstpage:1 lastpage:19 numberofpages:19 journal:GENES http://hdl.handle.net/2318/1714172 doi:10.3390/genes10040263 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85068426158 https://www.mdpi.com/2073-4425/10/4/263/pdf info:eu-repo/semantics/openAccess DNA methylation Epigenetic EpiRADseq Globe artichoke In vitro culture Somaclonal variation info:eu-repo/semantics/article 2019 ftunivtorino https://doi.org/10.3390/genes10040263 2023-10-10T22:25:07Z Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and ‘Spinoso sardo’ is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type ‘Spinoso sardo’ plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2897 differentially methylated loci (DML): 1998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the ‘Spinoso sardo’ non-conventional phenotype. Article in Journal/Newspaper DML Università degli studi di Torino: AperTo (Archivio Istituzionale ad Accesso Aperto) Genes 10 4 263 |
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Open Polar |
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Università degli studi di Torino: AperTo (Archivio Istituzionale ad Accesso Aperto) |
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ftunivtorino |
language |
English |
topic |
DNA methylation Epigenetic EpiRADseq Globe artichoke In vitro culture Somaclonal variation |
spellingShingle |
DNA methylation Epigenetic EpiRADseq Globe artichoke In vitro culture Somaclonal variation Cerruti E. Comino C. Acquadro A. Marconi G. Repetto A. M. Pisanu A. B. Pilia R. Albertini E. Portis E. Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach |
topic_facet |
DNA methylation Epigenetic EpiRADseq Globe artichoke In vitro culture Somaclonal variation |
description |
Globe artichoke represents one of the main horticultural species of the Mediterranean basin, and ‘Spinoso sardo’ is the most widespread and economically relevant varietal type in Sardinia, Italy. In the last decades, in vitro culture of meristematic apices has increased the frequency of aberrant plants in open-field production. These off-type phenotypes showed highly pinnate-parted leaves and late inflorescence budding, and emerged from some branches of the true-to-type ‘Spinoso sardo’ plants. This phenomenon cannot be foreseen and is reversible through generations, suggesting the occurrence of epigenetic alterations. Here, we report an exploratory study on DNA methylation patterns in off-type/true-to-type globe artichoke plants, using a modified EpiRADseq technology, which allowed the identification of 2897 differentially methylated loci (DML): 1998 in CG, 458 in CHH, and 441 in CHG methylation contexts of which 720, 88, and 152, respectively, were in coding regions. Most of them appeared involved in primary metabolic processes, mostly linked to photosynthesis, regulation of flower development, and regulation of reproductive processes, coherently with the observed phenotype. Differences in the methylation status of some candidate genes were integrated with transcriptional analysis to test whether these two regulation levels might interplay in the emergence and spread of the ‘Spinoso sardo’ non-conventional phenotype. |
author2 |
Cerruti E. Comino C. Acquadro A. Marconi G. Repetto A.M. Pisanu A.B. Pilia R. Albertini E. Portis E. |
format |
Article in Journal/Newspaper |
author |
Cerruti E. Comino C. Acquadro A. Marconi G. Repetto A. M. Pisanu A. B. Pilia R. Albertini E. Portis E. |
author_facet |
Cerruti E. Comino C. Acquadro A. Marconi G. Repetto A. M. Pisanu A. B. Pilia R. Albertini E. Portis E. |
author_sort |
Cerruti E. |
title |
Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach |
title_short |
Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach |
title_full |
Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach |
title_fullStr |
Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach |
title_full_unstemmed |
Analysis of DNA methylation patterns associated with in vitro propagated globe artichoke plants using an epiRADseq-based approach |
title_sort |
analysis of dna methylation patterns associated with in vitro propagated globe artichoke plants using an epiradseq-based approach |
publishDate |
2019 |
url |
http://hdl.handle.net/2318/1714172 https://doi.org/10.3390/genes10040263 https://www.mdpi.com/2073-4425/10/4/263/pdf |
genre |
DML |
genre_facet |
DML |
op_relation |
info:eu-repo/semantics/altIdentifier/pmid/30939865 info:eu-repo/semantics/altIdentifier/wos/WOS:000467302800013 volume:10 issue:263 firstpage:1 lastpage:19 numberofpages:19 journal:GENES http://hdl.handle.net/2318/1714172 doi:10.3390/genes10040263 info:eu-repo/semantics/altIdentifier/scopus/2-s2.0-85068426158 https://www.mdpi.com/2073-4425/10/4/263/pdf |
op_rights |
info:eu-repo/semantics/openAccess |
op_doi |
https://doi.org/10.3390/genes10040263 |
container_title |
Genes |
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10 |
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4 |
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263 |
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1781698058277355520 |