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Genes 2019, 10(4), 263; https://doi.org/10.3390/genes10040263

Analysis of DNA Methylation Patterns Associated with In Vitro Propagated Globe Artichoke Plants Using an EpiRADseq-Based Approach

1
Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, 10095 Grugliasco, Italy
2
Department of Agricultural, Food, and Environmental Sciences, University of Perugia, 06121 Perugia, Italy
3
Agris Sardegna—Agenzia Regionale per la Ricerca in Agricoltura—Servizio Ricerca sui Sistemi Colturali Erbacei, 09123 Cagliari, Italy
*
Author to whom correspondence should be addressed.
Received: 27 February 2019 / Revised: 22 March 2019 / Accepted: 26 March 2019 / Published: 1 April 2019
(This article belongs to the Section Plant Genetics and Genomics)
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Abstract

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. View Full-Text
Keywords: globe artichoke; in vitro culture; DNA methylation; EpiRADseq; epigenetics; somaclonal variation globe artichoke; in vitro culture; DNA methylation; EpiRADseq; epigenetics; somaclonal variation
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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. Genes 2019, 10, 263.

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