Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments

Apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) are two of the most important stone fruit species, and their climacteric nature is a major determinant in terms of fruit shelf-life period. The role of the main genes involved in the ripening process of these species has been exten...

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Detalles Bibliográficos
Autores: Ortuño-Hernández, Germán, Ruiz, David, Martínez-Gómez, Pedro, Salazar, Juan A.
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2024
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/365895
Acceso en línea:http://hdl.handle.net/10261/365895
https://api.elsevier.com/content/abstract/scopus_id/85187568274
Access Level:acceso abierto
Palabra clave:Prunus
Apricot
Japanese plum
Postharvest
Ethylene
Epigenetics
DNA methylation
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spelling Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatmentsOrtuño-Hernández, GermánRuiz, DavidMartínez-Gómez, PedroSalazar, Juan A.PrunusApricotJapanese plumPostharvestEthyleneEpigeneticsDNA methylationApricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) are two of the most important stone fruit species, and their climacteric nature is a major determinant in terms of fruit shelf-life period. The role of the main genes involved in the ripening process of these species has been extensively studied, however there is a need to expand our molecular knowledge at epigenetic level. To achieve this, postharvest monitoring of 'Goldrich' apricots and 'Santa Rosa' Japanese plums after 1-MCP (ethylene inhibitor) and Ethrel (ethylene precursor) treatments was carried out to delve deep into the epigenetic level using Whole Genome Bisulfite Sequencing (WGBS). Results showed over 12,000 and 9,000 genes with differentially methylated regions (DMRs) in 'Goldrich' and 'Santa Rosa' cultivars respectively. 1-MCP-treated apricot 'Goldrich' exhibited more hypomethylated regions, suggesting lower methylation levels compared to Ethrel treatment. While starch and sucrose metabolism exhibited the greatest number of partially methylated genes, other pathways showcased more significant differences. Thus, 4-coumarate-CoA ligase in phenylpropanoid biosynthesis, DELLA protein in hormone signal transduction, GDP-L-fucose synthase in amino sugar metabolism, D-lactate dehydratase in pyruvate metabolism, and hydroxymethylglutaryl-CoA reductase in 'Goldrich', as well as homocysteine S-methyltransferase in the cysteine and methionine metabolism, 1-phosphatidylinositol-4-phosphate 5-kinase in the inositol phosphate metabolism, pectinesterase in the pentose and glucuronate interconversions, malate dehydrogenase in the carbon metabolism, photosystem I subunit VI in photosynthesis, and aquaporin-4 as a membrane transporter in Japanese plum showed inverse gene expression-methylation patterns. These findings reveal variations in epigenetic regulation during fruit ripening in apricot and plum, influenced by ethylene modulating treatments, suggesting significant role of DNA methylation in this processThis research was sponsored and supported by Subprograma Regional ‘Saavedra Fajardo’ project N° 20397/SF/17 from the ‘Fundación Séneca’ of Murcia (Spain), by the Ministry of Science and Innovation (Spain) through the ‘Juan de la Cierva Incorporación’ postdoctoral fellowship N° IJC2018-036623-I, and ‘Apricot Breeding’ project (PID2020-116780RB-I00). Additionally, this study formed part of the AGROALNEXT program and was supported by MCIN with funding from European Union Next Generation EU (PRTR-C17.I1)Peer reviewedElsevier BVFundación SénecaMinisterio de Ciencia, Innovación y Universidades (España)Agencia Estatal de Investigación (España)European CommissionSalazar, Juan A. [0000-0003-0380-076X]Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]202420242024info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/365895https://api.elsevier.com/content/abstract/scopus_id/85187568274reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/IJC2018-036623-Iinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-116780RB-I00Scientia HorticulturaeThe underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1016/j.scienta.2024.113052https://doi.org/10.1016/j.scienta.2024.113052Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3658952026-05-22T06:33:51Z
dc.title.none.fl_str_mv Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
title Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
spellingShingle Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
Ortuño-Hernández, Germán
Prunus
Apricot
Japanese plum
Postharvest
Ethylene
Epigenetics
DNA methylation
title_short Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
title_full Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
title_fullStr Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
title_full_unstemmed Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
title_sort Differentially methylated DNA regions in apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) during fruit ripening after ethylene-related treatments
dc.creator.none.fl_str_mv Ortuño-Hernández, Germán
Ruiz, David
Martínez-Gómez, Pedro
Salazar, Juan A.
author Ortuño-Hernández, Germán
author_facet Ortuño-Hernández, Germán
Ruiz, David
Martínez-Gómez, Pedro
Salazar, Juan A.
author_role author
author2 Ruiz, David
Martínez-Gómez, Pedro
Salazar, Juan A.
author2_role author
author
author
dc.contributor.none.fl_str_mv Fundación Séneca
Ministerio de Ciencia, Innovación y Universidades (España)
Agencia Estatal de Investigación (España)
European Commission
Salazar, Juan A. [0000-0003-0380-076X]
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Prunus
Apricot
Japanese plum
Postharvest
Ethylene
Epigenetics
DNA methylation
topic Prunus
Apricot
Japanese plum
Postharvest
Ethylene
Epigenetics
DNA methylation
description Apricot (Prunus armeniaca L.) and Japanese plum (Prunus salicina L.) are two of the most important stone fruit species, and their climacteric nature is a major determinant in terms of fruit shelf-life period. The role of the main genes involved in the ripening process of these species has been extensively studied, however there is a need to expand our molecular knowledge at epigenetic level. To achieve this, postharvest monitoring of 'Goldrich' apricots and 'Santa Rosa' Japanese plums after 1-MCP (ethylene inhibitor) and Ethrel (ethylene precursor) treatments was carried out to delve deep into the epigenetic level using Whole Genome Bisulfite Sequencing (WGBS). Results showed over 12,000 and 9,000 genes with differentially methylated regions (DMRs) in 'Goldrich' and 'Santa Rosa' cultivars respectively. 1-MCP-treated apricot 'Goldrich' exhibited more hypomethylated regions, suggesting lower methylation levels compared to Ethrel treatment. While starch and sucrose metabolism exhibited the greatest number of partially methylated genes, other pathways showcased more significant differences. Thus, 4-coumarate-CoA ligase in phenylpropanoid biosynthesis, DELLA protein in hormone signal transduction, GDP-L-fucose synthase in amino sugar metabolism, D-lactate dehydratase in pyruvate metabolism, and hydroxymethylglutaryl-CoA reductase in 'Goldrich', as well as homocysteine S-methyltransferase in the cysteine and methionine metabolism, 1-phosphatidylinositol-4-phosphate 5-kinase in the inositol phosphate metabolism, pectinesterase in the pentose and glucuronate interconversions, malate dehydrogenase in the carbon metabolism, photosystem I subunit VI in photosynthesis, and aquaporin-4 as a membrane transporter in Japanese plum showed inverse gene expression-methylation patterns. These findings reveal variations in epigenetic regulation during fruit ripening in apricot and plum, influenced by ethylene modulating treatments, suggesting significant role of DNA methylation in this process
publishDate 2024
dc.date.none.fl_str_mv 2024
2024
2024
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/365895
https://api.elsevier.com/content/abstract/scopus_id/85187568274
url http://hdl.handle.net/10261/365895
https://api.elsevier.com/content/abstract/scopus_id/85187568274
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/IJC2018-036623-I
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-116780RB-I00
Scientia Horticulturae
The underlying dataset has been published as supplementary material of the article in the publisher platform at https://doi.org/10.1016/j.scienta.2024.113052
https://doi.org/10.1016/j.scienta.2024.113052
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv Elsevier BV
publisher.none.fl_str_mv Elsevier BV
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
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collection DIGITAL.CSIC. Repositorio Institucional del CSIC
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repository.mail.fl_str_mv
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