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The role of epigenetics in local adaptation in sessile oak trees: a population epigenetic association study

hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorBRANDT, Shannon
hal.structure.identifierBiologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt [BioForA]
hal.structure.identifierPhysiologie, Ecologie et Environnement [P2E]
dc.contributor.authorDUPLAN, Alexandre
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
hal.structure.identifierHelix Venture
dc.contributor.authorLESUR KUPIN, Isabelle
hal.structure.identifierSystème d'Information des GENomes des Animaux d'Elevage [SIGENAE]
hal.structure.identifierGénétique Animale et Biologie Intégrative [GABI]
hal.structure.identifierBiologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt [BioForA]
dc.contributor.authorROGIER, Odile
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
hal.structure.identifierBiologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt [BioForA]
dc.contributor.authorDIA SOW, Mamadou
hal.structure.identifierBiologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt [BioForA]
dc.contributor.authorDURUFLÉ, Harold
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorPLOMION, Christophe
hal.structure.identifierGénétique Diversité et Ecophysiologie des Céréales [GDEC]
dc.contributor.authorSALSE, Jérôme
hal.structure.identifierCentre National de Recherche en Génomique Humaine [CNRGH]
dc.contributor.authorTOST, Jörg
hal.structure.identifierBiologie intégrée pour la valorisation de la diversité des Arbres et de la Forêt [BioForA]
dc.contributor.authorSANCHEZ, Leopoldo
hal.structure.identifierBiodiversité, Gènes & Communautés [BioGeCo]
dc.contributor.authorDUVAUX, Ludovic
hal.structure.identifierPhysiologie, Ecologie et Environnement [P2E]
dc.contributor.authorMAURY, Stéphane
dc.date.conference2025-08-17
dc.description.abstractEnRapid climate change is forcing species to either adapt very quickly, shift their geographicdistributions, or face local extinction. This challenge is especially acute for long-lived, sessileorganisms such as trees, which cannot migrate easily and whose extended generation timeslimit the pace of evolutionary response through genetic variation alone. Epigenetic mechanisms,including DNA methylation, have been proposed as a means by which organisms may respondmore quickly to environmental shifts. In this study, we examine the role of DNA methylation inlocal adaptation across populations of sessile oak (Quercus petraea).We analysed DNA methylation patterns in 189 individuals from 22 populations spanning alatitudinal gradient from Southern France to Northern Germany. All individuals were grown in acommon garden experiment in Sillegny, France, which controlled for environmental variabilityand allowed us to isolate heritable components of epigenetic variation. Methylation data weregenerated using a targeted sequence capture approach focusing on regions known to beepigenetically variable, and targeting specific candidate genes (Lesur et al., 2024). Methylationdata was then imputed in all three contexts for using NIPALS as tested in Duplan et al. 2025.Exploratory data analysis revealed low variability and differentiation in the data. The global Fstfor the SNP data was 0.001, and the global Pst of the methylation data was 0.008 in all threecontexts. A PLS-DA across contexts by population also reflected the low variability as the firsttwo axes only explained <6% of the variation. Overall, we observed low levels of DNAmethylation variation across the genome, with fewer than 5% of SMPs exceeding 0.05inter-individual variation in any context (CG, CHG, CHH). For downstream analyses, weretained only the most variable 5% of SMPs per context.Multi-omic association analyses were conducted using a multi-locus mixed model (MLMM)framework that incorporated phenotypic, climatic, single nucleotide polymorphism (SNP), andmethylation (SMP) data. Despite the low overall variation, retained SMPs exhibited significantassociations with four different phenotypic traits and 26 different climatic variables. Additionally,40%, 49%, and 20% of tested SMPs in CG, CHG, and CHH contexts, respectively, were significantly associated with SNPs under the MLMM. There is however a significant amount ofspatial autocorrelation in the associated SMPs which may explain the high levels of association,this is expected as nearby methylation marks are known to experience co-methylation.Our findings indicate that while global DNA methylation variation is limited in our Q. petraeapopulations, specific methylation markers are associated with phenotypic traits andenvironmental gradients, pointing to a potential—but constrained—role for epigenetic variationin local adaptation in this species. Recognising this limited yet meaningful contribution is criticalfor understanding the mechanisms by which long-lived species may respond to rapid climatechange, especially during the early stages of adaptation when genetic responses may be tooslow.
dc.language.isoen
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/
dc.subject.enEpigenetic variation
dc.subject.enLocal adaptation
dc.subject.enSessile oak
dc.subject.enDNA methylation
dc.title.enThe role of epigenetics in local adaptation in sessile oak trees: a population epigenetic association study
dc.typeCommunication dans un congrès
dc.subject.halSciences du Vivant [q-bio]/Biodiversité/Evolution [q-bio.PE]
dc.subject.halInformatique [cs]/Bio-informatique [q-bio.QM]
dc.subject.halSciences de l'environnement/Milieux et Changements globaux
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des plantes
dc.subject.halSciences du Vivant [q-bio]/Génétique/Génétique des populations [q-bio.PE]
dc.subject.halSciences du Vivant [q-bio]/Sciences agricoles/Sylviculture, foresterie
bordeaux.conference.titleESEB 2025 - The Evolutionary Biology Congress
bordeaux.countryES
bordeaux.conference.cityBarcelone
bordeaux.peerReviewedoui
hal.identifierhal-05241621
hal.version1
hal.invitednon
hal.proceedingsnon
hal.conference.end2025-08-22
hal.popularnon
hal.audienceInternationale
hal.origin.linkhttps://hal.archives-ouvertes.fr//hal-05241621v1
bordeaux.COinSctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=BRANDT,%20Shannon&DUPLAN,%20Alexandre&LESUR%20KUPIN,%20Isabelle&ROGIER,%20Odile&DIA%20SOW,%20Mamadou&rft.genre=unknown


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