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|a 10.1093/jxb/erae266
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|a eng
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|a Lesur, Isabelle
|e verfasserin
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|a A strategy for studying epigenetic diversity in natural populations
|b proof of concept in poplar and oak
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|c 2024
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|a Text
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|a ƒaComputermedien
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|a ƒa Online-Ressource
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|a Date Completed 27.09.2024
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|a Date Revised 27.09.2024
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|a published: Print
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|a Citation Status MEDLINE
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|a © The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprintsoup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.
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|a In the last 20 years, several techniques have been developed for quantifying DNA methylation, the most studied epigenetic marks in eukaryotes, including the gold standard method, whole-genome bisulfite sequencing (WGBS). WGBS quantifies genome-wide DNA methylation but has several inconveniences rendering it less suitable for population-scale epigenetic studies. The high cost of deep sequencing and the large amounts of data generated prompted us to seek an alternative approach. Restricting studies to parts of the genome would be a satisfactory alternative had there not been a major limitation: the need to select upstream targets corresponding to differentially methylated regions as targets. Given the need to study large numbers of samples, we propose a strategy for investigating DNA methylation variation in natural populations, taking into account the structural complexity of genomes, their size, and their content in unique coding regions versus repeated regions as transposable elements. We first identified regions of highly variable DNA methylation in a subset of genotypes representative of the biological diversity in the population by WGBS. We then analysed the variations of DNA methylation in these targeted regions at the population level by sequencing capture bisulfite (SeqCapBis). The entire strategy was then validated by applying it to another species. Our strategy was developed as a proof of concept on natural populations of two forest species: Populus nigra and Quercus petraea
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|a Journal Article
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|a DNA methylation
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|a SeqCapBis
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|a WGBS
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|a WGS
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|a epigenetics
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|a epigenomics
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|a methylome
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|a natural population
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|a oak
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|a poplar
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|a transposon insertion polymorphism
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|a Rogier, Odile
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|a Sow, Mamadou Dia
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|a Boury, Christophe
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|a Duplan, Alexandre
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|a Senhaji-Rachik, Abdeljalil
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|a Civan, Peter
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|a Daron, Josquin
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|a Delaunay, Alain
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|a Duvaux, Ludovic
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|a Benoit, Vanina
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|a Guichoux, Erwan
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|a Le Provost, Grégoire
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|a Sanou, Edmond
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|a Ambroise, Christophe
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|a Plomion, Christophe
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|a Salse, Jérôme
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|a Tost, Jörg
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|a Maury, Stéphane
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|i Enthalten in
|t Journal of experimental botany
|d 1985
|g 75(2024), 18 vom: 27. Sept., Seite 5568-5584
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|x 1460-2431
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|g volume:75
|g year:2024
|g number:18
|g day:27
|g month:09
|g pages:5568-5584
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|u http://dx.doi.org/10.1093/jxb/erae266
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