Tree Genetics & Genomes

, 14:78 | Cite as

Narrow-sense heritability and PST estimates of DNA methylation in three Populus nigra L. populations under contrasting water availability

  • Mamadou Dia Sow
  • Vincent Segura
  • Sylvain Chamaillard
  • Véronique Jorge
  • Alain Delaunay
  • Clément Lafon-Placette
  • Régis Fichot
  • Patricia Faivre-Rampant
  • Marc Villar
  • Franck Brignolas
  • Stéphane MauryEmail author
Original Article
Part of the following topical collections:
  1. Complex Traits


In a context of climate change and forest decline, a better understanding of the sources of tree flexibility involved in phenotypic plasticity and adaptation is needed. These last years, the role of epigenetics in the response to environmental variations has been established in several model plants at the genotype level but little is known at the level of natural populations grown in pedoclimatic sites. Here, we focused on three French natural populations of black poplar, a key pioneer tree from watersheds, planted in common garden and subjected to controlled variations of water availability. We estimated common genetic parameters such as narrow-sense heritability (h2), phenotypic differentiation index (PST), and the overall genetic differentiation index (FST) from genome-wide SNPs to evaluate the extent of epigenetic variations. Indeed, global DNA methylation levels from individuals exposed to drought or irrigated in a common garden were used. We found that the three populations were not distinguished by their levels of DNA methylation. However, a moderate drought was associated to a significant decrease in DNA methylation in the populations. Narrow-sense heritability and PST estimates of DNA methylation were similar to those found for biomass productivity. Heritability and PST were higher when trees were subjected to drought than in control condition. Negative genetic correlations between global DNA methylation and height or biomass were detected in drought condition only. Altogether, our data highlight that global DNA methylation acts as a genetic marker of natural population differentiation under drought stress in a pedoclimatic context.


DNA methylation h2 PST FST Poplar Water availability 


Data archiving statement

The raw data containing the full list of genotypes, global DNA methylation levels, biomass, and height are included as Supplementary Table 1. The SNP data used in order to reconstruct genomic relationships between genotypes, within and between populations, and to estimate h2, PST, and FST for global DNA methylation are in Supplementary Tables 2 and 3.

Funding information

MDS obtained a PhD grant from the “Ministère de la Recherche et Enseignement Supérieur,” France. This work was funded by the “INRA DÉPARTEMENT EFPA,” France, with the project “PI EFPA-2010” and by the “Agence Nationale de la Recherche (ANR)” with the project “EPITREE” 2018-2021, ANR-17-CE32-0009-01,

Supplementary material

11295_2018_1293_MOESM1_ESM.xlsx (14 kb)
Supplementary Table 1 Global DNA methylation levels (Perc_mC) were calculated as mentioned in Zhu et al. (2013). The values of height and biomass were retrieved in Chamaillard et al. (2011). NOH for Nohèdes, RAM for Ramières and SPM for Saint-Pryvé Saint-Mesmin. WW and WD referred to irrigated and drought conditions, respectively. (XLSX 14 kb)
11295_2018_1293_MOESM2_ESM.xlsx (1.1 mb)
Supplementary Table 2 SNP genotypic data used to calculate h2, PST and FST estimates in the three geographical populations (NOH, RAM and SPM). These SNP were retrieved from Faivre-Rampant et al. 2016 and Le Paslier et al. 2016. The SNPs are denoted by SNP_IGA followed by the chromosome or scaffold number (V3.0 poplar; and the base position within the scaffold. (XLSX 1112 kb)
11295_2018_1293_MOESM3_ESM.xlsx (150 kb)
Supplementary Table 3 Details of the SNP data. The types of SNP, locus, sequence or position are mentioned. The SNPs were assembled with the V3.0 of the poplar genome ( (XLSX 149 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Mamadou Dia Sow
    • 1
  • Vincent Segura
    • 2
  • Sylvain Chamaillard
    • 1
  • Véronique Jorge
    • 2
  • Alain Delaunay
    • 1
  • Clément Lafon-Placette
    • 1
    • 3
  • Régis Fichot
    • 1
  • Patricia Faivre-Rampant
    • 4
  • Marc Villar
    • 2
  • Franck Brignolas
    • 1
  • Stéphane Maury
    • 1
    Email author
  1. 1.LBLGC, INRA, Université d’Orléans, EA 1207 USC 1328OrleansFrance
  2. 2.BioForA, INRA, ONFOrleansFrance
  3. 3.Department of Botany, Charles UniversityPragueCzech Republic
  4. 4.INRA, US1279 EPGV, CEA-IG/CNGEvryFrance

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