Introduction
Environmental temperature is a critical factor influencing the physiology and growth of marine teleosts. Epigenetic mechanisms, particularly DNA methylation, are increasingly recognized as potential mediators of phenotypic plasticity and short-term adaptation to climate change. However, the interplay between these epigenetic responses and the underlying genetic background remains poorly understood. In this study, we investigated the relationship between temperature, population origin, and the liver methylome in the European sea bass (Dicentrarchus labrax), a species with important ecological and economic value (Vandeputte et al., 2019). While previous work identified significant population differentiation in the methylome of the liver across populations (P = 0.004) linked to genome architecture (S��nchez-Baiz��n et al., Submitted), those results were limited to a single thermal regime. The current study expands this by examining how different populations respond to three thermal environments at the whole-methylome level while accounting for genetic variation.
Materials and methods
We implemented a robust experimental design involving ~4,000 individuals of from two distinct populations (Atlantic, AT; and East Mediterranean, EM). Fish were exposed to three different temperature regimes (mean temperatures: 14.5, 17 and 21.8°C) during two years (Crestel et al., 2025). At the end of the trial, liver samples were collected from 180 individuals. Phenotypic data, including body weight, length, Hepatosomatic Index (HSI), and condition factor (K), were recorded. We used whole-genome enzymatic methyl-seq (EM-seq) to analyze DNA methylation levels at single-nucleotide resolution. Bioinformatic analysis was performed using Methyl-seq nextflow pipeline (Ewels et al., 2025). Furthermore, we extracted SNPs from the same reads using BISCUIT package (Zhou et al., 2024). We performed variance partitioning through Redundancy Analysis and conducted meQTL mapping to differentiate between genetically determined and autonomous epigenetic marks. This will be complemented by applying regression-based models to identify DNA methylation levels associated with phenotypic traits of interest (e.g., Methylation ~Population x Temperature x Body weight) while controlling for multiple testing.
Table 1. Experimental design matrix (N=180), ensuring 30 biological replicates per group, providing sufficient statistical power for quantitative epigenetic modeling—a sample size that significantly exceeds standard practice in high-resolution whole genome studies.
Population
14.5°C
17°C
21.8°C
Total
AT
30
30
30
90
EM
30
30
30
90
180
Results and Discussion
The EM-seq sequencing effort produced a total of 926 Gb of high-quality data, with a mean alignment rate of 82% across the 180 libraries. Preliminary statistical analyses revealed significant differences in the methylome between the AT and EM populations, as well as a response to temperature treatments. Our ongoing analysis utilizes variance partitioning and meQTL mapping to dissect the source of this variation, specifically distinguishing between genetically- and environmentally-induced epigenetic marks. This distinction is critical to quantify the autonomous potential of the sea bass epigenome to contribute to evolution and thermal plasticity (Mueller et al., 2025). By categorizing identified regions into pure (environment), facilitated (genetic x environment), and obligated (genetic) epialleles, we aim to determine the extent to which these marks provide a substrate for selection. Furthermore, associating the direction of methylation change with continuous traits like body weight and HSI allows us to identify the regulatory mechanisms underpinning thermal short-term adaptation and robustness in different genetic backgrounds.
Conclusions
This study disentangles genetic and environmental contributions to methylation variation, revealing the methylome as a dynamic regulatory layer underlying population-specific thermal plasticity. Ongoing quantitative analyses will refine the relative roles of genetic control and autonomous epigenetic variation, providing insights into plasticity with direct relevance for aquaculture and ecological robustness under climate change.
Acknowledgements
This study is supported by the ANR FishNess project, CRECHE project (P120-0001-01-DF), and an Ifremer postdoctoral fellowship (2023–2026) awarded to NSB.
References
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S��nchez-Baiz��n, N., Crestel, D., Vergnet, A., McKenzie, D., Vandeputte, M., Allal, F., Submitted. Association between genome architecture and epigenetic divergence underlies phenotypic variation in European seabass populations.
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