Introduction
Environmentally induced changes in DNA methylation have been proposed as potential contributors to short-term adaptive responses to changing environments. To investigate whether epigenetic changes are involved in the resistance to temperature as an environmental stressor, we analyzed three genetically distinct European sea bass populations—Atlantic (AT), Western Mediterranean (WM), and Eastern Mediterranean (EM)—produced by artificial fertilization and reared under common garden conditions in a relatively warm thermal regime representative of the Eastern Mediterranean (rEM ). The primary objective of this study was to characterize the fin transcriptome and methylome to determine whether population-level differentiation is evident in these two omic layers. We then aimed to assess associations between omic patterns and phenotypic traits related to robustness, defined here as the capacity to resist environmental stressors and mitigate negative impacts on physiological performance and overall well-being.
Materials and Methods
After one year of exposure to the rEM thermal regime, 612 fish were slaughtered, and phenotypic data were collected, including body weight, body length, liver and gonad weight. Photographs of whole animals were also taken to allow later scoring of fin erosion level. From these , 72 individuals were randomly selected for transcriptome and methylome analyses. RNA and DNA were co-extracted from the same fin tissue using the Quick DNA/RNA Mini Prep Plus Kit. For transcriptomic analysis, RNA from these individuals was equimolarly pooled into 18 libraries (six per population), stratified by sex and population. For DNA methylation analysis, 12 equimolar pools (four per population) were prepared using only high-quality DNA. RNA-seq libraries were sequenced at ~30× coverage, while whole-genome DNA methylation was assessed using Enzymatic Methyl-seq (EM-seq) at ~25× coverage. Following quality control and bioinformatic processing, principal component analysis (PCA) was performed, differentially expressed genes (DEGs) were identified using DESeq2, and differentially methylated regions (DMRs) were detected using the MethylKit package in R.
General linear models are being used to assess whether expression and methylation biomarkers can be associated with phenotypic traits of interest linked to robustness . Additionally , we are working to determine which of these DMRs are influenced by underlying single nucleotide polymorphisms (SNPs) and which may constitute environmentally-driven epigenetic markers.
Results and Discussion
We observed significant differences among populations for several phenotypic traits, including condition factor and hepatosomatic index, which are associated with fish robustness. Transcriptome analysis identified 140 DEGs between EM and AT, 135 between WM and AT, and 119 between EM and WM (adjusted P < 0.05; |log₂ fold change| ≥ 0.5). Genes upregulated in the Mediterranean populations (EM and WM) were mainly associated with basal stress responses, whereas those upregulated in the Atlantic population (AT) were related to rapid stress response mechanisms, indicating population-specific molecular strategies to cope with warm environments. PCA of the methylome revealed significant differences between populations along the first three principal components. Differential methylation analysis identified 14,993 DMRs (EM vs AT), 8,391 (WM vs AT), and 4,983 (EM vs WM).
Further downstream analyses—linking DMRs and DEGs and phenotypic traits—will help pinpoint candidate biomarkers of robustness under the relatively warm regime representative of the species’ environmental range.
Conclusions
This study identifies candidate biomarkers of robustness from non-lethal fin tissue, contributing to the assessment of population vulnerability and promoting more sustainable aquaculture practices. It also enhances our understanding of genotype–environment interactions, local adaptation, and the potential impact of climate change on European sea bass populations.
Funding: Research funded by the ANR FishNess project and CRECHE (P120-0001-01-DF).