Development of epigenetic biomarkers with diagnostic and prognostic value to assess the long-lasting consequences of early temperature in European sea bass aquaculture. Dicentrarchus labrax

Epigenetic changes such as DNA methylation modifications at specific loci in the genome in response to environmental cues can appear long before the appearance of transcriptomic or other phenotypic changes with potential consequences for performance. Thus, epigenetic DNA methylation-based biomarkers hold great promise in aquaculture because they can have prognostic value. However, to the best of our knowledge, a clear demonstration of such biomarkers has not been provided yet. Temperature during early development is the main abiotic factor determining larval quality, with effects potentially persisting until adulthood and influencing performance. The objective of this study was to test whether epigenetic biomarkers could be used as reliable indicators of the quality of the thermal environment during European sea bass early development and their relation to long-lasting phenotypic (transcriptomic) consequences. We exposed European sea bass embryos and newley hatched larvae to different temperature regimes and sampled fish thereafter at different time points: at larval, juvenile and adult stages. Here, we provide an analytical strategy combining Reduced Representation Bisulfite sequencing (RRBS) and RNA-sequence to develop transcriptomic and epigenetic biomarkers with both prognostic and diagnostic value. Specifically, we report a series of DNA-methylation biomarkers linked to short-term, mid-term, long-term, and very-long term effects of temperature in both somatic and reproductive tissues. This study constitutes a first step toward providing the European sea bass farming sector with a set of epigenetic biomarkers that can be used to screen batches of larvae to determine the quality of their thermal environment and to anticipate their performance when juveniles and adults. Our study provides the way for similar developments for other farmed species.