Development of epigenetic biomarkers for the European sea bass (Dicentrachus labrax)

The European sea bass is a gonochoristic species that exhibits sexual size dimorphism in favor of females, the preferred sex in aquaculture, and has a polygenic system of sex determination, where both genetic factors and temperature contribute to population sex ratios. Thus, when reared at temperatures >17ºC, a proportion of the fish which would develop as females under cooler temperature become masculinized (neomales). Epigenetic biomarkers such as DNA methylation changes at specific loci (CpG), which are susceptible to environmental change, hold promise to complement genetic selection of broodstock and could help select fish with desired phenotypic traits resulting from the interplay between genetics and environment. Here, we aim to understand the nature of the epigenetic inheritance and the contribution of the genotype and of the environment to DNA methylation profiles. To this end, we created eight families by crossing one female with eight males which had been reared at different temperature treatments when young: two at low temperature (LT), three at high temperature (HT), and 3 HT neomales (NM). The offspring were also exposed to LT and HT during the thermosensitive period, thus creating a total of 32 groups for analysis (eight parents of three types, two temperatures and two sexes) and gonadal tissues were sampled when fish were over one year old. Based on genotypic (sex tendency) and phenotypic data of the offspring, we selected fish representative of each group by sex, temperature, and sire type. In total, we produced 130 libraries by Reduced Representation Bisulfite sequencing to analyze the DNA methylome of grandparents’ gametes (F0, n=2), sires and dam gametes (F1, n=9) and offspring juvenile gonad (F2, n=119). The obtained dataset generated a matrix of high dimensionality (130 samples x ~1,400,000 CpGs per sample). To make it more manageable, we contemplated several approaches to retain the most informative CpG positions. One included the definition of