Livestock animals have been domesticated for many generations and are genetically distinct from their wild ancestors. By contrast, by the advent of modern intensivefish farming, some aquacultured fish are still at the early stages of domestication, although they are raised in an environment very different from the their natural environment. Therefore, these fish species provide an excellent opportunity to study domestication effects in absence of genetic differentiation. Here, we use wild and farmed European sea bass (Dicentrarchus labrax), a fish known to develop morphological differences under an aquaculture environment and studied the effects of farming in muscle and testis using genome-wide NGS methods. We used Reduced Representation Bisulfite Sequencing (RRBS) for DNA methylation and RNA-seq for gene expression. We found differentially methylated sites (DMC) between wild and farmed sea bass in both tissues, with muscle presenting more than double the amount of DMCs compared to testis. The majority of DMCs were located close togenes and their cis-regulatory elements, within 500 bp upstream or 1500 bp downstream of the transcription start site (TSS). In accordance with DNA methylation data, there were more differentially expressed genes (DEG) in muscle than in testis. There were DEG that contained DMCs and GO-enrichment analysis showed the most affected processes in muscle and in testis. These results demonstrate a causal link between aquaculture environment and gene expression levels mediated, at least in part, by changes in DNA methylation levels

4th International Symposium on Genomics in Aquaculture (GIA 2016), 20-22 April 2016, Athens, Greece

Supported by Spanish Government grant “Epifarm” to FP

Peer Reviewed