Sammendrag
Introduction: Many studies in fish domestication have detected significant gene expression changes across generations. However, these changes cannot be explained entirely neither with the occurrence of mutations nor with changes in allele frequencies (Christie et al.,2016). DNA hydroxymethylation (5hmC) is one of the epigenetic modifications that can alter gene expression without causing any changes in the DNA sequence. It can serve both as an intermediate step in the demethylation process and as a stable epigenetic modification. The sustainable future of the aquaculture industry is relying more than ever on the domestication of fish species. Thus, a closer look into the epigenetic machinery of several cultivated fish species could provide significant insight into addressing these findings. Luyer et al.,(2017) provided recent evidence that hatchery conditions affect the epigenetic landscape, which has impact on the fitness of the species in question. However, methylation (5mC) analysis such as RRBS and WGBS cannot discriminate distinct epigenetic mechanisms such as 5mC and 5hmC. In this study, we compare for the first time the 5hmC profiles of wild Nile tilapia (Oreochromis niloticus) females and their female offspring reared in captivity. Our goal is to map the hydroxymethylome of these individuals, detect stable 5hmC loci and find inherited patterns and significant differences within the first stage of their domestication.
Materials and Methods: Fast muscle from wild female Nile tilapia was sampled from river Nile, Luxor, Egypt. Their eggs were kept in egg rockers until 3-5 days post-hatching and then transferred to Mørkvedbukta research station in Bodø, Norway. After 5 months, fast muscle samples were taken from the first generation in captivity. Global 5hmC levels were calculated by liquid chromatography/mass spectrometry (LC/MS) analysis while the hydroxymethylation mapping at a single nucleotide level was determined by the reduced representation hydroxymethylation profiling (RRHP, Zymo Research). The sequencing was performed on an Illumina HiSeq 4000 platform at the Norwegian Sequencing Center. In order to identify differentially hydroxymethylated regions we have used R, the limma package and the software Circos for data visualization.
Results and Discussion: The present study provides the first insight of 5hmC profiling during the first stage of domestication in fish. Our findings indicate significant differences between the wild and the first generation of reared Nile tilapia at both global 5hmC and single nucleotide levels (adj.p
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