Early fish domestication affects methylation of key genes involved in the rapid onset of the farmed phenotype

Abstract

Animal domestication is a process of environmental modulation and artificial selection leading to permanent phenotypic modifications. Recent studies showed that phenotypic changes occur very early in domestication, i.e., within the first generation in captivity, which raises the hypothesis that epigenetic mechanisms may play a critical role on the early onset of the domestic phenotype. In this context, we applied reduced representation bisulphite sequencing to compare methylation profiles between wild Nile tilapia females and their offspring reared under farmed conditions. Approximately 700 differentially methylated CpG sites were found, many of them associated not only with genes involved in muscle growth, immunity, autophagy and diet response but also related to epigenetic mechanisms, such as RNA methylation and histone modifications. This bottom-up approach showed that the phenotypic traits often related to domestic animals (e.g., higher growth rate and different immune status) may be regulated epigenetically and prior to artificial selection on gene sequences. Moreover, it revealed the importance of diet in this process, as reflected by differential methylation patterns in genes critical to fat metabolism. Finally, our study highlighted that the TGF-β1 signalling pathway may regulate and be regulated by several differentially methylated CpG-associated genes. This could be an important and multifunctional component in promoting adaptation of fish to a domestic environment while modulating growth and immunity-related traits.

Keywords: DNA methylation; Domestication; Oreochromis niloticus; epigenetics; muscle growth.

Figure 1.

Average weight (g) of 12 females from the wild and domestic groups. Domestic females were statistically heavier than small females (paired t-test, p-value <0.01).

Figure 2.

Number of total raw, quality-trimmed, adapter trimmed, uniquely mapped and multiply mapped reads in the domesticated- and wild female group.

Figure 3.

Genomic context of CpG sites found in the whole genome, our RRBS dataset and associated with hypo- and hypermethylated sites.

Figure 4.

Volcano plot representing q-value and methylation difference in all CpG sites compared between wild and domesticated fish. Red dots represent differentially methylated CpG sites (methylation difference >25%, FDR <0.01). Several genes associated with most extreme CpG methylation differences are indicated. In addition, blue dots highlight all the 15 DM CpG sites associated specifically with stub-1 gene.

Figure 5.

Chromosomal distribution of differentially methylated CpG sites between wild females and their progeny undergoing domestication (716 positions, FDR < 0.01, methylation difference >25%). Wild females are set as reference. Histograms pointing inwards (dark green) and outwards (dark red) represent hypomethylated and hypermethylated sites in domestic group, respectively.

Figure 6.

Principal component analysis of 12 fish separated in the domestic (d, blue) and wild group (w, red).

Figure 7.

Schematic representation of genes that are associated with differentially methylated CpGs (domestic VS wild females) and whose functions are related muscle growth, autophagy, immunity, diet or epigenetic regulation processes.

Figure 8.

Schematic representation of a gene network associated with differentially methylated CpGs (in blue) and whose functions are related to transforming growth factor beta 1 or to other genes relevant to the process of muscle growth (in black). Red/green and continuous/dashed arrows indicate positive/negative and direct/indirect regulation, respectively.