Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication. Major gene expression changes and epigenetic remodelling in Nile tilapia muscle after just one generation of domestication

Background: The historically recent domestication of fishes has been essential for mankind due to the overexploitation of natural stocks and the increasing protein demand to meet the needs of a growing human population. Selection for relevant traits, such as growth, during domestication is a complex process whose epigenetic basis is poorly understood. Results: We have determined changes that occur in the muscle transcriptome after a single generation of Nile tilapia (Oreochromis niloticus) domestication. There was a downregulation of 2015 genes in fish reared in captivity compared to their wild progenitors. In contrast, several myogenic and metabolic genes that can affect growth potential were upregulated. Methods: RNA was extracted and ribosomal RNA was removed using the Ribo-Zero gold rRNA removal kit. RNA libraries were prepared using the NEBNext Ultra II directional RNA library prep kit for Illumina. In total, we obtained 480 million 150 bp paired-end reads. Conclusion: Taken together, our data indicate that thousands of genes were differentially expressed within a single generation of fish domestication. Overall design: Fast muscle RNA-Seq from rRNA depleted libraries of 5-month old Wild type (W) and first generation of fish undergoing domestication (D) females in six replicates. W and D samples are genetically paired (i.e., each D sample corresponded to a W progenitor) and at the same ontogeny stage. The pairs are grouped according to their numbers (i.e. W53 - D53, W63 - D63)