Journal Article

Genomic Signatures of Domestication in European Seabass (Dicentrarchus labrax L.) Reveal a Potential Role for Epigenetic Regulation in Adaptation to Captivity

Moulistanos, Aristotelis, Karaiskou, Nikoleta, Papakostas, Spiros, Gkagkavouzis, Konstantinos, Papasakellariou, Konstantinos, Triantafyllidis, Alexandros, Kavakiotis, Ioannis, Antonopoulou, Efthimia

2024

Overview

Genome scans provide a comprehensive method to explore genome‐wide variation associated with traits under study. However, linking individual genes to broader functional groupings and pathways is often challenging, yet crucial for understanding the evolutionary mechanisms underlying these traits. This task is particularly relevant for multi‐trait processes such as domestication, which are influenced by complex interactions between numerous genetic and non‐genetic factors, including epigenetic regulation. As various traits within the broader spectrum of domestication are selected in concert over time, this process offers an opportunity to identify broader functional overlaps and understand the integrated genetic architecture underlying these traits. In this study, we analyzed approximately 600,000 SNPs from a Pool‐Seq experiment comparing eight natural‐origin and 12 farmed populations of European seabass in the Mediterranean Sea region. We implemented two genome scan approaches and focused on genomic regions supported by both methods, resulting in the identification of 96 candidate genes, including nine CpG islands, which highligt potential epigenetic influences. Many of these genes and CpG islands are in linkage groups previously associated with domestication‐related traits. The most significantly overrepresented molecular function was “oxidoreductase activity”. Furthermore, a dense network of interactions was identified, connecting 22 of the candidate genes. Within this network, the most significantly enriched pathways and central genes were involved in “chromatin organization”, highlighting another potential epigenetic mechanism. Altogether, our findings underscore the utility of interactome‐assisted pathway analysis in elucidating the genomic architecture of polygenic traits and suggest that epigenetic regulation may play a crucial role in the domestication of European seabass. Our study identified 96 candidate genes and nine CpG islands potentially linked to domestication in European seabass, many of which are associated with traits influenced by both genetic and epigenetic factors. The most enriched molecular functions were “oxidoreductase activity” and “chromatin organization”, indicating that epigenetic regulation may play a critical role in shaping domestication processes. Overall, our findings demonstrate the value of combining genome scans with interactome‐assisted pathway analysis to uncover the complex genetic architecture underlying polygenic traits like domestication.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc,Wiley
• Subject: Adaptation / artificial selection / Captivity / Chromatin / CpG islands / Datasets / Dicentrarchus labrax / Domestication / domestication genetics / Epigenetics / Farming / Fish / Gene loci / Gene regulation / Genes / Genetic factors / Genomes / genome‐wide variation / Genomic analysis / Genomics / interactome‐assisted pathway analysis / Islands / marine teleost / Oxidoreductase / Polygenic inheritance / Salmon / Single-nucleotide polymorphism