With the rapid development of aquaculture, many fish species are domesticated and brought into cultivation. In the process of domestication, the domesticated fish undergone intense selection pressures and develop some adaptations and phenotypic traits, namely selection signatures, such as growth and metabolism, immunity, foraging and learning behaviors. However, how this selection signatures emerges is still not clear and the knowledge of molecular epigenetic mechanisms underlying selection signatures in fish is still in its infancy. Thus, we used a farmed fish, grass carp (Ctenopharyngodon idellus), as model species to detect these selection signatures and identify the candidate differentially methylated genes that are closely associated with these selection signatures at the level of whole genome, investigating the role of DNA methylation in the emergence of selection signatures during domestication. Our results showed that domesticated grass carp demonstrated four selection signatures, including growth and metabolism, immunity, foraging and learning behaviors, and 38 candidate genes were found associated with these traits. 16 genes are significant candidate genes which play major roles in the growth and metabolism, such as IGF-1 , GK , GYS1, etc. 11 genes are related to immunity, including . The GRM1, TAS1R1 and TAS1R3 genes are essential for the adaptation of domesticated grass carp to commercial feed in artificial rearing condition. The C-FOS, POMC and CBP genes may be responsible for the acquisition of novel feeding habits and contribute to faster growth indirectly by enhancing food intake. The findings here in will provide new insights to expand our understanding about the role of epigenetic modifications in shaping physiological phenotypes in this and other teleost models, which can contribute to efficient breeding of aquaculture stocks and restocking programmes.

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