Changes in the liver of Tinca tinca under successive domestication using an integrated multi-omics approach

Domestication is the process of modifying the phenotype of a population through anthropic selection from human perspectives. Successive generations of domestication have influenced the physiological characteristics of tench Tinca tinca. In current study, we investigated gene and protein expression alterations in the liver of fifth-generation (F5). A total of 420 genes were found to be upregulated and 351 genes were downregulated, while 410 proteins were upregulated and 279 proteins were downregulated in domesticated T. tinca (DT). The integrated analysis of omics data revealed a total of 55 genes/proteins exhibiting consistent upregulation and 12 genes/proteins displaying consistent downregulation in DT. The upregulated genes/proteins in DT, such as SSR1, DERLIN2, OS9, DNAJB11, and HYOU1, exhibit enrichment in the protein processing in the endoplasmic reticulum pathway. Additionally, upregulated genes/proteins such as IL2RB, F13B, and IRF3 are associated with immune response. Conversely, downregulated genes/proteins in DT, including HSD11B1, CYP24A1, and COMT, play roles in hormone metabolism. These findings indicate that domestication can have a substantial impact on the physiological modifications related to protein processing, immune response, and hormone metabolism in DT. These adaptations potentially enhance their ability to thrive in artificial aquaculture environments, leading to improved growth and development. The exploration of genetic changes in DT will not only improve aquaculture practices but also provide significant insights into the broader process of domestication and its effects on physiological functions.