The Core Gene Expression Cascade during the Early Developmental Process Identifies Genetic Mechanisms for Salmonids Captive Breeding

Evidence for lower fitness of captive-reared salmonids in the wild has accumulated in recent years, raising serious concerns for long-term sustainability of wild populations. Comparative studies on the early developmental stages in Atlantic salmon have demonstrated genetic consequences related to energy metabolic, muscle, and immune-related gene expression in farmed/hybrid fish compared with wild. Thus, it is crucial to determine whether these genes are essential to infer the genetic mechanisms. We developed an exploratory graphical modeling approach to extract the key operating interactions rather than describing the entire gene interaction network. We obtained the maximum core expression cascade of 106 genes from a public dataset of farmed Atlantic salmon. An enrichment analysis determined that 13 of the 57 pre-identified farmed/hybrid/wild-differentially expressed genes were included in the core gene cascade (p=6.94×10^-11), and some had already reached a plateau before hatch. However, insulin-like growth factor 1 (IGF1), which explains the mechanisms of intended selection for rapid growth, was not included. Our results suggest the mechanisms for the fitness decline caused by captive breeding; that is, accumulated unintended domestication in captivity selects individuals adapted well to the captive environment with non-IGF1-dependent behavioral-related genes which reduce fitness of captive-reared fish in the wild.