Environment and genotype predict the genomic nature of domestication of salmonids as revealed by gene expression

Abstract

Billions of salmonids are produced annually by artificial reproduction for harvest and conservation. Morphologically, behaviourally and physiologically these fish differ from wild-born fish, including in ways consistent with domestication. Unlike most studied domesticates, which diverged from wild ancestors millennia ago, salmonids offer a tractable model for early-stage domestication. Here, we review a fundamental mechanism for domestication-driven differences in early-stage domestication, differentially expressed genes (DEGs), in salmonids. We found 34 publications examining DEGs under domestication driven by environment and genotype, covering six species, over a range of life-history stages and tissues. Three trends emerged. First, domesticated genotypes have increased expression of growth hormone and related metabolic genes, with differences magnified under artificial environments with increased food. Regulatory consequences of these DEGs potentially drive overall DEG patterns. Second, immune genes are often DEGs under domestication and not simply owing to release from growth-immune trade-offs under increased food. Third, domesticated genotypes exhibit reduced gene expression plasticity, with plasticity further reduced in low-complexity environments typical of production systems. Recommendations for experimental design improvements, coupled with tissue-specific expression and emerging analytical approaches for DEGs present tractable avenues to understand the evolution of domestication in salmonids and other species.

Premises for a digital twin of the Atlantic salmon in its world: Agency, robustness, subjectivity and prediction

“…Atlantic salmon has been under artificial selection in aquaculture for more than 50 years and 20 generations (Besnier et al., 2022). This has led to some genetic modifications in hormonal systems (Bull et al., 2022; Fleming et al., 2002) impacting physiology, behaviour, leading to faster growth (Debes & Hutchings, 2014; Houde et al., 2010; Solberg et al., 2020), higher stress tolerance (Solberg et al., 2013) and reduced vigilance (Fleming, 1998; Mobley et al., 2021). Domesticated and wild fish may thus differ in their propensity to alternative ontogenetic strategies (Harvey et al., 2018).…”

Parallel selection in domesticated Atlantic salmon from divergent founders including parallel selection on WGD-derived homeologous regions

“…Despite the very recent domestication, studies of Atlantic salmon have revealed rapid genetic changes in pathways for metabolism, immunity, and faster growth (Debes et al, 2012;Bicskei et al, 2014;Harvey et al, 2018;Jin et al, 2020;Bull et al, 2022). Moreover, signatures of domestication selection have also been observed in neurological genes (Bertolotti et al, 2020), and behavioral alterations, such as increased sensitivity to predation and increased tolerance to stress compared with the wild (Solberg et al, 2020).…”