Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon

Abstract

Farmed salmon strains have been selected to improve growth rates as well as other traits of commercial interest but the 2 million farmed salmon escaping annually may enhance the risk of extinction of wild populations through genetic and ecological interactions. Here, we compare the transcription profiles of 3557 genes in the progeny of farmed and wild Atlantic salmon from Norway and Canada grown in controlled conditions, and demonstrate that five to seven generations of artificial selection led to heritable changes in gene transcription profiles, the average magnitude of the differences being 25% and 18% for at least 1.4% and 1.7% of the expressed genes in juvenile salmon from Norway and Canada, respectively. Moreover, genes showing significant transcription profile differences in both farmed strains (16%) all exhibited parallel changes. These findings, along with the identification of several genes whose expression profiles were modified through artificial selection, provide new insights into the molecular basis of parallel evolution, and suggest how gene flow from farmed escapees may affect the genetic integrity of wild populations.

An assessment of the spatial scale of local adaptation in brown trout (Salmo trutta L.): footprints of selection at microsatellite DNA loci

“…This suggests that diversifying selection between wild and hatchery strain trout involves different loci than those under selection among wild populations. Although this latter point is based on analysis of relatively few loci, it does receive support from an analysis of transcriptome differences between farmed and wild Atlantic salmon (Roberge et al, 2006). Here, farmed and wild salmon showed considerable divergence, but different farmed strains of European and North American origin showed convergence at the transcriptome level, indicating parallel evolution during the domestication process.…”

Population Genomics of Marine Fishes: Next-Generation Prospects and Challenges

“…Therefore, it is not surprising that RNA-seq has become the technology of choice for quantifying differential gene expression (Deng et al, 2011;Smith et al, 2013). Gene expression analyses have allowed the identification of key molecular mechanisms underlying desired traits in farmed fish (Roberge et al, 2006;Ferraresso et al, 2008Ferraresso et al, , 2013, but have also been successfully applied to natural populations of marine fishes (Whitehead and Crawford, 2006;Larsen et al, 2007Larsen et al, , 2011Pujolar et al, 2012Pujolar et al, , 2013bCôté et al, 2014). Finally, transcriptomic analyses can be complemented and integrated with protein expression analysis to investigate the responses at the proteomic level for a deeper understanding of functional implications (Nie et al, 2007;Dalziel and Schulte, 2012).…”

Temporal change in genetic integrity suggests loss of local adaptation in a wild Atlantic salmon (Salmo salar) population following introgression by farmed escapees

“…Moreover, relaxed selection resulting from absence of predators, constant supply of food and medical treatment, as well as increased genetic drift caused by small effective population sizes may favor the accumulation of deleterious alleles. Furthermore, genetic changes unrelated to adaptation to captivity are bound to occur as a result of founder effects in the farmed populations (Roberge et al, 2006). Consequently, change in the genetic composition of captive populations has been observed in many studies on farmed Atlantic salmon of northern Europe (Skaala et al, 2004).…”