Comparing genomic signatures of domestication in two Atlantic salmon (Salmo salar L.) populations with different geographical origins

Abstract

Selective breeding and genetic improvement have left detectable signatures on the genomes of domestic species. The elucidation of such signatures is fundamental for detecting genomic regions of biological relevance to domestication and improving management practices. In aquaculture, domestication was carried out independently in different locations worldwide, which provides opportunities to study the parallel effects of domestication on the genome of individuals that have been selected for similar traits. In this study, we aimed to detect potential genomic signatures of domestication in two independent pairs of wild/domesticated Atlantic salmon populations of Canadian and Scottish origins, respectively. Putative genomic regions under divergent selection were investigated using a 200K SNP array by combining three different statistical methods based either on allele frequencies (LFMM, Bayescan) or haplotype differentiation (Rsb). We identified 337 and 270 SNPs potentially under divergent selection in wild and hatchery populations of Canadian and Scottish origins, respectively. We observed little overlap between results obtained from different statistical methods, highlighting the need to test complementary approaches for detecting a broad range of genomic footprints of selection. The vast majority of the outliers detected were population‐specific but we found four candidate genes that were shared between the populations. We propose that these candidate genes may play a role in the parallel process of domestication. Overall, our results suggest that genetic drift may have override the effect of artificial selection and/or point toward a different genetic basis underlying the expression of similar traits in different domesticated strains. Finally, it is likely that domestication may predominantly target polygenic traits (e.g., growth) such that its genomic impact might be more difficult to detect with methods assuming selective sweeps.

Relative genomic impacts of translocation history, hatchery practices, and farm selection in Pacific oysterCrassostrea gigasthroughout the Northern Hemisphere

“…An outlier was found in transient receptor potential cation channel subfamily M member 6 , and interestingly member 3-like from the same cation channel subfamily member was found to be a parallel domestication outlier in both Scottish and Canadian domestic Atlantic salmon (López et al, 2019). Several other genes identified here have also been identified as being involved in domestication processes, such as mitochondrial uncoupling protein 2 , which has undergone loss of function mutations in pig ( Sus scrofa domesticus ) domestication and potentially has led to the reduction of cold tolerance of pigs (Berg et al, 2006) as well as being found to be an outlier in domestic dogs Canis lupus familiaris (Udagawa et al, 2014).…”

Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects

“…2018c; López et al . ). Rainbow trout and coho salmon Chilean breeding populations were established based on improved germplasm introduced from multiple origins and the west coast of North America (e.g.…”

“…In Chile, commercial breeding programmes started being established in the late 1990s. Atlantic salmon breeding populations were created mainly based on improved germsplasm from Norwegian origin; however, North American and Scottish material was also introduced for the same purposes (Barr ıa et al 2018c;L opez et al 2018). Rainbow trout and coho salmon Chilean breeding populations were established based on improved germplasm introduced from multiple origins and the west coast of North America (e.g.…”

Multiple selection signatures in farmed Atlantic salmon adapted to different environments across Hemispheres

“…2015; L iu et al . 2016; López et al . 2018) exploration of selection signatures in additional populations will illuminate how genetic variation among the different strains, adapted to different culture conditions, across hemispheres has not been assessed yet.…”