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.
Highlights
Domestication, “the process by which captive animals adapted to man and the environment he provides,” has led to several genetic changes over generations in various animal and plant species (Price, 1984)
Despite Atlantic salmon populations having been intensely selected for growth-related traits on both sides of the Atlantic ocean, we found little overlap between the outlier genomic regions identified in previous studies of other Atlantic salmon strains selected for high growth rate (Gutierrez, Yáñez, & Davidson, 2015; Gutierrez, Yáñez, Fukui, et al, 2015)
A small number of parallel genomic regions putatively under selection belong to genes with molecular functions that might be associated with traits under domestication, such as behavior, immune response, and reproduction
Summary
Domestication, “the process by which captive animals adapted to man and the environment he provides,” has led to several genetic changes over generations in various animal and plant species (Price, 1984) This evolutionary process may induce similar phenotypic changes in populations of independent origins within the same species when the same phenotypic traits are subjected to similar selective pressures. Phenotypes of these animals have progressively evolved due to the combined influence of domestication selection through reproduction in captivity and human directional selective breeding (Andersson, 2012). Domestication has greatly impacted the phenotypes of domesticated aquatic species (e.g., Atlantic salmon [Salmo salar L.], rainbow trout [Oncorhynchus mykiss W.], tilapia [Oreochromis niloticus L.], common carp [Cyprinus carpio L.]) in which selective breeding programs have been implemented, focusing on specific economic objectives (Gjedrem, 2012; Rye, Gjerde, & Gjedrem, 2010)
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