Genome Scan for Selection Signatures in Atlantic Salmon Populations Using a High Density SNP Array

Detecting selection in domesticated species can provide insight into the biological process of artificial selection and the causal genes underlying phenotypic variation. In some cases artificial selection can drive genetic changes on a short time scale in domesticated animals. Atlantic salmon (Salmo salar) represent an ideal model for studying the genomic response to selection because some farmed populations of extant wild stocks have experienced intense artificial selection for traits such as growth for over 40 years.

We used a high density SNP chip to screen 151,509 SNPs for selection signatures in two independently domesticated strains and their respective wild ancestor populations. The genome-wide genetic differentiation between the domestic and wild populations as measured by F_ST was 0.16 for Canadian populations and 0.08 for Scottish populations. We performed F_ST outlier and cross-population extended haplotype homozyogisty tests to identity signals of artificial selection in the genome. The F_ST scans produced a subset of 160 and 93 outlier SNPs showing evidence of selection for Canadian and Scottish stocks respectively.

These identified outlier loci illustrate the usefulness of a high density, genotyping chip and provide a basis for further studies aimed at detecting genes involved in biological processes relevant to domestication and selection in Atlantic salmon.