Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits
Liu, Lei, University of Guelph
Ang, Keng Pee, University of Guelph
Elliott, J. A. K., Fisheries and Oceans Canada
Kent, Matthew Peter, Norwegian University of Life Sciences
Lien, Sigbjørn, Norwegian University of Life Sciences
MacDonald, Danielle, Fisheries and Oceans Canada
Boulding, Elizabeth Grace, University of Guelph
Published Nov 22, 2016 on Dryad.
Cite this dataset
Liu, Lei et al. (2016). Data from: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: testing co-localization among outlier markers, candidate genes, and QTLs for production traits [Dataset]. Dryad. https://doi.org/10.5061/dryad.53b58
Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, 3 of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease-resistance. Parallel comparisons using a wild, non-founder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.
TOB VS STW populations_text
raw dataset with 3980 SNP genotypes for two wild Atlantic salmon populations from the Tobique River and the Stewiacke River in the Bay of Fundy, Canada.