title: A genome scan for selection signatures comparing farmed Atlantic salmon with two wild populations: Testing colocalization among outlier markers, candidate genes, and quantitative trait loci for production traits.
abstract: 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, three 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, nonfounder 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.
authors.affiliation: Department of Integrative Biology University of Guelph Guelph ON Canada; Present address: School of Marine Sciences Ningbo University Ningbo China.
authors.forename: Lei
authors.initials: L
authors.lastname: Liu
authors.affiliation: Cooke Aquaculture Inc. Blacks Harbour NB Canada.
authors.forename: Keng Pee
authors.initials: KP
authors.lastname: Ang
authors.affiliation: Cooke Aquaculture Inc. Blacks Harbour NB Canada.
authors.forename: J A K
authors.initials: JA
authors.lastname: Elliott
authors.affiliation: Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway.
authors.forename: Matthew Peter
authors.initials: MP
authors.lastname: Kent
authors.affiliation: Department of Animal and Aquacultural Sciences (IHA) Center for Integrative Genetics (CIGENE) Norwegian University of Life Sciences Ås Norway.
authors.forename: Sigbjørn
authors.initials: S
authors.lastname: Lien
authors.affiliation: Saint Andrews Biological Station Department of Fisheries and Oceans Canada Saint Andrews NB Canada.
authors.forename: Danielle
authors.initials: D
authors.lastname: MacDonald
authors.affiliation: Department of Integrative Biology University of Guelph Guelph ON Canada.
authors.forename: Elizabeth Grace
authors.initials: EG
authors.lastname: Boulding
keywords: Atlantic salmon; SNP; artificial selection; candidate genes; continent of origin; domestication selection; outlier tests; population structure