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.

Can variation in standard metabolic rate explain context‐dependent performance of farmed Atlantic salmon offspring?

“…Both the reduced success of farmed salmon and their descendants in nature, and the negative effect of their presence for production of wild salmon, are likely related to genomic and phenotypic alterations that have occurred during the domestication process (Bolstad et al, 2017;Liu et al, 2017). Among the phenotypic alterations reported are increased growth rates (Gjedrem, 2000;Harvey et al, 2016;Solberg, Skaala, Nilsen, & Glover, 2013a) and changes in behavior, such as decreased response to predators, and increased aggression and social dominance (Einum & Fleming, 1997;Houde, Fraser, & Hutchings, 2010a;Johnsson, Höjesjö, & Fleming, 2001).…”

Genomic signatures of fine‐scale local selection in Atlantic salmon suggest involvement of sexual maturation, energy homeostasis and immune defence‐related genes

“…Several previous studies have used a 7K SNP array to identify regions of the genome putatively under differential selection among S. salar populations (Bourret, Dionne, Kent, Lien, & Bernatchez, ; Bourret, Kent et al., ; Gutierrez, Yáñez, & Davidson, ; Jeffery et al., ; Liu et al., ; Mäkinen, Vasemägi, McGinnity, Cross, & Primmer, ; Moore et al., ; Perrier, Bourret, Kent, & Bernatchez, ); discriminating populations (Karlsson, Moen, Lien, Glover, & Hindar, ) or associated with phenotypic traits (Gutierrez, Yáñez, Fukui, Swift, & Davidson, ; Johnston et al., ). To compare our results with the location of SNPs of interest identified in these studies, we obtained flanking sequences for the 7K SNPs from NCBI dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/) and aligned them with the S. salar genome using bwa‐mem with default parameters (Li, ; Li & Durbin, ).…”

Parallel evolution and adaptation to environmental factors in a marine flatfish: Implications for fisheries and aquaculture management of the turbot (Scophthalmus maximus)

“…Distinguishing between neutral and adaptive genetic variation has become a central issue in evolutionary biology, allowing for understanding of population structure in both historical/demographic and adaptive terms (Bernatchez, 2016; Nielsen, Hemmer‐Hansen, Larsen, & Bekkevold, 2009), thereby providing essential information for the conservation and management of wild populations. Genetic diversity in the wild represents, in turn, the raw material for the foundation of aquaculture broodstock and consequently, a reference to identify selection signatures for targeted traits in farmed populations through genome scanning (Liu et al., 2017). …”