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.
Highlights
| INTRODUCTION2013; Braastad & Bakken, 2002; Frantz et al, 2016). Subsequently, from 8,000 to 10,000 YBP, pigs, sheep, goats and cattle were domesticated as a source of food (Craig, 1981)
Animal domestication is one of the most important practical applications of evolutionary theory in human history
Motivation behind genome scans for selection signatures lies in the possibility of finding DNA markers associated with traits of economic interest that can be used for marker-assisted selection (López, Neira, & Yáñez, 2015; Yáñez, Houston, & Newman, 2014)
Summary
2013; Braastad & Bakken, 2002; Frantz et al, 2016). Subsequently, from 8,000 to 10,000 YBP, pigs, sheep, goats and cattle were domesticated as a source of food (Craig, 1981). The similar selection differentials applied to classic quantitative traits like growth are assumed to cause only minor changes in allele frequencies (Falconer & Mackay, 1996) that would be undetectable using outlier locus methodology (Wellenreuther & Hansson, 2016), but see Fontanesi et al (2015) Both single locus and quantitative traits might show rapid genetic divergence between aquaculture strains and wild populations of Atlantic salmon. We hypothesized that outlier analysis that compared the genomes of recently created North American aquaculture populations of Atlantic salmon from the Saint John River (SJR), with that of their putative wild founder population from the Tobique River, would be likely to identify genome regions underlying traits known to be under strong artificial selection in the hatchery environment. This allowed us to identify the genome regions, as well as some putative candidate genes, that have responded to either deliberate artificial selection for growth and late maturity or to accidental selection exerted by the hatchery environment
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