Population genomic analyses of early‐phase Atlantic Salmon (Salmo salar) domestication/captive breeding

Abstract

Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild Atlantic salmon (Salmo salarL.) populations are threatened by anthropogenic influences, and they are supplemented with captively bred fish. The Atlantic salmon is also widely used in selective breeding programs to increase the mean trait values for desired phenotypic traits. We analyzed a genomewide set of SNPs in three domesticated Atlantic salmon strains and their wild conspecifics to identify loci underlying domestication. The genetic differentiation between domesticated strains and wild populations was low (FST < 0.03), and domesticated strains harbored similar levels of genetic diversity compared to their wild conspecifics. Only a few loci showed footprints of selection, and these loci were located in different linkage groups among the different wild population/hatchery strain comparisons. Simulated scenarios indicated that differentiation in quantitative trait loci exceeded that in neutral markers during the early phases of divergence only when the difference in the phenotypic optimum between populations was large. This study indicates that detecting selection using standard approaches in the early phases of domestication might be challenging unless selection is strong and the traits under selection show simple inheritance patterns.

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

“…For example, the outlier BASS113_B6A_E01_397 that was found by Mäkinen et al. (2015) is within 3 cM of one of our consistent outlier SNPs (ESTNV_16810_167, Table 4) that is located on chromosome Ssa 12.…”

“…Recent outlier locus studies of salmonid fishes have primarily compared wild populations at different spatial scales (Freamo, O'Reilly, Berg, Lien, & Boulding, 2011; Vasemägi & Primmer, 2005) or have correlated outlier loci of wild populations with specific environmental variables (Bourret, Kent, et al., 2013; Bourret, Dionne, Kent, Lien, & Bernatchez, 2013; Narum, Campbell, Kozfkay, & Meyer, 2010; Perrier, Bourret, Kent, & Bernatchez et al., 2013). Of more relevance to Atlantic salmon domestication are four outlier studies comparing aquaculture strains with wild populations from the same region as their putative founder population(s) (Gutierrez, Yáñez, & Davidson, 2016; Karlsson, Moen, Lien, Glover, & Hindar, 2011; Mäkinen, Vasemägi, McGinnity, Cross, & Primmer, 2015; Vasemägi, Nilsson, & Primmer, 2005). …”

Wildlife Conservation: Is Domestication a Solution?

“…Yet, compared to the knowledge on the behavioral, physiological, morphological and genetic consequences of domestication among land vertebrates, there is very litle information on the consequences of domestication in ish [4 ]. "esides, much knowledge acquired has been on salmonids due to their economic importance for both human consumption and sport isheries (e.g., [50][51][52]). …”

“…The time spent in sea has decreased for both female and male sea trout, but not for "tlantic salmon [50]. "t last, several studies have been recently published that try to detect genomic diferences in recently domesticated species, such as the "tlantic salmon [51]. In their study, these authors analyzed a genome-wide set of single nucleotide polymorphisms (SNPs) in three domesticated "tlantic salmon (from ive to nine generations in captivity without wild inputs) and their wild conspeciics to identify loci underlying domestication.…”

“…They found that the genetic diferentiation between the two wild and domesticated was low and domesticated strains harbored similar level of genetic diversity compared to their wild conspeciics. Their study indicates that detecting selection in the irst generations of domestication could be tricky unless selection is strong and the traits under selection show simple inheritance paterns [51]. "ecause a genomewide response to selection can take many generations, as found for the "tlantic salmon, Christie et al [52] hypothesized that the earliest changes associated with domestication may irst manifest as heritable changes to global paterns of gene expression.…”