Abstract
Domestication of Atlantic salmon started approximately 40 years ago, using artificial selection through genetic improvement programs. Selection is likely to have imposed distinctive signatures on the salmon genome, which are often characterized by high genetic differentiation across population and/or reduction in genetic diversity in regions associated to traits under selection. The identification of such selection signatures may give insights into the candidate genomic regions of biological and commercial interest. Here, we used three complementary statistics to detect selection signatures, two haplotype-based (iHS and XP-EHH), and one FST-based method (BayeScan) among four populations of Atlantic salmon with a common genetic origin. Several regions were identified for these techniques that harbored genes, such as kind1 and chp2, which have been associated with growth-related traits or the kcnb2 gene related to immune system in Atlantic salmon, making them particularly relevant in the context of aquaculture. Our results provide candidate genes to inform the evolutionary and biological mechanisms controlling complex selected traits in Atlantic salmon.
Highlights
Domestication is a complex evolutionary process whereby wild animals or plant populations adapt to environmental conditions created by humans and so involves genetic and developmental changes over multiple generations (Price, 1984; Liu et al, 2017)
Domestication in most fish is relatively recent compared with terrestrial animals (Teletchea and Fontaine, 2014; López et al, 2015), but has expanded rapidly over the last decades (Lorenzen et al, 2012), and several breeding programs have been implemented in different aquatic species, such as Selection Signatures in Farmed Atlantic Salmon tilapia (Oreochromis niloticus L), rainbow trout (Oncorhynchus mykiss W), coho salmon (Oncorhynchus kisutch W), and Atlantic salmon (Salmo salar L) among others (Gjedrem, 2010; Gjedrem, 2012; Yáñez et al, 2014)
Genomic regions detected in this study strongly suggest selection on traits that could be associated with either natural or artificial selection, as they relate to the immune system, growth, and behavior, which are all often altered through domestication
Summary
Domestication is a complex evolutionary process whereby wild animals or plant populations adapt to environmental conditions created by humans and so involves genetic and developmental changes over multiple generations (Price, 1984; Liu et al, 2017). Domestication in most fish is relatively recent compared with terrestrial animals (Teletchea and Fontaine, 2014; López et al, 2015), but has expanded rapidly over the last decades (Lorenzen et al, 2012), and several breeding programs have been implemented in different aquatic species, such as Selection Signatures in Farmed Atlantic Salmon tilapia (Oreochromis niloticus L), rainbow trout (Oncorhynchus mykiss W), coho salmon (Oncorhynchus kisutch W), and Atlantic salmon (Salmo salar L) among others (Gjedrem, 2010; Gjedrem, 2012; Yáñez et al, 2014) The latter has become one of the most important aquaculture species (FAO, 2016), since it was first farmed in Norway during the 1960s. Domestication and subsequent artificial selection have produced stark phenotypic changes in farmed Atlantic salmon populations (Glover et al, 2017), as evidenced by differences in traits, such as growth and predator awareness, between wild and farmed populations (Thodesen et al, 1999; Glover et al, 2009; Solberg et al, 2012) (Einum and Fleming, 1997)
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