Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon

Vasemägi, Anti; Nilsson, Jan; McGinnity, Philip; Cross, Tom; O’Reilly, Patrick; Glebe, Brian; Peng, Bo; Berg, Paul Ragnar; Primmer, Craig Robert

Screen for Footprints of Selection during Domestication/Captive Breeding of Atlantic Salmon

2012

Vasemägi, Anti(Division of Genetics and Physiology, Department of Biology) | Nilsson, Jan(Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences) | McGinnity, Philip(Aquaculture and Fisheries Development Centre, School of Biological, Earth, and Environmental Sciences) | Cross, Tom(Aquaculture and Fisheries Development Centre, School of Biological, Earth, and Environmental Sciences) | O’Reilly, Patrick(Population Ecology Division, Department of Fisheries and Oceans) | Glebe, Brian(Fisheries and Oceans Canada, Department of Fisheries and Oceans) | Peng, Bo(Department of Genetics, The University of Texas M. D. Anderson Cancer Center) | Berg, Paul Ragnar(Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics) | Primmer, Craig Robert(Division of Genetics and Physiology, Department of Biology)

Domesticated animals provide a unique opportunity to identify genomic targets of artificial selection to the captive environment. Here, we screened three independent domesticated/captive Atlantic salmon (Salmo salar) strains and their wild progenitor populations in an effort to detect potential signals of domestication selection by typing of 261 SNPs and 70 microsatellite loci. By combining information from four different neutrality tests, in total ten genomic regions showed signs of directional selection based on multiple sources of evidence. Most of the identified candidate regions were rather small ranging from zero to a few centimorgans (cM) in the female Atlantic salmon linkage map. We also evaluated how adaptation from standing variation affects adjacent SNP and microsatellite variation along the chromosomes and, by using forward simulations with strong selection, we were able to generate genetic differentiation patterns comparable to the observed data. This study highlights the significance of standing genetic variation during the early stages of adaptation and represents a useful step towards identifying functional variants involved in domestication of Atlantic salmon.

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