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Comparative and Functional Genomics
Volume 2012, Article ID 628204, 14 pages
Research Article

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

1Division of Genetics and Physiology, Department of Biology, University of Turku, 20014 Turku, Finland
2Department of Aquaculture, Institute of Veterinary Medicine and Animal Science, Estonian University of Life Sciences, 51014 Tartu, Estonia
3Department of Wildlife, Fish, and Environmental Studies, Swedish University of Agricultural Sciences, 901 83 Umeå, Sweden
4Aquaculture and Fisheries Development Centre, School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland
5Marine Institute, Furnace, Newport, Co. Mayo, Ireland
6Population Ecology Division, Department of Fisheries and Oceans, Bedford Institute of Oceanography, Challenger Drive, Dartmouth, NS, Canada B2Y 4A2
7Fisheries and Oceans Canada, Department of Fisheries and Oceans, St. Andrews Biological Station, St. Andrews, NB, Canada E0G 2X0
8Department of Genetics, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
9Department of Animal and Aquacultural Sciences, Centre for Integrative Genetics, Norwegian University of Life Sciences, 1432 Aas, Norway

Received 17 August 2012; Revised 29 October 2012; Accepted 9 November 2012

Academic Editor: Mohamed Salem

Copyright © 2012 Anti Vasemägi et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


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.