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

• Published in: Evolutionary Applications
• Main Authors: Mäkinen, Hannu, Vasemägi, Anti, McGinnity, Philip, Cross, Tom F., Primmer, Craig R.
• Other Authors: Suomen Akatemia
• Format: Article in Journal/Newspaper
• Language: English
• Published: Wiley 2014
• Subjects: Almo; Atlantic salmon; Salmo salar
• Online Access: http://dx.doi.org/10.1111/eva.12230; https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Feva.12230; https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12230

Abstract Domestication can have adverse genetic consequences, which may reduce the fitness of individuals once released back into the wild. Many wild A tlantic salmon ( S almo salar L .) populations are threatened by anthropogenic influences, and they are supplemented with captively bred fish. The A tlantic 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 SNP s in three domesticated A tlantic salmon strains and their wild conspecifics to identify loci underlying domestication. The genetic differentiation between domesticated strains and wild populations was low ( F ST < 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.