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

Abstract Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North Ame...

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Bibliographic Details
Published in:Evolutionary Applications
Main Authors: Danielle Macdonald, Matthew Peter Kent, Sigbjørn Lien, Keng Pee Ang, J.A.K. Elliott, Lei Liu, Elizabeth G. Boulding
Format: Article in Journal/Newspaper
Language:English
Published: 2016
Subjects:
SNP
Online Access:http://europepmc.org/articles/PMC5322405
https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Feva.12450
https://onlinelibrary.wiley.com/doi/pdf/10.1111/eva.12450
https://onlinelibrary.wiley.com/doi/full-xml/10.1111/eva.12450
https://doi.org/10.1111/eva.12450
https://www.ncbi.nlm.nih.gov/pubmed/28250812
https://onlinelibrary.wiley.com/doi/abs/10.1111/eva.12450
https://brage.bibsys.no/xmlui/handle/11250/2469508
https://academic.microsoft.com/#/detail/2552674072
Description
Summary:Abstract Comparative genome scans can be used to identify chromosome regions, but not traits, that are putatively under selection. Identification of targeted traits may be more likely in recently domesticated populations under strong artificial selection for increased production. We used a North American Atlantic salmon 6K SNP dataset to locate genome regions of an aquaculture strain (Saint John River) that were highly diverged from that of its putative wild founder population (Tobique River). First, admixed individuals with partial European ancestry were detected using STRUCTURE and removed from the dataset. Outlier loci were then identified as those showing extreme differentiation between the aquaculture population and the founder population. All Arlequin methods identified an overlapping subset of 17 outlier loci, three of which were also identified by BayeScan. Many outlier loci were near candidate genes and some were near published quantitative trait loci (QTLs) for growth, appetite, maturity, or disease resistance. Parallel comparisons using a wild, nonfounder population (Stewiacke River) yielded only one overlapping outlier locus as well as a known maturity QTL. We conclude that genome scans comparing a recently domesticated strain with its wild founder population can facilitate identification of candidate genes for traits known to have been under strong artificial selection.