SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar)
Abstract Atlantic salmon ( S almo salar ) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic ar...
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crwiley:10.1111/mec.12003 2024-05-19T07:37:42+00:00 SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn 2012 http://dx.doi.org/10.1111/mec.12003 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.12003 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12003 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 Molecular Ecology volume 22, issue 3, page 532-551 ISSN 0962-1083 1365-294X journal-article 2012 crwiley https://doi.org/10.1111/mec.12003 2024-04-25T08:28:13Z Abstract Atlantic salmon ( S almo salar ) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium‐density A tlantic salmon single nucleotide polymorphism ( SNP ) array based on expressed sequence tags ( EST s) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNP s were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated E uropean and N orth A merican populations, and within E urope, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In E urope, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing B altic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture. Article in Journal/Newspaper Atlantic salmon Salmo salar Wiley Online Library Molecular Ecology 22 3 532 551 |
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English |
description |
Abstract Atlantic salmon ( S almo salar ) is one of the most extensively studied fish species in the world due to its significance in aquaculture, fisheries and ongoing conservation efforts to protect declining populations. Yet, limited genomic resources have hampered our understanding of genetic architecture in the species and the genetic basis of adaptation to the wide range of natural and artificial environments it occupies. In this study, we describe the development of a medium‐density A tlantic salmon single nucleotide polymorphism ( SNP ) array based on expressed sequence tags ( EST s) and genomic sequencing. The array was used in the most extensive assessment of population genetic structure performed to date in this species. A total of 6176 informative SNP s were successfully genotyped in 38 anadromous and freshwater wild populations distributed across the species natural range. Principal component analysis clearly differentiated E uropean and N orth A merican populations, and within E urope, three major regional genetic groups were identified for the first time in a single analysis. We assessed the potential for the array to disentangle neutral and putative adaptive divergence of SNP allele frequencies across populations and among regional groups. In E urope, secondary contact zones were identified between major clusters where endogenous and exogenous barriers could be associated, rendering the interpretation of environmental influence on potentially adaptive divergence equivocal. A small number of markers highly divergent in allele frequencies (outliers) were observed between (multiple) freshwater and anadromous populations, between northern and southern latitudes, and when comparing B altic populations to all others. We also discuss the potential future applications of the SNP array for conservation, management and aquaculture. |
format |
Article in Journal/Newspaper |
author |
Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn |
spellingShingle |
Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) |
author_facet |
Bourret, Vincent Kent, Matthew P. Primmer, Craig R. Vasemägi, Anti Karlsson, Sten Hindar, Kjetil McGinnity, Philip Verspoor, Eric Bernatchez, Louis Lien, Sigbjørn |
author_sort |
Bourret, Vincent |
title |
SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) |
title_short |
SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) |
title_full |
SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) |
title_fullStr |
SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) |
title_full_unstemmed |
SNP‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of Atlantic salmon ( Salmo salar) |
title_sort |
snp‐array reveals genome‐wide patterns of geographical and potential adaptive divergence across the natural range of atlantic salmon ( salmo salar) |
publisher |
Wiley |
publishDate |
2012 |
url |
http://dx.doi.org/10.1111/mec.12003 https://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1111%2Fmec.12003 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.12003 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Molecular Ecology volume 22, issue 3, page 532-551 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor http://doi.wiley.com/10.1002/tdm_license_1.1 |
op_doi |
https://doi.org/10.1111/mec.12003 |
container_title |
Molecular Ecology |
container_volume |
22 |
container_issue |
3 |
container_start_page |
532 |
op_container_end_page |
551 |
_version_ |
1799477053775413248 |