Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations
A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype–phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from Americ...
Published in: | Molecular Ecology Resources |
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Online Access: | https://hdl.handle.net/20.500.11794/301 https://doi.org/10.1111/1755-0998.12503 |
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ftunivlavalcorp:oai:corpus.ulaval.ca:20.500.11794/301 2024-06-23T07:51:16+00:00 Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations Yáñez, José Manuel Bernatchez, Louis Naswa, S. Lopez, M. E. Bassini, Liane Correa, Katharina Gilbey, John Norris, Ashie Neira Roa, Roberto Lhorente Caussade, Jean Paul Schnable, Patrick S. Newman, Scott Mileham, Alan Deeb, Nader Di Genova, Alex Maass, Alejandro 2016-03-16T13:01:08Z application/pdf https://hdl.handle.net/20.500.11794/301 https://doi.org/10.1111/1755-0998.12503 eng eng John Wiley & Sons Ltd 1755-0998 http://hdl.handle.net/20.500.11794/301 doi:10.1111/1755-0998.12503 http://purl.org/coar/access_right/c_16ec Saumon atlantique -- Génétique Polymorphisme génétique Séquence nucléotidique article de recherche COAR1_1::Texte::Périodique::Revue::Contribution à un journal::Article::Article de recherche 2016 ftunivlavalcorp https://doi.org/20.500.11794/30110.1111/1755-0998.12503 2024-06-10T23:42:53Z A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype–phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom® myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information. Keywords : Genomic selection; Next-generation sequencing; Pseudo-tetraploid; Salmo salar; SNP array Other/Unknown Material Atlantic salmon Salmo salar Université Laval: CorpusUL Molecular Ecology Resources 16 4 1002 1011 |
institution |
Open Polar |
collection |
Université Laval: CorpusUL |
op_collection_id |
ftunivlavalcorp |
language |
English |
topic |
Saumon atlantique -- Génétique Polymorphisme génétique Séquence nucléotidique |
spellingShingle |
Saumon atlantique -- Génétique Polymorphisme génétique Séquence nucléotidique Yáñez, José Manuel Bernatchez, Louis Naswa, S. Lopez, M. E. Bassini, Liane Correa, Katharina Gilbey, John Norris, Ashie Neira Roa, Roberto Lhorente Caussade, Jean Paul Schnable, Patrick S. Newman, Scott Mileham, Alan Deeb, Nader Di Genova, Alex Maass, Alejandro Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations |
topic_facet |
Saumon atlantique -- Génétique Polymorphisme génétique Séquence nucléotidique |
description |
A considerable number of single nucleotide polymorphisms (SNPs) are required to elucidate genotype–phenotype associations and determine the molecular basis of important traits. In this work, we carried out de novo SNP discovery accounting for both genome duplication and genetic variation from American and European salmon populations. A total of 9 736 473 nonredundant SNPs were identified across a set of 20 fish by whole-genome sequencing. After applying six bioinformatic filtering steps, 200 K SNPs were selected to develop an Affymetrix Axiom® myDesign Custom Array. This array was used to genotype 480 fish representing wild and farmed salmon from Europe, North America and Chile. A total of 159 099 (79.6%) SNPs were validated as high quality based on clustering properties. A total of 151 509 validated SNPs showed a unique position in the genome. When comparing these SNPs against 238 572 markers currently available in two other Atlantic salmon arrays, only 4.6% of the SNP overlapped with the panel developed in this study. This novel high-density SNP panel will be very useful for the dissection of economically and ecologically relevant traits, enhancing breeding programmes through genomic selection as well as supporting genetic studies in both wild and farmed populations of Atlantic salmon using high-resolution genomewide information. Keywords : Genomic selection; Next-generation sequencing; Pseudo-tetraploid; Salmo salar; SNP array |
format |
Other/Unknown Material |
author |
Yáñez, José Manuel Bernatchez, Louis Naswa, S. Lopez, M. E. Bassini, Liane Correa, Katharina Gilbey, John Norris, Ashie Neira Roa, Roberto Lhorente Caussade, Jean Paul Schnable, Patrick S. Newman, Scott Mileham, Alan Deeb, Nader Di Genova, Alex Maass, Alejandro |
author_facet |
Yáñez, José Manuel Bernatchez, Louis Naswa, S. Lopez, M. E. Bassini, Liane Correa, Katharina Gilbey, John Norris, Ashie Neira Roa, Roberto Lhorente Caussade, Jean Paul Schnable, Patrick S. Newman, Scott Mileham, Alan Deeb, Nader Di Genova, Alex Maass, Alejandro |
author_sort |
Yáñez, José Manuel |
title |
Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations |
title_short |
Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations |
title_full |
Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations |
title_fullStr |
Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations |
title_full_unstemmed |
Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar ) : validation in wild and farmed American and European populations |
title_sort |
genomewide single nucleotide polymorphism discovery in atlantic salmon (salmo salar ) : validation in wild and farmed american and european populations |
publisher |
John Wiley & Sons Ltd |
publishDate |
2016 |
url |
https://hdl.handle.net/20.500.11794/301 https://doi.org/10.1111/1755-0998.12503 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
1755-0998 http://hdl.handle.net/20.500.11794/301 doi:10.1111/1755-0998.12503 |
op_rights |
http://purl.org/coar/access_right/c_16ec |
op_doi |
https://doi.org/20.500.11794/30110.1111/1755-0998.12503 |
container_title |
Molecular Ecology Resources |
container_volume |
16 |
container_issue |
4 |
container_start_page |
1002 |
op_container_end_page |
1011 |
_version_ |
1802642298170769408 |