Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)
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{"title"=>"Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (Salmo salar)", "type"=>"journal", "authors"=>[{"first_name"=>"Alejandro P.", "last_name"=>"Gutierrez"}, {"first_name"=>"José M.", "last_name"=>"Yáñez"}, {"first_name"=>"Steve", "last_name"=>"Fukui"}, {"first_name"=>"Bruce", "last_name"=>"Swift"}, {"first_name"=>"William S.", "last_name"=>"Davidson"}], "year"=>2015, "source"=>"PLOS ONE", "identifiers"=>{"issn"=>"1932-6203", "pmid"=>"25757012", "doi"=>"10.1371/journal.pone.0119730", "isbn"=>"3814792009"}, "id"=>"68e2baf3-8335-3c16-819c-6f194cdb717c", "abstract"=>"Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼ 480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.", "link"=>"http://www.mendeley.com/research/genomewide-association-study-gwas-growth-rate-age-sexual-maturation-atlantic-salmon-salmo-salar", "reader_count"=>69, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>8, "Researcher"=>17, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>11, "Other"=>4, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>2, "Student > Doctoral Student"=>8, "Researcher"=>17, "Student > Ph. D. Student"=>12, "Student > Postgraduate"=>3, "Student > Master"=>11, "Other"=>4, "Student > Bachelor"=>4, "Lecturer"=>1, "Professor"=>6}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>54, "Veterinary Science and Veterinary Medicine"=>2, "Immunology and Microbiology"=>1, "Earth and Planetary Sciences"=>1}, "reader_count_by_subdiscipline"=>{"Immunology and Microbiology"=>{"Immunology and Microbiology"=>1}, "Earth and Planetary Sciences"=>{"Earth and Planetary Sciences"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>54}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>3}, "Environmental Science"=>{"Environmental Science"=>1}, "Veterinary Science and Veterinary Medicine"=>{"Veterinary Science and Veterinary Medicine"=>2}}, "reader_count_by_country"=>{"United States"=>1, "Finland"=>1, "France"=>1}, "group_count"=>5}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1942572"], "description"=>"<p>*Marker showing a chromosome-wide significance</p><p><sup>a</sup> Chromosome number assigned according to Phillips et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119730#pone.0119730.ref043\" target=\"_blank\">43</a>].</p><p><sup>b</sup> Positions obtained from female SNP map described by Lien et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119730#pone.0119730.ref038\" target=\"_blank\">38</a>].</p><p><sup>c</sup> Contig containing the marker sequence as result of BLAST alignment on <a href=\"http://www.asalbase.org\" target=\"_blank\">www.asalbase.org</a>.</p><p><sup>d</sup> The closest identified gene on the contig, according to BLASTx or BLASTn results.</p><p><sup>e</sup> p-value obtained from GRAMMAR analysis and subject to Bonferroni significance thresholds.</p><p><sup>f</sup> p-value obtained from genome wide permutation analysis.</p><p>Days to 5 kg association detected in the analysis.</p>", "links"=>[], "tags"=>["Ssa 13. Candidate genes", "maturation", "density SNP array", "association", "GWAS", "increases production times", "atlantic salmon", "marker", "Atlantic salmon aquaculture", "Cermaq Canada broodstock program"], "article_id"=>1330752, "categories"=>["Biological Sciences"], "users"=>["Alejandro P. Gutierrez", "José M. Yáñez", "Steve Fukui", "Bruce Swift", "William S. Davidson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119730.t001", "stats"=>{"downloads"=>0, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Days_to_5_kg_association_detected_in_the_analysis_/1330752", "title"=>"Days to 5 kg association detected in the analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-10 03:04:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1942574"], "description"=>"<p>** Markers showing a genome-wide significance.</p><p>* Markers showing a chromosome-wide significance.</p><p><sup>a</sup> Chromosome number assigned according to Phillips et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119730#pone.0119730.ref043\" target=\"_blank\">43</a>].</p><p><sup>b</sup> Positions obtained from female SNP map described by Lien et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119730#pone.0119730.ref038\" target=\"_blank\">38</a>].</p><p><sup>c</sup> Contig containing the marker sequence as result of BLAST alignment on <a href=\"http://www.asalbase.org\" target=\"_blank\">www.asalbase.org</a>.</p><p><sup>d</sup> The closest identified gene on the contig, according to BLASTx or BLASTn results.</p><p><sup>e</sup> p-value obtained from GRAMMAR analysis and subject to Bonferroni significance thresholds.</p><p><sup>f</sup> p-value obtained from genome wide permutation analysis.</p><p>Late maturation association detected in the analysis.</p>", "links"=>[], "tags"=>["Ssa 13. Candidate genes", "maturation", "density SNP array", "association", "GWAS", "increases production times", "atlantic salmon", "marker", "Atlantic salmon aquaculture", "Cermaq Canada broodstock program"], "article_id"=>1330754, "categories"=>["Biological Sciences"], "users"=>["Alejandro P. Gutierrez", "José M. Yáñez", "Steve Fukui", "Bruce Swift", "William S. Davidson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119730.t003", "stats"=>{"downloads"=>0, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Late_maturation_association_detected_in_the_analysis_/1330754", "title"=>"Late maturation association detected in the analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-10 03:04:23"}
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  • {"files"=>["https://ndownloader.figshare.com/files/1942568"], "description"=>"<p>Horizontal dotted line represents the genome-wide significant threshold.</p>", "links"=>[], "tags"=>["Ssa 13. Candidate genes", "maturation", "density SNP array", "association", "GWAS", "increases production times", "atlantic salmon", "marker", "Atlantic salmon aquaculture", "Cermaq Canada broodstock program"], "article_id"=>1330748, "categories"=>["Biological Sciences"], "users"=>["Alejandro P. Gutierrez", "José M. Yáñez", "Steve Fukui", "Bruce Swift", "William S. Davidson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119730.g001", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_from_GWAS_for_days_to_5_kg_/1330748", "title"=>"Results from GWAS for days to 5 kg.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2015-03-10 03:04:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1942576"], "description"=>"<div><p>Early sexual maturation is considered a serious drawback for Atlantic salmon aquaculture as it retards growth, increases production times and affects flesh quality. Although both growth and sexual maturation are thought to be complex processes controlled by several genetic and environmental factors, selection for these traits has been continuously accomplished since the beginning of Atlantic salmon selective breeding programs. In this genome-wide association study (GWAS) we used a 6.5K single-nucleotide polymorphism (SNP) array to genotype ∼480 individuals from the Cermaq Canada broodstock program and search for SNPs associated with growth and age at sexual maturation. Using a mixed model approach we identified markers showing a significant association with growth, grilsing (early sexual maturation) and late sexual maturation. The most significant associations were found for grilsing, with markers located in Ssa10, Ssa02, Ssa13, Ssa25 and Ssa12, and for late maturation with markers located in Ssa28, Ssa01 and Ssa21. A lower level of association was detected with growth on Ssa13. Candidate genes, which were linked to these genetic markers, were identified and some of them show a direct relationship with developmental processes, especially for those in association with sexual maturation. However, the relatively low power to detect genetic markers associated with growth (days to 5 kg) in this GWAS indicates the need to use a higher density SNP array in order to overcome the low levels of linkage disequilibrium observed in Atlantic salmon before the information can be incorporated into a selective breeding program.</p></div>", "links"=>[], "tags"=>["Ssa 13. Candidate genes", "maturation", "density SNP array", "association", "GWAS", "increases production times", "atlantic salmon", "marker", "Atlantic salmon aquaculture", "Cermaq Canada broodstock program"], "article_id"=>1330756, "categories"=>["Biological Sciences"], "users"=>["Alejandro P. Gutierrez", "José M. Yáñez", "Steve Fukui", "Bruce Swift", "William S. Davidson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119730", "stats"=>{"downloads"=>2, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Genome_Wide_Association_Study_GWAS_for_Growth_Rate_and_Age_at_Sexual_Maturation_in_Atlantic_Salmon_Salmo_salar_/1330756", "title"=>"Genome-Wide Association Study (GWAS) for Growth Rate and Age at Sexual Maturation in Atlantic Salmon (<i>Salmo salar</i>)", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-10 03:04:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/1942573"], "description"=>"<p>** Markers showing a genome-wide significance.</p><p><sup>a</sup> Chromosome number assigned according to Phillips et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119730#pone.0119730.ref043\" target=\"_blank\">43</a>].</p><p><sup>b</sup> Positions obtained from female SNP map described by Lien et al. [<a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0119730#pone.0119730.ref038\" target=\"_blank\">38</a>].</p><p><sup>c</sup> Contig containing the marker sequence as result of BLAST alignment on <a href=\"http://www.asalbase.org\" target=\"_blank\">www.asalbase.org</a>.</p><p><sup>d</sup> The closest identified on the contig, according to BLASTx or BLASTn results.</p><p><sup>e</sup> p-value obtained from GRAMMAR analysis and subject to Bonferroni significance thresholds.</p><p><sup>f</sup> p-value obtained from genome wide permutation analysis.</p><p>Grilsing association detected in the analysis.</p>", "links"=>[], "tags"=>["Ssa 13. Candidate genes", "maturation", "density SNP array", "association", "GWAS", "increases production times", "atlantic salmon", "marker", "Atlantic salmon aquaculture", "Cermaq Canada broodstock program"], "article_id"=>1330753, "categories"=>["Biological Sciences"], "users"=>["Alejandro P. Gutierrez", "José M. Yáñez", "Steve Fukui", "Bruce Swift", "William S. Davidson"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0119730.t002", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Grilsing_association_detected_in_the_analysis_/1330753", "title"=>"Grilsing association detected in the analysis.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2015-03-10 03:04:23"}
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{"start_date"=>"2015-01-01T00:00:00Z", "end_date"=>"2015-12-31T00:00:00Z", "subject_areas"=>[]}
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