Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon
Abstract Background Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as surv...
Published in: | Genetics Selection Evolution |
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Online Access: | http://dx.doi.org/10.1186/s12711-020-0529-8 http://link.springer.com/content/pdf/10.1186/s12711-020-0529-8.pdf http://link.springer.com/article/10.1186/s12711-020-0529-8/fulltext.html |
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crspringernat:10.1186/s12711-020-0529-8 2023-05-15T15:30:32+02:00 Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjørn Primmer, Craig R. Barson, Nicola J. AquaGen AS SkatteFUNN program Research Council of Norway Academy of Finland Natural Sciences and Engineering Research Council of Canada 2020 http://dx.doi.org/10.1186/s12711-020-0529-8 http://link.springer.com/content/pdf/10.1186/s12711-020-0529-8.pdf http://link.springer.com/article/10.1186/s12711-020-0529-8/fulltext.html en eng Springer Science and Business Media LLC http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/ CC-BY Genetics Selection Evolution volume 52, issue 1 ISSN 1297-9686 Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics journal-article 2020 crspringernat https://doi.org/10.1186/s12711-020-0529-8 2022-01-14T15:39:50Z Abstract Background Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest. Results Here, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes ( P -values: 8.7 × 10 −133 –9.8 × 10 −8 ), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans. Discussion These results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations. Article in Journal/Newspaper Atlantic salmon Springer Nature (via Crossref) Genetics Selection Evolution 52 1 |
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Open Polar |
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Springer Nature (via Crossref) |
op_collection_id |
crspringernat |
language |
English |
topic |
Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics |
spellingShingle |
Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjørn Primmer, Craig R. Barson, Nicola J. Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
topic_facet |
Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics |
description |
Abstract Background Understanding genetic architecture is essential for determining how traits will change in response to evolutionary processes such as selection, genetic drift and/or gene flow. In Atlantic salmon, age at maturity is an important life history trait that affects factors such as survival, reproductive success, and growth. Furthermore, age at maturity can seriously impact aquaculture production. Therefore, characterizing the genetic architecture that underlies variation in age at maturity is of key interest. Results Here, we refine our understanding of the genetic architecture for age at maturity of male Atlantic salmon using a genome-wide association study of 11,166 males from a single aquaculture strain, using imputed genotypes at 512,397 single nucleotide polymorphisms (SNPs). All individuals were genotyped with a 50K SNP array and imputed to higher density using parents genotyped with a 930K SNP array and pedigree information. We found significant association signals on 28 of 29 chromosomes ( P -values: 8.7 × 10 −133 –9.8 × 10 −8 ), including two very strong signals spanning the six6 and vgll3 gene regions on chromosomes 9 and 25, respectively. Furthermore, we identified 116 independent signals that tagged 120 candidate genes with varying effect sizes. Five of the candidate genes found here were previously associated with age at maturity in other vertebrates, including humans. Discussion These results reveal a mixed architecture of large-effect loci and a polygenic component that consists of multiple smaller-effect loci, suggesting a more complex genetic architecture of Atlantic salmon age at maturity than previously thought. This more complex architecture will have implications for selection on this key trait in aquaculture and for management of wild salmon populations. |
author2 |
AquaGen AS SkatteFUNN program Research Council of Norway Academy of Finland Natural Sciences and Engineering Research Council of Canada |
format |
Article in Journal/Newspaper |
author |
Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjørn Primmer, Craig R. Barson, Nicola J. |
author_facet |
Sinclair-Waters, Marion Ødegård, Jørgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjørn Primmer, Craig R. Barson, Nicola J. |
author_sort |
Sinclair-Waters, Marion |
title |
Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_short |
Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_full |
Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_fullStr |
Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_full_unstemmed |
Beyond large-effect loci: large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon |
title_sort |
beyond large-effect loci: large-scale gwas reveals a mixed large-effect and polygenic architecture for age at maturity of atlantic salmon |
publisher |
Springer Science and Business Media LLC |
publishDate |
2020 |
url |
http://dx.doi.org/10.1186/s12711-020-0529-8 http://link.springer.com/content/pdf/10.1186/s12711-020-0529-8.pdf http://link.springer.com/article/10.1186/s12711-020-0529-8/fulltext.html |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_source |
Genetics Selection Evolution volume 52, issue 1 ISSN 1297-9686 |
op_rights |
http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/ |
op_rightsnorm |
CC-BY |
op_doi |
https://doi.org/10.1186/s12711-020-0529-8 |
container_title |
Genetics Selection Evolution |
container_volume |
52 |
container_issue |
1 |
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1766360986861699072 |