Beyond large-effect loci : large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon
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, rep...
Published in: | Genetics Selection Evolution |
---|---|
Main Authors: | , , , , , , |
Other Authors: | , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
BioMed Central Ltd
2020
|
Subjects: | |
Online Access: | http://hdl.handle.net/10138/313659 |
id |
ftunivhelsihelda:oai:helda.helsinki.fi:10138/313659 |
---|---|
record_format |
openpolar |
spelling |
ftunivhelsihelda:oai:helda.helsinki.fi:10138/313659 2024-01-07T09:42:12+01:00 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 Odegard, Jorgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjorn Primmer, Craig R. Barson, Nicola J. Organismal and Evolutionary Biology Research Programme Evolution, Conservation, and Genomics Institute of Biotechnology 2020-03-27T08:19:01Z 11 application/pdf http://hdl.handle.net/10138/313659 eng eng BioMed Central Ltd 10.1186/s12711-020-0529-8 Funding was provided by AquaGen AS, SkatteFUNN program (Research Council of Norway), Research Council of Norway (Grant Number 254852 - QuantEscape2), Academy of Finland (Grant Numbers 307593 and 302873), and a Natural Sciences and Engineering Research Council of Canada postgraduate scholarship. Sinclair-Waters , M , Odegard , J , Korsvoll , S A , Moen , T , Lien , S , Primmer , C R & Barson , N J 2020 , ' Beyond large-effect loci : large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon ' , Genetics Selection Evolution , vol. 52 , no. 1 , 9 . https://doi.org/10.1186/s12711-020-0529-8 ORCID: /0000-0002-3687-8435/work/71185313 ORCID: /0000-0001-7371-4547/work/71185491 9dfdc201-eae0-488a-9206-0959ecd62c06 http://hdl.handle.net/10138/313659 000514633300001 cc_by openAccess info:eu-repo/semantics/openAccess SEXUAL-MATURATION COMMON VARIANTS COMPLEX TRAITS SNP ANALYSIS POPULATION ASSOCIATION EVOLUTION DOMINANCE GENOMICS SALAR 1181 Ecology evolutionary biology Article publishedVersion 2020 ftunivhelsihelda 2023-12-14T00:14:16Z 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 x 10(-133)-9.8 x 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. Peer reviewed Article in Journal/Newspaper Atlantic salmon HELDA – University of Helsinki Open Repository Genetics Selection Evolution 52 1 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
SEXUAL-MATURATION COMMON VARIANTS COMPLEX TRAITS SNP ANALYSIS POPULATION ASSOCIATION EVOLUTION DOMINANCE GENOMICS SALAR 1181 Ecology evolutionary biology |
spellingShingle |
SEXUAL-MATURATION COMMON VARIANTS COMPLEX TRAITS SNP ANALYSIS POPULATION ASSOCIATION EVOLUTION DOMINANCE GENOMICS SALAR 1181 Ecology evolutionary biology Sinclair-Waters, Marion Odegard, Jorgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjorn 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 |
SEXUAL-MATURATION COMMON VARIANTS COMPLEX TRAITS SNP ANALYSIS POPULATION ASSOCIATION EVOLUTION DOMINANCE GENOMICS SALAR 1181 Ecology evolutionary biology |
description |
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 x 10(-133)-9.8 x 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. Peer reviewed |
author2 |
Organismal and Evolutionary Biology Research Programme Evolution, Conservation, and Genomics Institute of Biotechnology |
format |
Article in Journal/Newspaper |
author |
Sinclair-Waters, Marion Odegard, Jorgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjorn Primmer, Craig R. Barson, Nicola J. |
author_facet |
Sinclair-Waters, Marion Odegard, Jorgen Korsvoll, Sven Arild Moen, Thomas Lien, Sigbjorn 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 |
BioMed Central Ltd |
publishDate |
2020 |
url |
http://hdl.handle.net/10138/313659 |
genre |
Atlantic salmon |
genre_facet |
Atlantic salmon |
op_relation |
10.1186/s12711-020-0529-8 Funding was provided by AquaGen AS, SkatteFUNN program (Research Council of Norway), Research Council of Norway (Grant Number 254852 - QuantEscape2), Academy of Finland (Grant Numbers 307593 and 302873), and a Natural Sciences and Engineering Research Council of Canada postgraduate scholarship. Sinclair-Waters , M , Odegard , J , Korsvoll , S A , Moen , T , Lien , S , Primmer , C R & Barson , N J 2020 , ' Beyond large-effect loci : large-scale GWAS reveals a mixed large-effect and polygenic architecture for age at maturity of Atlantic salmon ' , Genetics Selection Evolution , vol. 52 , no. 1 , 9 . https://doi.org/10.1186/s12711-020-0529-8 ORCID: /0000-0002-3687-8435/work/71185313 ORCID: /0000-0001-7371-4547/work/71185491 9dfdc201-eae0-488a-9206-0959ecd62c06 http://hdl.handle.net/10138/313659 000514633300001 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
container_title |
Genetics Selection Evolution |
container_volume |
52 |
container_issue |
1 |
_version_ |
1787423131945664512 |