Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods
Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fit...
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/351357 2024-01-07T09:42:12+01:00 Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods Sinclair-Waters, Marion Nome, Torfinn Wang, Jing Lien, Sigbjorn Kent, Matthew P. Saegrov, Harald Floro-Larsen, Bjorn Bolstad, Geir H. Primmer, Craig R. Barson, Nicola J. Evolution, Conservation, and Genomics Organismal and Evolutionary Biology Research Programme Institute of Biotechnology Biosciences Helsinki Institute of Sustainability Science (HELSUS) 2022-12-02T22:47:05Z 10 application/pdf http://hdl.handle.net/10138/351357 eng eng Nature Publishing Group 10.1038/s41437-022-00570-w Sinclair-Waters , M , Nome , T , Wang , J , Lien , S , Kent , M P , Saegrov , H , Floro-Larsen , B , Bolstad , G H , Primmer , C R & Barson , N J 2022 , ' Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods ' , Heredity , vol. 129 , pp. 356–365 . https://doi.org/10.1038/s41437-022-00570-w ORCID: /0000-0002-3687-8435/work/124033402 ORCID: /0000-0001-7371-4547/work/124033974 36357776 818eeb98-d19f-403a-8fc6-6f950ca702ba http://hdl.handle.net/10138/351357 000881655000001 cc_by openAccess info:eu-repo/semantics/openAccess Reproductive strategies Polygenic characters Genetic-variability Selection balance Evolution Adaptation Genome Age Traits Maturity 1182 Biochemistry cell and molecular biology Article publishedVersion 2022 ftunivhelsihelda 2023-12-14T00:06:07Z Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations. Peer reviewed Article in Journal/Newspaper Atlantic salmon Salmo salar HELDA – University of Helsinki Open Repository Heredity 129 6 356 365 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
Reproductive strategies Polygenic characters Genetic-variability Selection balance Evolution Adaptation Genome Age Traits Maturity 1182 Biochemistry cell and molecular biology |
spellingShingle |
Reproductive strategies Polygenic characters Genetic-variability Selection balance Evolution Adaptation Genome Age Traits Maturity 1182 Biochemistry cell and molecular biology Sinclair-Waters, Marion Nome, Torfinn Wang, Jing Lien, Sigbjorn Kent, Matthew P. Saegrov, Harald Floro-Larsen, Bjorn Bolstad, Geir H. Primmer, Craig R. Barson, Nicola J. Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods |
topic_facet |
Reproductive strategies Polygenic characters Genetic-variability Selection balance Evolution Adaptation Genome Age Traits Maturity 1182 Biochemistry cell and molecular biology |
description |
Characterizing the role of different mutational effect sizes in the evolution of fitness-related traits has been a major goal in evolutionary biology for a century. Such characterization in a diversity of systems, both model and non-model, will help to understand the genetic processes underlying fitness variation. However, well-characterized genetic architectures of such traits in wild populations remain uncommon. In this study, we used haplotype-based and multi-SNP Bayesian association methods with sequencing data for 313 individuals from wild populations to test the mutational composition of known candidate regions for sea age at maturation in Atlantic salmon (Salmo salar). We detected an association at five loci out of 116 candidates previously identified in an aquaculture strain with maturation timing in wild Atlantic salmon. We found that at four of these five loci, variation explained by the locus was predominantly driven by a single SNP suggesting the genetic architecture of this trait includes multiple loci with simple, non-clustered alleles and a locus with potentially more complex alleles. This highlights the diversity of genetic architectures that can exist for fitness-related traits. Furthermore, this study provides a useful multi-SNP framework for future work using sequencing data to characterize genetic variation underlying phenotypes in wild populations. Peer reviewed |
author2 |
Evolution, Conservation, and Genomics Organismal and Evolutionary Biology Research Programme Institute of Biotechnology Biosciences Helsinki Institute of Sustainability Science (HELSUS) |
format |
Article in Journal/Newspaper |
author |
Sinclair-Waters, Marion Nome, Torfinn Wang, Jing Lien, Sigbjorn Kent, Matthew P. Saegrov, Harald Floro-Larsen, Bjorn Bolstad, Geir H. Primmer, Craig R. Barson, Nicola J. |
author_facet |
Sinclair-Waters, Marion Nome, Torfinn Wang, Jing Lien, Sigbjorn Kent, Matthew P. Saegrov, Harald Floro-Larsen, Bjorn Bolstad, Geir H. Primmer, Craig R. Barson, Nicola J. |
author_sort |
Sinclair-Waters, Marion |
title |
Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods |
title_short |
Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods |
title_full |
Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods |
title_fullStr |
Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods |
title_full_unstemmed |
Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods |
title_sort |
dissecting the loci underlying maturation timing in atlantic salmon using haplotype and multi-snp based association methods |
publisher |
Nature Publishing Group |
publishDate |
2022 |
url |
http://hdl.handle.net/10138/351357 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
10.1038/s41437-022-00570-w Sinclair-Waters , M , Nome , T , Wang , J , Lien , S , Kent , M P , Saegrov , H , Floro-Larsen , B , Bolstad , G H , Primmer , C R & Barson , N J 2022 , ' Dissecting the loci underlying maturation timing in Atlantic salmon using haplotype and multi-SNP based association methods ' , Heredity , vol. 129 , pp. 356–365 . https://doi.org/10.1038/s41437-022-00570-w ORCID: /0000-0002-3687-8435/work/124033402 ORCID: /0000-0001-7371-4547/work/124033974 36357776 818eeb98-d19f-403a-8fc6-6f950ca702ba http://hdl.handle.net/10138/351357 000881655000001 |
op_rights |
cc_by openAccess info:eu-repo/semantics/openAccess |
container_title |
Heredity |
container_volume |
129 |
container_issue |
6 |
container_start_page |
356 |
op_container_end_page |
365 |
_version_ |
1787423132814934016 |