Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus
Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore...
Published in: | Molecular Ecology |
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ftunivhelsihelda:oai:helda.helsinki.fi:10138/350333 2024-01-07T09:42:13+01:00 Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus Sinclair-Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig Evolution, Conservation, and Genomics Organismal and Evolutionary Biology Research Programme Institute of Biotechnology Helsinki Institute of Sustainability Science (HELSUS) Biosciences 2022-10-29T21:50:42Z 9 application/pdf http://hdl.handle.net/10138/350333 eng eng Wiley 10.1111/mec.16256 Sinclair-Waters , M , Piavchenko , N , Ruokolainen , A , Aykanat , T , Erkinaro , J & Primmer , C 2022 , ' Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus ' , Molecular Ecology , vol. 31 , no. 2 , pp. 562-570 . https://doi.org/10.1111/mec.16256 ORCID: /0000-0002-3687-8435/work/106791645 ORCID: /0000-0001-7371-4547/work/106791768 7ea08dfc-175e-4a15-be46-a5a5df9f4545 http://hdl.handle.net/10138/350333 000717946700001 unspecified openAccess info:eu-repo/semantics/openAccess 1181 Ecology evolutionary biology Atlantic salmon candidate gene genotype-phenotype association maturation vgll3 WIDE ASSOCIATION GENETIC-BASIS AGE POPULATION PROTEIN Article acceptedVersion 2022 ftunivhelsihelda 2023-12-14T00:11:27Z Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity. Peer reviewed Article in Journal/Newspaper Atlantic salmon Salmo salar HELDA – University of Helsinki Open Repository Molecular Ecology 31 2 562 570 |
institution |
Open Polar |
collection |
HELDA – University of Helsinki Open Repository |
op_collection_id |
ftunivhelsihelda |
language |
English |
topic |
1181 Ecology evolutionary biology Atlantic salmon candidate gene genotype-phenotype association maturation vgll3 WIDE ASSOCIATION GENETIC-BASIS AGE POPULATION PROTEIN |
spellingShingle |
1181 Ecology evolutionary biology Atlantic salmon candidate gene genotype-phenotype association maturation vgll3 WIDE ASSOCIATION GENETIC-BASIS AGE POPULATION PROTEIN Sinclair-Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus |
topic_facet |
1181 Ecology evolutionary biology Atlantic salmon candidate gene genotype-phenotype association maturation vgll3 WIDE ASSOCIATION GENETIC-BASIS AGE POPULATION PROTEIN |
description |
Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation. By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity. Peer reviewed |
author2 |
Evolution, Conservation, and Genomics Organismal and Evolutionary Biology Research Programme Institute of Biotechnology Helsinki Institute of Sustainability Science (HELSUS) Biosciences |
format |
Article in Journal/Newspaper |
author |
Sinclair-Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig |
author_facet |
Sinclair-Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig |
author_sort |
Sinclair-Waters, Marion |
title |
Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus |
title_short |
Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus |
title_full |
Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus |
title_fullStr |
Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus |
title_full_unstemmed |
Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus |
title_sort |
refining the genomic location of single nucleotide polymorphism variation affecting atlantic salmon maturation timing at a key large-effect locus |
publisher |
Wiley |
publishDate |
2022 |
url |
http://hdl.handle.net/10138/350333 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_relation |
10.1111/mec.16256 Sinclair-Waters , M , Piavchenko , N , Ruokolainen , A , Aykanat , T , Erkinaro , J & Primmer , C 2022 , ' Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large-effect locus ' , Molecular Ecology , vol. 31 , no. 2 , pp. 562-570 . https://doi.org/10.1111/mec.16256 ORCID: /0000-0002-3687-8435/work/106791645 ORCID: /0000-0001-7371-4547/work/106791768 7ea08dfc-175e-4a15-be46-a5a5df9f4545 http://hdl.handle.net/10138/350333 000717946700001 |
op_rights |
unspecified openAccess info:eu-repo/semantics/openAccess |
container_title |
Molecular Ecology |
container_volume |
31 |
container_issue |
2 |
container_start_page |
562 |
op_container_end_page |
570 |
_version_ |
1787423144551645184 |