Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus
Abstract 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...
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Online Access: | http://dx.doi.org/10.1111/mec.16256 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16256 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.16256 |
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crwiley:10.1111/mec.16256 2024-06-23T07:51:20+00:00 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 R. H2020 European Research Council Academy of Finland 2021 http://dx.doi.org/10.1111/mec.16256 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16256 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.16256 en eng Wiley http://onlinelibrary.wiley.com/termsAndConditions#vor Molecular Ecology volume 31, issue 2, page 562-570 ISSN 0962-1083 1365-294X journal-article 2021 crwiley https://doi.org/10.1111/mec.16256 2024-06-06T04:23:42Z Abstract 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. Article in Journal/Newspaper Atlantic salmon Salmo salar Wiley Online Library Molecular Ecology 31 2 562 570 |
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English |
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Abstract 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. |
author2 |
H2020 European Research Council Academy of Finland |
format |
Article in Journal/Newspaper |
author |
Sinclair‐Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig R. |
spellingShingle |
Sinclair‐Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig R. Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus |
author_facet |
Sinclair‐Waters, Marion Piavchenko, Nikolai Ruokolainen, Annukka Aykanat, Tutku Erkinaro, Jaakko Primmer, Craig R. |
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 |
2021 |
url |
http://dx.doi.org/10.1111/mec.16256 https://onlinelibrary.wiley.com/doi/pdf/10.1111/mec.16256 https://onlinelibrary.wiley.com/doi/full-xml/10.1111/mec.16256 |
genre |
Atlantic salmon Salmo salar |
genre_facet |
Atlantic salmon Salmo salar |
op_source |
Molecular Ecology volume 31, issue 2, page 562-570 ISSN 0962-1083 1365-294X |
op_rights |
http://onlinelibrary.wiley.com/termsAndConditions#vor |
op_doi |
https://doi.org/10.1111/mec.16256 |
container_title |
Molecular Ecology |
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31 |
container_issue |
2 |
container_start_page |
562 |
op_container_end_page |
570 |
_version_ |
1802642393188532224 |