Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches

Understanding the genetic architecture of adaptive traits is a common goal in evolutionary biology. However, there are relatively few well-characterized genetic architectures for adaptive traits in non-model systems, particularly in wild populations. In this thesis, we further characterize the genet...

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Main Author: Sinclair-Waters, Marion
Other Authors: Peichel, Catherine, University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology, Doctoral Programme in Wildlife Biology, Institute of Biotechnology, Helsingin yliopisto, bio- ja ympäristötieteellinen tiedekunta, Luonnonvaraisten eliöiden tutkimuksen tohtoriohjelma, Helsingfors universitet, bio- och miljövetenskapliga fakulteten, Doktorandprogrammet i forskning om vilda organismer, Primmer, Craig, Barson, Nicola
Format: Doctoral or Postdoctoral Thesis
Language:English
Published: Helsingin yliopisto 2021
Subjects:
Online Access:http://hdl.handle.net/10138/335021
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spelling ftunivhelsihelda:oai:helda.helsinki.fi:10138/335021 2023-08-20T04:05:13+02:00 Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches Sinclair-Waters, Marion Peichel, Catherine University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology Doctoral Programme in Wildlife Biology Institute of Biotechnology Helsingin yliopisto, bio- ja ympäristötieteellinen tiedekunta Luonnonvaraisten eliöiden tutkimuksen tohtoriohjelma Helsingfors universitet, bio- och miljövetenskapliga fakulteten Doktorandprogrammet i forskning om vilda organismer Primmer, Craig Barson, Nicola 2021-10-07T04:37:11Z application/pdf http://hdl.handle.net/10138/335021 eng eng Helsingin yliopisto Helsingfors universitet University of Helsinki URN:ISBN:978-951-51-7525-0 http://hdl.handle.net/10138/335021 URN:ISBN:978-951-51-7526-7 Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty. This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited. Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden. evolutionary genomics Text 1181 Ekologia, evoluutiobiologia 1181 Ekologi, evolutionsbiologi 1181 Ecology, evolutionary biology Doctoral dissertation (article-based) Artikkeliväitöskirja Artikelavhandling doctoralThesis 2021 ftunivhelsihelda 2023-07-28T06:11:35Z Understanding the genetic architecture of adaptive traits is a common goal in evolutionary biology. However, there are relatively few well-characterized genetic architectures for adaptive traits in non-model systems, particularly in wild populations. In this thesis, we further characterize the genetic architecture of age at maturity in Atlantic salmon using a combination of genomic-enabled approaches. First, a large-scale genome-wide association study of ~11000 male Atlantic salmon, with ~500K single nucleotide polymorphisms (SNPs) genotypes, was used to identify loci underlying age at maturity. Significant associations were found on 28 of the 29 Atlantic salmon chromosomes, including two strong signals at the six6 and vgll3 gene regions. Furthermore, 116 candidate loci with varying effect sizes were identified revealing a mixed genetic architecture with a combination of large-effect loci and a polygenic component consisting of multiple smaller-effect loci. A combination of multi-SNP association methods and individual-level sequencing data was then used to resolve the genetic architecture within the 116 candidate loci for Atlantic salmon age at maturity. The genetic architecture within these candidate loci was relatively simple, where the association was driven by a single mutation. Finally, ~6000 male Atlantic salmon with a high frequency of recombinant alleles at a known large-effect locus spanning two linked genes, vgll3 and akap11, were reared to maturation age. Vgll3 SNP variation was strongly associated with maturation timing, however, akap11 SNP variation showed little to no association with maturation timing, suggesting that variation linked to vgll3 is driving the association at this large-effect locus. Together, these findings further refine our understanding of the genetic architecture for Atlantic salmon age at maturity. Additionally, this thesis provides an analytical framework for characterizing the genetic architecture of adaptive traits in non-model systems. Tässä väitöskirjassa hyödynnetään ... Doctoral or Postdoctoral Thesis Atlantic salmon Salmo salar Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto
institution Open Polar
collection Helsingfors Universitet: HELDA – Helsingin yliopiston digitaalinen arkisto
op_collection_id ftunivhelsihelda
language English
topic evolutionary genomics
spellingShingle evolutionary genomics
Sinclair-Waters, Marion
Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches
topic_facet evolutionary genomics
description Understanding the genetic architecture of adaptive traits is a common goal in evolutionary biology. However, there are relatively few well-characterized genetic architectures for adaptive traits in non-model systems, particularly in wild populations. In this thesis, we further characterize the genetic architecture of age at maturity in Atlantic salmon using a combination of genomic-enabled approaches. First, a large-scale genome-wide association study of ~11000 male Atlantic salmon, with ~500K single nucleotide polymorphisms (SNPs) genotypes, was used to identify loci underlying age at maturity. Significant associations were found on 28 of the 29 Atlantic salmon chromosomes, including two strong signals at the six6 and vgll3 gene regions. Furthermore, 116 candidate loci with varying effect sizes were identified revealing a mixed genetic architecture with a combination of large-effect loci and a polygenic component consisting of multiple smaller-effect loci. A combination of multi-SNP association methods and individual-level sequencing data was then used to resolve the genetic architecture within the 116 candidate loci for Atlantic salmon age at maturity. The genetic architecture within these candidate loci was relatively simple, where the association was driven by a single mutation. Finally, ~6000 male Atlantic salmon with a high frequency of recombinant alleles at a known large-effect locus spanning two linked genes, vgll3 and akap11, were reared to maturation age. Vgll3 SNP variation was strongly associated with maturation timing, however, akap11 SNP variation showed little to no association with maturation timing, suggesting that variation linked to vgll3 is driving the association at this large-effect locus. Together, these findings further refine our understanding of the genetic architecture for Atlantic salmon age at maturity. Additionally, this thesis provides an analytical framework for characterizing the genetic architecture of adaptive traits in non-model systems. Tässä väitöskirjassa hyödynnetään ...
author2 Peichel, Catherine
University of Helsinki, Faculty of Biological and Environmental Sciences, Organismal and Evolutionary Biology
Doctoral Programme in Wildlife Biology
Institute of Biotechnology
Helsingin yliopisto, bio- ja ympäristötieteellinen tiedekunta
Luonnonvaraisten eliöiden tutkimuksen tohtoriohjelma
Helsingfors universitet, bio- och miljövetenskapliga fakulteten
Doktorandprogrammet i forskning om vilda organismer
Primmer, Craig
Barson, Nicola
format Doctoral or Postdoctoral Thesis
author Sinclair-Waters, Marion
author_facet Sinclair-Waters, Marion
author_sort Sinclair-Waters, Marion
title Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches
title_short Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches
title_full Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches
title_fullStr Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches
title_full_unstemmed Refining the genetic architecture of Atlantic salmon (Salmo salar) maturation using genomics-enabled approaches
title_sort refining the genetic architecture of atlantic salmon (salmo salar) maturation using genomics-enabled approaches
publisher Helsingin yliopisto
publishDate 2021
url http://hdl.handle.net/10138/335021
genre Atlantic salmon
Salmo salar
genre_facet Atlantic salmon
Salmo salar
op_relation URN:ISBN:978-951-51-7525-0
http://hdl.handle.net/10138/335021
URN:ISBN:978-951-51-7526-7
op_rights Julkaisu on tekijänoikeussäännösten alainen. Teosta voi lukea ja tulostaa henkilökohtaista käyttöä varten. Käyttö kaupallisiin tarkoituksiin on kielletty.
This publication is copyrighted. You may download, display and print it for Your own personal use. Commercial use is prohibited.
Publikationen är skyddad av upphovsrätten. Den får läsas och skrivas ut för personligt bruk. Användning i kommersiellt syfte är förbjuden.
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