Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia

Abstract Arctic charr (Salvelinus alpinus) is a niche‐market high‐value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole‐genome re‐sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord;...

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Main Authors: Fotis Pappas, Khrystyna Kurta, Tytti Vanhala, Henrik Jeuthe, Ørjan Hagen, José Beirão, Christos Palaiokostas
Format: Article
Language:English
Published: Wiley 2023-04-01
Series:Evolutionary Applications
Subjects:
Online Access:https://doi.org/10.1111/eva.13537
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author Fotis Pappas
Khrystyna Kurta
Tytti Vanhala
Henrik Jeuthe
Ørjan Hagen
José Beirão
Christos Palaiokostas
author_facet Fotis Pappas
Khrystyna Kurta
Tytti Vanhala
Henrik Jeuthe
Ørjan Hagen
José Beirão
Christos Palaiokostas
author_sort Fotis Pappas
collection DOAJ
description Abstract Arctic charr (Salvelinus alpinus) is a niche‐market high‐value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole‐genome re‐sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.
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spelling doaj.art-7a82c400edeb461085cc633761c9feca2023-04-26T05:41:35ZengWileyEvolutionary Applications1752-45712023-04-0116479781310.1111/eva.13537Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from ScandinaviaFotis Pappas0Khrystyna Kurta1Tytti Vanhala2Henrik Jeuthe3Ørjan Hagen4José Beirão5Christos Palaiokostas6Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala SwedenDepartment of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala SwedenDepartment of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala SwedenDepartment of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala SwedenFaculty of Bioscience and Aquaculture Nord University Bodø NorwayFaculty of Bioscience and Aquaculture Nord University Bodø NorwayDepartment of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala SwedenAbstract Arctic charr (Salvelinus alpinus) is a niche‐market high‐value species for Nordic aquaculture. Similar to other salmonids, both anadromous and landlocked populations are encountered. Whole‐genome re‐sequencing (22X coverage) was performed on two farmed populations of anadromous (Sigerfjord; n = 24) and landlocked (Arctic Superior; n = 24) origin from Norway and Sweden respectively. More than 5 million SNPs were used to study their genetic diversity and to scan for selection signatures. The two populations were clearly distinguished through principal component analysis, with the mean fixation index being ~0.12. Furthermore, the levels of genomic inbreeding estimated from runs of homozygosity were 6.23% and 8.66% for the Norwegian and the Swedish population respectively. Biological processes that could be linked to selection pressure associated primarily with the anadromous background and/or secondarily with domestication were suggested. Overall, our study provided insights regarding the genetic composition of two main strains of farmed Arctic charr from Scandinavia. At the same time, ample genomic resources were produced in the magnitude of millions of SNPs that could assist the transition of Nordic Arctic charr farming in the genomics era.https://doi.org/10.1111/eva.13537Arctic charrgenetic diversityselective sweepswhole‐genome resequencing
spellingShingle Fotis Pappas
Khrystyna Kurta
Tytti Vanhala
Henrik Jeuthe
Ørjan Hagen
José Beirão
Christos Palaiokostas
Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
Evolutionary Applications
Arctic charr
genetic diversity
selective sweeps
whole‐genome resequencing
title Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
title_full Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
title_fullStr Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
title_full_unstemmed Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
title_short Whole‐genome re‐sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia
title_sort whole genome re sequencing provides key genomic insights in farmed arctic charr salvelinus alpinus populations of anadromous and landlocked origin from scandinavia
topic Arctic charr
genetic diversity
selective sweeps
whole‐genome resequencing
url https://doi.org/10.1111/eva.13537
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