Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production
Aquaculture of the lumpfish ( Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the...
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ftdoajarticles:oai:doaj.org/article:c1060813b15a4e17aa2b266a4560236d 2023-12-31T10:04:49+01:00 Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production Simo Njabulo Maduna Ólöf Dóra Bartels Jónsdóttir Albert Kjartan Dagbjartarson Imsland Davíð Gíslason Patrick Reynolds Lauri Kapari Thor Arne Hangstad Kristian Meier Snorre B. Hagen 2023-09-01T00:00:00Z https://doi.org/10.3390/genes14101870 https://doaj.org/article/c1060813b15a4e17aa2b266a4560236d EN eng MDPI AG https://www.mdpi.com/2073-4425/14/10/1870 https://doaj.org/toc/2073-4425 doi:10.3390/genes14101870 2073-4425 https://doaj.org/article/c1060813b15a4e17aa2b266a4560236d Genes, Vol 14, Iss 10, p 1870 (2023) 3RAD adaptive variation aquaculture cleaner fish C. lumpus genotype–environment association Genetics QH426-470 article 2023 ftdoajarticles https://doi.org/10.3390/genes14101870 2023-12-03T01:37:01Z Aquaculture of the lumpfish ( Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype–environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our ‘global’ sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway. Article in Journal/Newspaper Atlantic salmon North Atlantic Directory of Open Access Journals: DOAJ Articles Genes 14 10 1870 |
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Directory of Open Access Journals: DOAJ Articles |
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English |
topic |
3RAD adaptive variation aquaculture cleaner fish C. lumpus genotype–environment association Genetics QH426-470 |
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3RAD adaptive variation aquaculture cleaner fish C. lumpus genotype–environment association Genetics QH426-470 Simo Njabulo Maduna Ólöf Dóra Bartels Jónsdóttir Albert Kjartan Dagbjartarson Imsland Davíð Gíslason Patrick Reynolds Lauri Kapari Thor Arne Hangstad Kristian Meier Snorre B. Hagen Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production |
topic_facet |
3RAD adaptive variation aquaculture cleaner fish C. lumpus genotype–environment association Genetics QH426-470 |
description |
Aquaculture of the lumpfish ( Cyclopterus lumpus L.) has become a large, lucrative industry owing to the escalating demand for “cleaner fish” to minimise sea lice infestations in Atlantic salmon mariculture farms. We used over 10K genome-wide single nucleotide polymorphisms (SNPs) to investigate the spatial patterns of genomic variation in the lumpfish along the coast of Norway and across the North Atlantic. Moreover, we applied three genome scans for outliers and two genotype–environment association tests to assess the signatures and patterns of local adaptation under extensive gene flow. With our ‘global’ sampling regime, we found two major genetic groups of lumpfish, i.e., the western and eastern Atlantic. Regionally in Norway, we found marginal evidence of population structure, where the population genomic analysis revealed a small portion of individuals with a different genetic ancestry. Nevertheless, we found strong support for local adaption under high gene flow in the Norwegian lumpfish and identified over 380 high-confidence environment-associated loci linked to gene sets with a key role in biological processes associated with environmental pressures and embryonic development. Our results bridge population genetic/genomics studies with seascape genomics studies and will facilitate genome-enabled monitoring of the genetic impacts of escapees and allow for genetic-informed broodstock selection and management in Norway. |
format |
Article in Journal/Newspaper |
author |
Simo Njabulo Maduna Ólöf Dóra Bartels Jónsdóttir Albert Kjartan Dagbjartarson Imsland Davíð Gíslason Patrick Reynolds Lauri Kapari Thor Arne Hangstad Kristian Meier Snorre B. Hagen |
author_facet |
Simo Njabulo Maduna Ólöf Dóra Bartels Jónsdóttir Albert Kjartan Dagbjartarson Imsland Davíð Gíslason Patrick Reynolds Lauri Kapari Thor Arne Hangstad Kristian Meier Snorre B. Hagen |
author_sort |
Simo Njabulo Maduna |
title |
Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production |
title_short |
Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production |
title_full |
Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production |
title_fullStr |
Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production |
title_full_unstemmed |
Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production |
title_sort |
genomic signatures of local adaptation under high gene flow in lumpfish—implications for broodstock provenance sourcing and larval production |
publisher |
MDPI AG |
publishDate |
2023 |
url |
https://doi.org/10.3390/genes14101870 https://doaj.org/article/c1060813b15a4e17aa2b266a4560236d |
genre |
Atlantic salmon North Atlantic |
genre_facet |
Atlantic salmon North Atlantic |
op_source |
Genes, Vol 14, Iss 10, p 1870 (2023) |
op_relation |
https://www.mdpi.com/2073-4425/14/10/1870 https://doaj.org/toc/2073-4425 doi:10.3390/genes14101870 2073-4425 https://doaj.org/article/c1060813b15a4e17aa2b266a4560236d |
op_doi |
https://doi.org/10.3390/genes14101870 |
container_title |
Genes |
container_volume |
14 |
container_issue |
10 |
container_start_page |
1870 |
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1786836240955342848 |