Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval Production
Aquaculture of the lumpfish (<i>Cyclopterus lumpus</i> 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)...
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MDPI AG
2023-09-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/10/1870 |
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| 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 |
| collection | DOAJ |
| description | Aquaculture of the lumpfish (<i>Cyclopterus lumpus</i> 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. |
| first_indexed | 2024-03-11T10:15:07Z |
| format | Article |
| id | doaj.art-c1060813b15a4e17aa2b266a4560236d |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T10:15:07Z |
| publishDate | 2023-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-c1060813b15a4e17aa2b266a4560236d2023-11-16T10:29:38ZengMDPI AGGenes2073-44252023-09-011410187010.3390/genes14101870Genomic Signatures of Local Adaptation under High Gene Flow in Lumpfish—Implications for Broodstock Provenance Sourcing and Larval ProductionSimo Njabulo Maduna0Ólöf Dóra Bartels Jónsdóttir1Albert Kjartan Dagbjartarson Imsland2Davíð Gíslason3Patrick Reynolds4Lauri Kapari5Thor Arne Hangstad6Kristian Meier7Snorre B. Hagen8Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, NorwayAkvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, IcelandAkvaplan-Niva Iceland Office, Akralind 6, 201 Kópavogur, IcelandMatís, Vínlandsleið 12, 113 Reykjavík, IcelandGIFAS AS, Gildeskål, 8140 Inndyr, NorwayAkvaplan-Niva, Framsenteret, 9296 Tromsø, NorwayLumarine AS, Stadionveien 21, 4632 Kristiansand, NorwayLerøy Aurora, Stortorget 1D, 9008 Tromsø, NorwayDepartment of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, NorwayAquaculture of the lumpfish (<i>Cyclopterus lumpus</i> 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.https://www.mdpi.com/2073-4425/14/10/18703RADadaptive variationaquaculturecleaner fish<i>C. lumpus</i>genotype–environment association |
| spellingShingle | 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 Genes 3RAD adaptive variation aquaculture cleaner fish <i>C. lumpus</i> genotype–environment association |
| title | 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_short | 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 |
| topic | 3RAD adaptive variation aquaculture cleaner fish <i>C. lumpus</i> genotype–environment association |
| url | https://www.mdpi.com/2073-4425/14/10/1870 |
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