SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array
Abstract Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environme...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Wiley
2023-05-01
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| Series: | Evolutionary Applications |
| Subjects: | |
| Online Access: | https://doi.org/10.1111/eva.13552 |
| _version_ | 1797823535126675456 |
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| author | Jennifer C. Nascimento‐Schulze Tim P. Bean Carolina Peñaloza Josephine R. Paris James R. Whiting Alexis Simon Bonnie A. Fraser Ross D. Houston Nicolas Bierne Robert P. Ellis |
| author_facet | Jennifer C. Nascimento‐Schulze Tim P. Bean Carolina Peñaloza Josephine R. Paris James R. Whiting Alexis Simon Bonnie A. Fraser Ross D. Houston Nicolas Bierne Robert P. Ellis |
| author_sort | Jennifer C. Nascimento‐Schulze |
| collection | DOAJ |
| description | Abstract Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium‐density 60 K SNP‐array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole‐genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change. |
| first_indexed | 2024-03-13T10:25:27Z |
| format | Article |
| id | doaj.art-0e91656d7b4b4d42b28e228603421bf7 |
| institution | Directory Open Access Journal |
| issn | 1752-4571 |
| language | English |
| last_indexed | 2024-03-13T10:25:27Z |
| publishDate | 2023-05-01 |
| publisher | Wiley |
| record_format | Article |
| series | Evolutionary Applications |
| spelling | doaj.art-0e91656d7b4b4d42b28e228603421bf72023-05-19T10:52:16ZengWileyEvolutionary Applications1752-45712023-05-011651044106010.1111/eva.13552SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐arrayJennifer C. Nascimento‐Schulze0Tim P. Bean1Carolina Peñaloza2Josephine R. Paris3James R. Whiting4Alexis Simon5Bonnie A. Fraser6Ross D. Houston7Nicolas Bierne8Robert P. Ellis9Biosciences, Faculty of Health and Life Sciences University of Exeter Exeter UKThe Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Midlothian UKThe Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Midlothian UKBiosciences, Faculty of Health and Life Sciences University of Exeter Exeter UKBiosciences, Faculty of Health and Life Sciences University of Exeter Exeter UKISEM University of Montpellier, CNRS, IRD Montpellier FranceBiosciences, Faculty of Health and Life Sciences University of Exeter Exeter UKBenchmark Genetics Midlothian UKISEM University of Montpellier, CNRS, IRD Montpellier FranceBiosciences, Faculty of Health and Life Sciences University of Exeter Exeter UKAbstract Blue mussels from the genus Mytilus are an abundant component of the benthic community, found in the high latitude habitats. These foundation species are relevant to the aquaculture industry, with over 2 million tonnes produced globally each year. Mussels withstand a wide range of environmental conditions and species from the Mytilus edulis complex readily hybridize in regions where their distributions overlap. Significant effort has been made to investigate the consequences of environmental stress on mussel physiology, reproductive isolation, and local adaptation. Yet our understanding on the genomic mechanisms underlying such processes remains limited. In this study, we developed a multi species medium‐density 60 K SNP‐array including four species of the Mytilus genus. SNPs included in the platform were called from 138 mussels from 23 globally distributed mussel populations, sequenced using a whole‐genome low coverage approach. The array contains polymorphic SNPs which capture the genetic diversity present in mussel populations thriving across a gradient of environmental conditions (~59 K SNPs) and a set of published and validated SNPs informative for species identification and for diagnosis of transmissible cancer (610 SNPs). The array will allow the consistent genotyping of individuals, facilitating the investigation of ecological and evolutionary processes in these taxa. The applications of this array extend to shellfish aquaculture, contributing to the optimization of this industry via genomic selection of blue mussels, parentage assignment, inbreeding assessment and traceability. Further applications such as genome wide association studies (GWAS) for key production traits and those related to environmental resilience are especially relevant to safeguard aquaculture production under climate change.https://doi.org/10.1111/eva.13552aquaculturemusselsMytiluspopulation genomicsSNPSNP chip |
| spellingShingle | Jennifer C. Nascimento‐Schulze Tim P. Bean Carolina Peñaloza Josephine R. Paris James R. Whiting Alexis Simon Bonnie A. Fraser Ross D. Houston Nicolas Bierne Robert P. Ellis SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array Evolutionary Applications aquaculture mussels Mytilus population genomics SNP SNP chip |
| title | SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array |
| title_full | SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array |
| title_fullStr | SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array |
| title_full_unstemmed | SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array |
| title_short | SNP discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 K SNP‐array |
| title_sort | snp discovery and genetic structure in blue mussel species using low coverage sequencing and a medium density 60 k snp array |
| topic | aquaculture mussels Mytilus population genomics SNP SNP chip |
| url | https://doi.org/10.1111/eva.13552 |
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