Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis)
Accurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01159/full |
| _version_ | 1819136222542430208 |
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| author | Luke E. Holman Christopher M. Hollenbeck Thomas J. Ashton Ian A. Johnston Ian A. Johnston |
| author_facet | Luke E. Holman Christopher M. Hollenbeck Thomas J. Ashton Ian A. Johnston Ian A. Johnston |
| author_sort | Luke E. Holman |
| collection | DOAJ |
| description | Accurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile animals or taxa where sampling tissue is difficult or may cause mortality (e.g. bivalve mollusks). Here, we demonstrate a novel, non-invasive technique for sampling DNA based on the collection of environmental DNA using European Flat Oysters (Ostrea edulis) as an example. The live animals are placed in individual containers until sufficient genetic material is released into the seawater which is then recovered by filtration. We compared the results of tissue and eDNA derived SNP genotype calls using a PCR based genotyping platform. We found that 100% accurate genotype calls from eDNA are possible, but depend on appropriate filtration and the dilution of the sample throughout the workflow. We also developed an additional low-cost DNA extraction technique which provided >99% correct SNP genotype calls in comparison to tissue. It was concluded that eDNA sampling can be used in hatchery and selective breeding programs applicable to any aquatic organism for which direct tissue sampling may result in animal welfare concerns or mortality. |
| first_indexed | 2024-12-22T10:31:33Z |
| format | Article |
| id | doaj.art-7d1358b768c84fb28eaafe8a6ce0cd19 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-22T10:31:33Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-7d1358b768c84fb28eaafe8a6ce0cd192022-12-21T18:29:18ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-11-011010.3389/fgene.2019.01159483038Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis)Luke E. Holman0Christopher M. Hollenbeck1Thomas J. Ashton2Ian A. Johnston3Ian A. Johnston4School of Ocean and Earth Science, National Oceanography Centre Southampton, University of Southampton, Southampton, United KingdomXelect Ltd, Horizon House, Scotland, United KingdomXelect Ltd, Horizon House, Scotland, United KingdomXelect Ltd, Horizon House, Scotland, United KingdomScottish Oceans Institute, School of Biology, University of St Andrews, Scotland, United KingdomAccurate SNP (single nucleotide polymorphism) genotype information is critical for a wide range of selective breeding applications in aquaculture, including parentage assignment, marker-assisted, and genomic selection. However, the sampling of tissue for genetic analysis can be invasive for juvenile animals or taxa where sampling tissue is difficult or may cause mortality (e.g. bivalve mollusks). Here, we demonstrate a novel, non-invasive technique for sampling DNA based on the collection of environmental DNA using European Flat Oysters (Ostrea edulis) as an example. The live animals are placed in individual containers until sufficient genetic material is released into the seawater which is then recovered by filtration. We compared the results of tissue and eDNA derived SNP genotype calls using a PCR based genotyping platform. We found that 100% accurate genotype calls from eDNA are possible, but depend on appropriate filtration and the dilution of the sample throughout the workflow. We also developed an additional low-cost DNA extraction technique which provided >99% correct SNP genotype calls in comparison to tissue. It was concluded that eDNA sampling can be used in hatchery and selective breeding programs applicable to any aquatic organism for which direct tissue sampling may result in animal welfare concerns or mortality.https://www.frontiersin.org/article/10.3389/fgene.2019.01159/fullbroodstockhatchery managementsingle nucleotide polymorphism genotypingmollusk aquacultureminimally invasive samplingnon-invasive genetic sampling |
| spellingShingle | Luke E. Holman Christopher M. Hollenbeck Thomas J. Ashton Ian A. Johnston Ian A. Johnston Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis) Frontiers in Genetics broodstock hatchery management single nucleotide polymorphism genotyping mollusk aquaculture minimally invasive sampling non-invasive genetic sampling |
| title | Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis) |
| title_full | Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis) |
| title_fullStr | Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis) |
| title_full_unstemmed | Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis) |
| title_short | Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis) |
| title_sort | demonstration of the use of environmental dna for the non invasive genotyping of a bivalve mollusk the european flat oyster ostrea edulis |
| topic | broodstock hatchery management single nucleotide polymorphism genotyping mollusk aquaculture minimally invasive sampling non-invasive genetic sampling |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.01159/full |
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