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Demonstration of the use of environmental DNA for the non-invasive genotyping of a bivalve mollusk, the European Flat Oyster (Ostrea edulis)

Demonstration of the use of environmental DNA for the non-invasive genotyping of a bivalve mollusk, the European Flat Oyster (Ostrea edulis)
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 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.

1664-8021
1-7
Holman, Luke E.
3d57aba8-c261-413b-a053-e7bed35adba0
Hollenbeck, Christopher M.
cc6cc8a2-d79d-489d-9328-11ba4ef36da8
Ashton, Thomas J.
bad56965-07b8-45dc-8b09-c806bc340c32
Johnston, Ian A.
31b5afe1-ae80-444c-bcbc-2ff332fac180
Holman, Luke E.
3d57aba8-c261-413b-a053-e7bed35adba0
Hollenbeck, Christopher M.
cc6cc8a2-d79d-489d-9328-11ba4ef36da8
Ashton, Thomas J.
bad56965-07b8-45dc-8b09-c806bc340c32
Johnston, Ian A.
31b5afe1-ae80-444c-bcbc-2ff332fac180

Holman, Luke E., Hollenbeck, Christopher M., Ashton, Thomas J. and Johnston, Ian A. (2019) 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, 10, 1-7, [1159]. (doi:10.3389/fgene.2019.01159).

Record type: Article

Abstract

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.

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fgene-10-01159 - Version of Record
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Accepted/In Press date: 22 October 2019
Published date: 19 November 2019

Identifiers

Local EPrints ID: 439832
URI: http://eprints.soton.ac.uk/id/eprint/439832
ISSN: 1664-8021
PURE UUID: 9b31cf22-a437-47e8-bd74-c1131e6a223a
ORCID for Luke E. Holman: ORCID iD orcid.org/0000-0002-8139-3760

Catalogue record

Date deposited: 05 May 2020 16:31
Last modified: 26 Nov 2021 02:32

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Contributors

Author: Luke E. Holman ORCID iD
Author: Christopher M. Hollenbeck
Author: Thomas J. Ashton
Author: Ian A. Johnston

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