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

Luke Holman, Christopher Michael Hollenbeck, Thomas J. Ashton, Ian A. Johnston

Research output: Contribution to journalArticlepeer-review

5 Citations (Scopus)
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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.
Original languageEnglish
Article number1159
Number of pages7
JournalFrontiers in Genetics
Volume10
DOIs
Publication statusPublished - 19 Nov 2019

Keywords

  • Broodstock
  • Hatchery management
  • Single nucleotide polymorphism genotyping
  • Mollusk aquaculture
  • Minimally invasive sampling
  • Non-invasive genetic sampling

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