Demonstration of the Use of Environmental DNA for the Non-Invasive Genotyping of a Bivalve Mollusk, the European Flat Oyster (Ostrea edulis)

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.

Managing human-mediated range shifts: understanding spatial, temporal and genetic variation in marine non-native species

“…Cumulatively, these studies have demonstrated the value of DNA evidence for the management of NNS. Furthermore, observations from both laboratory [47,48] and field studies [49][50][51][52][53][54] have shown that eDNA can provide population genetics inference, but very little work has used this approach to study NNS [55].…”

Forty questions of importance to the policy and practice of native oyster reef restoration in Europe

“…Given the low abundance of oysters in many locations, reaching this sample size can present a challenge in itself. eDNA analysis represents a potential opportunity to overcome these difficulties in sampling (Holman, Hollenbeck, Ashton, & Johnston, 2019; Mérou, Lecadet, Pouvreau, & Arzul, 2020). In a hatchery setting, production of O. edulis spat is an ongoing challenge (Lapègue, Beaumont, Boudry, & Goulletquer, 2007).…”

Genome resequencing clarifies phylogeny and reveals patterns of selection in the toxicogenomics model Pimephales promelas

“…Although frequency estimates can be derived for DNA pooled from archived samples or new collections, we ultimately expect the most efficient approach to quantifying contemporary allele-frequencies will be from environmental DNA samples. Conceptually similar eDNA genotyping assays have already been applied to diverse management needs, such as determining the proportion of conspecific carp derived from a non-native source ( Uchii, Doi & Minamoto, 2016 ), noninvasive genotyping of cultured oysters ( Holman et al, 2019 ), and noninvasive haplotyping of whale sharks ( Dugal et al, 2022 ).…”