Author: Chelsea E. Frank
Environmental DNA (eDNA) is a useful tool for management of aquatic ecosystems, as its applications provide a non-invasive method for species detection. Compared to other molecular technologies (e.g., metabarcoding) for analyzing target species eDNA presence/absence, OpenArrayTM chips provide a time and cost-effective quantification method. As part of Activity 1, our goal at GEN-FISH was to determine the location and abundance of over 200 of Canada’s freshwater fish species with our fish survey toolkit. As part of this toolkit, we implemented a species-specific approach to designing and optimizing OpenArrayTM qPCR assays for taxonomically (e.g., salmonid and non-teleost) and/or geographically (e.g., Atlantic Canada, Western Canada, the Prairies, and Southern Ontario) related freshwater fishes. Initially we developed OpenArrayTM chips to test the sensitivity and specificity of COI and CytB primer sets at a rapid pace. This testing was then followed by utilizing the remaining OpenArrayTM chips to determine species presence via eDNA quantification, from over 500 water bodies across Canada. While we are limited in the focus of species in which primer sets appropriate for OpenArrayTM technologies have been developed, this enables us to take a more direct approach in aquatic management with respect to breadth of application (e.g., conservation and management). With a specific number of species-specific assays within a chip, we can highlight the focus of these technologies to provide information on species of concern (e.g., invasive or endangered) without harm to the species present within those environments.