Real-time PCR assays for identification of commonly entrained freshwater species from the great lakes

  • Danielle BourqueEmail author
  • Amanda Naaum
  • Doug Bradley
  • Jennifer Daley
  • Paul Patrick
  • Robert Hanner
Methods and Resources Article


Entrainment studies, mandated by The Final Rule, require facilities to identify entrained organisms to “the lowest taxon possible”, usually species. The life stages most commonly captured present challenges to traditional taxonomic approaches, and DNA barcoding also presents time- and cost-related barriers to routine screening. Real-time PCR offers a rapid DNA-based solution with high target specificity. Four real-time qPCR assays were designed, validated, and optimized for multiplexing of freshwater species of interest to entrainment monitoring: Yellow Perch (Perca flavescens), Round Whitefish (Prosopium cylindraceum), Walleye (Sander vitreus), and Lake Whitefish (Coregonus clupeaformis). These assays provide a means to reduce the number of unidentified entrained eggs and larvae, thus providing improved data quality for impact assessments. They also represent a rapid and low-cost means to achieve accurate identification of target species, and species of conservation concern.


Entrainment Quantitative PCR Yellow perch Round whitefish Lake whitefish Walleye 



This study was funded by the Fish Protection Program at the Electric Power Research Institute, the CANDU Owners Group Inc., and ARCADIS SENES Canada Inc.

The Investigators would like to thank the following for their technical assistance, concept discussions and idea refinements: Doug Dixon (EPRI), Jon Black (EPRI), Peter Ernst (CANDU Owners Group), Steven Crookes (University of Guelph), Kevin Morey (University of Guelph), Elaine Mason (Ecometrix) and Jason Parks (Ministry of Natural Resources, Ontario).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflicts of interest.


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Integrative BiologyUniversity of GuelphGuelphCanada
  2. 2.LimnoTechAnn ArborUSA
  3. 3.Petrudev Inc.MiltonCanada

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