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

Abstract

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.