evaluation of target specificity and sensitivity of three qPCR assays for detecting environmental DNA from Northern Pike (Esox lucius)

• Published in: Conservation genetics resources Vol. 7; no. 3; pp. 615 - 617
• Main Authors: Olsen, Jeffrey B, Lewis, Cara J, Massengill, Robert L, Dunker, Kristine J, Wenburg, John K
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-09-2015; Springer Nature B.V
• Subjects: Animal Genetics and Genomics; Biodiversity; Biomedical and Life Sciences; Conservation Biology/Ecology; Copy number; Cytochrome; Cytochrome b; cytochrome-c oxidase; Deoxyribonucleic acid; DNA; Ecology; Environmental DNA; Esox lucius; Esox masquinongy; Evolutionary Biology; fluorescence; freshwater fish; genes; Life Sciences; Mitochondrial DNA; Plant Genetics and Genomics; Predation; probability; quantitative polymerase chain reaction; Technical Note; eDNA; Invasive species; Northern Pike
• ISSN: 1877-7252; 1877-7260
• DOI: 10.1007/s12686-015-0459-x

We developed and evaluated three qPCR assays for detecting environmental DNA from northern pike (Esox lucius). The assays target the cytochrome oxidase 1 (EluCOI), control region (EluCR), and cytochrome b (EluCytB) genes of the mitochondrial DNA. Target specificity, assessed using the fluorescence signal (at 45 cycles) to noise (at 1 cycle) ratio (S/N), showed strong amplification in northern pike (mean S/N = 2.62, 3.52, 2.69 for EluCOI, EluCR, EluCytB). The mean S/N estimates from fifteen non-esocid freshwater fishes were about 1.0, as expected for no amplification. EluCR showed evidence of amplification (mean S/N = 3.16) in muskellunge (Esox masquinongy). The sensitivity tests indicated EluCOI has a higher detection probability than EluCR and EluCytB at low (20 copies/reaction) copy number. The results favor using EluCOI although EluCytB and EluCR are viable assays for the detection of northern pike eDNA.