Development of a quantitative PCR assay for detection of redside shiner (Richardsonius balteatus) from environmental DNA

• Published in: BMC research notes Vol. 12; no. 1; pp. 782 - 4
• Main Authors: Hoy, Marshal S, Ostberg, Carl O
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 29.11.2019; BioMed Central; BMC
• Subjects: Animals; Aquatic invasive species; Biological Assay; Cyprinidae - genetics; Cytochrome; Deoxyribonucleic acid; DNA; Endangered & extinct species; Environmental DNA; Environmental DNA - analysis; Estuaries; Fishes; Gene expression; Introduced species; Polymerase chain reaction; qPCR; Quality control; Real-Time Polymerase Chain Reaction - methods; Redside shiner; Reproducibility of Results; Research Note; Reservoirs (Water); Richardsonius balteatus; Rivers; Sampling; Sympatric populations; Sympatry - genetics; Water sampling; Elwha River; Ross Lake; United States > US; Skagit River; Redside shiner; Water sampling; qPCR; Aquatic invasive species
• ISSN: 1756-0500; 1756-0500
• DOI: 10.1186/s13104-019-4819-6

A quantitative PCR (qPCR) assay for the detection of redside shiner (Richardsonius balteatus) environmental DNA (eDNA) was designed as a side product of a larger project aimed at using eDNA to determine the presence and geographic extent of native and non-native fishes in the reservoirs and associated tributaries above the three mainstem dams (Ross, Diablo, Gorge) on the Skagit River, Washington, USA. The eDNA survey results can be used to help guide additional sampling efforts that include traditional sampling methods, such as electrofishing and netting. The redside shiner qPCR assay (RSSCOI_540-601) was validated by testing for sensitivity using redside shiner genomic DNA from three different populations and by testing for specificity against 30 potentially sympatric species. No non-target amplification was observed in our validation tests. We then evaluated the assay on field-collected water samples where there are known populations of redside shiner and a negative control site where the target species is known to be absent. The field-collected water samples tested positive at the redside shiner sites and tested negative at the negative control site. The assay could provide resource managers with an effective means for surveying and monitoring redside shiner populations.