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Improving detection of the silver carp using eDNA

Researchers from the United States have worked on optimizing DNA extraction techniques and amplification protocols for the detection of the Silver carp from environmental samples.

In June 2015, Amberg et al. published a paper entitled “Improving efficiency and reliability of environmental DNA analysis for silver carp” in the “Journal of Great Lakes research”.

Summary: Natural resource agencies have established surveillance programs which use environmental DNA (eDNA) for the early detection of bighead carp Hypophthalmichthys nobilis and silver carp Hypophthalmichthys molitrix before they establish populations within the Great Lakes. This molecular monitoring technique must be highly accurate and precise for confident interpretation and also efficient, both in detection threshold and cost. Here, the researchers compared two DNA extraction techniques and compared a new quantitative PCR (qPCR) assay with the conventional PCR (cPCR) assay used by monitoring programs. Both the qPCR and cPCR assays were able to amplify the DNA of silver carp present in environmental samples taken from locations where mixed populations of bigheaded carps existed. However, the qPCR assay had substantially fewer PCR positive samples which were subsequently determined not to contain DNA of bigheaded carps than the cPCR assay. Additionally, the qPCR assay was able to amplify the DNA of bigheaded carps even in the presence of inhibitors that blocked amplification with cPCR. Also, the selection of an appropriate DNA extraction method can significantly alter the efficiency of eDNA surveillance programs by lowering detection limits and by decreasing costs associated with sample processing. The results reported herein are presently being incorporated into eDNA surveillance programs to decrease the costs, increase DNA yield and increase the confidence that assays are amplifying the target DNA. These results are critical to enhancing researchers’ ability to accurately and confidently interpret the results reported from monitoring programs using eDNA for early detection of invasive species.

Reference: Amberg, J.J., McCalla, S.G., Monroe, E., Lance, R.,  Baerwaldt, K., Gaikowski, M.P. (2015). Improving efficiency and reliability of environmental DNA analysis for silver carp. Journal of Great Lakes Research, 41(2): 367-373.

To learn more about this article, you can download: Amberg et al. 2015.pdf