A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus)


Environmental DNA (eDNA) is increasingly applied as a highly sensitive way to detect aquatic animals non-invasively. However, distinguishing closely related taxa can be particularly challenging. Previous studies of ancient DNA and genetic diet analysis have used blocking primers to enrich target template in the presence of abundant, non-target DNA. Here we apply a blocking primer to increase the specificity of a TaqMan assay for eDNA detection of rare and endangered bull trout (Salvelinus confluentus) in the presence of the closely related (Salvelinus namaycush). We found that addition of a blocking primer substantially increased assay specificity without compromising sensitivity or quantification ability.

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The authors thank the McCutheon Lab at the University of Montana for use of their spectrophotometer. TW is supported by a NSF Graduate Research Fellowship (Grant No. DGE-1313190).

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Correspondence to Taylor M. Wilcox.

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Wilcox, T.M., Schwartz, M.K., McKelvey, K.S. et al. A blocking primer increases specificity in environmental DNA detection of bull trout (Salvelinus confluentus). Conservation Genet Resour 6, 283–284 (2014). https://doi.org/10.1007/s12686-013-0113-4

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  • Environmental DNA
  • Bull trout
  • Blocking primer
  • Complex templates