Multiplex real-time polymerase chain reaction for identifying potato cyst nematodes, Globodera pallida and Globodera rostochiensis, and the tobacco cyst nematode, Globodera tabacum

Because the potato cyst nematodes (PCNs), Globodera rostochiensis and Globodera pallida, and tobacco cyst nematode (TCN), Globodera tabacum, may occur in the same geographic regions, their accurate identification is essential for implementing appropriate regulatory and crop loss mitigating strategies. Molecular methods for differentiating PCNs based on the internal genomic transcribed spacer (ITS) sequences have been developed but the potential of the many DNA amplification-based test formats have not yet been fully explored and most published work has not included TCN. In our study, the two PCN species and TCN could be distinguished by melting curve analysis of ITS amplicons generated in an EvaGreen-based real-time polymerase chain reaction (PCR) test. However, a multiplex real-time Taqman PCR test, which is also based on ITS sequences, was developed in this study with primers and probes modified with locked nucleic acids and proved to be superior for identification of one or more Globodera spp. in samples containing DNA from cysts and (or) second-stage juveniles. The test was specific for the PCN and TCN species with efficiencies of 0.91, 1.02, and 0.89 for G. rostochiensis, G. pallida. and G. tabacum tabacum, respectively. The multiplex, real-time PCR test was useful for distinguishing PCNs and TCN from other nematodes as well as their identification to species level in a single assay, correctly identifying each species in a DNA template from mixed populations.