Looking for a needle in a hay-stack: diagnostic kits for the detection of plant parasitic nematodes in complex DNA backgrounds.

Recently, many agricultural laboratories have invested in the set up of a molecular laboratory in the expectation that DNA-based identification and detection of plant pathogens, including nematodes, will be the golden standard in the near future. However, as molecular methods for the detection of some specific (quarantine) nematodes have the potential to fully replace the current microscopic routine screening of (soil) samples, there is a strong need to check for their accuracy and performance. Whereas a molecular method in itself may be far more precise and accurate than a microscopic method ever can be, its accuracy will largely depend on the biological information that was used to develop it. Its performance will depend on the robustness of the method and the test performed. On the basis of a phylum-wide, small subunit ribosomal DNA (SSU rDNA)-based framework consisting of ~ 2,500 full-length nematode sequences, we have developed over 20 diagnostic Q-PCR tests for plant pathogenic nematodes. Some nematode species have a dubious reputation as parasites of major crops such as potato, sugar beet and soybean. Among the most notorious ones are cyst (e.g. Globodera rostochiensis and G. pallida), root knot (e.g. Meloidogyne chitwoodi, M. fallax and M. minor), stem and bulb (e.g Ditylenchus dipsaci and D. destructor), and foliar nematodes (various Aphelenchoides species). By using this SSU rDNA framework, we could define unique DNA sequence signatures that enable ‘blind’ identification of these individual nematode species in highly complex DNA backgrounds. A number of examples will be presented during this meeting.