The last decade has seen some large advances in diagnostics, many of which can be used for potato disease detection and diagnosis. The current state of the art for diagnostics is real-time PCR (polymerase chain reaction), the cornerstone technique of many diagnostic labs. It offers unrivaled sensitivity in disease detection and is therefore useful when screening asymptomatic tissue or for testing soil samples.
Presently, it is possible to test soil samples for the presence of DNA associated with potato pathogens. There has been success with quantifying levels of Spongospora (powdery scab) and Colletotrichum (black dot) and directly linking this to risk of disease developing. With other soil-borne diseases such as Verticillium wilt and Rhizoctonia diseases, there has been less success, possibly due to these diseases being caused by a complex of several strains of the pathogen—and in the case of Rhizoctonia, the importance of seed-borne inoculum. Further work is therefore needed on all these pathogens to correlate the diagnostic result to observations of disease, particularly for local conditions.
Although real-time PCR has its advantages, it is still a lab-based method requiring several hours to perform the DNA extraction method and the PCR. For these reasons, there has recently been much interest in isothermal methods for detecting DNA. In isothermal methods, a DNA replication reaction takes place at a constant temperature (usually 65 degrees Celsius), whereas in PCR the temperature is cycled up to 95 degrees Celsius and back to 60 degrees to split the DNA and then replicate it. Since isothermal reactions take place at a constant temperature, they do not need expensive equipment to be carried out.
At the University of Idaho, we have been using one isothermal method called LAMP (Loop-mediated Amplification) for the detection of various potato pathogens. Recent assays developed include Pythium ultimum (Pythium leak), Phytophthora infestans (late blight), Liberibacter (zebra chip), Clavibacter michiganensis subsp. sepedonicus (ring rot), Alternaria solani (early blight), and Botrytis cinerea (gray mold). Several further assays are in development including one for Phytophthora erythroseptica (pink rot) and for Verticillium dahliae (wilt).
Work so far has shown LAMP is excellent for the confirmation of diagnosis from asymptomatic and symptomatic material. However, new research is attempting to use it in an automated sampler, which will detect the spores for several pathogens in the first instance. This device will not only trap the spores, but extract the DNA, test it using LAMP, and then report the results wirelessly to the lab or grower. This device could easily be adapted to detect A. solani, B. cinerea or even P. infestans in potato-growing areas. This ambitious project also hopes to develop markers to test for fungicide resistance and to incorporate this into the test. Therefore, not only will we be able to inform growers of when to spray, but also what to spray.
In addition to methods detecting specific pathogens, there have been huge advances in next-generation sequencing (NGS) technologies, with prices decreasing while quality and quantity of data increase. Although NGS is still some way from routine use in a frontline diagnostic lab, it offers an incredible amount of data for the cost and has proven useful in discovering new viruses. There are currently efforts to use such sequencing technologies to determine the vast array of organisms present in the soil, which will gain us a whole new understanding of soil health.
Over the next decade we will see the emergence of technologies other than molecular-based ones. The use of drones in agriculture has enormous potential. A drone with the appropriate instruments could allow, even enhance, early disease detection. There are already efforts under way to build up large banks of imaging data to facilitate this. Even more remote detection of plant diseases could be possible through the use of sophisticated imaging systems on satellites. However, key to the use of all these technologies is thorough method validation and determining the meaning of the diagnostic result, then linking it into specific actions. Growers, consultants and scientists will need to collaborate closely to produce such meaningful diagnostics.
This article appears in the November 2016 issue of Potato Grower.