Finding the Culprit

Published online: Mar 12, 2021 Articles James Woodhall, University of Idaho
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This article appears in the March 2021 issue of Potato Grower.

Soil-borne diseases make up more than their fair share of potato samples we receive for diagnosis in the lab here in Parma, Idaho. There are probably several good reasons for this, the foremost being that the diseases are difficult to manage, detect and diagnose. Diagnosing soil-borne diseases always generates a few surprises each year. Recently, we received some samples infected with potato mop-top virus (PMTV) where only surface blemishes were present. Usually we see internal symptoms with PMTV and tobacco rattle virus (TRV). Thankfully, molecular diagnostics were available to confirm the diagnosis in this instance. 

All too often when we see symptoms of the soil-borne diseases, it is too late to do anything about it. Therefore, any strategy for managing soil-borne diseases needs to be lon-term over the whole rotation, and numerous tactics need to be employed to ensure success. Such tactics for managing soil-borne diseases include suitable rotations, fumigation, in-furrow fungicide treatments, tillage, varietal resistance and not introducing inoculum on equipment or with seed. Unfortunately, not all of these tactics are available for all diseases; for instance, in-furrow fungicides are not available for viruses like PMTV and TRV. However, you need to build a variety of tactics into your disease management plans. Even if on its own a tactic appears to only have a minimal effect, an accumulation of minor gains will have an impact, particularly over the long term.

Soil testing is one way to monitor the success or failure of managing these diseases. I do not recommend that soil testing is routine and completed on every field all the time, but I do recommend the technology is used if there is a particular issue of concern. Presently, a variety of labs can test for the causal agents of early die (Verticillium), powdery scab (Spongospora), black dot (Colletotrichum), black scurf (Rhizoctonia) and common scab (Streptomcyces) using direct soil DNA extraction and TaqMan PCR. More recently, labs have started developing soil RNA extraction methods to enable soils to be directly tested for PMTV and TRV. Prior to the availability of the soil RNA extraction methods, labs could bait for PMTV and TRV by planting tomatoes and/or tobacco in the test soil and after two to three weeks and testing the roots for the presence of the virus. While an effective method, it cannot provide a rapid result and quantification is not as clear.  

Despite such advances in detection technology, particularly in the lab, there are still limitations and knowledge gaps in deploying these molecular tests for TRV and PMTV. These include lack of data on the relationship between inoculum detected and disease. This is often complicated by the fact that diseases can also be seed-borne, and they often have a highly clustered distribution of a pathogen within a typical potato field. Also, there is the cost of the test itself and sampling. With such a clustered distribution, numerous individual sampling points are often required for a representative sample, although these can be combined to form an aggregate sample, typically over four to 10 acres. Large fields require possibly hundreds of induvial sampling points and several samples sent into the lab. 

Another drawback of the method is a wide variety of molecular methods employed in labs. Each lab may have its own extraction methodology with different chemistry and sample size processed. Some of the published methods only extract RNA from 1 gram of soil, although at Parma we extract RNA from 300 grams of soil with our new method of testing soil for PMTV and TRV. Therefore, results can vary a lot between different labs, although each lab will produce a consistent result. It is therefore important to build up a relationship with your diagnostic lab, especially if you are conducting long-term monitoring projects.


James Woodhall is an assistant professor and extension plant pathologist based at the University of Idaho’s Parma Research & Extension Center. He can be contacted at