Improving decision making for the management of potato diseases using real-time predictive diagnostics
The aim of the project was to develop diagnostic technology for disease management and decision making purposes. It focussed on backleg-causing bacteria (Pectobacterium species) on seed tubers and Rhizoctonia, black dot, powdery scab and PMTV in field soils. It combined work on real-time PCR assays with the development of seed and soil sampling strategies.
Techniques for the extraction of pathogen DNA from soil were developed and used in conjunction with the assays. Information on inoculum levels on seed and daughter tubers, as well as in soil, was collected. Disease in daughter crops was also assessed and all the information was used to look for relationships between seed/soil inoculum and disease, with the aim of developing risk thresholds.
Seed inoculum can cause disease, but at relatively low levels compared to soil inoculum. The level of soil inoculum can be used to predict the risk of progeny disease. Disease risk categories have been set, based on the amount of soil inoculum detected (as determined with real-time PCR). These categories of disease risk can be used to inform growers of the agronomic factors they need to consider to reduce the incidence and severity of black dot on progeny tubers.
Both seed and soil-borne inoculum can cause disease. However, it is not the level of inoculum that is important in determining the extent of disease but rather environmental conditions. If any seed or soil inoculum is detected then there is a risk of disease given suitable conditions for its development. In wetter summers when powdery scab is more prevalent compared to drier years, higher levels of soil inoculum do increase the risk of disease occurring.
Despite a great deal of effort to make the sampling protocols as robust and reliable as possible, they were not adequate in providing a consistent estimate of soil-borne inoculum for R. solani. The occurrence of disease when mini-tubers were grown in soil where no inoculum was detected highlights the problem. A new strategy for soil sampling needs to be developed which reflects the patchy and perhaps fluctuating occurrence of R. solani mycelium in fields.
There was a good correlation between levels of soil-borne PMTV inoculum, as measured by PCR analysis on tomato bait plant roots, and detection of PMTV in progeny tubers. This correlation was improved by considering the results from both soil- and seed PCR tests. However, there was poor correlation between the detection of seed-borne PMTV and detection of virus in progeny tubers.
Real-time PCR analysis allowed high throughput detection, quantification and identification of Pectobacterium and Dickeya populations on potato tuber stocks. Although the incidence of infection (% stocks infected) was high, the average inoculum load of Pectobacterium atrosepticum (previously known as Erwinia carotovora subsp. atroseptica) on seed from each stock was generally low in all 3 years studied. Blackleg incidence was correspondingly low in 2005 and 2006 but was higher in 2007 in response to wetter spring and early summer weather.
Further data from a wider variety of seed stocks with a higher range of inoculum levels is needed before the accuracy of blackleg prediction under varying climatic conditions can be assessed. Some correlation was observed between P. atrosepticum levels on seed and on progeny tubers in two out of three years. No correlation was found in 2007, when bacterial numbers probably increased rapidly under wetter conditions irrespective of the initial inoculum level on the seed.
Downloads20086 Diagnostics Final Report R253_0
About this project
To provide information which would allow DNA-based diagnostic tests to be used for disease risk assessment.