Diagnostic assays: quantitative tools for investigating the epidemiology of skin blemish and storage rot diseases and making disease risk assessments

Abstract

The requirement of the potato industry for high quality healthy tubers is well established and blemish diseases are therefore of particular concern. In recent years, quantitative molecular diagnostic assays based on real-time PCR have been developed for many pests and pathogens of potato. These diagnostic assays are now being used as tools to study outstanding questions in the epidemiology of potato diseases including blemish diseases such as black dot, powdery scab and black scurf and storage rots caused by Fusarium spp. Examples of various investigations designed to examine the relative contribution of seed- and soil-borne inoculum in causing disease on progeny tubers and the effect of environmental factors on the incidence and severity of disease are described. To enable real-time PCR diagnostic assays to be used not only for research purposes, but also more directly in the management of potato diseases, diagnostic results must be associated with factors affecting the risk of disease. Therefore, a comprehensive system of soil and seed tuber sampling, testing and disease monitoring has been initiated in a project funded by the British Potato Council to validate these assays and enable results to be translated into disease risk. Some of the techniques employed in this validation, and results of experiments focusing on black dot (Colletotrichum coccodes), are presented. The refinement of a direct soil DNA extraction method and the detection and quantification of target DNA in both seed and progeny tubers are described. Consideration is given to the development of appropriate diagnostic assays, their use in conjunction with relevant and robust sampling techniques and a direct soil DNA extraction method, and the interpretation of results to inform disease risk assessment and control strategies through collaboration with the potato industry.