Monitoring important soil-borne plant pathogens in Swedish crop production using real-time PCR

Sammanfattning: The global demand for food will increase considerably in the nearest future and among the major constraints to agricultural productivity are biotic stresses caused by microorganisms. In this thesis, the causal agents of four of the most important soil-borne diseases threatening the Swedish production of oilseed rape, sugar beets and red clover were selected as targets for developing diagnostic assays using real-time PCR. The disease risk assessment of clubroot in oilseed rape was improved by developing a real-time PCR assay for quantification of the causal pathogen Plasmodiophora brassicae directly in soil samples. Broad disease risk categories including a threshold level for growing resistant cultivars were established. A real-time PCR assay for quantification of Aphanomyces cochlioides, the oomycete causing root rot in sugar beets, was also developed in the present study. The potential use of this assay as a tool in disease risk assessment was demonstrated for fields with high risk of infection. Real-time PCR was used to monitor the plant- and airborne inoculum of Sclerotinia sclerotiorum, the causal fungus of Sclerotinia stem rot, in spring oilseed rape. We found that determining the presence of S. sclerotiorum on petals was not useful for stem rot risk assessment since (i) the inoculum incidence on petals varied during flowering, (ii) there was no clear relationship between petal infection and stem rot incidence and (iii) spore release and flowering were not synchronized at one of the field experimental sites. Real-time PCR detection of the incidence of S. sclerotiorum DNA on leaves revealing the field-borne inoculum and quantification of the airborne inoculum are likely more reliable tools for predicting the potential risk of disease. The pathogen complex causing red clover root rot was monitored over three years in two field experiments. Fusarium avenaceum, Phoma spp. and Cylindrocarpon destructans were detected in red clover roots early in the seeding year using real-time PCR and the levels of pathogen DNA generally increased during the following years. Significant linear relationships were found between the amount of pathogen DNA and disease severity index.