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Title: PCR based identification of Pythium spp. causing cavity spot in carrots and sensitive detection in soil samples

item Wanner, Leslie

Submitted to: Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/22/2007
Publication Date: 3/23/2008
Citation: Klemsdal, S., Herrero, M., Wanner, L.A., Lund, G., Hermansen, A. 2007. Pcr based identification of pythium spp. causing cavity spot in carrots and sensitive detection in soil samples . Plant Pathology. 57: 877-886

Interpretive Summary: Carrots are subject to losses from disease during cultivation, and also during months of storage at low temperature before they are marketed, resulting in large and variable economic loss to producers. Methods to predict the incidence of disease in the field and in stored crops are needed to limit these losses. Cavity spot is a major disease of carrot, causing rot both in the field and in the harvested crop during long-term cold storage. The disease is caused by a poorly-characterized complex of soil pathogenic organisms. Molecular tools have been developed to specifically and sensitively identify these soil pathogens on carrot roots after harvest. The tools also can be used in soil samples, both before planting and at the end of the season prior to long-term storage of the harvested crop. These tools enable researchers to predict which lots of stored carrots are subject to losses due to cavity spot during cold storage, and to assess what field locations are at highest risk for the disease.

Technical Abstract: Cavity spot is caused by several Pythium species and is one of the most economically important diseases of carrot (Daucus carota L.). Diagnosis of the pathogens in soil and in carrot tissue has been complicated. On the bases of ITS sequences PCR primers were designed for the identification of the five Pythium species found to be most important for the development of carrot cavity spot in Norway, P. intermedium, P. sulcatum, P. sylvaticum, P. violae and P. “vipa”. The P. “vipa” isolates had a unique ITS sequence and differed morphologically from all other Pythium species and probably represent a new species. The PCR primers were species-specific with no cross-reaction to other Pythium species or to other fungal strains from carrot. The detection limits varied for the different primer pairs. The two most sensitive assays allowed detection of as little as 5 fg DNA. All five Pythium species could be detected in lesions from diseased carrots. Weak positive signals were obtained from some carrot samples without symptoms. PCR assays allowed detection of pathogens in soil. In samples of soil known to produce cavity spots on cropped carrots, strong signals were obtained. In several soil samples more than one of the five Pythium species could be detected. The utilization of this diagnostic PCR assay in analysis of field soil and carrot tissue could be exploited to reduce the incidence of this serious carrot disease.