Identification and characterization of the fungal pathogens inhabiting the root zone of sweet cherry (Prunus avium L.) in the Okanagan Valley of British Columbia.

Differences in tree vigour within and among sweet cherry (Prunus avium L.) orchards, is a continuing problem for the BC tree fruit industry and is believed to be associated with maladies such as cankers, dieback, root rots and replant disease. However, a general lack of knowledge exists regarding the pathogens associated with these diseases of cherry. Therefore the objective of this study was to identify fungal species in the rhizosphere that are associated with root rots and replant disease of cherry. A survey of both commercial and research cherry orchards was conducted to identify and assess pathogenicity of the predominant fungi colonizing roots or inhabiting the rhizosphere. Fungi were isolated from necrotic and discoloured cherry root tissues, orchard soils and/or wooden toothpicks inserted into soils as bait. Fungal species recovered from the sampling were identified using morphological characteristics and DNA sequencing of the ITS, β-tubulin and EF1 genes. Pathogenicity testing for some of the most prominent fungal species identified (Fusarium, Ilyonectria and Rhizoctonia spp.) were conducted in the greenhouse by inoculating Mazzard rootstock. All isolates tested, produced significant regions of vascular discolouration extending from the inoculation point. Ilyonectria macrodidima (Halleen, Schroers & Crous) P. Chaverri & C. Salgado and Fusarium oxysporum Schlecht. emend. Snyder & Hansen produced the largest areas of necrosis and were re-isolated at rates of 57% and 66%, respectively. Additionally, oligonucleotide probes for the species found in our survey were designed or modified using available sequences and assembled in a DNA-macroarray as part of the development of a diagnostic assay.