Rapid Colorimetric Detection of the Fungal Phytopathogen Synchytrium endobioticum Using Cyanine dye-Indicated PNA Hybridization

Abstract

Synchytrium endobioticum is a parasitic fungus that is considered to be the most important potato pathogen worldwide. Spread of the fungus can result in catastrophic impacts to agriculture and economy, as it is very infective and can survive in spore form for over 70 years. To date, the gold standard for S. endobioticum identification relies on visual classification by highly trained personnel. This paper presents the colorimetric detection of S. endobioticum from potato wart samples using a peptide nucleic acid (PNA) probe and a cyanine dye. A segment of the 18S ribosomal RNA gene was sequenced for several S. endobioticum pathotypes and used to design a species-specific PNA probe. The probe was used in a rapid colorimetric hybridization assay that detected RNA from infected wart tissue down to 10−17 mol within 15 min. This technique demonstrates potential for rapid identification of potato wart in non-laboratory settings with minimally trained staff.