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Diagnostics of phytopathogen fungi Septoria tritici and Stagonospora nodorum by fluorescent amplification-based specific hybridization (FLASH) PCR


A PCR system in the fluorescent amplification-based specific hybridization (FLASH) format was developed for the detection and identification of two important wheat pathogenic fungi Septoria tritici (teleomorph of Mycosphaerella graminicola) and Stagonospora nodorum (teleomorph of Phaeosphaeria nodorum), which cause spots on leaves and glumes, respectively. The pathogen detection system is based on the amplification of a genome fragment in the internal transcribed spacer 1 (ITS1) region and a site encoding the 5.8S ribosomal RNA. The forward primers to ITS1 and a universal reverse primer and a beacon type probe to the 5.8S ribosomal RNA region were chosen to provide the detection of the products in the FLASH format. This system was tested on different isolates of the pathogens, and on infected soil, leaf, and seed samples.

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fluorescent amplification-based specific hybridization


polymerase chain reaction


internal control


internal transcribed spacer


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Correspondence to S. K. Zavriev.

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Original Russian Text © S.L. Abramova, D.Yu. Ryazantsev, T.M. Voinova, S.K. Zavriev, 2008, published in Bioorganicheskaya Khimiya, 2008, Vol. 34, No. 1, pp. 107–113.

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Abramova, S.L., Ryazantsev, D.Y., Voinova, T.M. et al. Diagnostics of phytopathogen fungi Septoria tritici and Stagonospora nodorum by fluorescent amplification-based specific hybridization (FLASH) PCR. Russ J Bioorg Chem 34, 97–102 (2008).

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Key words

  • diagnostics
  • PCR
  • phytopathogen
  • septoriosis
  • Septoria tritici
  • Stagonospora nodorum
  • wheat