Real-time assays for detection of Phytophthora spp. and identification of an avr3a gene variant
A study was carried out for identification and detection of Phytophthora spp. from soil and plant samples, collected from Solanaceous crops in Egypt and Italy. The samples were screened with specific and universal primers of Phytophthora 18S, ITS1–ITS2 and 28S regions, followed by PCR product sequencing. The Phytophthora spp. detected were P. infestans (Egypt) and P. parasitica (Italy). A molecular beacon probe was also developed based on the avr3a gene of P. infestans to detect a variant associated with virulence traits. The probe was suitable for avr3a allele identification from P. infestans and also from P. parasitica PCR products.
Keywordsavr3a ITS Molecular beacon Phytophthora infestans Phytophthora parasitica Virulence
Research developed as part of STT higher degree requirements. Study partially funded by the EU Commission, Joint Master Degree Tempus Project No. 543865. The authors thank prof. Sanaa Haroon (Fayum University, Egypt) for travel assistance and coordination, and Dr Michelina Ruocco, IPSP CNR, Portici, for suggestions and isolate CBS 120920.
Compliance with ethical standards
Conflict of interest
The authors declare no conflict of interest.
Human and animal rights
Research does not involve human participants and/or animals.
All authors gave informed consent to publish the manuscript.
- Ausubel FM, Brent R, Kingston RE, Moore DD, Seidmann JG, Struhl K (1990) Current protocols in molecular biology, vol 3. Wiley, New York, p A.3–D.1Google Scholar
- Clément JAJ, Baldwin TK, Magalon H, Glais I, Gracianne C, Andrivon D, Jacquot E (2013) Specific detection and quantification of virulent/avirulent Phytophthora infestans isolates using a real-time PCR assay that targets polymorphisms of the Avr3a gene. Lett Appl Microb 56:322–332CrossRefGoogle Scholar
- Drenth A, Guest DI (2004) Principles of Phytophthora disease management. In: Drenth A, Guest DI (eds) Diversity and management of Phytophthora in Southeast Asia, ACIAR Monograph, vol 114. Australian Centre for International Agricultural Research, Canberra, Australia, pp 154–160Google Scholar
- El-Ganainy S, Ahmed Y, Soliman M, Ismail A, Tohamy A, Randall E, Cooke D (2016) A shift in the population of Phytophthora infestans on Egyptian potato crops. Phytopathology 106:140Google Scholar
- El-Korany AE (2008) Occurrence of oospores of Phytophthora infestans in the field and under controlled conditions. J Agric Environ Sci Alex Univ 7:31–52Google Scholar
- Ersek T, Schoelz JE, English JT (1994) PCR amplification of species-specific DNA sequences can distinguish among Phytophthora species. Appl Environ Microb 60:2616–2621Google Scholar
- Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41:95e98Google Scholar