, Volume 39, Issue 2, pp 165–174 | Cite as

Molecular, physiological and pathogenic variability of Pyrenochaeta lycopersici associated with corky rot disease of tomato plants in Turkey

  • Harun Bayraktar
  • Erçin Oksal


Isolates of Pyrenochaeta lycopersici, the causal agent of corky root rot on tomato plants, were assessed for physiological and genetic characteristics using conventional and molecular techniques. All isolates were able to produce necrosis on tomato roots and classified into temperature group according to the optimal growth temperatures. Specific-PCR assays and DNA sequence analysis of the ribosomal DNA (rDNA) internal transcribed spacer region confirmed the existence of both types (Type 1 and Type 2) of the pathogen among the isolates tested. All isolates were identified as Type 2 except for isolate Pl-4, which was classified as Type 1. Restriction fragment length polymorphism (RFLP) analysis with six enzymes resulted in three distinct banding patterns among the isolates depending on the length and restriction profiles of the rDNA intergenic spacer region. Inter-simple sequence-repeat analysis revealed a high level of genetic diversity among the isolates in agreement with the data of RFLP analysis. These results indicated that there were three different intraspecific groups among Turkish isolates of P. lycopersici. The presented study is the first attempting to characterize Turkish isolates of P. lycopersici. The results obtained will be useful in screening of tomato seedlings for resistance to P. lycopersici.


Corky root rot DNA sequencing Intraspecific variability ISSR PCR detection RFLP 


  1. Alves-Santos, F. M., Benito, E. P., Eslava, A. P., & Diaz-Minguez, J. M. (1999). Genetic diversity of Fusarium oxysporum strains from common bean fields in Spain. Applied and Environmental Microbiology, 65, 3335–3340.PubMedGoogle Scholar
  2. Appel, D. J., & Gordon, T. R. (1995). Intraspecific variation within populations of Fusarium oxysporum based on RFLP analysis of the intergenic spacer region of the rDNA. Experimental Mycology, 19, 120–128.PubMedCrossRefGoogle Scholar
  3. Balmas, V., Scherm, B., Ghignone, S., Mohamed-Salem, A. O., Cacciola, S. O., & Migheli, Q. (2005). Characterization of Phoma tracheiphila by RAPD-PCR, microsatellite-primed PCR and ITS rDNA sequencing and development of specific primers for in planta PCR detection. European Journal of Plant Pathology, 111, 235–247.CrossRefGoogle Scholar
  4. Bubici, G., Amenduni, M., Colella, C., D’Amico, M., & Cirulli, M. (2006). Efficacy of acibenzolar-S-methyl and two strobilurins, azoxystrobin and trifloxystrobin, for the control of corky root of tomato and verticillium wilt of eggplant. Crop Protection, 25, 814–820.CrossRefGoogle Scholar
  5. Campbell, R. N., Hall, D. H., & Schweers, V. H. (1982). Corky root of tomato in California caused by Pyrenochaeta lycopersici and control by soil fumigation. Plant Disease, 66, 657–661.CrossRefGoogle Scholar
  6. Clerjeau, M. (1976). Exigences thermiques de croissance et ďaggressivité de divers isolats de Pyrenochaeta lycopersici Schneider et Gerlach. Annales de Phytopathologie, 8, 9–15.Google Scholar
  7. Clerjeau, M., & Conus, M. (1973). Méthode rapide de contamination de jeune plantules de tomate par Pyrenochaeta lycopersici. Annales de Phytopathologie, 5, 143–150.Google Scholar
  8. Ekengren, S. K. (2008). Cutting the Gordian knot: taking a stab at corky root rot of tomato. Plant Biotechnology, 25, 265–269.CrossRefGoogle Scholar
  9. Faostat. (2010). Food and Agriculture Organization of the United Nations. Accessed 20 June 2010.
  10. Grove, G. G., & Campbell, R. N. (1987). Host range and survival in soil of Pyrenochaeta lycopersici. Plant Disease, 71, 806–809.CrossRefGoogle Scholar
  11. Hockey, A. G., & Jeves, T. M. (1984). Isolation and identification of Pyrenochaeta lycopersici, causal agent of tomato brown root rot. Transactions of the British Mycological Society, 82, 151–152.CrossRefGoogle Scholar
  12. Infantino, A., Aragona, M., Brunetti, A., Lahoz, E., Oliva, A., & Porta-Puglia, A. (2003). Molecular and physiological characterization of Italian isolates of Pyrenochaeta lycopersici. Mycological Research, 107, 707–716.PubMedCrossRefGoogle Scholar
  13. Infantino, A., & Pucci, N. (2005). A PCR-based assay for the detection and identification of Pyrenochaeta lycopersici. European Journal of Plant Pathology, 112, 337–347.CrossRefGoogle Scholar
  14. Jana, T., Sharma, T. R., & Singh, N. K. (2005). SSR-based detection of genetic variability in the charcoal root rot pathogen Macrophomina phaseolina. Mycological Research, 109, 81–86.PubMedCrossRefGoogle Scholar
  15. Longato, S., & Bonfante, P. (1997). Molecular identification of mycorrhizal fungi by direct amplification of microsatellite regions. Mycological Research, 101, 425–432.CrossRefGoogle Scholar
  16. Lu, G., Cannon, P. F., Reid, A., & Simmons, C. M. (2004). Diversity and molecular relationships of endophytic Colletotrichum isolates from the Iwokrama Forest Reserve, Guyana. Mycological Research, 108, 53–63.PubMedCrossRefGoogle Scholar
  17. McGrath, D. M., & Campbell, R. N. (1983). Improved methods for inducing sporulation of Pyrenochaeta lycopersici. Plant Disease, 67, 1245–1248.CrossRefGoogle Scholar
  18. Mishra, P. K., Fox, R. T. V., & Culham, A. (2002). Restriction analysis of PCR amplified nrDNA regions revealed intraspecific variation within populations of Fusarium culmorum. FEMS Microbiology Letters, 215, 291–296.PubMedCrossRefGoogle Scholar
  19. Ozan, S., & Maden, S. (2004). Root and crown rot and wilt of tomatoes caused by fungal diseases in Ankara province. Plant Protection Bulletin, 44(1–4), 105–120.Google Scholar
  20. Pecchia, S., Mercatelli, E., & Vannacci, G. (1998). PCR amplification and characterization of the intergenic spacer region of the ribosomal DNA in Pyrenophora graminea. FEMS Microbiology Letters, 166, 21–27.PubMedCrossRefGoogle Scholar
  21. Pohronezny, K. L., & Volin, R. B. (1991). Corky root rot. In J. B. Jones, J. P. Jones, R. E. Stall, & T. A. Zitter (Eds.), Compendium of tomato diseases (pp. 12–13). Minneapolis, MN, USA: APS Press.Google Scholar
  22. Reader, U., & Broda, P. (1985). Rapid preparation of DNA from filamentous fungi. Letters in Applied Microbiology, 1, 17–20.CrossRefGoogle Scholar
  23. Rohlf, F. I. (1998). NTSYS-pc. Numerical taxonomy and multivariate analysis system, Version 2.0. New York, NY: Applied Biostatistics.Google Scholar
  24. Sambrook, J., Fritsch, E. F., & Maniatis, T. (1989). Molecular cloning: A laboratory manual (2nd ed.). New York, NY: Cold Spring Harbor Laboratory Press.Google Scholar
  25. Sneath, P. H. A., & Sokal, R. R. (1973). Numerical taxonomy: the principles and practice of numerical classification. San Francisco, CA, USA: Freeman.Google Scholar
  26. Sugiura, T., Horinouchi, H., Taguchi, Y., & Hyahamachi, M. (2003). Two types of Pyrenochaeta lycopersici, causal pathogen of corky root of tomato. Proceedings of the 8th International Congress of Plant Pathology (Christchurch, New Zealand).Google Scholar
  27. White, T. J., Bruns, T. D., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR protocols: a guide to methods and applications (pp. 315–322). San Diego, CA, USA: Academic.Google Scholar
  28. White, J. G., & Scott, A. C. (1973). Formation and ultrastructure of microsclerotia of Pyrenochaeta lycopersici. The Annals of Applied Biology, 73, 163–166.CrossRefGoogle Scholar
  29. Yıldız, M., Yıldız, F., & Delen, N. (1991). Türkiye’de sera domateslerinde kök hastalıkları etmenlerinin saptanmasına yönelik çalışmalar. VI. Türkiye Fitopatoloji Kongresi (İzmir, Türkiye), (pp. 183–186).Google Scholar
  30. Yücel, S. (1994). Survey studies on fungal diseases of covered vegetable areas in Mediterranean region. Plant Protection Bulletin, 34(1–2), 23–34.Google Scholar

Copyright information

© Springer Science & Business Media BV 2011

Authors and Affiliations

  1. 1.Department of Plant Protection, Faculty of AgricultureUniversity of AnkaraAnkaraTurkey
  2. 2.Plant Protection Central Research InstituteAnkaraTurkey

Personalised recommendations