Abstract
The isolation of Pyrenochaeta lycopersici, causal agent of corky root of tomato, is difficult because of its slow growth and poor sporulation. Identification is complicated due the existence of two morphologically similar forms, Types 1 and 2, that differ in several physiological and molecular features. For the rapid and unambiguous identification of isolates, two oligonucleotide primer pairs were designed using ITS region sequences. Specific PCR products of 147 and 209 bp were obtained for isolates of Type 1 and Type 2, respectively. Specificity of both primer pairs was verified using several fungal and bacterial species. As little as 0.7 pg of target DNA could be detected with the protocol. A nested PCR procedure was necessary for the detection of the fungus in plant tissue. This technique will be of use in epidemiological studies and in the implementation of control strategies.
Similar content being viewed by others
References
SF Altschul TL Madden AA Schaffer J Zhang Z Zhang W Miller DJ Lipman (1997) ArticleTitleGapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Research 25 3389–3402 Occurrence Handle10.1093/nar/25.17.3389 Occurrence Handle9254694
PD Bridge DK Arora (1998) Interpretation of PCR methods for species definition PD Bridge DK Arora CA Reddy RP Elander (Eds) Application of PCR in Mycology CAB International Wallingford UK 63–80
G Cascone A D’Emilio G Polizzi R Grillo (2000) ArticleTitleEffectiveness of greenhouse soil solarization with different plastic mulches in controlling corky root and root-knot on tomato plants Acta Horticulturae 532 145–150
JL Cenis (1992) ArticleTitleRapid extraction of fungal DNA for PCR amplification Nucleic Acids Research 20 2380 Occurrence Handle1594460
W Chen LE Gray JE Kurle CR Grau (1999) ArticleTitleSpecific detection of Phialophora gregata and Plectosporium tabacinum in infected soybean plants using polymerase chain reaction Molecular Ecology 8 871–877 Occurrence Handle10.1046/j.1365-294X.1999.00645.x
DW Cullen AK Lees IK Toth JM Duncan (2002) ArticleTitleDetection of Colletotrichum coccodes from soil and potato tubers by conventional and quantitative real-time PCR Plant Pathology 51 281–292 Occurrence Handle10.1046/j.1365-3059.2002.00690.x
R Faggian SR Bulman AC Lawrie IJ Porter (1999) ArticleTitleSpecific Polymerase Chain Reaction primers for the detection of Plasmodiophora brassicae in soil and water Phytopathology 89 392–397
S Ghignone G Tamietti M Girlanda (2003) ArticleTitleDevelopment of specific PCR primers for identification and detection of Rhizopycnis vagum European Journal of Plant Pathology 109 861–870 Occurrence Handle10.1023/A:1026171307719
GG Grove RN Campbell (1987) ArticleTitleHost range and survival in soil of Pyrenochaeta lycopersici Plant Disease 71 806–809
D Higgins J Thompson T Gibson JD Thompson DG Higgins TJ Gibson (1994) ArticleTitleCLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Research 22 4673–4680 Occurrence Handle7984417
AG Hockey TM Jeves (1984) ArticleTitleIsolation and identification of Pyrenochaeta lycopersici, causal agent of tomato brown root rot Transactions of the British Mycological Society 82 151–152
A Infantino G Di Giambattista A Porta-Puglia (2000) ArticleTitleFirst report of Pyrenochaeta lycopersici on melon in Italy Petria 10 195–198
A Infantino M Aragona A Brunetti E Lahoz A Oliva A Porta-Puglia (2003) ArticleTitleMolecular and physiological characterization of Italian isolates of Pyrenochaeta lycopersici Mycological Research 107 707–716 Occurrence Handle10.1017/S0953756203007962 Occurrence Handle12951797
MA Innis DH Gelfand (1990) Optimization of PCRs MA Innis DH Gelfand JJ Sninsky TJ. White (Eds) PCR Protocols. A Guide to Methods and Applications Academic Press San Diego, USA 3–12
A Johansson HC Turner GJ McKay AE Brown (1998) ArticleTitleA PCR-based method to distinguish fungi of the rice sheath-blight complex, Rhizoctonia solani, R. oryzae and R. oryzae-sativae FEMS Microbiology Letters 162 289–294 Occurrence Handle10.1016/S0378-1097(98)00136-0 Occurrence Handle9627963
P Konstantinova PJM Bonants MPE Gent-Pelzer Particlevan P Zouwen Particlevan der R Bulk Particlevan den (2002) ArticleTitleDevelopment of specific primers for detection and identification of Alternaria spp. in carrot material by PCR and comparison with blotter and plating assays Mycological Research 106 23–33 Occurrence Handle10.1017/S0953756201005160
S Kumar K Tamura M Nei (2004) ArticleTitleMEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment Briefings in Bioinformatics 5 150–163 Occurrence Handle15260895
BR Lovic RD Martin ME Miller (1995) ArticleTitleSequence analysis of the ITS region of rDNA in Monosporascus spp. to evaluate its potential for PCR-mediated detection Phytopathology 85 655–661
RR Martin D James CA Lévesque (2000) ArticleTitleImpacts of molecular diagnostic technologies on plant disease management Annual Review of Phytopathology 38 207–239 Occurrence Handle10.1146/annurev.phyto.38.1.207 Occurrence Handle11701842
MG Milgroom (1997) ArticleTitleGenetic variation and the application of genetic markers for studying plant pathogen populations Journal of Plant Pathology 78 1–13
KL Pohronezny RB Volin (1991) Corky root rot JB Jones JP Jones RE Stall TA Zitter (Eds) Compendium of Tomato Diseases APS Press St. Paul, Minnesota, USA 12–13
A Porta-Puglia N Pucci G Di Giambattista A Infantino (2001) ArticleTitleFirst report of Rhizopycnis vagum associated with tomato roots in Italy Plant Disease 85 1210
E Punithalingam P Holiday (1973) Pyrenochaeta lycopersici. CMI Description of Pathogenic Fungi and Bacteria No. 398. Commonwealth Agricultural Bureau Kew, UK.
S Rozen HJ Skaletsky (2000) Primer3 on the WWW for general users and for biologist programmers S Krawetz S Misener (Eds) Bioinformatics Methods and Protocols: Methods in Molecular Biology Humana Press Totowa, NJ 365–386
O Salazar MCA Julian V Rubio (2000) ArticleTitlePrimers based on specific rDNA-ITS sequences for PCR detection of Rhizoctonia solani, R. solani AG2 subgroups and ecological types, and binucleate Rhizoctonia Mycological Research 104 281–285 Occurrence Handle10.1017/S0953756299001355
R Schneider W Gerlach (1966) ArticleTitlePyrenochaeta lycopersici nov. spec., der Erreger der Korkwurzelkrankheit der Tomate Phytopathologische Zeitschrift 56 117–122
Sugiura T, Horinouchi H, Taguchi Y and 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 2–7 February 2003, p. 346
G Tamietti D Valentino (1990) ArticleTitleA semi-selective medium for the isolation of Pyrenochaeta lycoperici from soil Phytopatologia Mediterranea 29 90–94
TJ White T Bruns S Lee J Taylor (1990) Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics MA Innis DH Gelfand JJ Sninsky TJ White (Eds) PCR Protocols, a Guide to Methods and Applications Academic Press San Diego, USA 315–322
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Infantino, A., Pucci, N. A PCR-based assay for the detection and identification of Pyrenochaeta lycopersici. Eur J Plant Pathol 112, 337–347 (2005). https://doi.org/10.1007/s10658-005-6605-7
Accepted:
Issue Date:
DOI: https://doi.org/10.1007/s10658-005-6605-7