Real-time polymerase chain reaction: Applications to studies on soilborne pathogens

Canadian Journal of Plant Pathology

Volumn 27, Issue 3, 2005, Pages 300-313

  Okubara, Patricia A ^a   Schroeder, Kurtis L ^a   Paulitz, Timothy C ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

Author keywords

Molecular beacon; Phytophthora; Pythium; Quantitative polymerase chain reaction; Real time chemistry; Scorpion

Indexed keywords

BACTERIA (MICROORGANISMS); PHYTOPHTHORA; PYTHIUM; SCORPIONES;

EID: 29644443436     PISSN: 07060661     EISSN: 17152992     Source Type: Journal    
DOI: 10.1080/07060660509507229     Document Type: Article

References (83)

1. Ali-Shtayeh, M. S., Lim-Ho, C. L., and Dick, M. W., 1986. An improved method and medium for quantitative estimates of populations of Pythium species from soil. Trans. Br. Mycol. Soc., 86:39–47.
2. Bach, H.-J., Jessen, I., Schloter, M., and Munch, J. C., 2003. A TaqMan-PCR protocol for quantification and differentiation of the phytopathogenic Clavibacter michiganensis subspecies. J. Microbiol. Methods, 52:85–91.
3. Bell, K. S., Roberts, J., Verrall, S., Cullen, D. W., Williams, N. A., Harrison, J. G., Toth, I. K., Cooke, D. E. L., Duncan, J. M., and Claxton, J. R., 1999. Detection and quantification of Spongo spora subterranea f. sp. subterranea in soils and on tubers using specific PCR primers. Eur. J. Plant Pathol., 105:905–915.
4. Böhm, J., Hahn, A., Schubert, R., Bahnweg, G., Adler, N., Nechwatal, J., Oehlmann, R., and Osswald, W., 1999. Real-time quantitative PCR:DNA determination in isolated spores of the mycorrhizal fungus Glomus mosseae and monitoring of Phytophthora infestans and Phytophthora citricola in their respective host plants. J. Phytopathol. (Berlin), 147:409–416.
5. Bonants, P. J. M., van Gent-Pelzer, M. P. E., Hooftman, R., Cooke, D. E. L., Guy, D. C., and Duncan, J. M., 2004. A combination of baiting and different PCR formats, including measurement of real-time quantitative fluorescence, for the detection of Phytophthora fragariae in strawberry plants. Eur. J. Plant Pathol., 110:689–702.
6. Bustin, S. A., ed. 2004. A-Z of quantitative PCR, IUL biotechnology series, 5, La Jolla, Calif:International University Line.
7. Bustin, S. A., and Nolan, T., 2004. Pitfalls of quantitative real-time reverse-transcription polymerase chain reaction. J. Biomol. Tech., 15:155–166.
8. Campbell, C. L., and Madden, L. V., 1990. Introduction to plant disease epidemiology, New York:John Wiley & Sons.
9. Conway, K. E., 1985. Selective medium for isolation of Pythium spp. from soil. Plant Dis., 69:393–395.
10. Cooke, D. E. L., and Duncan, J. M., 1997. Phylogenetic analysis of Phytophthora species based on ITS1 and ITS2 sequences of the ribosomal RNA gene repeat. Mycol. Res., 101:667–677.
11. Cullen, D. W., and Hirsch, P. R., 1998. Simple and rapid method for direct extraction of microbial DNA from soil for PCR. Soil Biol. Biochem., 30:983–993.
12. Cullen, D. W., Lees, A. K., Toth, I. K., and Duncan, J. M., 2001. Conventional PCR and real-time quantitative PCR detection of Helminthosporium solani in soil and on potato tubers. Eur. J. Plant Pathol., 107:387–398.
13. Cullen, D. W., Lees, A. K., Toth, I. K., and Duncan, J. M., 2002. Detection of Colletotrichum coccodes from soil and potato tubers by conventional and quantitative real-time PCR. Plant Pathol. (Oxford), 51:281–292.
14. Dheda, K., Huggett, J. F., Bustin, S. A., Johnson, M. A., Rook, G., and Zumla, A., 2004. Validation of housekeeping genes for normalizing RNA expression in real-time PCR. BioTechniques, 37:112–119.
15. Didenko, V. V., 2001. DNA probes using fluorescence resonance energy transfer (FRET):designs and applications. BioTechniques, 31:1106–1121.
16. Filion, M., St-Arnaud, M., and Jabaji-Hare, S. H., 2003. Direct quantification of fungal DNA from soil substrate using real-time PCR. J. Microbiol. Methods, 53:67–76.
17. Frederick, R. D., Snyder, K. E., Tooley, P. W., Berthier-Schaad, Y., Peterson, G. L., Bonde, M. R., Schaad, N. W., and Knorr, D. A., 2000. Identification and differentiation of Tilletia indica and T. walkeri using polymerase chain reaction. Phytopathology, 90:951–960.
18. Freeman, W. M., Walker, S. J., and Vrana, K. E., 1999. Quantitative RT-PCR:pitfalls and potential. BioTechniques, 26:112–125.
19. Gao, X., Jackson, T. A., Lambert, K. N., and Li, S., 2004. Detection and quantification of Fusarium solani f. sp. glycines in soybean roots with real-time quantitative polymerase chain reaction. Plant Dis, 88:1372–1380.
20. Gilliland, G., Perrin, S., Blanchard, K., and Bunn, H. F., 1990. Analysis of cytokine mRNA and DNA:detection and quantitation by competitive polymerase chain reaction. Proc. Natl. Acad. Sci. USA, 87:2725–2729.
21. Ginzinger, D. G., 2002. Gene quantification using real-time quantitative PCR:an emerging technology hits the mainstream. Exp. Hematol, 30:503–512.
22. Giulietti, A., Overbergh, L., Valckx, D., Decallonne, B., Bouillon, R., and Mathieu, C., 2001. An overview of real-time quantitative PCR:applications to quantify cytokine gene expression. Methods, 25:386–401.
23. Guillemette, T., Iacomi-Vasilescu, B., and Simoneau, P., 2004. Conventional and real-time PCR-based assay for detecting pathogenic Alternaria brassicae in cruciferous seed. Plant Dis., 88:490–496.
24. Hayden, K. J., Rizzo, D., Tse, J., and Garbelotto, M., 2004. Detection and quantification of Phytophthora ramorum from California forests using a real-time polymerase chain reaction assay. Phytopathology, 94:1075–1083.
25. Heid, C. A., Stevens, J., Livak, K. J., and Williams, P. M., 1996. Real time quantitative PCR. Genome Res., 6:986–994.
26. Ippolito, A., Schena, L., Nigro, F., Ligorio, V. S., and Yaseen, T., 2004. Real-time detection of Phytophthora nicotianae and P. citrophthora in citrus roots and soil. Eur. J. Plant Pathol., 110:833–843.
27. Klein, D., 2002. Quantification using real-time PCR technology; applications and limitations. Trends Mol. Med, 8:257–260.
28. Kranz, J., 1988. “ Measuring plant disease ”. In Experimental techniques in plant disease epidemiology, Edited by:Kranz, J., and Rotem, J., 35–50. Berlin:Springer.
29. Kutyavin, I. V., Afonina, I. A., Mills, A., Gorn, V. V., Lukhtanov, E. A., Belousov, E. S., Singer, M. J., Walburger, D. K., Lokhov, S. G., Gall, A. A., Dempcy, R., Reed, M. W., Meyer, R. B., and Hedgpeth, J., 2000. 3'-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures. Nucleic Acids Res., 28:655–661.
30. Lees, A. K., Cullen, D. W., Sullivan, L., and Nicolson, M. J., 2002. Development of conventional and quantitative real-time PCR assays for the detection and identification of Rhizoctonia solani AG-3 in potato and soil. Plant Pathol, 51:293–302.
31. Lévesque, C. A., and de Cock, A. W. A. M., 2004. Molecular phylogeny and taxonomy of the genus Pythium. Mycol. Res., 108:1363–1383.
32. Lévesque, C. A., Harlton, C. E., and de Cock, A. W. A. M., 1998. Identification of some oomycetes by reverse dot blot hybridization. Phytopathology, 88:213–222.
33. -DDCT method. Methods, 25:402–408.
34. Lloyd-Jones, G., Laurie, A. D., and Tizzard, A. C., 2005. Quantification of the Pseudomonas population in New Zealand soils by fluorogenic PCR assay and culturing techniques. J. Microbiol. Methods, 60:217–224.
35. Mahuku, G. S., and Platt, H. W., 2002. Quantifying Verticillium dahliae in soils collected from potato fields using a competitive PCR assay. Am. J. Potato Res., 79:107–117.
36. Martin, F. N., Tooley, P. W., and Blomquist, C., 2004. Molecular detection of Phytophthora ramorum, the causal agent of sudden oak death in California, and two additional species commonly recovered from diseased plant material. Phytopathology, 94:621–631.
37. McCartney, H. A., Foster, S. J., Fraaije, B. A., and Ward, E., 2003. Molecular diagnostics for fungal plant pathogens. Pest Manag. Sci., 59:129–142.
38. McDonald, B. A., 1997. The population genetics of fungi:tools and techniques. Phytopathology, 87:448–453.
39. McMaugh, S. J., and Lyon, B. R., 2003. Real-time quantitative RT-PCR assays of gene expression in plant roots during fungal pathogenesis. BioTechniques, 34:982–986.
40. Mhlanga, M. M., and Malmberg, L., 2001. Using molecular beacons to detect single-nucleotide polymorphisms with real-time PCR. Methods, 25:463–471.
41. Mircetich, S. M., and Kraft, J. M., 1973. Efficiency of various selective media in determining Pythium population in soil. Myco pathol. Mycol. Appl, 50:151–161.
42. Mocellin, S., Rossi, C. R., Pilati, P., Nitti, D., and Marincola, F. M., 2003. Quantitative real-time PCR:a powerful ally in cancer research. Trends Mol. Med., 9:189–195.
43. (r) green I monitoring during amplification. BioTechniques, 24:954–962.
44. Nazarenko, I. A., Bhatnagar, S. K., and Hohman, R. J., 1997. A closed tube format for amplification and detection of DNA based on energy transfer. Nucleic Acids Res, 25:2516–2521.
45. Nicholson, P., Rezanoor, H. N., Simpson, D. R., and Joyce, D., 1997. Differentiation and quantification of the cereal eyespot fungi Tapesia yallundae and Tapesia acuformis using a PCR assay. Plant Pathol, 46:842–856.
46. Nicholson, P., Turner, A. S., Edwards, S. G., Bateman, G. L., Morgan, L. W., Parry, D. W., Marshall, J., and Nuttall, M., 2002. Development of stem-base pathogens on different cultivars of winter wheat determined by quantitative PCR. Eur. J. Plant Pathol., 108:163–177.
47. Paulitz, T. C., and Rossi, R., 2004. Spatial distribution of Rhizo ctonia solani and Rhizoctonia oryzae at three different scales in direct-seeded wheat. Can. J. Plant Pathol, 26:419
48. Paulitz, T. C., and Schroeder, K. L., 2005. A new method for the quantification of Rhizoctonia solani and R. oryzae from soil. Plant Dis, 89:767–772.
49. Paulitz, T. C., Zhang, H., and Cook, R. J., 2003. Spatial distribution of Rhizoctonia oryzae and rhizoctonia root rot in direct-seeded cereals. Can. J. Plant Pathol., 25:295–303.
50. Pepper, I. L., and Dowd, S. E., 2002. “ PCR applications for plant and soil microbes ”. In Environmental microbiology., 2nd ed., Edited by:Hurst, C. J., Crawford, R. L., Knudsen, G. R., McInerney, M. J., and Stetzenbach, L. D., 573–582. Washington, D.C:ASM Press.
51. Pfaffl, M. W., 2001. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res., 29:e45 [online]
52. Rachdawong, S., Cramer, C. L., Grabau, E. A., Stromberg, V. K., Lacy, G. H., and Stromberg, E. L., 2002. Gaeumannomyces graminis vars. avenae, graminis, and tritici identified using PCR amplification of avenacinase-like genes. Plant Dis, 86:652–660.
53. Reischer, G. H., Lemmens, M., Farnleitner, A., Adler, A., and Mach, R. L., 2004. Quantification of Fusarium graminearum in infected wheat species specific real-time PCR applying a TaqMan probe. J. Microbiol. Methods, 59:141–146.
54. Ruppel, E. G., Schneider, C. L., Hecker, J. R., and Hogaboam, G. J., 1979. Creating epiphytotics of Rhizoctonia root rot and evaluation for resistance to Rhizoctonia solani in sugarbeet field plots. Plant Dis. Rep., 63:1245–1248.
55. Saiki, R. K., Scharf, S., Faloona, F., Mullis, K. B., Horn, G. T., Erlich, H. A., and Arnheim, N., 1985. Enzymatic amplification of β-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science (Washington, D.C.), 230:1350–1354.
56. Schaad, N. W., 1999. Detection of Clavibacter michiganensis subsp. sepedonicus in potato tubers by BIO-PCR and an automated real-time fluorescence detection system. Plant Dis., 83:1095–1100.
57. Schaad, N. W., and Frederick, R. D., 2002. Real-time PCR and application for rapid plant disease diagnostics. Can. J. Plant Pathol., 24:250–258.
58. Schaad, N. W., Frederick, R. D., Shaw, J., Schneider, W. L., Hickson, R., Petrillo, M. D., and Luster, D. G., 2003. Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annu. Rev. Phytopathol, 41:305–324.
59. Schena, L., Nigro, F., Ippolito, A., and Gallitelli, D., 2004. Real-time quantitative PCR:a new technology to detect and study phytopathogenic and antagonistic fungi. Eur. J. Plant Pathol., 110:893–908.
60. Schmittgen, T. D., Zakrajsek, B. A., Mills, A. G., Gorn, V., Singer, M. J., and Reed, M. W., 2000. Quantitative reverse transcription–polymerase chain reaction to study mRNA decay:comparison of endpoint and real-time methods. Anal. Biochem., 285:104–194.
61. Shengqi, W., Xiaohong, W., Suhong, C., and Wei, Guan., 2002. A new fluorescent quantitative polymerase chain reaction technique. Anal. Biochem., 309:206–211.
62. Sneh, B., Katan, J., Henis, Y., and Wahl, I., 1966. Methods for evaluating inoculum density of Rhizoctonia in naturally infested soil. Phytopathology, 56:74–78.
63. Solinas, A., Brown, L. J., McKeen, C., Mellor, J. M., Nichol, J. T. G., Thelwell, N., and Brown, T., 2001. Duplex Scorpion primers in SNP analysis and FRET applications. Nucleic Acids Res, 29:e96 [online]
64. (r) assay and molecular beacons probes. BioTechniques, 28:732–738.
65. Thelwell, N., Millington, S., Solinas, A., Booth, J., and Brown, T., 2000. Mode of action and application of scorpion primers to mutation detection. Nucleic Acids Res, 28:3752–3761.
66. Tsai, Y.-L., and Olson, B. H., 1992. Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl. Environ. Microbiol, 58:2292–2295.
67. Tyagi, S., and Kramer, R. J., 1996. Molecular beacons:probes that fluoresce upon hybridization. Nature Biotechnol., 14:303–308.
68. Tyagi, S., Marras, S. A. E., and Kramer, F. R., 2000. Wavelength-shifting molecular beacons. Nature Biotechnol, 18:1191–1196.
69. Van de Graaf, P., Lees, A. K., Cullen, D. W., and Duncan, J. M., 2003. Detection and quantification of Spongospora subterranea in soil, water and plant tissue using real-time PCR. Eur. J. Plant Pathol., 109:589–597.
70. Vandemark, G. J., and Barker, B. M., 2003. Quantifying Phytophthora medicaginis in susceptible and resistant alfalfa with a real-time fluorescent PCR assay. J. Phytopathol. (Berlin), 151:577–583.
71. Vandemark, G. J., Barker, B. M., and Gritsenko, M. A., 2002. Quantifying Aphanomyces euteiches in alfalfa with a fluorescent polymerase chain reaction assay. Phytopathology, 92:265–272.
72. Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., and Speleman, F., 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol, 3:1–12.
73. Waalwijk, C., van der Heide, R., de Vries, I., van der Lee, T., Schoen, C., Costrel-de Corainville, G., Häuser-Hahn, I., Kastelein, P., Köhl, J., Lonnet, P., Demarquet, T., and Kema, G. H. J., 2004. Quantitative detection of Fusarium species in wheat using TaqMan. Eur. J. Plant Pathol., 110:481–494.
74. Wang, C., Gao, D., Vaglenov, A., and Kaltenboeck, B., 2004. One-step real-time duplex reverse transcription PCRs simultaneously quantify analyte and housekeeping gene mRNAs. BioTechniques, 36:508–519.
75. Ward, E., Foster, S. J., Fraaije, B. A., and McCartney, H. A., 2004. Plant pathogen diagnostics:immunological and nucleic acid-based approaches. Ann. Appl. Biol., 145:1–16.
76. Weller, S. A., and Stead, D. E., 2002. Detection of root mat associated Agrobacterium strains from plant material and other sample types by post-enrichment TaqMan PCR. J. Appl. Microbiol, 92:118–126.
77. Weller, S. A., Elphinstone, J. G., Smith, N. C., Boonham, N., and Stead, D. E., 2000. Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Appl. Environ. Microbiol., 66:2853–2858.
78. Whitcombe, D., Theaker, J., Guy, S. P., Brown, T., and Little, S., 1999. Detection of PCR products using self-probing amplicons and fluorescence. Nature Biotechnol, 17:804–807.
79. Wilhelm, J., Pingoud, A., and Hahn, M., 2003. SoFAR:software for fully automated evaluation of real-time PCR data. BioTechniques, 34:324–332.
80. Winton, L. M., Stone, J. K., Watrud, L. S., and Hansen, E. M., 2002. Simultaneous one-tube quantification of host and pathogen DNA with real-time polymerase chain reaction. Phyto pathology, 92:112–116.
81. Wittwer, C. T., Ririe, K. M., Andrew, R. V., David, D. A., Gundry, R. A., and Balis, U. J., 1997. The LightCycler™:a microvolume multisample fluorimeter with rapid temperature control. BioTechniques, 22:176–181.
82. Wittwer, C. T., Herrmann, M. G., Gundry, C. N., and Elenitoba-Johnson, K. S. J., 2001. Real-time multiplex PCR assays. Methods, 25:430–442.
83. Yin, J. L., Shackel, N. A., Zekry, A., McGuinness, P. H., Richard, C., van der Putten, K., McCaughan, G. W., Eris, J. M., and Bishop, G. A., 2001. Real-time reverse-transcriptase–polymerase chain reaction (RT-PCR) for measurement of cytokine and growth factor mRNA expression with fluorogenic probes or SYBR green I. Immunol. Cell Biol, 79:213–221.