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. 2006 Jul 13;116(1):1–19. doi: 10.1007/s10658-006-9037-0

Advances in molecular phytodiagnostics – new solutions for old problems

Rick Mumford 1,✉, Neil Boonham 1, Jenny Tomlinson 1, Ian Barker 1
PMCID: PMC7087944  PMID: 32214677

Abstract

In the last decade, developments in molecular (nucleic acid-based) diagnostic methods have made significant improvements in the detection of plant pathogens. By using methods such as the polymerase chain reaction (PCR), the range of targets that can now be reliably diagnosed has grown to the extent that there are now extremely few, known pathogens that cannot be identified accurately by using laboratory-based diagnostics. However, while the detection of pathogens in individual, infected samples is becoming simpler, there are still many scenarios that present a major challenge to diagnosticians and plant pathologists. Amongst these are the detection of pathogens in soil or viruses in their vectors, high throughput testing and the development of generic methods, that allow samples to be simultaneously screened for large numbers of pathogens. Another major challenge is to develop robust technologies that avoid the reliance on well-equipped central laboratories and making reliable diagnostics available to pathologists in the field or in less-developed countries. In recent years, much of the research carried out on phytodiagnostics has focussed in these areas and as a result many novel, routine diagnostic tests are becoming available. This has been possible due to the introduction of new molecular technologies such real-time PCR and microarrays. These advances have been complemented by the development of new nucleic acid extraction methods, increased automation, reliable internal controls, assay multiplexing and generic amplification methods. With developments in new hardware, field-portable real-time PCR is now also a reality and offers the prospect of ultra-rapid, on-site molecular diagnostics for the first time. In this paper, the development and implementation of new diagnostic methods based upon novel molecular techniques is presented, with specific examples given to demonstrate how these new methods can be used to overcome some long-standing problems.

Keywords: on-site testing, real-time PCR, TaqMan, microarrays, molecular diagnostics, phytodiagnostics

Footnotes

An erratum to this article can be found at http://dx.doi.org/10.1007/s10658-006-9084-6

References

  1. Barker I, Hims M, Boonham N, Fisher T, Elmore J, Mumford RA (2005) Latest developments in diagnostics for potato diseases. In: Champion G, Dale MFB, Jaggard K, Parker WE, Pickup J, Stevens M (eds) Protection and production of sugar beet and potatoes. Aspects of Applied Biology No. 76 (pp. 147–150): Association of Applied Biologists, Wellesbourne, UK
  2. Bates JA, Taylor EJA. Scorpions ARMS primers for SNP real-time PCR detection and quantification of Pyrenophora teres. Molecular Plant Pathology. 2001;2:275–280. doi: 10.1046/j.1464-6722.2001.00074.x. [DOI] [PubMed] [Google Scholar]
  3. Bates JA, Taylor EJA, Kenyon DM, Thomas JE. The application of real-time PCR to the identification, detection and quantification of Pyrenophora species in the barley seed. Molecular Plant Pathology. 2001;2:49–57. doi: 10.1046/j.1364-3703.2001.00049.x. [DOI] [PubMed] [Google Scholar]
  4. Belanger SD, Boissinot M, Menard C, Picard FJ, Bergeron MG. Rapid detection of Shiga toxin-producing bacteria in feces by multiplex PCR with molecular beacons on the smart cycler. Journal of Clinical Microbiology. 2002;40:1436–1440. doi: 10.1128/JCM.40.4.1436-1440.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Belgrader P, Benett W, Hadley D, Long G, Mariella R, Milanovich F, Nasarabadi S, Nelson W, Richards J, Stratton P. Rapid pathogen detection using a microchip PCR array instrument. Clinical Chemistry. 1998a;44:2191–2194. [PubMed] [Google Scholar]
  6. Belgrader P, Benett W, Hadley D, Richards J, Stratton P, Mariella R, Milanovich F. PCR detection of bacteria in seven minutes. Science. 1999a;284:449–450. doi: 10.1126/science.284.5413.449. [DOI] [PubMed] [Google Scholar]
  7. Belgrader P, Hansford D, Kovacs GTA, Venkateswaran K, Mariella R, Milanovich F, Nasarabadi S, Okuzumi M, Pourahmadi F, Northrup MA. A minisonicator to rapidly disrupt bacterial spores for DNA analysis. Analytical Chemistry. 1999b;71:4232–4236. doi: 10.1021/ac990347o. [DOI] [PubMed] [Google Scholar]
  8. Belgrader P, Smith JK, Weedn VW, Northrup MA. Rapid PCR for identity testing using a battery-powered miniature thermal cycler. Journal of Forensic Sciences. 1998b;43:315–319. [PubMed] [Google Scholar]
  9. Bentley HA, Belloni DR, Tsongalis GJ. Parameters involved in the conversion of real-time PCR assays from the ABI Prism 7700 to the Cepheid SmartCycler II. Clinical Biochemistry. 2005;38:183–186. doi: 10.1016/j.clinbiochem.2004.10.009. [DOI] [PubMed] [Google Scholar]
  10. Bentsink L, Leone GOM, van Beckhoven JRCM, van Schijndel HB, van Gemen B, van der Wolf JM. Amplification of RNA by NASBA allows direct detection of viable cells of Ralstonia solanacearum in potato. Journal of Applied Microbiology. 2002;93:647–655. doi: 10.1046/j.1365-2672.2002.01725.x. [DOI] [PubMed] [Google Scholar]
  11. Bertolini E, Olmos A, Martinez MC, Gorris MT, Cambra M. Single-step multiplex RT-PCR for simultaneous and colourimetric detection of six RNA viruses in olive trees. Journal of Virological Methods. 2001;96:33–41. doi: 10.1016/s0166-0934(01)00313-5. [DOI] [PubMed] [Google Scholar]
  12. Bianco PA, Casati P, Marziliano N. Detection of phytoplasmas associated with grapevine flavescence Doree disease using real-time PCR. Journal of Plant Pathology. 2004;86:257–261. [Google Scholar]
  13. Bodrossy L, Stralis-Pavese N, Murrell JC, Radajewski S, Weilharter A, Sessitsch A. Development and validation of a diagnostic microbial microarray for methanotrophs. Environmental Microbiology. 2003;5:566–582. doi: 10.1046/j.1462-2920.2003.00450.x. [DOI] [PubMed] [Google Scholar]
  14. Bohm J, Hahn A, Schubert R, Bahnweg G, Adler N, Nechwatal J, Oehlmann R, Osswald W. 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. Journal of Phytopathology. 1999;147:409–416. [Google Scholar]
  15. Bonants PJM, van Gent-Pelzer MPE, Hooftman R, Cooke DEL, Guy DC, Duncan JM. A combination of baiting and different PCR formats, including measurement of real-time quantitative fluorescence, for the detection of Phytophthora fragariae in strawberry plants. European Journal of Plant Pathology. 2004;110:689–702. [Google Scholar]
  16. Boonham N, Perez LG, Mendez MS, Peralta EL, Blockley A, Walsh K, Barker I, Mumford RA. Development of a real-time RT-PCR assay for the detection of Potato spindle tuber viroid. Journal of Virological Methods. 2004;116:139–146. doi: 10.1016/j.jviromet.2003.11.005. [DOI] [PubMed] [Google Scholar]
  17. Boonham N, Smith P, Walsh K, Tame J, Morris J, Spence N, Bennison J, Barker I. The detection of Tomato spotted wilt virus (TSWV) in individual thrips using real time fluorescent RT-PCR (TaqMan) Journal of Virological Methods. 2002;101:37–48. doi: 10.1016/s0166-0934(01)00418-9. [DOI] [PubMed] [Google Scholar]
  18. Boonham N, Walsh K, Smith P, Madagan K, Graham I, Barker I. Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. Journal of Virological Methods. 2003;108:181–187. doi: 10.1016/s0166-0934(02)00284-7. [DOI] [PubMed] [Google Scholar]
  19. Bos L. Disease diagnosis and routine virus detection. In: Bos L, editor. Plant Viruses, Unique and Intriguing Pathogens. Leiden, The Netherlands: Backhuys Publishers; 1999. pp. 193–216. [Google Scholar]
  20. Bystricka D, Lenz O, Mraz I, Dedic P, Sip M. DNA microarray: parallel detection of potato viruses. Acta Virologica. 2003;47:41–44. [PubMed] [Google Scholar]
  21. Bystricka D, Lenz O, Mraz I, Piherova L, Kmoch S, Sip M. Oligonucleotide-based microarray: A new improvement in microarray detection of plant viruses. Journal of Virological Methods. 2005;128:176–182. doi: 10.1016/j.jviromet.2005.04.009. [DOI] [PubMed] [Google Scholar]
  22. Call DR. Challenges and opportunities for pathogen detection using DNA microarrays. Critical Reviews in Microbiology. 2005;31:91–99. doi: 10.1080/10408410590921736. [DOI] [PubMed] [Google Scholar]
  23. Christensen DR, Hartman LJ, Loveless BM, Frye MS, Shipley MA, Bridge DL, Richards MJ, Kaplan RS, Garrison J, Baldwin CD, Kulesh DA, Norwood DA. Detection of biological threat agents by real-time PCR: Comparison of assay performance on the RAPID, the LightCycler, and the smart cycler platforms. Clinical Chemistry. 2006;52:141–145. doi: 10.1373/clinchem.2005.052522. [DOI] [PubMed] [Google Scholar]
  24. Cullen DW, Lees AK, Toth IK, Duncan JM. Conventional PCR and quantitative real-time PCR detection of Helminthosporium solani in soil and on potato tubers. European Journal of Plant Pathology. 2001;107:387–398. [Google Scholar]
  25. Cullen DW, Lees AK, Toth IK, Duncan JM. Detection of Colleotrichum coccodes from soil and potato tubers by conventional PCR and quantitative real-time PCR. Plant Pathology. 2002;51:281–292. [Google Scholar]
  26. Danks C, Barker I. On-site detection of plant pathogens using lateral-flow devices. OEPP/EPPO Bulletin. 2000;30:421–426. [Google Scholar]
  27. Deyong Z, Willingmann P, Heinze C, Adam G, Pfunder M, Frey B, Frey JE. Differentiation of cucumber mosaic virus isolates by hybridization to oligonucleotides in a microarray format. Journal of Virological Methods. 2005;123:101–108. doi: 10.1016/j.jviromet.2004.09.021. [DOI] [PubMed] [Google Scholar]
  28. Dodds JA, Morris TJ, Jordan RL. Plant viral double-stranded RNA. Annual Review of Phytopathology. 1984;22:151–168. [Google Scholar]
  29. Doyle JJ, Doyle JL. A rapid DNA isolation procedure from small quantities of fresh leaf tissues. Phytochemistry Bulletin. 1987;19:11–15. [Google Scholar]
  30. Ekins RP. Multi-analyte immunoassay. Journal of Pharmaceutical and Biomedical Analysis. 1989;7:155–168. doi: 10.1016/0731-7085(89)80079-2. [DOI] [PubMed] [Google Scholar]
  31. Emanuel PA, Bell R, Dang JL, McClanahan R, David JC, Burgess RJ, Thompson J, Collins L, Hadfield T. Detection of Francisella tularensis within infected mouse tissues by using a hand-held PCR thermocycler. Journal of Clinical Microbiology. 2003;41:689–693. doi: 10.1128/JCM.41.2.689-693.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  32. Eun AJC, Seoh ML, Wong SM. Simultaneous quantitation of two orchid viruses by the TaqMan real-time RT-PCR. Journal of Virological Methods. 2000;87:151–160. doi: 10.1016/S0166-0934(00)00161-0. [DOI] [PMC free article] [PubMed] [Google Scholar]
  33. Fabre F, Kervarrec C, Mieuzet L, Riault G, Vialatte A, Jacquot E. Improvement of Barley yellow dwarf virus-PAV detection in single aphids using a fluorescent real time RT-PCR. Journal of Virological Methods. 2003;110:51–60. doi: 10.1016/s0166-0934(03)00097-1. [DOI] [PubMed] [Google Scholar]
  34. Fessehaie A, De Boer SH, Levesque AC. An oligonucleotide array for the identification and differentiation of bacteria pathogenic on potato. Phytopathology. 2003;93:262–269. doi: 10.1094/PHYTO.2003.93.3.262. [DOI] [PubMed] [Google Scholar]
  35. Fraaije BA, Lovell DJ, Coelho JM, Baldwin S, Hollomon DW. PCR-based assays to assess wheat varietal resistance to blotch (Septoria tritici and Stagonospora nodorum) and rust (Puccinia striiformis and Puccinia recondita) diseases. European Journal of Plant Pathology. 2001;107:905–917. [Google Scholar]
  36. Franke-Whittle IH, Klammer SH, Insam H. Design and application of an oligonucleotide microarray for the investigation of compost microbial communities. Journal of Microbiological Methods. 2005;62:37–56. doi: 10.1016/j.mimet.2005.01.008. [DOI] [PubMed] [Google Scholar]
  37. Fukuta S, Iida T, Mizukami Y, Ishida A, Ueda J, Kanbe M, Ishimoto Y. Detection of Japanese yam mosaic virus by RT-LAMP. Archives of Virology. 2003a;148:1713–1720. doi: 10.1007/s00705-003-0134-5. [DOI] [PubMed] [Google Scholar]
  38. Fukuta S, Kato S, Yoshida K, Mizukami Y, Ishida A, Ueda J, Kanbe M, Ishimoto Y. Detection of tomato yellow leaf curl virus by loop-mediated isothermal amplification reaction. Journal of Virological Methods. 2003b;112:35–40. doi: 10.1016/s0166-0934(03)00187-3. [DOI] [PubMed] [Google Scholar]
  39. Fukuta S, Ohishi K, Yoshida K, Mizukami Y, Ishida A, Kanbe M. Development of immunocapture reverse transcription loop-mediated isothermal amplification for the detection of tomato spotted wilt virus from chrysanthemum. Journal of Virological Methods. 2004;121:49–55. doi: 10.1016/j.jviromet.2004.05.016. [DOI] [PubMed] [Google Scholar]
  40. Gallagher WM, Bergin OE, Rafferty M, Kelly ZD, Nolan IM, Fox EJ, Culhane AC, McArdle L, Fraga MF, Hughes L, Currid CA, O’mahony F, Byrne A, Murphy AA, Moss C, McDonnell S, Stallings RL, Plumb JA, Esteller M, Brown R, Dervan PA, Easty DJ. Multiple markers for melanoma progression regulated by DNA methylation: insights from transcriptomic studies. Carcinogenesis. 2005;26:1856–1867. doi: 10.1093/carcin/bgi152. [DOI] [PubMed] [Google Scholar]
  41. Germini A, Rossi S, Zanetti A, Corradini R, Fogher C, Marchelli R. Development of a peptide nucleic acid array platform for the detection of genetically modified organisms in food. Journal of Agricultural and Food Chemistry. 2005;53:3958–3962. doi: 10.1021/jf050016e. [DOI] [PubMed] [Google Scholar]
  42. Hadidi A, Czosnek H, Barba M. DNA microarrays and their potential applications for the detection of plant viruses, viroids and phytoplasmas. Journal of Plant Pathology. 2004;86:97–104. [Google Scholar]
  43. Harju VA, Skelton A, Clover GRG, Ratti C, Boonham N, Henry CM, Mumford RA. The use of real-time RT-PCR (TaqMan) and post-ELISA virus release for the detection of beet necrotic yellow vein virus types containing RNA 5 and its comparison with conventional RT-PCR. Journal of Virological Methods. 2005;123:73–80. doi: 10.1016/j.jviromet.2004.09.009. [DOI] [PubMed] [Google Scholar]
  44. Hartung JS, Pruvost OP, Villemot I, Alvarez A. Rapid and sensitive colormetric detection of Xanthomonas axonopodis pv. citri by immunocapture and a nested-polymerase chain reaction assay. Phytopathology. 1996;86:95–101. [Google Scholar]
  45. Hearps A, Zhang Z, Alexandersen S. Evaluation of the portable Cepheid SmartCycler real-time PCR machine for the rapid diagnosis of foot-and-mouth disease. Veterinary Record. 2002;150:625–628. doi: 10.1136/vr.150.20.625. [DOI] [PubMed] [Google Scholar]
  46. Henson JM, French R. The polymerase chain reaction and plant disease diagnosis. Annual Review of Phytopathology. 1993;31:81–109. doi: 10.1146/annurev.py.31.090193.000501. [DOI] [PubMed] [Google Scholar]
  47. Higgins JA, Cooper M, Schroeder-Tucker L, Black S, Miller D, Karns JS, Manthey E, Breeze R, Perdue ML. A field investigation of Bacillus anthracis contamination of US Department of Agriculture and other Washington, DC, buildings during the anthrax attack of October 2001. Applied and Environmental Microbiology. 2002;69:593–599. doi: 10.1128/AEM.69.1.593-599.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Higgins JA, Nasarabadi S, Karns JS, Shelton DR, Cooper M, Gbakima A, Koopman RP. A handheld real time thermal cycler for bacterial pathogen detection. Biosensors and Bioelectronics. 2003;18:1115–1123. doi: 10.1016/s0956-5663(02)00252-x. [DOI] [PubMed] [Google Scholar]
  49. Hilscher C, Vahrson W, Dittmer DP. Faster quantitative real-time PCR protocols may lose sensitivity and show increased variability. Nucleic Acids Research. 2005;33:e182. doi: 10.1093/nar/gni181. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. Holland PM, Abramson RD, Watson R, Gelfand DH. Detection of specific polymerase chain reaction product by utilizing the 5’ to 3’ exonuclease activity of Thermus aquaticus DNA polymerase. Proceedings of the National Academy of Sciences. 1991;88:7276–7280. doi: 10.1073/pnas.88.16.7276. [DOI] [PMC free article] [PubMed] [Google Scholar]
  51. Hsu YC, Yeh TJ, Chang YC. A new combination of RT-PCR and reverse dot blot hybridization for rapid detection and identification of potyviruses. Journal of Virological Methods. 2005;128:54–60. doi: 10.1016/j.jviromet.2005.04.002. [DOI] [PubMed] [Google Scholar]
  52. Hull R. The potential for using dot-blot hybridisation in the detection of plant viruses. In: Jones RAC, Torrance L, editors. Developments in Applied Biology 1: Developments and Applications in Virus Testing. Wellesbourne, UK: Association of Applied Biologists; 1986. pp. 3–12. [Google Scholar]
  53. Ito T, Ieki H, Ozaki K. Simultaneous detection of six citrus viroids and Apple stem grooving virus from citrus plants by multiplex reverse transcription polymerase chain reaction. Journal of Virological Methods. 2002;106:235–239. doi: 10.1016/s0166-0934(02)00147-7. [DOI] [PubMed] [Google Scholar]
  54. Iwamoto T, Sonobe T, Hayashi K. Loop-mediated isothermal amplification for direct detection of Mycobacterium tuberculosis complex, M. avium, and M. intracellulare in sputum samples. Journal of Clinical Microbiology. 2003;41:2616–2622. doi: 10.1128/JCM.41.6.2616-2622.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  55. Klatser PR, Kuijper S, van Ingen CW, Kolk AHJ. Stabilized, freeze-dried PCR mix for detection of mycobacteria. Journal of Clinical Microbiology. 1998;36:1798–1800. doi: 10.1128/jcm.36.6.1798-1800.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Klerks MM, Leone GOM, Verbeek M, van den Heuvel JFJM, Schoen CD. Development of a multiplex AmpliDet RNA for the simultaneous detection of Potato leafroll virus and Potato virus Y in potato tubers. Journal of Virological Methods. 2001;93:115–125. doi: 10.1016/s0166-0934(01)00258-0. [DOI] [PubMed] [Google Scholar]
  57. Kox LFF, Boxman ILA, Jansen CCC, Roenhorst JW. Reliability of nucleic acid amplification techniques. Modified target RNA as exogenous internal standard for a real-time RT-PCR for Potato spindle tuber viroid. EPPO Bulletin. 2005;35:117–124. [Google Scholar]
  58. Landegren U, Schallmeiner E, Nilsson M, Fredriksson S, Baner J, Gullberg M, Jarvius J, Gustafsdottir S, Dahl F, Soderberg O, Ericsson O, Stenberg J. Molecular tools for a molecular medicine: analyzing genes, transcripts and proteins using padlock and proximity probes. Journal of Molecular Recognition. 2004;17:194–197. doi: 10.1002/jmr.664. [DOI] [PubMed] [Google Scholar]
  59. Lee GP, Min BE, Kim CS, Choi SH, Harn CH, Kim SU, Ryu KH. Plant virus cDNA chip hybridization for detection and differentiation of four cucurbit-infecting Tobamoviruses. Journal of Virological Methods. 2003;110:19–24. doi: 10.1016/s0166-0934(03)00082-x. [DOI] [PubMed] [Google Scholar]
  60. Leone G, van Schijndel H, van Gemen B, Kramer FR, Schoen CD. Molecular beacon probes combined with amplification by NASBA enable homogeneous, real-time detection of RNA. Nucleic Acids Research. 1998;26:2150–2155. doi: 10.1093/nar/26.9.2150. [DOI] [PMC free article] [PubMed] [Google Scholar]
  61. Leone G, van Schijndel HB, van Gemen B, Schoen CD. Direct detection of potato leafroll virus in potato tubers by immunocapture and the isothermal nucleic acid amplification method NASBA. Journal of Virological Methods. 1997;66:19–27. doi: 10.1016/s0166-0934(97)02203-9. [DOI] [PubMed] [Google Scholar]
  62. Lievens B, Brouwer M, Vanachter ACRC, Levesque CA, Cammue BPA, Thomma BPHJ. Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. FEMS Microbiology Letters. 2003;223:113–122. doi: 10.1016/S0378-1097(03)00352-5. [DOI] [PubMed] [Google Scholar]
  63. Lin H, Moh JS, Ou YC, Shen SY, Tsai YM, Chang Chien CC, Liu JM, Ma YY. A simple method for the detection and genotyping of high-risk human papillomavirus using seminested polymerase chain reaction and reverse hybridization. Gynecologic Oncology. 2005;96:84–91. doi: 10.1016/j.ygyno.2004.09.043. [DOI] [PubMed] [Google Scholar]
  64. Marko NF, Frank B, Quackenbush J, Lee NH (2005) A robust method for the amplification of RNA in the sense orientation. BMC Genomics 6: 27 [http://www.biomedcentral.com/1471-2164/6/27] [DOI] [PMC free article] [PubMed]
  65. Mavrodieva V, Levy L, Gabriel DW. Improved sampling methods for real-time polymerase chain reaction diagnosis of citrus canker from field samples. Phytopathology. 2004;94:61–68. doi: 10.1094/PHYTO.2004.94.1.61. [DOI] [PubMed] [Google Scholar]
  66. Mori Y, Kitao M, Tomita N, Notomi T. Real-time turbidimetry of LAMP reaction for quantifying template DNA. Journal of Biochemical and Biophysical Methods. 2004;59:145–157. doi: 10.1016/j.jbbm.2003.12.005. [DOI] [PubMed] [Google Scholar]
  67. Mumford R, Barker I, Walsh K, Boonham N. The reliable detection of Potato mop-top and Tobacco rattle viruses directly from potato tubers, using a multiplex TaqMan assay. Phytopathology. 2000;90:448–453. doi: 10.1094/PHYTO.2000.90.5.448. [DOI] [PubMed] [Google Scholar]
  68. Mumford RA, Skelton A, Metcalfe E, Walsh K, Boonham N. The reliable detection of Barley yellow and mild mosaic viruses using real-time PCR (TaqMan) Journal of Virological Methods. 2004b;117:153–159. doi: 10.1016/j.jviromet.2004.01.006. [DOI] [PubMed] [Google Scholar]
  69. Mumford RA, Skelton A, Posthuma KI, Kirby MJ, Boonham N, Adams AN. The improved detection of Strawberry crinkle virus using real-time RT-PCR (TaqMan®) Acta Horticulturae. 2004a;656:81–86. [Google Scholar]
  70. Nagamine K, Hase T, Notomi T. Accelerated reaction by loop-mediated isothermal amplification using loop primers. Molecular and Cellular Probes. 2002;16:223–229. doi: 10.1006/mcpr.2002.0415. [DOI] [PubMed] [Google Scholar]
  71. Nagamine K, Watanabe K, Ohtsuka K, Hase T, Notomi T. Loop-mediated isothermal amplification reaction using a nondenatured template. Clinical Chemistry. 2001;47:1742–1743. [PubMed] [Google Scholar]
  72. Nicolaisen M. Partial molecular characterization of Dahlia mosaic virus and its detection by PCR. Plant Disease. 2003;87:945–948. doi: 10.1094/PDIS.2003.87.8.945. [DOI] [PubMed] [Google Scholar]
  73. Nicolaisen M, Justesen AF, Thrane U, Skouboe P, Holmstrom K. An oligonucleotide microarray for the identification and differentiation of trichothecene producing and non-producing Fusarium species occurring on cereal grain. Journal of Microbiological Methods. 2005;62:57–69. doi: 10.1016/j.mimet.2005.01.009. [DOI] [PubMed] [Google Scholar]
  74. Nicolaisen M, Rasmussen HN, Husted K, Nielsen SL. Reverse transcription-detection of immobilized, amplified product in a one-phase system (RT-DIAPOPS) for the detection of potato virus Y. Plant Pathology. 2001;50:124–129. [Google Scholar]
  75. Nie XZ. Reverse transcription loop-mediated isothermal amplification of DNA for detection of Potato virus Y. Plant Disease. 2005;89:605–610. doi: 10.1094/PD-89-0605. [DOI] [PubMed] [Google Scholar]
  76. Nilsson M, Malmgren H, Samiotaki M, Kwiatkowski M, Chowdhary BP, Landegren U. Padlock probes: circularizing oligonucleotides for localized DNA detection. Science. 1994;265:2085–2088. doi: 10.1126/science.7522346. [DOI] [PubMed] [Google Scholar]
  77. Nolasco G, De Blas C, Torres V, Ponz F. A method combining immunocapture and PCR amplification in a microtitre plate for the detection of plant viruses and subviral pathogens. Journal of Virological Methods. 1993;45:201–218. doi: 10.1016/0166-0934(93)90104-y. [DOI] [PubMed] [Google Scholar]
  78. Notomi T, Okayama H, Masubuchi H, Yonekawa T, Watanabe K, Amino N, Hase T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Research. 2000;28:e63. doi: 10.1093/nar/28.12.e63. [DOI] [PMC free article] [PubMed] [Google Scholar]
  79. O’Donnell J, Canning E, Young LGA (1996) Detection of Potato virus Y using ligase chain reaction (LCR), in combination with a microtitre plate based method for product detection. In: Marshall G (ed) Diagnostics in Crop Production: BCPC Symposium Proceedings No. 65 (pp. 187–192) British Crop Protection Council, Farnham, UK
  80. Okuda M, Matsumoto M, Tanaka Y, Subandiyah S, Iwanami T. Characterization of the tufB-secE-nusG-rplKAJL-rpoB gene cluster of the citrus greening organism and detection by loop-mediated isothermal amplification. Plant Disease. 2005;89:705–711. doi: 10.1094/PD-89-0705. [DOI] [PubMed] [Google Scholar]
  81. Olmos A, Bertolini E, Gil M, Cambra M. Real-time assay for quantitative detection of non-persistently transmitted Plum pox virus RNA targets in single aphids. Journal of Virological Methods. 2005;128:151–155. doi: 10.1016/j.jviromet.2005.05.011. [DOI] [PubMed] [Google Scholar]
  82. Olmos A, Dasi MA, Candresse T, Cambra M. Print-capture PCR: a simple and highly sensitive method for the detection of plum pox virus (PPV) in plant tissues. Nucleic Acids Research. 1996;24:2192–2193. doi: 10.1093/nar/24.11.2192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  83. Persson K, Hamby K, Ugozzoli LA. Four-color multiplex reverse transcription polymerase chain reaction - overcoming its limitations. Analytical Biochemistry. 2005;344:33–42. doi: 10.1016/j.ab.2005.06.026. [DOI] [PubMed] [Google Scholar]
  84. Pfunder M, Holzgang O, Frey JE. Development of microarray-based diagnostics of voles and shrews for use in biodiversity monitoring studies, and evaluation of mitochondrial cytochrome oxidase I vs. cytochrome b as genetic markers. Molecular Ecology. 2004;13:1277–1286. doi: 10.1111/j.1365-294X.2004.02126.x. [DOI] [PubMed] [Google Scholar]
  85. Puchta H, Sanger HL. Sequence analysis of minute amounts of viroid RNA using the polymerase chain reaction (PCR) Archives of Virology. 1989;106:335–340. doi: 10.1007/BF01313962. [DOI] [PubMed] [Google Scholar]
  86. Ragozzino E, Faggioli F, Barba M. Development of a one tube-one step RT-PCR protocol for the detection of seven viroids in four genera: Apscaviroid, Hostuviroid, Pelamoviroid and Pospiviroid. Journal of Virological Methods. 2004;121:25–29. doi: 10.1016/j.jviromet.2004.05.012. [DOI] [PubMed] [Google Scholar]
  87. Raja S, Ching J, Xi LQ, Hughes SJ, Chang R, Wong W, McMillan W, Gooding WE, McCarty KS, Chestney M, Luketich JD, Godfrey TE. Technology for automated, rapid, and quantitative PCR or reverse transcription-PCR clinical testing. Clinical Chemistry. 2005;51:882–890. doi: 10.1373/clinchem.2004.046474. [DOI] [PubMed] [Google Scholar]
  88. Rowhani A, Biardi L, Routh G, Daubert SD, Golino DA. Development of a sensitive colorimetric-PCR assay for detection of viruses in woody plants. Plant Disease. 1998;82:880–884. doi: 10.1094/PDIS.1998.82.8.880. [DOI] [PubMed] [Google Scholar]
  89. Rowhani A, Maningas MA, Lile LS, Daubert SD, Golino DA. Development of a detection system for viruses of woody plants based on PCR analysis of immobilised virions. Phytopathology. 1995;85:347–352. [Google Scholar]
  90. Rudi K, Rud I, Holck A. A novel multiplex quantitative DNA array based PCR (MQDA-PCR) for quantification of transgenic maize in food and feed. Nucleic Acids Research. 2003;31:e62. doi: 10.1093/nar/gng061. [DOI] [PMC free article] [PubMed] [Google Scholar]
  91. Rudi K. Application of 16S rDNA arrays for analyses of microbial communities. Recent Research Developments in Bacteriology. 2003;1:35–44. [Google Scholar]
  92. Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Ehrlich HA. Primer directed enzymic amplification of DNA with a thermostable polymerase. Science. 1988;239:487–491. doi: 10.1126/science.2448875. [DOI] [PubMed] [Google Scholar]
  93. Saiki RK, Scharf S, Faloona F, Mullis KB, Horn GT, Erlich HA, Arnheim N. Enzymatic amplification of Beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anaemia. Science. 1985;230:1350–1354. doi: 10.1126/science.2999980. [DOI] [PubMed] [Google Scholar]
  94. Schaad NW, Frederick RD. Real-time PCR and its application for rapid plant disease diagnostics. Canadian Journal of Plant Pathology. 2002;24:250–258. doi: 10.1080/07060660209507006. [DOI] [Google Scholar]
  95. Schaad NW, Berthier-Schaad Y, Sechler A, Knorr D. Detection of Clavibacter michiganensis subsp sepedonicus in potato tubers by BIO-PCR and an automated real-time fluorescence detection system. Plant Disease. 1999;83:1095–1100. doi: 10.1094/PDIS.1999.83.12.1095. [DOI] [PubMed] [Google Scholar]
  96. Schaad NW, Frederick RD, Shaw J, Schneider WL, Hickson R, Petrillo MD, Luster DG. Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. Annual Review of Phytopathology. 2003;41:305–324. doi: 10.1146/annurev.phyto.41.052002.095435. [DOI] [PubMed] [Google Scholar]
  97. Schaad NW, Opgenorth D, Gaush P. Real-time polymerase chain reaction for one-hour on-site diagnosis of Pierce’s disease of grape in early season symptomatic vines. Phytopathology. 2002;92:721–728. doi: 10.1094/PHYTO.2002.92.7.721. [DOI] [PubMed] [Google Scholar]
  98. Schena L, Nigro F, Ippolito A. Identification and detection of Rosellinia necatrix by conventional and real-time Scorpion-PCR. European Journal of Plant Pathology. 2002;108:355–366. [Google Scholar]
  99. Schena L, Nigro F, Ippolito A, Gallitelli D. Real-time quantitative PCR: a new technology to detect and study phytopathogenic and antagonistic fungi. European Journal of Plant Pathology. 2004;110:893–908. [Google Scholar]
  100. Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467–470. doi: 10.1126/science.270.5235.467. [DOI] [PubMed] [Google Scholar]
  101. Schneider WL, Sherman DJ, Stone AL, Damsteegt VD, Frederick RD. Specific detection and quantification of Plum pox virus by real-time fluorescent reverse transcription-PCR. Journal of Virological Methods. 2004;120:97–105. doi: 10.1016/j.jviromet.2004.04.010. [DOI] [PubMed] [Google Scholar]
  102. Schoen CD, Knorr D, Leone G. Detection of potato leafroll virus in dormant potato tubers by immunocapture and a fluorogenic 5’ nuclease RT-PCR assay. Phytopathology. 1996;86:993–999. [Google Scholar]
  103. Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Research. 1996;6:639–645. doi: 10.1101/gr.6.7.639. [DOI] [PubMed] [Google Scholar]
  104. Shoemaker DD, Lashkari DA, Morris D, Mittmann M, Davis RW. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nature Genetics. 1996;14:450–456. doi: 10.1038/ng1296-450. [DOI] [PubMed] [Google Scholar]
  105. Stralis-Pavese N, Sessitsch A, Weilharter A, Reichenauer T, Riesing J, Csontos J, Murrell JC, Bodrossy L. Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environmental Microbiology. 2004;6:347–363. doi: 10.1111/j.1462-2920.2004.00582.x. [DOI] [PubMed] [Google Scholar]
  106. Sun ZF, Hu CQ, Ren CH, Shen Q. Sensitive and rapid detection of infectious hypodermal and hematopoietic necrosis virus (IHHNV) in shrimps by loop-mediated isothermal amplification. Journal of Virological Methods. 2006;131:41–46. doi: 10.1016/j.jviromet.2005.07.011. [DOI] [PubMed] [Google Scholar]
  107. Szemes M, Bonants P, de Weerd M, Bane J, Landegre U, Schoen CD. Diagnostic application of padlock probes-multiplex detection of plant pathogens using universal microarrays. Nucleic Acids Research. 2005;33:e70. doi: 10.1093/nar/gni069. [DOI] [PMC free article] [PubMed] [Google Scholar]
  108. ‘t Hoen PA, de Kort F, van Ommen GJ, den Dunnen JT. Fluorescent labelling of cRNA for microarray applications. Nucleic Acids Research. 2003;31:e20. doi: 10.1093/nar/gng020. [DOI] [PMC free article] [PubMed] [Google Scholar]
  109. Tamaoki M, Matsuyama T, Nakajima N, Aono M, Kubo A, Saji H. A method for diagnosis of plant environmental stresses by gene expression profiling using a cDNA macroarray. Environmental Pollution. 2004;131:137–145. doi: 10.1016/j.envpol.2004.01.008. [DOI] [PubMed] [Google Scholar]
  110. Thai HTC, Le MQ, Vuong CD, Parida M, Minekawa H, Notomi T, Hasebe F, Morita K. Development and evaluation of a novel loop-mediated isothermal amplification method for rapid detection of severe acute respiratory syndrome coronavirus. Journal of Clinical Microbiology. 2004;42:1956–1961. doi: 10.1128/JCM.42.5.1956-1961.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  111. Thelwell N, Millington S, Solinas A, Booth J, Brown T. Mode of action and application of Scorpion primers to mutation detection. Nucleic Acids Research. 2000;28:3752–3761. doi: 10.1093/nar/28.19.3752. [DOI] [PMC free article] [PubMed] [Google Scholar]
  112. Tomlinson JA, Boonham N, Hughes KJD, Griffin RL, Barker I. On-site DNA extraction and real-time PCR for detection of Phytophthora ramorum in the field. Applied and Environmental Microbiology. 2005;71:6702–6710. doi: 10.1128/AEM.71.11.6702-6710.2005. [DOI] [PMC free article] [PubMed] [Google Scholar]
  113. van Beckhoven JRCM, Stead DE, van der Wolf JM. Detection of Clavibacter michiganensis subsp. sepedonicus by AmpliDet RNA, a new technology based on real time monitoring of NASBA amplicons with a molecular beacon. Journal of Applied Microbiology. 2002;93:840–849. doi: 10.1046/j.1365-2672.2002.01765.x. [DOI] [PubMed] [Google Scholar]
  114. Van Gelder RN, von Zastrow ME, Yool A, Dement WC, Barchas JD, Eberwine JH. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proceedings of the National Academy of Sciences. 1990;87:1663–1667. doi: 10.1073/pnas.87.5.1663. [DOI] [PMC free article] [PubMed] [Google Scholar]
  115. Van Kessel JS, Karns JS, Perdue ML. Using a portable real-time PCR assay to detect Salmonella in raw milk. Journal of Food Protection. 2003;66:1762–1767. [PubMed] [Google Scholar]
  116. Vora GJ, Meador CE, Stenger DA, Andreadis JD. Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Applied and Environmental Microbiology. 2004;70:3047–3054. doi: 10.1128/AEM.70.5.3047-3054.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
  117. Walsh K, Boonham N, Barker I, Collins DW. Development of a sequence-specific real-time PCR to the melon thrips Thrips palmi (Thysanoptera; Thripidae) Journal of Applied Entomology. 2005;129:272–279. [Google Scholar]
  118. Ward LI, Fenn MGE, Henry CM. A rapid method for direct detection of Polymyxa DNA in soil. Plant Pathology. 2004;53:485–490. [Google Scholar]
  119. Weekes RJ, Barker I, Wood KR. An RT-PCR test for the detection of tomato spotted wilt tospovirus incorporating immunocapture and colorimetric estimation. Journal of Phytopathology. 1996;144:575–580. [Google Scholar]
  120. Weller SA, Elphinstone JG, Smith NC, Boonham N, Stead DE. Detection of Ralstonia solanacearum strains with a quantitative, multiplex, real-time, fluorogenic PCR (TaqMan) assay. Applied and Environmental Microbiology. 2000;66:2853–2858. doi: 10.1128/aem.66.7.2853-2858.2000. [DOI] [PMC free article] [PubMed] [Google Scholar]
  121. Wetzel T, Candresse T, Macquaire G, Ravelonandro M, Dunez J. A highly sensitive immunocapture polymerase chain reaction method for plum pox potyvirus detection. Journal of Virological Methods. 1992;39:27–37. doi: 10.1016/0166-0934(92)90122-t. [DOI] [PubMed] [Google Scholar]
  122. Wilson WJ, Wiedmann M, Dillard HR, Batt CA. Identification of Erwinia stewartii by a ligase chain-reaction assay. Applied and Environmental Microbiology. 1994;60:278–284. doi: 10.1128/aem.60.1.278-284.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  123. Winton LM, Manter DK, Stone JK, Hansen EA. Comparison of biochemical, molecular, and visual methods to quantify Phaeocryptopus gaeumannii in Douglas-Fir foliage. Phytopathology. 2003;93:121–126. doi: 10.1094/PHYTO.2003.93.1.121. [DOI] [PubMed] [Google Scholar]
  124. Wong ML, Medrano JF. Real-time PCR for mRNA quantitation. Biotechniques. 2005;39:75–85. doi: 10.2144/05391RV01. [DOI] [PubMed] [Google Scholar]
  125. Yamakawa H, Yokoyama S, Hirano T, Kitamura H, Ohara O. A simple and robust method for preparation of cDNA nylon microarrays. DNA Research. 2004;11:353–360. doi: 10.1093/dnares/11.5.353. [DOI] [PubMed] [Google Scholar]
  126. Zhang AW, Hartman GL, Curio-Penny B, Pedersen WL, Becker KB. Molecular detection of Diaporthe phaseolorum and Phomopsis longicolla from soybean seeds. Phytopathology. 1999;89:796–804. doi: 10.1094/PHYTO.1999.89.9.796. [DOI] [PubMed] [Google Scholar]
  127. Zhang DY, Liu B. Detection of target nucleic acids and proteins by amplification of circularizable probes. Expert Review of Molecular Diagnostics. 2003;3:237–248. doi: 10.1586/14737159.3.2.237. [DOI] [PubMed] [Google Scholar]

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