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Exploiting generic platform technologies for the detection and identification of plant pathogens

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Abstract

The detection and identification of plant pathogens currently relies upon a very diverse range of techniques and skills, from traditional culturing and taxonomic skills to modern molecular-based methods. The wide range of methods employed reflects the great diversity of plant pathogens and the hosts they infect. The well-documented decline in taxonomic expertise, along with the need to develop ever more rapid and sensitive diagnostic methods has provided an impetus to develop technologies that are both generic and able to complement traditional skills and techniques. Real-time polymerase chain reaction (PCR) is emerging as one such generic platform technology and one that is well suited to high-throughput detection of a limited number of known target pathogens. Real-time PCR is now exploited as a front line diagnostic screening tool in human health, animal health, homeland security, biosecurity as well as plant health. Progress with developing generic techniques for plant pathogen identification, particularly of unknown samples, has been less rapid. Diagnostic microarrays and direct nucleic acid sequencing (de novo sequencing) both have potential as generic methods for the identification of unknown plant pathogens but are unlikely to be suitable as high-throughput detection techniques. This paper will review the application of generic technologies in the routine laboratory as well as highlighting some new techniques and the trend towards multi-disciplinary studies.

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References

  • Armstrong, K. F., & Ball, S. L. (2005). DNA barcodes for biosecurity: invasive species identification. Philosophical Transactions of the Royal Society B, 360, 1813–1823.

    Article  CAS  Google Scholar 

  • Ball, S. L., & Armstrong, K. F. (2006). DNA barcodes for insect pest identification: a test case with tussock moths (Lepidoptera: Lymantriidae). Canadian Journal of Forest Research, 36, 337–350.

    Article  CAS  Google Scholar 

  • Blaxter, M. (2003). Molecular systematics: counting angels with DNA. Nature, 421, 122–124.

    Article  PubMed  CAS  Google Scholar 

  • Blaxter, M. (2004). The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society B, 359, 669–679.

    Article  CAS  Google Scholar 

  • Boonham, N., Tomlinson, J., & Mumford, R. (2007). Microarrays for rapid identification of plant viruses. Annual review of Phytopathology, 45, 307–328.

    Article  PubMed  CAS  Google Scholar 

  • Boonham, N., Walsh, K., Mumford, R. A., & Barker, I. (2000). The use of multiplex real-time PCR (TaqMan®) for the detection of potato viruses. EPPO Bulletin, 30, 427–430.

    Article  Google Scholar 

  • Brunner, P. C., Fleming, C., & Frey, J. E. (2002). A molecular identification key for economically important thrips species (Thysanoptera: Thripidae) using direct sequencing and a PCR-RFLP-based approach. Agricultural and Forest Entomology, 4, 127–136.

    Article  Google Scholar 

  • Clare, E. L., Lim, B. K., Engstron, M. D., Eger, J. L., & Hebert, P. D. N. (2007). DNA bar coding of neotropical bats: species identification and discovery within Guyana. Molecular Ecology Notes, 7, 184–190.

    Article  CAS  Google Scholar 

  • Clark, M. F., & Adams, A. N. (1977). Characteristics of the microplate method of Enzyme-Linked Immunosorbent Assay for the detection of plant viruses. Journal of General Virology, 34, 475–483.

    Google Scholar 

  • Coomans, A. (2002). Present status and future of nematode systematics. Nematology, 4, 573–582.

    Article  Google Scholar 

  • Cox-Foster, D. L., Conlan, S., Holmes, E. C., Palacios, G., Evans, J. D., Moran, N. A., et al. (2007). A metagenomic survey of microbes in honey bee colony collapse disorder. Science, 318(5848), 283–287, Oct 12, Epub 2007 Sep 6.

    Article  PubMed  CAS  Google Scholar 

  • Gandelman, O., Church, V. L., Moore, C., Carne, C., Jalal, H., Murray, J. A. H., et al. (2006). Bioluminescent alternative to real-time PCR (BART). Luminescence, 21, 276–277.

    Google Scholar 

  • Hajibabaei, M., Singer, G. A. C., Clare, E. L., & Hebert, P. D. N. (2007). Design and applicability of DNA arrays and DNA barcodes in biodiversity monitoring. BMC Biology, 5, 24.

    Article  PubMed  CAS  Google Scholar 

  • Hebert, P. D. N., Cywinska, A., Ball, S. L., & deWaard, J. R. (2003a). Biological identification through DNA barcodes. Proceedings of the Royal Society London B, 270, 313–321.

    Article  CAS  Google Scholar 

  • Hebert, P. D. N., Ratnasingham, S., & deWaard, J. R. (2003b). Bar coding animal life: Cytochrome C oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society London B, 270, S96–S99.

    Article  CAS  Google Scholar 

  • Hebert, P. D. N., Stoeckle, M. Y., Zemlak, T. S., & Francis, C. M. (2004). Identification of birds through DNA barcodes. PloS Biology, 2, e312.

    Article  PubMed  CAS  Google Scholar 

  • Hill, S. A., & Jackson, E. A. (1984). An investigation of the reliability of ELISA as a practical test for detecting Potato leaf roll virus and Potato virus Y in tubers. Plant Pathology, 33, 21–26.

    Article  Google Scholar 

  • Hopkins, G. W., & Freckleton, R. P. (2002). Declines in the numbers of amateur and professional taxonomists: implications for conservation. Animal Conservation, 5, 245–249.

    Article  Google Scholar 

  • Hulcr, J., Miller, S. E., Setliff, G. P., Darrow, K., Mueller, N. D., Hebert, P. D. N., et al. (2007). DNA bar coding confirms polyphagy in a generalist moth, Homona mermerodes (Lepidoptera: Tortricidae). Molecular Ecology Notes, 7, 549–557.

    Article  CAS  Google Scholar 

  • Jaffrezic-Renault, N., Martelet, C., Chevolot, Y., & Cloarec, J. P. (2007). Biosensors and bio-bar code assays based on biofunctionalized magnetic microbeads. Sensors, 7, 589–614.

    Article  CAS  Google Scholar 

  • Kerr, K. C. R., Stoeckle, M. Y., Dove, C. J., Weight, L. A., Francis, C. M., & Hebert, P. D. N. (2007). Comprehensive DNA barcode coverage of North American Birds. Molecular Ecology Notes, 7, 535–543.

    Article  CAS  PubMed  Google Scholar 

  • Klerks, M. M., Leone, G. O. M., Verbeek, M., van den Heuvel, J. F. J. M., & Schoen, C. D. (2001). 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, 93, 115–125.

    Article  PubMed  CAS  Google Scholar 

  • Leone, G., van Schijndel, H. B., van Gemen, B., & Schoen, C. D. (1997). Direct detection of Potato leafroll virus in potato tubers by immunocapture and the isothermal nucleic acid amplification method NASBA. Journal of Virological Methods, 66, 19–27.

    Article  PubMed  CAS  Google Scholar 

  • Ledford, H. (2007). Rapid sequencer puts virus in the frame for deaths. Nature, 447, 12–13.

    Google Scholar 

  • Mumford, R. A., Barker, I., & Wood, K. R. (1994). The detection of Tomato Spotted Wilt Virus using the polymerase chain reaction. Journal of Virological Methods, 46(3), 303–311.

    Article  PubMed  CAS  Google Scholar 

  • Mumford, R., Boonham, N., Tomlinson, J., & Barker, I. (2006). Advances in molecular phytodiagnostics - new solutions for old problems. European Journal of Plant Pathology, 116, 1–19.

    Article  CAS  Google Scholar 

  • Nelson, L. A., Wallman, J. F., & Dowton, M. (2007). Using COI barcodes to identify forensically and medically important blowflies. Medical and Veterinary Entomology, 21, 44–52.

    Article  PubMed  CAS  Google Scholar 

  • Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., Watanabe, K., Amino, N., & Hase, T. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28, e63.

  • O’Donnell, K. J., Canning, E., & Young, L. G. A. (1996). Detection of Potato virus Y using ligase chain reaction (LCR), in combination with a microtitre plate based method for product detection. In G. Marshall (Ed.) Diagnostics in Crop Production: BCPC Symposium Proceedings No. 65 (pp. 187–192). Farnham, UK: British Crop Protection Council.

    Google Scholar 

  • Pfunder, M., Holzgana, O., & Frey, J. E. (2004). 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, 13, 1277–1286.

    Article  PubMed  CAS  Google Scholar 

  • Puchta, H., & Sanger, H. L. (1989). Sequence analysis of minute amounts of viroid RNA using the polymerase chain reaction (PCR). Archives of Virology, 106, 335–340.

    Article  PubMed  CAS  Google Scholar 

  • Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The barcode of life data system. Molecular Ecology Notes, 7, 355–364. (www.barcodinglife.org).

    Article  CAS  PubMed  Google Scholar 

  • Schoen, C. D., Knorr, D., & Leone, G. (1996). Detection of Potato leafroll virus in dormant potato tubers by immunocapture and a fluorogenic 5ô nuclease RT-PCR assay. Phytopathology, 86, 993–999.

    Article  CAS  Google Scholar 

  • Seifert, K. A., Samson, R. A., deWaard, J. R., Houbraken, J., Levesque, C. A., Moncalvo, J. M., et al. (2007). Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case. Proceedings of the National Academy of Sciences USA, 104, 3901–3906.

    Article  CAS  Google Scholar 

  • Spiegel, S., & Martin, R. R. (1993). Improved detection of Potato leafroll virus in dormant potato tubers and microtubers by the polymerase chain reaction and ELISA. Annals of Applied Biology, 122, 493–500.

    Article  CAS  Google Scholar 

  • Stoeckle, M. (2003). Taxonomy, DNA and the barcode of life. BioScience, 53, 2, 3.

    Article  Google Scholar 

  • Tan, E., Wong, J., Nguyen, D., Zhang, Y., Erwin, B., Van Ness, L. K., et al. (2005). Isothermal DNA amplification coupled with DNA nanosphere-based colorimetric detection. Analytical Chemistry, 77, 7984–7992.

    Article  PubMed  CAS  Google Scholar 

  • Tomlinson, J. A., Barker, I., & Boonham, N. (2007). Faster, simpler, more specific methods for improved molecular detection of Phytophthora ramorum in the field. Applied and Environmental Microbiology, 73, 4040–4047.

    Article  PubMed  CAS  Google Scholar 

  • Vincent, M., Xu, Y., & Kong, H. M. (2004). Helicase-dependent isothermal DNA amplification. EMBO Reports, 5, 795–800.

    Article  PubMed  CAS  Google Scholar 

  • Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. N. (2005). DNA bar coding Australia’s fish species. Philosophical Transactions of The Royal Society of London B, 360, 1847–1857.

    Article  CAS  Google Scholar 

  • Yi, J. Z., Zhang, W. D., & Zhang, D. Y. (2006). Molecular Zipper: A fluorescent probe for real-time isothermal DNA amplification. Nucleic Acids Research, 34, e81.

    Article  PubMed  CAS  Google Scholar 

  • Zhang, D., Wu, J., Ye, F., Feng, T., Lee, I., & Yin, B. J. (2006). Amplification of circularizable probes for the detection of target nucleic acids and proteins. Clinica Chimica Acta, 363, 61–70.

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to acknowledge funding from Plant Health Division and Chief Scientist Group of Defra (www.bio-chip.co.uk), and also the European Union for funding under the fifth framework programme (www.diagchip.co.uk) and also the sixth framework programme (www.portcheck.eu.com) project (SSPE-CT-2004-502348). In addition the authors would like to acknowledge the help and support provided through the COST project ‘Agricultural Biomarkers for Array Technology’ (http://www.cost853.ch/).

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Correspondence to Neil Boonham.

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Boonham, N., Glover, R., Tomlinson, J. et al. Exploiting generic platform technologies for the detection and identification of plant pathogens. Eur J Plant Pathol 121, 355–363 (2008). https://doi.org/10.1007/s10658-008-9284-3

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  • DOI: https://doi.org/10.1007/s10658-008-9284-3

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