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Diagnostic Tools for Plant Biosecurity

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Part of the book series: Plant Pathology in the 21st Century ((ICPP,volume 8))

Abstract

There is now a wide range of diagnostic tools in the armoury to help prevent or control damaging disease outbreaks. When applied in the context of biosecurity, they have immense power to protect the plants on which food, feed, fuel and fibre supplies rely. Diagnoses which used to rely on culturing organisms, examining spores, or testing viruses on indicator plants, often taking many weeks to complete, can now be achieved in a matter of hours. Moreover, the advent of in-field diagnostic tests allows growers, agronomists or plant health and seeds inspectors to get a reliable test result without sending a sample to a laboratory. Remote sensing, using ground vehicles, unmanned aerial vehicles, or satellite technology, can bring a new dimension to surveillance, detection and diagnostic systems. Pathogen variation can be characterised rapidly by molecular marker techniques, potentially accelerating the process of identifying new pathotypes or fungicide resistant strains which threaten plant productivity. Metagenomic methods will undoubtedly play a part in non-targeted diagnostics, and identifying new threats to biosecurity. While diagnostic methods have advanced rapidly, their use in disease management in the field must be supported by robust sampling methods, treatment thresholds, and in depth understanding of disease risks.

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References

  • Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M, Samuitiene M, Boonham N (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 10:537–545

    Article  CAS  PubMed  Google Scholar 

  • Aksenov AA, Pasamontes A, Peirano DJ, Zhao W, Dandekar AM, Fiehn O, Ehsani R, Davis CE (2014) Detection of Huanglongbing disease using differential mobility spectrometry. Anal Chem 86:2481–2488

    Article  CAS  PubMed  Google Scholar 

  • Anderson PK, Cunningham AA, Patel NG, Morales FJ, Epstein PR, Daszak P (2004) Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. Trends Ecol Evol 19:535–544

    Article  PubMed  Google Scholar 

  • Atkins SD, Clark IM (2004) Fungal molecular diagnostics – a mini review. J Appl Genet 45:3–15

    PubMed  Google Scholar 

  • Atkins SD, Clark IM, Sosnowska D, Hirsch PR, Kerry BR (2003) Detection and quantification of Plectosphaerella cucumerina, a potential biological control agent of potato cyst nematodes, by using conventional PCR, Real-Time PCR, selective media, and baiting. Appl Environ Microbiol 69:4788–4793

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Barba M, Czosnek H, Hadidi A (2014) Historical perspective, development and applications of next-generation sequencing in plant virology. Viruses 6:106–136

    Article  PubMed  PubMed Central  Google Scholar 

  • Bauriegel E, Giebel A, Geyer M, Schmidt U, Herppich WB (2011) Early detection of Fusarium infection in wheat using hyper-spectral imaging. Comput Electron Agric 75:304–312

    Article  Google Scholar 

  • Bilodeau GJ, Koike ST, Uribe P, Martin FN (2012) Development of an assay for rapid detection and quantification of Verticillium dahliae in soil. Phytopathology 102:331–343

    Article  CAS  PubMed  Google Scholar 

  • Boonham N, Kreuze J, Winter S, van der Vlugt R, Bergervoet J, Tomlinson J, Mumford R (2014) Methods in virus diagnostics: from ELISA to next generation sequencing. Virus Res 186:20–31

    Article  CAS  PubMed  Google Scholar 

  • Bradshaw RE, Foster SJ, Monahan BJ (2006) Molecular diagnostic tools for detection of plant pathogen fungi. In: Rao JR, Fleming CC, Moore JE, (eds) Molecular diagnostics – current technology and application, Horizon Biosciences, p 47–66

    Google Scholar 

  • Brasier CM (2008) The biosecurity threat to the UK and global environment from international trade in plants. Plant Pathol 57:792–808

    Article  Google Scholar 

  • Cai H, Parks JW, Wall TA, Stott MA, Stambaugh A, Alfons K, Griffiths A, Mathies RA, Carrion R, Patterson JL, Hawkins AR, Schimdt H (2015) Optofluidic analysis system for amplification-free, direct detection of Ebola infection Nature Science Reports 5, doi:10.1038/srep14494

  • Camargo-Rodriguez AV, Smith J (2009) An image-processing based algorithm to automatically identify plant disease visual symptoms. Biosyst Eng 102:9–21

    Article  Google Scholar 

  • Camargo-Rodriguez AV, Molina JP, Cadena-Torres J, Jimenez N, Kim JT (2012) Intelligent systems for the assessment of crop disorders. Comput Electron Agric 85:1–7

    Article  Google Scholar 

  • Charlermroj R, Himananto O, Seepiban C, Kumpoosiri M, Warin N, Oplatowska M (2013) Multiplex detection of plant pathogens using a microsphere immunoassay technology. PLoS One 8(4):e62344. doi:10.1371/journal.pone.0062344

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cullen DW, Lees AK, Toth IK, Bell KS, Duncan JM (2000) Detection and quantification of fungal and bacterial potato pathogens in plants and soil. EPPO Bull 30:485–488

    Article  Google Scholar 

  • De Boer SH, Lopez MM (2012) New grower friendly methods for plant pathogen monitoring. Annu Rev Phytopathol 50:197–218

    Article  PubMed  Google Scholar 

  • Deora A, Gossen BD, Amirsadeghi S, McDonald MR (2015) A multiplex qPCR assay for detection and quantification of Plasmodiophora brassicae in soil. Plant Dis 99:1002–1009

    Article  CAS  Google Scholar 

  • Doan H, Zhang S, Davis RM (2014) Development and evaluation of AmplifyRP Acceler8 diagnostic assay for the detection of Fusarium oxysporum f. sp. vasinfectum race 4 in cotton. Plant Health Prog doi:10.1094/PHP-RS-13-0115

  • Fang Y, Ramasamy RP (2015) Current and prospective methods for plant disease detection. Biosensors 5:537–561

    Article  PubMed  PubMed Central  Google Scholar 

  • Faulstich K, Gruler R, Eberhard M, Lentzsch D, Haberstroh K (2009) Handheld and portable reader devices for lateral flow immunoassays. In: Wong RC, Tse HY (eds) Lateral flow immunoassay. Humana, New York, pp 157–183

    Google Scholar 

  • Fujinaga M, Ogiso H, Tsuchiya N, Saito H (2001) Physiological specialization of Fusarium oxysporum f. sp. lactucae, a causal organism of Fusarium root Rot of crisp head lettuce in Japan. J Gen Plant Pathol 67:205–206

    Article  Google Scholar 

  • Fujinaga M, Ogiso H, Tuchiya N, Saito H, Yamanaka S, Nozue M, Kojima M (2003) Race 3, a new race of Fusarium oxysporum f. sp. lactucae determined by a differential system with commercial cultivars. J Gen Plant Pathol 69:23–28

    Article  Google Scholar 

  • Garibaldi A, Gilardi G, Gullino ML (2002) First report of Fusarium oxysporum on lettuce in Europe. Plant Dis 86:1052

    Article  Google Scholar 

  • Garibaldi A, Gilardi G, Ortu G, Gullino ML (2012) First report of Plectosphaerella cucumerina on greenhouse cultured wild rocket (Diplotaxis tenuifolia) in Italy. Plant Dis 96:1825

    Article  Google Scholar 

  • Ghaffari R, Laothawornkitkul J, Iliescu D, Hines E, Leeson M, Napier R, Moore JP, Paul ND, Hewitt CN (2012) Plant pest and disease diagnosis using electronic nose and support vector machine approach. J Plant Dis Prot 119:200–220

    Article  CAS  Google Scholar 

  • Gilles T, Evans N, Fitt BDL, Jeger MJ (2000) Epidemiology in relation to methods for forecasting light leaf spot (Pyrenopeziza brassicae) severity on winter oilseed rape (Brassica napus) in the UK. Eur J Plant Pathol 106:593–605

    Article  Google Scholar 

  • Gladders P, Smith JA, Kirkpatrick L, Clewes E, Grant C, Barbara D, Barnes AV, Lane CR (2011) First record of verticillium wilt (Verticillium longisporum) in winter oilseed rape in the UK New Disease Reports 23: 8

    Google Scholar 

  • Greninger AL, Naccache SN, Federman S, Yu G, Mbala P, Bres V, Bouquet J, Stryke D, Somasekar S, Linnen J, Dodd R, Mulembakani P, Schneider B, Muyembe J, Stramer D, Chiu CY (2015) Genome Med 7:99. doi:10.1186/s13073-015-0220-9

    Article  PubMed  PubMed Central  Google Scholar 

  • Gullino ML, Gilardi G, Garibaldi A (2004) New Fusarium wilts on vegetable crops in Italy. Commun Agric Appl Biol Sci 69:405–413

    CAS  PubMed  Google Scholar 

  • Gullino ML, Gilardi G, Garibaldi A (2014) Seed-borne fungal pathogens of leafy vegetables. In: Gulliono ML, Munkvold G (eds) Global perspectives on the health of seeds and plant propogaton material. Springer, p 47–56

    Google Scholar 

  • Hausladen H, Leiminger J (2007) Potato early blight in Germany (Alternaria solani – Alternaria alternata), PPO Special report no. 12, Westerdijk CE, Schepers HTAM, (eds) Applied Plant Research BV, Wageningen.

    Google Scholar 

  • Hovmøller MS, Walter S, Bayles RA, Hubbard A, Flath K, Sommerfeldt N, Leconte M, Czembor P, Rodriguez-Algaba J, Thach T, Hansen JG, Lassen P, Justesen AF, Ali S, de Vallavieille-Pope C (2015) Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region. Plant Pathol 65(3):402–411. doi:10.1111/ppa.12433

    Article  Google Scholar 

  • Huang W, Lamb D, Niu Z, Liu L, Wang J (2007) Identification of yellow rust in wheat using in situ spectral reflectance measurements and airborne hyperspectral imaging. Precis Agric 8:187–197

    Article  Google Scholar 

  • Hubbard A, Lewis CM, Yoshida K, Ramirez-Gonzalez RH, de Vallavielle-Pope C, Thomas J, Kamoun S, Bayles R, Uauy C, Saunders DGO (2015) Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biology 16:23. doi:10.1186/s13059-015-0590-8

    Article  PubMed  PubMed Central  Google Scholar 

  • Isack Y, Benichis M, Gillet D, Gamliel A (2014) A selective agar medium for isolation, enumeration and morphological identification of Fusarium proliferatum. Phytoparasitica 4:541–547

    Article  Google Scholar 

  • Jackson SL, Bayliss KL (2011) Spore traps need improvement to fulfil plant biosecurity requirements. Plant Pathol 60:801–810

    Article  Google Scholar 

  • Kennedy R, Wakeham AJ (2008) Development of detection systems for the sporangia of Peronospora destructor. Eur J Plant Pathol 122:147–155

    Article  CAS  Google Scholar 

  • Kostov K, Verstappen ECP, Bergervoet JHW, de Weerdt M, Schoen CD, Slavov S, Bonants PJM (2015) Multiplex detection and identification of Phytophthora spp. using target-specific primer extension and Luminex xTAG technology. Plant Pathol 65(6):1008–1021. doi:10.1111/ppa.12481

    Article  Google Scholar 

  • Lane CR, Hobden E, Walker L, Barton VC, Inman AJ, Hughes KJD, Swan H, Colyer A, Barker I (2007) Evaluation of a rapid diagnostic field test kit for identification of Phytophthora species, including P. ramorum and P. kernoviae at the point of inspection. Plant Pathol 56:828–835

    Article  Google Scholar 

  • Lin YH, Lai PJ, Chang TH, Wan YL, Huang JW, Huang JH, Chang PFL (2014) Genetic diversity and identification of race 3 of Fusarium oxysporum f. sp. lactucae in Taiwan. Eur J Plant Pathol 140:721–733

    Article  CAS  Google Scholar 

  • Mahlein A (2016) Plant disease detection by imaging sensors – parallels and specific demands for precision agriculture and plant phenotyping. Plant Dis 100:241–251

    Article  Google Scholar 

  • Martinelli F, Scalenghe R, Salvatore D, Panno S, Scuderi G, Ruisi P, Villa P, Stroppiana D, Boschetti M, Goulart LR, Davis CE, Dandekar AM (2014) Advanced methods of plant disease detection. A review. Agron Sustain Dev 35:1–25. doi:10.1007/s13593-014-0246-1

    Article  Google Scholar 

  • Miles TD, Martin FN, Coffey MD (2015) Development of rapid isothermal amplification assays for detection of Phytophthora spp. In plant tissue. Phytopathology 105:265–278

    Article  CAS  PubMed  Google Scholar 

  • Mirik M, Ansley RJ, Price JA, Workneh F, Rush CM (2013) Remote monitoring of wheat streak mosaic progression using Sub-pixel classification of landsat 5 TM imagery for site specific disease management in winter wheat. Adv Remote Sens 2:16–28

    Article  Google Scholar 

  • Oerke EC, Dehne HW, Schnbeck F, Weber A (1994) Crop production and crop protection: estimated losses in major food and cash crops. Elsevier, Amsterdam

    Google Scholar 

  • Pasquali M, Dematheis F, Gullino ML, Garibaldi A (2007) Identification of race 1 of Fusarium oxysporum f. sp. lactucae on lettuce by inter-retrotransposon sequence-characterized amplified region technique. Phytopathology 97:987–996

    Article  CAS  PubMed  Google Scholar 

  • Pautasso M, Doring TF, Garbelotto M, Pellis L, Jeger MJ (2012) Impacts of climate change on plant diseases – opinions and trends. Eur J Plant Pathol 133:295–313

    Article  Google Scholar 

  • Qu XS, Wanner LA, Christ BJ (2010) Multiplex real-time PCR (TaqMan) assay for the simultaneous detection and discrimination of potato powdery and common scab diseases and pathogens. J Appl Microbiol 110:769–777

    Article  Google Scholar 

  • Rogers P, Whitby S, Dando M (1999) Biological warfare against crops. Sci Am 280:70–75

    Article  CAS  PubMed  Google Scholar 

  • Rutolo M, Covington JA, Clarkson J, Iliescu D (2014) Detection of potato storage disease via Gas analysis: a pilot study using field asymmetric Ion mobility spectrometry. Sensors 14:15939–15952

    Article  PubMed  PubMed Central  Google Scholar 

  • Sankaran S, Mishra A, Ehsani R, Davis C (2010) A review of advanced techniques for detecting plant diseases. Comput Electron Agric 72:1–13

    Article  Google Scholar 

  • Schmale DG, Ross SD (2015) Highways in the Sky: scales of atmospheric transport of plant pathogens. Annu Rev Phytopathol 53:591–611

    Article  CAS  PubMed  Google Scholar 

  • Singh RP, Hodson DP, Jin Y, Lagudah ES, Ayliffe MA, Bhavani MN, Rouse S, Pretorius SA, Szabo LJ, Huerta Espinosa J, Basnet BR, Lan C, Hovmoller MS (2015) Emergence and spread of new races wheat of stem rust: continued threat to food security and prospects of genetic control. Phytopathology 105:872–884

    Article  PubMed  Google Scholar 

  • Thiessen LD, Keune JA, Neill TM, Turechek WW, Grove GG, Mahaffee WF (2016) Development of a grower conducted inoculum detection assay for management of grape powdery mildew. Plant Pathol 65:238–249

    Article  CAS  Google Scholar 

  • Thornton CR, Groenhof AC, Forrest R, Lamotte R (2004) A one-step, immunochromatographic lateral flow device specific to Rhizoctonia solani and certain related species, and its use to detect and quantify R. solani in soil. Phytopathology 94:280–288

    Article  CAS  PubMed  Google Scholar 

  • Waage JK, Mumford JD (2008) Agricultural biosecurity. Philos Trans R Soc Lond B Biol Sci 363:863–876

    Article  CAS  PubMed  Google Scholar 

  • Wahabzada M, Mahlein A-K, Bauckhage C, Steiner U, Oerke E-C, Kersting K (2015) Metro maps of plant disease dynamics – automated mining of differences using hyperspectral images. PLoS One 10(1):e0116902. doi:10.1371/journal.pone.0116902

    Article  PubMed  PubMed Central  Google Scholar 

  • Wakeham A (2015) Validation of the clubroot lateral flow in UK commercial Brassica cropping systems. Report CP 099a, AHDB Horticultural Development Council

    Google Scholar 

  • West JS, Kimber RBE (2015) Innovations in air sampling to detect plant pathogens. Ann Appl Biol 166:4–17

    Article  PubMed  PubMed Central  Google Scholar 

  • West JS, Canning GGM, Heard S, Wili SG (2013) Proceedings of future IPM in Europe. development of the miniature virtual impactor – MVI – for long-term and automated air sampling to detect plant pathogen spores., 19–21 March 2013, Riva del Garda, Italy. (Abstract)

    Google Scholar 

  • Woodall JW, Webb KM, Giltrap PM, Adams IP, Peters JC, Budge GE, Boonham N (2012) A new large scale soil DNA extraction procedure and real time PCR assay for the detection of Sclerotium cepivorum in soil. Eur J Plant Pathol 134:467–473

    Article  Google Scholar 

  • Yuan L, Zhang J, Shi Y, Nie C, Wei L, Wang J (2014) Damage mapping of powdery mildew in winter wheat with high-resolution satellite image. Remote Sens 6:3611–3623

    Article  Google Scholar 

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Correspondence to Jane E. Thomas .

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Thomas, J.E., Wood, T.A., Gullino, M.L., Ortu, G. (2017). Diagnostic Tools for Plant Biosecurity. In: Gullino, M., Stack, J., Fletcher, J., Mumford, J. (eds) Practical Tools for Plant and Food Biosecurity. Plant Pathology in the 21st Century, vol 8. Springer, Cham. https://doi.org/10.1007/978-3-319-46897-6_10

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