New grower-friendly methods for plant pathogen monitoring.

Accurate plant disease diagnoses and rapid detection and identification of plant pathogens are of utmost importance for controlling plant diseases and mitigating the economic losses they incur. Technological advances have increasingly simplified the tools available for the identification of pathogens to the extent that, in some cases, this can be done directly by growers and producers themselves. Commercially available immunoprinting kits and lateral flow devices (LFDs) for detection of selected plant pathogens are among the first tools of what can be considered grower-friendly pathogen monitoring methods. Research efforts, spurned on by point-of-care needs in the medical field, are paving the way for the further development of on-the-spot diagnostics and multiplex technologies in plant pathology. Grower-friendly methods need to be practical, robust, readily available, and cost-effective. Such methods are not restricted to on-the-spot testing but extend to laboratory services, which are sometimes more practicable for growers, extension agents, regulators, and other users of diagnostic tests.

[1]  K. Pierce,et al.  Linear-After-The-Exponential (LATE)–PCR: An advanced method of asymmetric PCR and its uses in quantitative real-time analysis , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[2]  D. Geiser,et al.  The promise and pitfalls of sequence-based identification of plant-pathogenic fungi and oomycetes. , 2010, Phytopathology.

[3]  C. Thornton,et al.  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. , 2004, Phytopathology.

[4]  D. Gramaje,et al.  Fungal Trunk Pathogens in the Grapevine Propagation Process: Potential Inoculum Sources, Detection, Identification, and Management Strategies. , 2011, Plant disease.

[5]  J. Compton,et al.  Nucleic acid sequence-based amplification , 1991, Nature.

[6]  T. Kikuchi,et al.  A rapid and precise diagnostic method for detecting the Pinewood nematode Bursaphelenchus xylophilus by loop-mediated isothermal amplification. , 2009, Phytopathology.

[7]  B. Thomma,et al.  Detecting single nucleotide polymorphisms using DNA arrays for plant pathogen diagnosis. , 2006, FEMS microbiology letters.

[8]  Peter Daszak,et al.  Emerging infectious diseases of plants: pathogen pollution, climate change and agrotechnology drivers. , 2004, Trends in ecology & evolution.

[9]  Zhanhong Ma,et al.  Rapid and Precise Detection of Latent Infections of Wheat Stripe Rust in Wheat Leaves using Loop‐Mediated Isothermal Amplification , 2011 .

[10]  C. D'arcy,et al.  Essential Plant Pathology , 2006 .

[11]  N. Tisserat,et al.  Nucleic Acid-Based Pathogen Detection in Applied Plant Pathology. , 2008, Plant disease.

[12]  D. Shank,et al.  Isothermal in vitro amplification of DNA by a restriction enzyme/DNA polymerase system. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[13]  J. M. van der Wolf,et al.  Multiplex microsphere immuno-detection of potato virus Y, X and PLRV. , 2008, Journal of virological methods.

[14]  Daniel Malamud,et al.  An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acids , 2010, Biomedical microdevices.

[15]  J. García,et al.  Plum Pox Virus and Sharka Disease , 2007 .

[16]  G. Schmitz,et al.  Bead-Based Multiplex Analysis/Bead-basierte Multiplexanalyse , 2003 .

[17]  B. Liaw,et al.  Hybridization probe for femtomolar quantification of selected nucleic acid sequences on a disposable electrode. , 2006, Analytical chemistry.

[18]  R. Frederick,et al.  Advances in molecular-based diagnostics in meeting crop biosecurity and phytosanitary issues. , 2003, Annual review of phytopathology.

[19]  B. Thomma,et al.  Recent developments in pathogen detection arrays: implications for fungal plant pathogens and use in practice. , 2005, Phytopathology.

[20]  T. Iwanami,et al.  Characterization of the tufB-secE-nusG-rplKAJL-rpoB Gene Cluster of the Citrus Greening Organism and Detection by Loop-Mediated Isothermal Amplification. , 2005, Plant disease.

[21]  B. Duffy,et al.  A rapid lateral-flow immunoassay for phytosanitary detection of Erwinia amylovora and on-site fire blight diagnosis. , 2011, Journal of microbiological methods.

[22]  I. Kato,et al.  Highly efficient isothermal DNA amplification system using three elements of 5'-DNA-RNA-3' chimeric primers, RNaseH and strand-displacing DNA polymerase. , 2007, Journal of biochemistry.

[23]  David J. Ecker,et al.  Ibis T5000: a universal biosensor approach for microbiology , 2008, Nature Reviews Microbiology.

[24]  M. Cambra,et al.  MOLECULAR METHODS FOR DETECTION AND QUANTITATION OF VIRUS IN APHIDS , 2006 .

[25]  C. Brasier,et al.  The biosecurity threat to the UK and global environment from international trade in plants , 2008 .

[26]  C. Lévesque,et al.  Oligonucleotide Array for Identification and Detection of Pythium Species , 2006, Applied and Environmental Microbiology.

[27]  J. West,et al.  Detection of airborne plant pathogens: halting epidemics before they start , 2009 .

[28]  Gwo-Bin Lee,et al.  Extraction of genomic DNA and detection of single nucleotide polymorphism genotyping utilizing an integrated magnetic bead-based microfluidic platform , 2009 .

[29]  Eun Kyu Lee,et al.  Loop Mediated Isothermal Amplification of DNA , 2008 .

[30]  K Watanabe,et al.  Loop-mediated isothermal amplification reaction using a nondenatured template. , 2001, Clinical chemistry.

[31]  N. Boonham,et al.  Faster, Simpler, More-Specific Methods for Improved Molecular Detection of Phytophthora ramorum in the Field , 2007, Applied and Environmental Microbiology.

[32]  J. Dunez,et al.  Virus and Virus-Like Diseases of Pome and Stone Fruits , 2011 .

[33]  K. L. Bayliss,et al.  Spore traps need improvement to fulfil plant biosecurity requirements , 2011 .

[34]  M. López,et al.  Molecular Tools for Detection of Plant Pathogens 13 1 Are Molecular Tools Solving the Challenges Posed by Detection of Plant Pathogenic Bacteria and Viruses ? , 2016 .

[35]  F. Beed,et al.  Plant disease diagnostic capabilities and networks. , 2009, Annual review of phytopathology.

[36]  B. Lockhart,et al.  Characterization of a Potexvirus infecting Hosta spp. , 1996 .

[37]  T. Notomi,et al.  Isolation of single-stranded DNA from loop-mediated isothermal amplification products. , 2002, Biochemical and biophysical research communications.

[38]  Linda M. Pilarski,et al.  On-chip PCR amplification of genomic and viral templates in unprocessed whole blood , 2011 .

[39]  J. Delgado,et al.  Pyrosequencing Reveals a Highly Diverse and Cultivar-Specific Bacterial Endophyte Community in Potato Roots , 2010, Microbial Ecology.

[40]  Ning Zhang,et al.  Dimeric oligonucleotide probes enhance diagnostic macroarray performance. , 2011, Journal of microbiological methods.

[41]  K. Madagan,et al.  Detection of potato viruses using microarray technology: towards a generic method for plant viral disease diagnosis. , 2003, Journal of virological methods.

[42]  N. Lin,et al.  Immunological detection of plant viruses and a mycoplasmalike organism by direct tissue blotting on nitrocellulose membranes. , 1990 .

[43]  T. Notomi,et al.  Accelerated reaction by loop-mediated isothermal amplification using loop primers. , 2002, Molecular and cellular probes.

[44]  Geertruida A. Posthuma-Trumpie,et al.  Lateral flow (immuno)assay: its strengths, weaknesses, opportunities and threats. A literature survey , 2009, Analytical and bioanalytical chemistry.

[45]  Richard F. Lee,et al.  Routine detection of citrus tristeza virus by direct immunoprinting-ELISA method using specific monoclonal and recombinant antibodies. , 2000 .

[46]  B. Landa,et al.  Region-wide analysis of genetic diversity in Verticillium dahliae populations infecting olive in southern Spain and agricultural factors influencing the distribution and prevalence of vegetative compatibility groups and pathotypes. , 2011, Phytopathology.

[47]  K L Manjunath,et al.  Detection of 'Candidatus Liberibacter asiaticus' in Diaphorina citri and its importance in the management of citrus huanglongbing in Florida. , 2008, Phytopathology.

[48]  F. Nigro,et al.  INCIDENCE OF VERTICILLIUM WILT ON OLIVE IN APULIA AND GENETIC DIVERSITY OF VERTICILLIUM DAHLIAE ISOLATES FROM INFECTED TREES , 2005 .

[49]  Michael G. Mauk,et al.  A disposable, integrated loop-mediated isothermal amplification cassette with thermally actuated valves , 2011, Microfluidics and nanofluidics.

[50]  A. Wheeler,et al.  The Digital Revolution: A New Paradigm for Microfluidics , 2009 .

[51]  G. Murray,et al.  An enhanced protocol for the quarantine detection of Tilletia indica and economic comparison with the current standard , 2010, Australasian Plant Pathology.

[52]  Neil Boonham,et al.  Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. , 2009, Molecular plant pathology.

[53]  B. Thomma,et al.  Design and development of a DNA array for rapid detection and identification of multiple tomato vascular wilt pathogens. , 2003, FEMS microbiology letters.

[54]  C. Lévesque,et al.  An oligonucleotide array for the identification and differentiation of bacteria pathogenic on potato. , 2003, Phytopathology.

[55]  Scotland Leman,et al.  PAMDB, a multilocus sequence typing and analysis database and website for plant-associated microbes. , 2010, Phytopathology.

[56]  R. Hamelin,et al.  Fungal pathogen (mis-) identifications: a case study with DNA barcodes on Melampsora rusts of aspen and white poplar. , 2009, Mycological research.

[57]  D. Golino,et al.  Pathogen testing and certification of Vitis and Prunus species. , 2005, Annual review of phytopathology.

[58]  Kenneth B. Johnson,et al.  Evaluation of Loop-Mediated Isothermal Amplification for Rapid Detection of Erwinia amylovora on Pear and Apple Fruit Flowers. , 2011, Plant disease.

[59]  T. Been,et al.  Development and Evaluation of Sampling Methods for Fields with Infestation Foci of Potato Cyst Nematodes (Globodera rostochiensis and G. pallida). , 2000, Phytopathology.

[60]  N. Boonham,et al.  Faster, Simpler, More-Specific Methods for Improved Molecular Detection of Phytophthora ramorum in the Field , 2007, Applied and Environmental Microbiology.

[61]  F. Rezzonico,et al.  Application of Whole-Cell Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry for Rapid Identification and Clustering Analysis of Pantoea Species , 2010, Applied and Environmental Microbiology.

[62]  N. Boonham,et al.  On-Site DNA Extraction and Real-Time PCR for Detection of Phytophthora ramorum in the Field , 2005, Applied and Environmental Microbiology.

[63]  Wenbin Li,et al.  Optimized Quantification of Unculturable Candidatus Liberibacter Spp. in Host Plants Using Real-Time PCR. , 2008, Plant disease.

[64]  Xiang Li Selection of polymerase chain reaction primers from an RNA intergenic spacer region for specific detection of Clavibacter michiganensis subsp. sepedonicus. , 1995 .

[65]  M. Wenneker,et al.  Possibilities of avoidance and control of bacterial plant diseases when using pathogen-tested (certified) or - treated planting material , 2002 .

[66]  Takashi Kawana,et al.  Tolerance of loop-mediated isothermal amplification to a culture medium and biological substances. , 2007, Journal of biochemical and biophysical methods.

[67]  Michael Eberhard,et al.  Handheld and Portable Reader Devices for Lateral Flow Immunoassays , 2009 .

[68]  A. Moreno,et al.  Quantitative detection of Citrus tristeza virus in plant tissues and single aphids by real-time RT-PCR , 2008, European Journal of Plant Pathology.

[69]  Jos Houbraken,et al.  Prospects for fungus identification using CO1 DNA barcodes, with Penicillium as a test case , 2007, Proceedings of the National Academy of Sciences.

[70]  Gregor Rothe,et al.  Bead‐Based Multiplex Analysis , 2003 .

[71]  Jan LW Rademaker,et al.  THE THREE DS OF PCR-BASED GENOMIC ANALYSIS OF PHYTOBACTERIA: Diversity, Detection, and Disease Diagnosis. , 1999, Annual review of phytopathology.

[72]  Yasuyoshi Mori,et al.  Loop-mediated isothermal amplification (LAMP) of gene sequences and simple visual detection of products , 2008, Nature Protocols.

[73]  P. R. Scott,et al.  Plant disease: a threat to global food security. , 2005, Annual review of phytopathology.

[74]  D. Geiser,et al.  Macroarray Detection of Solanaceous Plant Pathogens in the Fusarium solani Species Complex. , 2007, Plant disease.

[75]  Shinji Kawano,et al.  Rapid and sensitive detection of “Candidatus Liberibacter asiaticus” by cycleave isothermal and chimeric primer-initiated amplification of nucleic acids , 2008, Journal of General Plant Pathology.

[76]  J. Frey,et al.  Design and development of a DNA microarray for rapid identification of multiple European quarantine phytopathogenic bacteria , 2009, European Journal of Plant Pathology.

[77]  R. Sampath,et al.  Identification of bacterial plant pathogens using multilocus polymerase chain reaction/electrospray ionization-mass spectrometry. , 2008, Phytopathology.

[78]  I. Barker,et al.  On‐site detection of plant pathogens using lateral‐flow devices* , 2000 .

[79]  Adhemar Pereira de Barros,et al.  HUANGLONGBING: A DESTRUCTIVE, NEWLY-EMERGING, CENTURY-OLD DISEASE OF CITRUS 1 , 2006 .

[80]  Kendra Cox,et al.  Sequence specific detection of DNA using nicking endonuclease signal amplification (NESA) , 2007, Nucleic acids research.

[81]  Eiichi Honda,et al.  Colorimetric detection of loop-mediated isothermal amplification reaction by using hydroxy naphthol blue. , 2009, BioTechniques.

[82]  Garnsey,et al.  Riverside International Organization of Citrus Virologists Conference Proceedings ( 1957-2010 ) Title Direct Tissue Blot Immunoassay ( DTBIA ) for Detection of Citrus Tristeza Virus ( CTV ) Permalink , 2007 .

[83]  Satoshi Tsuneda,et al.  Real-time quantitative LAMP (loop-mediated isothermal amplification of DNA) as a simple method for monitoring ammonia-oxidizing bacteria. , 2006, Journal of biotechnology.

[84]  Richard B. Fair,et al.  Digital microfluidics: is a true lab-on-a-chip possible? , 2007 .

[85]  T. Gottwald Current epidemiological understanding of citrus Huanglongbing . , 2010, Annual review of phytopathology.

[86]  Development of a simplified NASBA protocol for detecting viable cells of the citrus pathogen Xanthomonas citri subsp. citri under different treatments , 2010 .

[87]  M. López,et al.  PCR DETECTION AND IDENTIFICATION OF PLANT-PATHOGENIC BACTERIA: UPDATED REVIEW OF PROTOCOLS (1989-2007) , 2009 .

[88]  J. Wolf,et al.  An enrichment microsphere immunoassay for the detection of Pectobacterium atrosepticum and Dickeya dianthicola in potato tuber extracts , 2007, European Journal of Plant Pathology.

[89]  N. Boonham,et al.  Advances in molecular phytodiagnostics – new solutions for old problems , 2006, European journal of plant pathology.

[90]  福田 至朗,et al.  Simplification of template DNA preparation for the loop-mediated isothermal amplification (LAMP) method to detect tomato yellow leaf curl virus , 2005 .

[91]  M. Cambra,et al.  Direct sample preparation methods for the detection of Plum pox virus by real-time RT-PCR. , 2010, International microbiology : the official journal of the Spanish Society for Microbiology.

[92]  M. Saito,et al.  Electrochemical genosensor for the rapid detection of GMO using loop-mediated isothermal amplification. , 2009, The Analyst.

[93]  Tim R. Gottwald,et al.  Citrus Canker: The Pathogen and Its Impact , 2002 .

[94]  M. Fukaya,et al.  Simplification of template DNA preparation for the loop-mediated isothermal amplification (LAMP) method to detect tomato yellow leaf curl virus , 2005 .

[95]  Doyoung Byun,et al.  A disposable, self-contained PCR chip. , 2009, Lab on a chip.

[96]  A. M. Alvarez Integrated approaches for detection of plant pathogenic bacteria and diagnosis of bacterial diseases. , 2003, Annual review of phytopathology.

[97]  B. Sobral,et al.  Plant Pathogen Forensics: Capabilities, Needs, and Recommendations , 2006, Microbiology and Molecular Biology Reviews.

[98]  Peter A. Emanuel,et al.  Detection of Francisella tularensis within Infected Mouse Tissues by Using a Hand-Held PCR Thermocycler , 2003, Journal of Clinical Microbiology.

[99]  Neil Boonham,et al.  Application of high-throughput DNA sequencing in phytopathology. , 2011, Annual review of phytopathology.

[100]  A. Moreno,et al.  Calculation of diagnostic parameters of advanced serological and molecular tissue-print methods for detection of Citrus tristeza virus: a model for other plant pathogens. , 2012, Phytopathology.

[101]  S. D. De Boer,et al.  Minireview/Minisynthèse Prospect for functional eradication of the bacterial ring rot disease of potato , 2011 .

[102]  L. Navarro,et al.  Incidence and epidemiology of Citrus tristeza virus in the Valencian community of Spain. , 2000, Virus research.

[103]  Investigation of the molecular mechanism of ICAN, a novel gene amplification method. , 2007, Journal of biochemistry.

[104]  A. Moreno,et al.  Estimation of the accuracy of two diagnostic methods for the detection of Plum pox virus in nursery blocks by latent class models , 2012 .

[105]  D. Gramaje,et al.  Fungal grapevine trunk pathogens associated with Syrah decline in Spain , 2009 .

[106]  C. Lévesque,et al.  Development of a DNA Macroarray for Detection and Monitoring of Economically Important Apple Diseases. , 2005, Plant disease.

[107]  N. Boonham,et al.  Microarrays for rapid identification of plant viruses. , 2007, Annual review of phytopathology.

[108]  Kenneth B. Johnson,et al.  DEVELOPMENT OF A RAPID DETECTION METHOD FOR ERWINIA AMYLOVORA BY LOOP-MEDIATED ISOTHERMAL AMPLIFICATION (LAMP) , 2008 .

[109]  C. Fournier-Wirth,et al.  Nanotechnologies for pathogen detection: Future alternatives? , 2010, Biologicals : journal of the International Association of Biological Standardization.

[110]  R. P. Koopman,et al.  Corrigendum to “A handheld real time thermal cycler for bacterial pathogen detection” [Biosens. Bioelectron. 18 (2003) 1115–1123] , 2004 .

[111]  U. Landegren,et al.  Diagnostic application of padlock probes—multiplex detection of plant pathogens using universal microarrays , 2005, Nucleic acids research.

[112]  Y. Fujiwara,et al.  Detection of Potato spindle tuber viroid by Reverse Transcription Loop-mediated Isothermal Amplification. , 2010 .

[113]  M. A. Machado,et al.  In planta multiplication and graft transmission of ‘Candidatus Liberibacter asiaticus’ revealed by Real-Time PCR , 2009, European Journal of Plant Pathology.

[114]  David J. Galas,et al.  Isothermal reactions for the amplification of oligonucleotides , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[115]  Jitae Kim,et al.  A PCR reactor with an integrated alumina membrane for nucleic acid isolation. , 2010, The Analyst.

[116]  Douglas R Call,et al.  Challenges and Opportunities for Pathogen Detection Using DNA Microarrays , 2005, Critical reviews in microbiology.

[117]  D. Thompson Control and monitoring: control strategies for Plum pox virus in Canada , 2006 .

[118]  M. López,et al.  Innovative tools for detection of plant pathogenic viruses and bacteria , 2003, International microbiology : the official journal of the Spanish Society for Microbiology.

[119]  E. Adipala,et al.  Efficacy of different fungicide spray schedules for control of potato late blight in Southwestern Uganda , 2003 .

[120]  M. Ghanim,et al.  Oligonucleotide microarray-based detection and genotyping of Plum pox virus. , 2008, Journal of virological methods.

[121]  R. Henrik Nilsson,et al.  Taxonomic Reliability of DNA Sequences in Public Sequence Databases: A Fungal Perspective , 2006, PloS one.