Current and emerging molecular technologies for the diagnosis of plant diseases – An overview
DOI:
https://doi.org/10.18006/2022.10(2).294.305Keywords:
ELISA, PCR, Real-time PCR, LAMP, Biosensor, NGSAbstract
Plant diseases caused by numerous pathogens such as bacteria, viruses, and fungi are responsible for substantial economic losses in the agricultural industry worldwide. Specific, sensitive, and efficient diagnostic tools have been developed worldwide to mitigate and prevent the pathogenic threat. The diagnostic tools have revolutionized from classical methods to more advanced molecular diagnostic approaches such as enzyme-linked immunosorbent assay (ELISA), conventional polymerase chain reaction (PCR), real-time PCR, loop-mediated isothermal amplification (LAMP), biosensor, and next-generation sequencing (NGS). Hence, this review describes the current and emerging molecular diagnostic tools to distinguish and identify pathogens in crops.
References
Azizi, M. M. F., Ismail, S. I., Hata, E. M., Zulperi, D., et al. (2019a). First report of Pantoea stewartii subsp. indologenes causing leaf blight on rice in Malaysia. Plant Disease,103, 1407-1407 DOI: https://doi.org/10.1094/PDIS-08-18-1403-PDN
Azizi, M. M. F., Zulperi, D., Rahman, M. A. A., Abdul-Basir, B., et al. (2019b). First report of Pantoea ananatis causing leaf blight disease of rice in Peninsular Malaysia. Plant Disease,103,2122 DOI: https://doi.org/10.1094/PDIS-01-19-0191-PDN
Bastien, P., Procop, G.W., & Reischl, U. (2008). Quantitative real-time PCR is not more sensitive than “conventional” PCR. Journal of Clinical Microbiology,46,1897–1900 DOI: https://doi.org/10.1128/JCM.02258-07
Behjati, S., & Tarpey, P.S. (2013). What is next generation sequencing?. Archives of Disease in Childhood-Education and Practice, 98, 236-238 DOI: https://doi.org/10.1136/archdischild-2013-304340
Boonham, N., Glover, R., Tomlinson, J., & Mumford, R. (2008). Exploiting generic platform technologies for the detection and identification of plant pathogens. European Journal of Plant Pathology,121, 355-363 DOI: https://doi.org/10.1007/s10658-008-9284-3
Carneiro, G.A., Matić, S., Ortu, G., Garibaldi, A., et al. (2017). Development and validation of a TaqMan real-time PCR assay for the specific detection and quantification of Fusariumfujikuroi in rice plants and seeds. Phytopathology,107, 885-892 DOI: https://doi.org/10.1094/PHYTO-10-16-0371-R
Chalupowicz, L., Dombrovsky, A., Gaba, V., Luria, N., et al. (2019). Diagnosis of plant diseases using the Nanopore sequencing platform. Plant Pathology, 68, 229-238 DOI: https://doi.org/10.1111/ppa.12957
Chen, Z.D., Kang, H.J., Chai, A.L., Shi, Y.X., et al. (2020). Development of a loop-mediated isothermal amplification (LAMP) assay for rapid detection of Pseudomonas syringaepv. tomato in planta. European Journal of Plant Pathology,156, 739-750 DOI: https://doi.org/10.1007/s10658-019-01923-8
Clark, L.C., & Lyons, C. (1962). Electrode systems for continuous monitoring in cardiovascular surgery. Annals of the New York Academy of sciences, 102, 29-45 DOI: https://doi.org/10.1111/j.1749-6632.1962.tb13623.x
Crosslin, J.M., Vandemark, G.J., & Munyaneza, J.E. (2006). Development of a real-time, quantitative PCR for detection of the Columbia basin potato purple top phytoplasma in plants and beet leafhoppers. Plant Disease, 90, 663-667 DOI: https://doi.org/10.1094/PD-90-0663
Cruickshanks, H.A., McBryan, T., Nelson, D.M., et al. (2013). Senescent cells harbour features of the cancer epigenome. Nature Cell Biology, 15, 1495-1506 DOI: https://doi.org/10.1038/ncb2879
Darmanis, S., Nong, R.Y., Vänelid, J., Siegbhan, A., et al. (2011) ProteinSeq: High-performance proteomic analyses by proximity ligation and next generation sequencing. PLoS One, 6, e25583 DOI: https://doi.org/10.1371/journal.pone.0025583
Dhama, K., Karthik, K., Chakraborty, S., Tiwari, T., et al. (2014). Loop-mediated isothermal amplification of DNA (LAMP): a new diagnostic tool lights the world of diagnosis of animal and human pathogens: a review. Pakistan journal of biological sciences, 17, 151-166 DOI: https://doi.org/10.3923/pjbs.2014.151.166
Di Resta, C., Galbiati, S., Carrera, P., & Ferrari, M. (2018). Next-generation sequencing approach for the diagnosis of human diseases: open challenges and new opportunities. Ejifcc, 29, 4
Díaz-Cruz G. A, Smith, C. M, Wiebe, K. F., Villanueva, S.M., et al. (2019). Applications of next-generation sequencing for large-scale pathogen diagnoses in soybean. Plant Disease, 103, 1075-1083 DOI: https://doi.org/10.1094/PDIS-05-18-0905-RE
Fang, Y., & Ramasamy, R .P. (2015). Current and Prospective Methods for Plant Disease Detection. Biosensors, 5, 537-561 DOI: https://doi.org/10.3390/bios5030537
Francois, P., Tangomo, M., Hibbs, J., Bonetti, E.J., et al. (2011). Robustness of a loop-mediated isothermal amplification reaction for diagnostic applications. FEMS Immunology & Medical Microbiology, 62, 41-48 DOI: https://doi.org/10.1111/j.1574-695X.2011.00785.x
Franken, A. A. J. M., Zilverentant, J. F., Boonekamp, P. M., & Schots, A. (1992). Specificity of polyclonal and monoclonal-antibodies for the identification of Xanthomonascampestrispv. campestris. Netherlands Journal of Plant Pathology,98, 81-94 DOI: https://doi.org/10.1007/BF01996321
Gachon, C., Mingam, A., & Charrier, B. (2004). Real-time PCR: What relevance to plant studies?. Journal of Experimental Botany, 55,1445–1454 DOI: https://doi.org/10.1093/jxb/erh181
Hajia, M. (2018). Limitations of different PCR protocols used in diagnostic laboratories: a short review. Modern Medical Laboratory Journal, 1, 1-6 DOI: https://doi.org/10.30699/mmlj17-01-01
Haji-Hashemi, H. Safarnejad, M.R., Norouzi, P., Ebrahimi, M., et al. (2019). Simple and effective label free electrochemical immunosensor for Fig mosaic virus detection. Analytical Biochemistry, 566,102-106 DOI: https://doi.org/10.1016/j.ab.2018.11.017
Hardinge, P., & Murray, J. A. H. (2019). Reduced false positives and improved reporting of Loop-mediated isothermal amplification using quenched fluorescent primers. Scientific Reports, 9, 1–13 DOI: https://doi.org/10.1038/s41598-019-43817-z
He, S., Chen, H., Wei, Y., An, T., & Liu, S. (2020). Development of a DNA-based real-time PCR assay for the quantification of Colletotrichumcamelliae growth in tea (Camellia sinensis). Plant Methods, 16, 1-11 DOI: https://doi.org/10.1186/s13007-020-00564-x
Hubbard, A., Lewis, C. M., Yoshida, K., Ramirez-Gonzalez, R.H., et al. (2015). Field pathogenomics reveals the emergence of a diverse wheat yellow rust population. Genome Biology,16,1-15 DOI: https://doi.org/10.1186/s13059-015-0590-8
Ichiki, T. U., Shiba, T., Matsukura, K., Ueno, T., et al. (2013). Detection and diagnosis of rice-infecting viruses. Frontiers in Microbiology, 4, 289 DOI: https://doi.org/10.3389/fmicb.2013.00289
Kanzi, A. M., San, J. E., Chimukangara, B., Ueno, T., et al. (2020). Next Generation Sequencing and Bioinformatics Analysis of Family Genetic Inheritance. Frontiers in Genetics,11, 1250 DOI: https://doi.org/10.3389/fgene.2020.544162
Karimi, K., Arzanlou, M., Pertot, I. (2020). Development of novel species-specific primers for the specific identification of Colletotrichum nymphaeae based on conventional PCR and LAMP techniques. European Journal of Plant Pathology,156, 463-475 DOI: https://doi.org/10.1007/s10658-019-01895-9
Kavita, V. (2017) DNA biosensors—a review. Journal Bioengineering and Biomedical Science, 7, 222 DOI: https://doi.org/10.4172/2155-9538.1000222
Kehoe, M. A., Coutts, B. A., Buirchell, B. J., Jones, R. A. (2014). Plant virology and next generation sequencing: experiences with a Potyvirus. PLoS One, 9, e104580 DOI: https://doi.org/10.1371/journal.pone.0104580
Klap, C., Luria, N., Smith, E., Bakelman, E., et al. (2020). The Potential Risk of Plant-Virus Disease Initiation by Infected Tomatoes. Plants, 9, 623 DOI: https://doi.org/10.3390/plants9050623
Koyun, A., Ahlatcolu, E., Koca, Y., & Kara, S. (2012). Biosensors and their principles. A Roadmap of Biomedical Engineers and Milestones. InTech, 117-142 DOI: https://doi.org/10.5772/48824
Lafar, S., Zro, K., & Ennaji, M. M. (2020). Capripoxvirus Diseases: Current updates and developed strategies for control. In Ennaji, M.M. (Ed.). Emerging and Reemerging Viral Pathogens. United States: Academic Press DOI: https://doi.org/10.1016/B978-0-12-819400-3.00028-4
Lau, H. Y., & Botella, J. R. (2017). Advanced DNA-based point-of-care diagnostic methods for plant diseases detection. Frontiers in Plant Science, 8, 2016 DOI: https://doi.org/10.3389/fpls.2017.02016
Lau, H. Y., Palanisamy, R., Trau, M., & Botella, J. R. (2014). Molecular inversion probe: a new tool for highly specific detection of plant pathogens. PloS One, 9, e111182 DOI: https://doi.org/10.1371/journal.pone.0111182
Lau, H. Y., Wu, H., & Wee, E. J., (2017). Specific and sensitive isothermal electrochemical biosensor for plant pathogen DNA detection with colloidal gold nanoparticles as probes. Scientific Reports, 7,1-7 DOI: https://doi.org/10.1038/srep38896
Lievens, B., Brouwer, M., Vanachter, A. C., Cammue, B. P, & Thomma, B. P. (2006). Real-time PCR for detection and quantification of fungal and oomycete tomato pathogens in plant and soil samples. Plant Science, 171, 155-165 DOI: https://doi.org/10.1016/j.plantsci.2006.03.009
Liu, L., Li, Y., Li, S., Hu, N., et al. (2012). Comparison of next-generation sequencing systems. Journal of Biomedicine and Biotechnology, 251364. doi: 10.1155/2012/251364 DOI: https://doi.org/10.1155/2012/251364
Luigi, M., Manglli, A., Bertin, S., Donati, L., et al. (2020). Development and validation of a specific real-time PCR protocol for the detection of tomato leaf curl New Delhi virus. European Journal of Plant Pathology,157, 969-974 DOI: https://doi.org/10.1007/s10658-020-02038-1
Luna-Moreno, D., Sánchez-Álvarez, A., Islas-Flores, I., Canto-Canche, B., et al. (2019). Early detection of the fungal banana black Sigatoka pathogen Pseudocercospora fijiensis by an SPR immunosensor method. Sensors, 19,465 DOI: https://doi.org/10.3390/s19030465
Malapi-Wight, M., Salgado-Salazar, C., Demers, J. E., Clement, D.L., et al. (2016). Sarcococca blight: Use of whole-genome sequencing for fungal plant disease diagnosis. Plant Disease,100, 1093–1100 DOI: https://doi.org/10.1094/PDIS-10-15-1159-RE
McCartney, H. A., Foster, S. J., Fraaije, B. A., & Ward, E. (2003). Molecular diagnostics for fungal plant pathogens. Pest Management Science: formerly Pesticide Science, 59, 129-142 DOI: https://doi.org/10.1002/ps.575
Mori, Y., Hirano, T., & Notomi, T. (2006). Sequence specific visual detection of LAMP reactions by addition of cationic polymers. BMC biotechnology, 6, 1-10 DOI: https://doi.org/10.1186/1472-6750-6-3
Mullis, K. B. (1990). The unusual origin of the polymerase chain reaction. Scientific American, 262, 56-61 DOI: https://doi.org/10.1038/scientificamerican0490-56
Mullis, K. B., & Faloona, F. A. (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods in Enzymology,155, 335–350 DOI: https://doi.org/10.1016/0076-6879(87)55023-6
Murugan, L., Krishnan, N., Venkataravanappa, V., Saha, S., et al. (2020). Molecular characterization and race identification of Fusarium oxysporum f. sp. lycopersici infecting tomato in India. 3 Biotech, 10, 1-12 DOI: https://doi.org/10.1007/s13205-020-02475-z
Myerson, L. A., & Reaser, J. K. (2002). Biosecurity: Moving toward a comprehensive approach. Bioscience, 52,593-600 DOI: https://doi.org/10.1641/0006-3568(2002)052[0593:BMTACA]2.0.CO;2
Navin, N., Kendall, J., Troge, J., Rodgers, L., et al. (2011).Tumour evolution inferred by single-cell sequencing. Nature, 472, 90-94 DOI: https://doi.org/10.1038/nature09807
Notomi, T., Okayama, H., Masubuchi, H., Yonekawa, T., et al. (2000). Loop-mediated isothermal amplification of DNA. Nucleic Acids Research, 28, E63 DOI: https://doi.org/10.1093/nar/28.12.e63
Oono, Y., Kobayashi, F., Kawahara, Y., Yazawa, T., et al. (2013). Characterisation of the wheat (triticumaestivum L.) transcriptome by de novo assembly for the discovery of phosphate starvation-responsive genes: gene expression in Pi-stressed wheat. BMC Genomics, 14, 1-14 DOI: https://doi.org/10.1186/1471-2164-14-77
Pabinger, S., Dander, A., Fischer, M., Snajder, R., et al. (2014). A survey of tools for variant analysis of next-generation genome sequencing data. Briefings in bioinformatics, 15, 256-278 DOI: https://doi.org/10.1093/bib/bbs086
Panteghini, M., & Forest, J. C. (2005). Standardization in laboratory medicine: new challenges. Clinica Chimica Acta, 355, 1-12 DOI: https://doi.org/10.1016/j.cccn.2004.12.003
Peña-Bahamonde, J., Nguyen, H. N., Fanourakis, S. K., & Rodrigues, D. F. (2018). Recent advances in graphene-based biosensor technology with applications in life sciences. Journal of Nanobiotechnology,16,75 DOI: https://doi.org/10.1186/s12951-018-0400-z
Piombo, E., Abdelfattah, A., Droby, S., Wisniewski, M., et al. (2021). Metagenomics approaches for the detection and surveillance of emerging and recurrent plant pathogens. Microorganisms, 9, 188 DOI: https://doi.org/10.3390/microorganisms9010188
Qin, D. (2019). Next-generation sequencing and its clinical application. Cancer Biology and Medicine,16,4-10 DOI: https://doi.org/10.20892/j.issn.2095-3941.2018.0055
Qin, J., Li, R., Raes, J., Arumugam, M., et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature,464,59-65 DOI: https://doi.org/10.1038/nature08821
Rahman, M., Heng, L.Y., & Futra, D., (2017). A highly sensitive electrochemical DNA biosensor from acrylic-gold nanocomposite for the determination of arowana fish gender. Nanoscale Research Letters,12,484 DOI: https://doi.org/10.1186/s11671-017-2254-y
Rajesh T, & Jaya M (2017) Next-generation sequencing methods. In Christian, L., Sanroman, D., Du, M. (Eds.), Current Developments in Biotechnology and Bioengineering.Amsterdam: Elsevier DOI: https://doi.org/10.1016/B978-0-444-63667-6.00007-9
Rani, A., Donovan, N., & Mantri, N. (2019). Review: The future of plant pathogen diagnostics in a nursery production system. Biosensors and Bioelectronics,145,111631 DOI: https://doi.org/10.1016/j.bios.2019.111631
Rizzo, D, M., Lichtveld, M., Mazet, J. A., Togami, E., & Miller, S. A. (2021). Plant health and its effects on food safety and security in a One Health framework: Four case studies. One Health Outlook, 3, 1-9 DOI: https://doi.org/10.1186/s42522-021-00038-7
Ronholm, J. (2018). Game Changer-Next Generation Sequencing and Its Impact on Food Microbiology. Frontiers in Microbiology, 9, 363 DOI: https://doi.org/10.3389/fmicb.2018.00363
Sakamoto, S., Putalun, W., Vimolmangkang, S., Phoolcharoen, W., et al. (2018). Enzyme-linked immunosorbent assay for the quantitative/qualitative analysis of plant secondary metabolites. Journal of Natural Medicines, 72, 32-42 DOI: https://doi.org/10.1007/s11418-017-1144-z
Sakudo, A., Suganuma, Y., Kobayashi, T., Onodera, T., Ikuta, K. (2006). Near-infrared spectroscopy: promising diagnostic tool for viral infections. Biochemical and Biophysical Research Communications,341, 279-284 DOI: https://doi.org/10.1016/j.bbrc.2005.12.153
Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences,74, 5463–5467 DOI: https://doi.org/10.1073/pnas.74.12.5463
Sarkes, A., Fu, H., Feindel, D., Harding, M., & Feng, J. (2020). Development and evaluation of a loop-mediated isothermal amplification (LAMP) assay for the detection of Tomato brown rugose fruit virus (ToBRFV). PLoS One,15,e0230403 DOI: https://doi.org/10.1371/journal.pone.0230403
Savary, S., Bregaglio, S., Willocquet, L., Gustafson, D., et al. (2017). Crop health and its global impacts on the components of food security. Food Security, 9, 311–27 DOI: https://doi.org/10.1007/s12571-017-0659-1
Scala, V., Pucci, N., & Loreti, S. (2018). The diagnosis of plant pathogenic bacteria: A state of art. Frontiers in Bioscience, 10, 449-460 DOI: https://doi.org/10.2741/e832
Shweta, H. M., Kumar, M. P., Teli, K., Kunduru, B., & Shekar, B. C. (2018). Isolation, identification and molecular characterization of Ralstonia solanacerum isolates collected from Southern Karnataka. Journal of Applied and Natural Science, 10, 886-893 DOI: https://doi.org/10.31018/jans.v10i3.1747
Skottrup, P. D, Nicolaisen, M., & Justesen, A. F. (2008). Towards on-site pathogen detection using antibody-based sensors. Biosensors and Bioelectronics, 24,339-348 DOI: https://doi.org/10.1016/j.bios.2008.06.045
Smith, C. J., & Osborn, A. M. (2009). Advantages and limitations of quantitative PCR (Q-PCR)-based approaches in microbial ecology. FEMS microbiology ecology, 67, 6-20 DOI: https://doi.org/10.1111/j.1574-6941.2008.00629.x
Stackhouse, T., Martinez-Espinoza, A. D., & Ali, M. E. (2020). Turfgrass disease diagnosis: Past, present, and future. Plants, 9, 1544 DOI: https://doi.org/10.3390/plants9111544
Tian, Y. L., Zhao, Y. Q., Chen, B. H., Chen, S., et al. (2020). Real-time PCR assay for detection of Dickeyafangzhongdai causing bleeding canker of pear disease in China. Journal of Integrative Agriculture,19, 898-905 DOI: https://doi.org/10.1016/S2095-3119(19)62881-9
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 DOI: https://doi.org/10.1128/AEM.00161-07
Tomlinson, J., & Boonham, N. (2008). Potential of LAMP for detection of plant pathogens. CAB Reviews: Perspectives in Agriculture, Veterinary Science, Nutrition and Natural Resources, 3, 1-7 DOI: https://doi.org/10.1079/PAVSNNR20083066
Vigneshvar, S., Sudhakumari, C. C., Senthilkumaran, B., & Prakash, H. (2016). Recent advances in biosensor technology for potential applications–an overview. Frontiers in Bioengineering and Biotechnology, 4, 11 DOI: https://doi.org/10.3389/fbioe.2016.00011
Vincelli, P., Tisserat, N. (2008). Nucleic acid–based pathogen detection in applied plant pathology. Plant Disease, 92, 660-669 DOI: https://doi.org/10.1094/PDIS-92-5-0660
Waliullah, S., Ling, K. S., Cieniewicz, E. J., Oliver. J.E., et al. (2020). Development of loop-mediated isothermal amplification
assay for rapid detection of Cucurbit leaf crumple virus. International Journal of Molecular Sciences, 21, 1756
Walker, T. M., Ip, C. L .C., Harell, R. H., Evans, J.T., et al. (2013). Whole-genome sequencing to delineate Mycobacterium tuberculosis outbreaks: a retrospective observational study. The Lancet Infectious Diseases, 13, 137-146 DOI: https://doi.org/10.1016/S1473-3099(12)70277-3
Wang, Z., Yu, D., Li. X., Zeng, M., et al. (2012). The development and application of a Dot-ELISA assay for diagnosis of southern rice black streaked dwarf disease in the field. Viruses, 4, 167-183 DOI: https://doi.org/10.3390/v4010167
White, S., Schultz, T., & Enuameh, Y. A. K. (2011). Synthesizing evidence of diagnostic accuracy. Philadelphia: Lippincott Williams & Wilkins
Zhang, M., Chen, R., Zhou, X., & Wu, J. (2018). Monoclonal antibody-based serological detection methods for wheat dwarf virus. Virologica Sinica, 33, 173-180 DOI: https://doi.org/10.1007/s12250-018-0024-3
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