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Lacomme C, Holmes R, Evans F. Molecular and serological methods for the diagnosis of viruses in potato tubers. Methods Mol Biol 2015; 1302:161-176. [PMID: 25981254 DOI: 10.1007/978-1-4939-2620-6_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Viruses cause important diseases to potato crops. Monitoring virus content in plant material for quarantine or seed certification scheme purposes is essential to prevent the spread of viruses and to minimize the impact of viral diseases. There are currently two main methods for virus diagnosis in potato tubers: growing-on ELISA testing which requires breaking tuber dormancy followed by an ELISA test on grown plantlets and direct real-time RT-PCR testing on tubers. This chapter will describe both methods that can be adapted for large-scale virus testing activities.
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Affiliation(s)
- Christophe Lacomme
- Science and Advice for Scottish Agriculture (SASA), Roddinglaw Road, Edinburgh, EH12 9FJ, UK,
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2
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Fageria MS, Singh M, Nanayakkara U, Pelletier Y, Nie X, Wattie D. Monitoring Current-Season Spread of Potato virus Y in Potato Fields Using ELISA and Real-Time RT-PCR. PLANT DISEASE 2013; 97:641-644. [PMID: 30722193 DOI: 10.1094/pdis-03-12-0283-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The current-season spread of Potato virus Y (PVY) was investigated in New Brunswick, Canada, in 11 potato fields planted with six different cultivars in 2009 and 2010. In all, 100 plants selected from each field were monitored for current-season PVY infections using enzyme-linked immunosorbent assay (ELISA) and real-time reverse-transcription polymerase chain reaction (RT-PCR) assay. Average PVY incidence in fields increased from 0.6% in 2009 and 2% in 2010 in the leaves to 20.3% in 2009 and 21.9% in 2010 in the tubers at the time of harvest. In individual fields, PVY incidence in tubers reached as high as 37% in 2009 and 39% in 2010 at the time of harvest. Real-time RT-PCR assay detected more samples with PVY from leaves than did ELISA. A higher number of positive samples was also detected with real-time RT-PCR from growing tubers compared with the leaves collected from the same plant at the same sampling time. PVY incidence determined from the growing tubers showed a significant positive correlation with the PVY incidence of tubers after harvest. Preharvest testing provides another option to growers to either top-kill the crop immediately to secure the seed market when the PVY incidence is low or leave the tubers to develop further for table or processing purposes when incidence of PVY is high.
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Affiliation(s)
| | - Mathuresh Singh
- Agricultural Certification Services, Fredericton, NB, Canada E3B 8B7
| | - Upeksha Nanayakkara
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada E3B 4Z7
| | - Yvan Pelletier
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada E3B 4Z7
| | - Xianzhou Nie
- Potato Research Centre, Agriculture and Agri-Food Canada, Fredericton, NB, Canada E3B 4Z7
| | - David Wattie
- New Brunswick Department of Agriculture, Aquaculture and Fisheries, Wicklow, NB, Canada E7L 3S4
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Mehle N, Ravnikar M. Plant viruses in aqueous environment - survival, water mediated transmission and detection. WATER RESEARCH 2012; 46:4902-17. [PMID: 22871317 DOI: 10.1016/j.watres.2012.07.027] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 07/12/2012] [Accepted: 07/15/2012] [Indexed: 05/09/2023]
Abstract
The presence of plant viruses outside their plant host or insect vectors has not been studied intensively. This is due, in part, to the lack of effective detection methods that would enable their detection in difficult matrixes and in low titres, and support the search for unknown viruses. Recently, new and sensitive methods for detecting viruses have resulted in a deeper insight into plant virus movement through, and transmission between, plants. In this review, we have focused on plant viruses found in environmental waters and their detection. Infectious plant pathogenic viruses from at least 7 different genera have been found in aqueous environment. The majority of the plant pathogenic viruses so far recovered from environmental waters are very stable, they can infect plants via the roots without the aid of a vector and often have a wide host range. The release of such viruses from plants can lead to their dissemination in streams, lakes, and rivers, thereby ensuring the long-distance spread of viruses that otherwise, under natural conditions, would remain restricted to limited areas. The possible sources and survival of plant viruses in waters are therefore discussed. Due to the widespread use of hydroponic systems and intensive irrigation in horticulture, the review is focused on the possibility and importance of spreading viral infection by water, together with measures for preventing the spread of viruses. The development of new methods for detecting multiple plant viruses at the same time, like microarrays or new generation sequencing, will facilitate the monitoring of environmental waters and waters used for irrigation and in hydroponic systems. It is reasonable to expect that the list of plant viruses found in waters will thereby be expanded considerably. This will emphasize the need for further studies to determine the biological significance of water-mediated transport.
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Affiliation(s)
- Nataša Mehle
- National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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Cheng J, Jiang Y, Rao P, Wu H, Dong Q, Wu Z, Ding X, Guo J. Development of a single-tube multiplex real-time PCR for detection and identification of five pathogenic targets by using melting-curve analysis with EvaGreen. Arch Virol 2012; 158:379-86. [PMID: 23053522 DOI: 10.1007/s00705-012-1493-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 08/21/2012] [Indexed: 12/18/2022]
Abstract
SYBR Green I (SG) is widely used in real-time PCR applications as an intercalating dye. Preferential binding of SG during PCR and inhibition of PCR often result in failure to detect multiple amplicons in multiplex reactions. In the present study, a novel single-tube, multiplex real-time PCR with EvaGreen dye (EG) was developed and evaluated for simultaneous detection of pathogenic targets by using five potato viruses as models. The PCR products obtained using five sets of specific primers were analyzed by melting curve analysis. The assay could specifically detect and differentiate the five potato viruses by producing a distinct peak for each amplification product and exhibited a high reproducibility with coefficients of variation from 0.01 to 0.25 %. Detection sensitivity of the assay ranged from 100 to 500 copies/μL for each virus. The results of this study demonstrate that multiplex real-time PCR and melting-curve analysis with EG is a sensitive, specific and inexpensive method for simultaneous detection of multiple pathogens.
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Affiliation(s)
- Juhui Cheng
- College of Life Sciences, Zhejiang Sci-Tech University, 2nd street, Xiasha, Hangzhou, 310018, China
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Real-time PCR assay for the discrimination and quantification of wheat and barley strains of Wheat dwarf virus. Virus Genes 2011; 44:349-55. [DOI: 10.1007/s11262-011-0699-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 12/03/2011] [Indexed: 10/14/2022]
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A single tube, quantitative real-time RT-PCR assay that detects four potato viruses simultaneously. J Virol Methods 2009; 161:289-96. [DOI: 10.1016/j.jviromet.2009.06.027] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 06/26/2009] [Accepted: 06/30/2009] [Indexed: 11/23/2022]
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Boonham N, Laurenson L, Weekes R, Mumford R. Direct detection of plant viruses in potato tubers using real-time PCR. Methods Mol Biol 2009; 508:249-258. [PMID: 19301760 DOI: 10.1007/978-1-59745-062-1_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Virus indexing of seed potatoes can be carried out by growing eye plugs to produce small plants and then testing them by ELISA, but this method is time consuming. Direct testing of the eye plugs by ELISA is not reliable, and so a method has been developed for the routine testing of seed potatoes for virus by PCR.
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Affiliation(s)
- Neil Boonham
- Central Science Laboratories, Sand Hutton, York, UK
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Agindotan BO, Shiel PJ, Berger PH. Simultaneous detection of potato viruses, PLRV, PVA, PVX and PVY from dormant potato tubers by TaqMan real-time RT-PCR. J Virol Methods 2007; 142:1-9. [PMID: 17276522 DOI: 10.1016/j.jviromet.2006.12.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2006] [Revised: 12/12/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
The requirements of sprouting dormant potato tubers for biological or serological assays or RNA extraction for nucleic acid and PCR assays add to the cost of virus screening. Recently, cheaper, reliable and more rapid methods for the screening of potato tuber-seed pieces for viruses have been developed that do not require sprouted tubers for indexing, including TaqMan real-time RT-PCR. Although the assays are often designed for minimal time and reagent use, they still require a time-consuming and laborious RNA extraction step. This paper describes an assay where four common potato-infecting viruses, Potato leafroll virus, Potato virus A, Potato virus X and Potato virus Y, were detected simultaneously from total RNA and saps of dormant potato tubers in a quadruplex real-time RT-PCR. Factors critical for the detection of these viruses in saps of dormant potato tubers included: optimum dilution and inhibition of RNAses, and the optimization of the reverse transcription and PCR steps. Potato virus detection directly from tuber saps was comparable to that from purified total plant RNA, and this represents significant savings of time and expense. The TaqMan system developed in this study detected between 200 and 400 copies of potato virus RNA.
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Affiliation(s)
- Bright O Agindotan
- University of Idaho, Department of Plant, Soil and Entomological Sciences, Moscow, ID 83844-2339, USA
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Fox A, Evans F, Browning I. Direct tuber testing for Potato Y potyvirus by real-time RT-PCR and ELISA: reliable options for post-harvest testing? ACTA ACUST UNITED AC 2005. [DOI: 10.1111/j.1365-2338.2005.00805.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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McCartney HA, Foster SJ, Fraaije BA, Ward E. Molecular diagnostics for fungal plant pathogens. PEST MANAGEMENT SCIENCE 2003; 59:129-142. [PMID: 12587866 DOI: 10.1002/ps.575] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Accurate identification of fungal phytopathogens is essential for virtually all aspects of plant pathology, from fundamental research on the biology of pathogens to the control of the diseases they cause. Although molecular methods, such as polymerase chain reaction (PCR), are routinely used in the diagnosis of human diseases, they are not yet widely used to detect and identify plant pathogens. Here we review some of the diagnostic tools currently used for fungal plant pathogens and describe some novel applications. Technological advances in PCR-based methods, such as real-time PCR, allow fast, accurate detection and quantification of plant pathogens and are now being applied to practical problems. Molecular methods have been used to detect several pathogens simultaneously in wheat, and to study the development of fungicide resistance in wheat pathogens. Information resulting from such work could be used to improve disease control by allowing more rational decisions to be made about the choice and use of fungicides and resistant cultivars. Molecular methods have also been applied to the study of variation in plant pathogen populations, for example detection of different mating types or virulence types. PCR-based methods can provide new tools to monitor the exposure of a crop to pathogen inoculum that are more reliable and faster than conventional methods. This information can be used to improve disease control decision making. The development and application of molecular diagnostic methods in the future is discussed and we expect that new developments will increase the adoption of these new technologies for the diagnosis and study of plant disease.
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Affiliation(s)
- H Alastair McCartney
- Plant Pathogen Interactions Division, IACR-Rothamsted, Harpenden, Herts AL5 2JQ, UK
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Boonham N, Walsh K, Preston S, North J, Smith P, Barker I. The detection of tuber necrotic isolates of Potato virus Y, and the accurate discrimination of PVY(O), PVY(N) and PVY(C) strains using RT-PCR. J Virol Methods 2002; 102:103-12. [PMID: 11879698 DOI: 10.1016/s0166-0934(02)00008-3] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potato tuber necrotic ringspot disease (PTNRD) is a damaging disease of potatoes, causing unsightly necrotic rings on the surface of tubers. The causal agent is thought to be tuber necrotic isolates of Potato virus Y, known as PVY(NTN). The disease spoils tubers for processing and table use, and the lack of a diagnostic method makes control especially difficult. The development of an RT-PCR assay for the reliable detection of PVY(NTN) and discrimination of all the main strains of PVY (PVY(O), PVY(N) and PVY(C)) is described. An assay was developed, exploiting a recombination site in the coat protein of PVY(NTN), allowing more reliable diagnosis of these isolates. Although the conserved nucleotide differences observed between the strains was very small, competitive PCR and mutagenically separated PCR were both employed in the development of a robust assay. The assay was found to be more reliable than the most commonly used RT-PCR method, and should prove to be an important tool in the confirmation of symptoms and for the detection of PVY(NTN) in symptomless tissue, in disease surveys and seed health schemes.
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Affiliation(s)
- Neil Boonham
- Central Science Laboratory, Sand Hutton, YO41 1LZ, York, UK.
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