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Luigi M, Taglienti A, Corrado CL, Cardoni M, Botti S, Bissani R, Casati P, Passera A, Miotti N, De Jonghe K, Everaert E, Olmos A, Ruiz-García AB, Faggioli F. Development and Validation of a Duplex RT-qPCR for Detection of Peach Latent Mosaic Viroid and Comparison of Different Nucleic-Acid-Extraction Protocols. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091802. [PMID: 37176860 PMCID: PMC10181016 DOI: 10.3390/plants12091802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023]
Abstract
Peach latent mosaic viroid (PLMVd) is an important pathogen that causes disease in peaches. Control of this viroid remains problematic because most PLMVd variants are symptomless, and although there are many detection tests in use, the reliability of PCR-based methods is compromised by the complex, branched secondary RNA structure of the viroid and its genetic diversity. In this study, a duplex RT-qPCR method was developed and validated against two previously published single RT-qPCRs, which were potentially able to detect all known PLMVd variants when used in tandem. In addition, in order to simplify the sample preparation, rapid-extraction protocols based on the use of crude sap or tissue printing were compared with commercially available RNA purification kits. The performance of the new procedure was evaluated in a test performance study involving five participant laboratories. The new method, in combination with rapid-sample-preparation approaches, was demonstrated to be feasible and reliable, with the advantage of detecting all different PLMVd isolates/variants assayed in a single reaction, reducing costs for routine diagnosis.
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Affiliation(s)
- Marta Luigi
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Anna Taglienti
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Carla Libia Corrado
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
| | - Marco Cardoni
- CAV-Centro Attività Vivaistiche, 48018 Faenza, Italy
| | - Simona Botti
- CAV-Centro Attività Vivaistiche, 48018 Faenza, Italy
| | - Rita Bissani
- CAV-Centro Attività Vivaistiche, 48018 Faenza, Italy
| | - Paola Casati
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Alessandro Passera
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Niccolò Miotti
- Department of Agricultural and Environmental Sciences-Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy
| | - Kris De Jonghe
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Ellen Everaert
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Antonio Olmos
- IVIA Instituto Valenciano de Investigaciones Agrarias, 46113 Valencia, Spain
| | - Ana B Ruiz-García
- IVIA Instituto Valenciano de Investigaciones Agrarias, 46113 Valencia, Spain
| | - Francesco Faggioli
- CREA Research Centre for Plant Protection and Certification, 00156 Rome, Italy
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2
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Lee HJ, Cho IS, Ju HJ, Jeong RD. Development of a reverse transcription droplet digital PCR assay for sensitive detection of peach latent mosaic viroid. Mol Cell Probes 2021; 58:101746. [PMID: 34102255 DOI: 10.1016/j.mcp.2021.101746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Peach latent mosaic viroid (PLMVd) represents a continuing threat to peach tree production worldwide. In this study, a sensitive and accurate quantification of PLMVd in peach leaves was established using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The quantitative linearity, accuracy, and sensitivity of RT-ddPCR for the detection of PLMVd were comparatively assessed to those of reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) assay. The specificity assay shows no amplification in major peach viruses, apple chlorotic leaf spot virus and prunus necrotic ring spot virus and negative control. Furthermore, the levels of PLMVd transcripts determined using RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. Our results also indicated that the RT-ddPCR assay is at least two-fold more sensitive than qPCR and could therefore, be used to detect PLMVd in field samples. Moreover, optimization of RT-ddPCR was found to enhance the sensitivity of PLMVd detection in the peach leaf samples with low viral loads. In summary, the established RT-ddPCR assay represents a promising alternative method for the precise quantitative detection of PLMVd; it would be particularly applicable for diagnosing PLMVd infections in plant quarantine inspection and PLMVd-free certification program.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, Republic of Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju-si, 54896, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea.
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Pappi PG, Fotiou I, Efthimiou KE, Katis NI, Maliogka VI. Development of three duplex real-time RT-PCR assays for the sensitive and rapid detection of a phytoplasma and five viral pathogens affecting stone fruit trees. Mol Cell Probes 2020; 53:101621. [PMID: 32603761 DOI: 10.1016/j.mcp.2020.101621] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/27/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Three duplex real-time reverse-transcription polymerase chain reaction (real-time RT-PCR) assays based on TaqMan chemistry, were developed for the simultaneous detection and specific quantification of apple chlorotic leafspot virus (ACLSV), plum pox virus (PPV), prunus necrotic ringspot virus (PNRSV), prune dwarf virus (PDV), peach latent mosaic viroid (PLMVd) and the European stone fruit yellows (ESFY) phytoplasma, which are considered among the most important pathogens affecting stone fruit trees. The quantitative RT-PCR (RT-qPCR) assays were optimized using RNA transcripts (linearized plasmid was used for the assay optimization of the ESFY phytoplasma) of known concentrations. No differences in sensitivity were recorded between the duplex and singleplex RT-qPCR assays. The amplification efficiency of the duplex assays reached 91.1-95.8%, while the linear range of quantification was from 20 to 2 × 107 RNA/linearized plasmid transcripts for PLMVd and ESFY phytoplasma, 40 to 4 × 107 RNA transcripts for ACLSV, PPV and PDV, and 102 to 108 RNA transcripts for PNRSV, respectively. The duplex RT-qPCR assays, which were validated using both characterized isolates from all pathogens and field samples from Prunus species in Northern Greece, exhibited a broad detection range. Overall, the developed methods comprise useful tools that could be applied for the simultaneous and reliable detection of graft-transmissible pathogens in certification programs of Prunus spp.
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Affiliation(s)
- Polyxeni G Pappi
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Ioanna Fotiou
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Konstantinos E Efthimiou
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Nikolaos I Katis
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece
| | - Varvara I Maliogka
- Laboratory of Plant Pathology, School of Agriculture, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, University Campus, Thessaloniki, Greece.
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Serra P, Bertolini E, Martínez MC, Cambra M, Flores R. Interference between variants of peach latent mosaic viroid reveals novel features of its fitness landscape: implications for detection. Sci Rep 2017; 7:42825. [PMID: 28211491 PMCID: PMC5314366 DOI: 10.1038/srep42825] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 01/13/2017] [Indexed: 12/05/2022] Open
Abstract
Natural populations of peach latent mosaic viroid (PLMVd) are complex mixtures of variants. During routine testing, TaqMan rtRT-PCR and RNA gel-blot hybridization produced discordant results with some PLMVd isolates. Analysis of the corresponding populations showed that they were exclusively composed of variants (of class II) with a structural domain different from that of the reference and many other variants (of class I) targeted by the TaqMan rtRT-PCR probe. Bioassays in peach revealed that a representative PLMVd variant of class II replicated without symptoms, generated a progeny with low nucleotide diversity, and, intriguingly, outcompeted a representative symptomatic variant of class I when co-inoculated in equimolecular amounts. A number of informative positions associated with the higher fitness of variants of class II have been identified, and novel sets of primers and probes for universal or specific TaqMan rtRT-PCR detection of PLMVd variants have been designed and tested.
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Affiliation(s)
- Pedro Serra
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Spain
| | - Edson Bertolini
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
- Departamento de Fitossanidade, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil
| | - M. Carmen Martínez
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Mariano Cambra
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Ricardo Flores
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Spain
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Kushalappa AC, Gunnaiah R. Metabolo-proteomics to discover plant biotic stress resistance genes. TRENDS IN PLANT SCIENCE 2013; 18:522-31. [PMID: 23790252 DOI: 10.1016/j.tplants.2013.05.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Revised: 04/26/2013] [Accepted: 05/17/2013] [Indexed: 05/23/2023]
Abstract
Plants continuously encounter various environmental stresses and use qualitative and quantitative measures to resist pathogen attack. Qualitative stress responses, based on monogenic inheritance, have been elucidated and successfully used in plant improvement. By contrast, quantitative stress responses remain largely unexplored in plant breeding, due to complex polygenic inheritance, although hundreds of quantitative trait loci for resistance have been identified. Recent advances in metabolomic and proteomic technologies now offer opportunities to overcome the hurdle of polygenic inheritance and identify candidate genes for use in plant breeding, thus improving the global food security. In this review, we describe a conceptual background to the plant-pathogen relationship and propose ten heuristic steps streamlining the application of metabolo-proteomics to improve plant resistance to biotic stress.
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Affiliation(s)
- Ajjamada C Kushalappa
- Plant Science Department, McGill University, Sainte-Anne-de-Bellevue, Quebec, H9X 3V9, Canada.
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Zhang Y, Yin J, Jiang D, Xin Y, Ding F, Deng Z, Wang G, Ma X, Li F, Li G, Li M, Li S, Zhu S. A universal oligonucleotide microarray with a minimal number of probes for the detection and identification of viroids at the genus level. PLoS One 2013; 8:e64474. [PMID: 23734201 PMCID: PMC3667192 DOI: 10.1371/journal.pone.0064474] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 04/15/2013] [Indexed: 11/19/2022] Open
Abstract
A major challenge in the agricultural industry is the development of techniques that can screen plant samples for viroid infection. Microarrays are promising in this regard, as their high throughput nature can potentially allow for the detection of a range of viroids in a single test. In this paper we present a microarray that can detect a wide spectrum of all 8 reported viroid genera including 37 known plant viroid species. The array was constructed using an automated probe design protocol which generated a minimal number of probes to detect viroids at the genus level. The designed microarray showed a high specificity and sensitivity when tested with a set of standard virus samples. Finally, the microarray was applied to screen infected field samples, with Hop stunt viroid infection identified as the major disease causing pathogen for an infected citrus sample.
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Affiliation(s)
- Yongjiang Zhang
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Jun Yin
- School of Medicine and Medical Science, Conway Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Dongmei Jiang
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanyan Xin
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Fang Ding
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ziniu Deng
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, China
| | - Guoping Wang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Xianfeng Ma
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, China
| | - Fang Li
- Horticulture and Landscape College, Hunan Agricultural University, Changsha, China
| | - Guifen Li
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Mingfu Li
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Shifang Li
- State Key Laboratory of Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuifang Zhu
- Chinese Academy of Inspection and Quarantine, Beijing, China
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Abreu PMV, Piccin JG, Rodrigues SP, Buss DS, Ventura JA, Fernandes PMB. Molecular diagnosis of Papaya meleira virus (PMeV) from leaf samples of Carica papaya L. using conventional and real-time RT-PCR. J Virol Methods 2011; 180:11-7. [PMID: 22193169 DOI: 10.1016/j.jviromet.2011.12.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Revised: 12/01/2011] [Accepted: 12/06/2011] [Indexed: 01/02/2023]
Abstract
Papaya meleira virus (PMeV) is the causal agent of papaya sticky disease. This study describes two methods for molecular diagnosis of PMeV using conventional and real-time PCR. These methods were shown to be more efficient than current methods of viral detection using extraction of PMeV dsRNA and observation of symptoms in the field. The methods described here were used to evaluate the effect of inoculation of papaya plants with purified PMeV dsRNA on the progress of PMeV infection. A single inoculation with PMeV dsRNA was observed to delay the progress of the virus infection by several weeks. The possibility of vertical transmission of PMeV was also investigated. No evidence was found for PMeV transmission through seeds collected from diseased fruit. The implications of these results for the epidemiology of PMeV and the management of papaya sticky disease are discussed.
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Affiliation(s)
- Paolla M V Abreu
- Núcleo de Biotecnologia, Universidade Federal do Espírito Santo, Av. Marechal Campos, 1468, 29040-090, Vitória, ES, Brazil
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