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Shymanovich T, Saville AC, Paul R, Wei Q, Ristaino JB. Rapid Detection of Viral, Bacterial, Fungal, and Oomycete Pathogens on Tomatoes with Microneedles, LAMP on a Microfluidic Chip, and Smartphone Device. PHYTOPATHOLOGY 2024:PHYTO12230481R. [PMID: 38829831 DOI: 10.1094/phyto-12-23-0481-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
Abstract
Rapid detection of plant diseases before they escalate can improve disease control. Our team has developed rapid nucleic acid extraction methods with microneedles and combined these with loop-mediated amplification (LAMP) assays for pathogen detection in the field. In this work, we developed LAMP assays for early blight (Alternaria linariae, A. alternata, and A. solani) and bacterial spot of tomato (Xanthomonas perforans) and validated these LAMP assays and two previously developed LAMP assays for tomato spotted wilt virus and late blight. Tomato plants were inoculated, and disease severity was measured. Extractions were performed using microneedles, and LAMP assays were run in tubes (with hydroxynaphthol blue) on a heat block or on a newly designed microfluidic slide chip on a heat block or a slide heater. Fluorescence on the microfluidic chip slides was visualized using EvaGreen and photographed on a smartphone. Plants inoculated with X. perforans or tomato spotted wilt virus tested positive prior to visible disease symptoms, whereas Phytophthora infestans and A. linariae were detected at the time of visual disease symptoms. LAMP assays were more sensitive than PCR, and the limit of detection was 1 pg of DNA for both A. linariae and X. perforans. The LAMP assay designed for early blight detected all three species of Alternaria that infect tomato and is thus an Alternaria spp. assay. This study demonstrates the utility of rapid microneedle extraction followed by LAMP on a microfluidic chip for rapid diagnosis of four important tomato pathogens.
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Affiliation(s)
- Tatsiana Shymanovich
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
| | - Amanda C Saville
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
| | - Rajesh Paul
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC
| | - Qingshan Wei
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC
- Emerging Plant Disease and Global Food Security Cluster, Plant Sciences Initiative, North Carolina State University, Raleigh, NC
| | - Jean Beagle Ristaino
- Department of Entomology and Plant Pathology, North Carolina State University, Raleigh, NC
- Emerging Plant Disease and Global Food Security Cluster, Plant Sciences Initiative, North Carolina State University, Raleigh, NC
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Çelik A, Emiralioğlu O, Yeken MZ, Çiftçi V, Özer G, Kim Y, Baloch FS, Chung YS. A novel study on bean common mosaic virus accumulation shows disease resistance at the initial stage of infection in Phaseolus vulgaris. Front Genet 2023; 14:1136794. [PMID: 37021006 PMCID: PMC10067576 DOI: 10.3389/fgene.2023.1136794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/06/2023] [Indexed: 04/07/2023] Open
Abstract
Accurate and early diagnosis of bean common mosaic virus (BCMV) in Phaseolus vulgaris tissues is critical since the pathogen can spread easily and have long-term detrimental effects on bean production. The use of resistant varieties is a key factor in the management activities of BCMV. The study reported here describes the development and application of a novel SYBR Green-based quantitative real-time PCR (qRT-PCR) assay targeting the coat protein gene to determine the host sensitivity to the specific NL-4 strain of BCMV. The technique showed high specificity, validated by melting curve analysis, without cross-reaction. Further, the symptoms development of twenty advanced common bean genotypes after mechanical BCMV-NL-4 infection was evaluated and compared. The results showed that common bean genotypes exhibit varying levels of host susceptibility to this BCMV strain. The YLV-14 and BRS-22 genotypes were determined as the most resistant and susceptible genotypes, respectively, in terms of aggressiveness of symptoms. The accumulation of BCMV was analyzed in the resistant and susceptible genotypes 3, 6, and 9 days following the inoculation by the newly developed qRT-PCR. The mean cycle threshold (Ct) values showed that the viral titer was significantly lower in YLV-14, which was evident in both root and leaf 3 days after the inoculation. The qRT-PCR thus facilitated an accurate, specific, and feasible assessment of BCMV accumulation in bean tissues even in low virus titers, allowing novel clues in selecting resistant genotypes in the early stages of infection, which is critical for disease management. To the best of our knowledge, this is the first study of a successfully performed qRT-PCR to estimate BCMV quantification.
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Affiliation(s)
- Ali Çelik
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yoonha Kim
- Laboratory of Crop Production, Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
- *Correspondence: Ali Çelik, ; Göksel Özer, ; Faheem Shehzad Baloch, ; Yong Suk Chung,
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Rubio L, Giménez K, Romero J, Font-San-Ambrosio MI, Alfaro-Fernández A, Galipienso L. Detection and absolute quantitation of watermelon mosaic virus by real-time RT-PCR with a TaqMan probe. J Virol Methods 2021; 300:114416. [PMID: 34896120 DOI: 10.1016/j.jviromet.2021.114416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 10/20/2021] [Accepted: 12/08/2021] [Indexed: 10/19/2022]
Abstract
Watermelon mosaic virus (WMV) causes serious damage to several crops worldwide, mainly cucurbits. Disease control is based on preventing spread and search for natural resistances for plant breeding, which requires tools for sensitive detection and precise quantitation. We developed a procedure based on reverse transcription followed by real-time quantitative polymerase chain reaction (RT-qPCR) with a primer pair and a TaqMan® probe specific for WMV. The primers and probe were designed from conserved sequence stretches to target a wide range of WMV isolates. A standard curve performed with transcripts enabled estimation of WMV RNA copies per ng of total RNA, with a wide dynamic range and sensitivity (104 to 1011). This RT-qPCR was assayed with field samples from different cucurbits and used to evaluate the temporal accumulation in pumpkin plants.
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Affiliation(s)
- Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain.
| | - Karen Giménez
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | - Juan Romero
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
| | | | - Ana Alfaro-Fernández
- Grupo de Virología, Instituto Agroforestal Mediterráneo, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Luis Galipienso
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
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Bouagga S, Urbaneja A, Depalo L, Rubio L, Pérez-Hedo M. Zoophytophagous predator-induced defences restrict accumulation of the tomato spotted wilt virus. PEST MANAGEMENT SCIENCE 2020; 76:561-567. [PMID: 31283098 DOI: 10.1002/ps.5547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/13/2019] [Accepted: 07/04/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND The use of zoophytophagous predators in protected crops has been widely adopted to manage pests in southern Europe. We hypothesized that plant defence responses would be induced by zoophytophagous predators and this induction could affect plant virus occurrence; the phytophagy of these predators induces plant defences similarly to that of viral infection. Therefore, we evaluated whether or not mirid predator-activated plant defences limited the accumulation of Tomato Spotted Wilt Virus (TSWV) in mechanically infected sweet pepper. RESULTS Our results revealed TSWV accumulation in mirid-punctured plants to be significantly lower than in intact plants. This is most likely associated with the upregulation of the jasmonate acid pathway triggered by mirid phytophagy. CONCLUSION Activation of induced defences by mirid predators has been demonstrated for the first time to limit the accumulation of TSWV in sweet pepper. This novel approach can offer new control strategies for the management of plant diseases. © 2019 Society of Chemical Industry.
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Affiliation(s)
- Sarra Bouagga
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), Moncada, Spain
| | - Alberto Urbaneja
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), Moncada, Spain
| | - Laura Depalo
- DISTAL Department of Agricultural and Food Sciences, Alma Mater Studiorum. Università di Bologna, Bologna, Italy
| | - Luís Rubio
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), Moncada, Spain
| | - Meritxell Pérez-Hedo
- Instituto Valenciano de Investigaciones Agrarias (IVIA), Centro de Protección Vegetal y Biotecnología, (IVIA), Moncada, Spain
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Rubio L, Galipienso L, Ferriol I. Detection of Plant Viruses and Disease Management: Relevance of Genetic Diversity and Evolution. FRONTIERS IN PLANT SCIENCE 2020; 11:1092. [PMID: 32765569 PMCID: PMC7380168 DOI: 10.3389/fpls.2020.01092] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/02/2020] [Indexed: 05/04/2023]
Abstract
Plant viruses cause considerable economic losses and are a threat for sustainable agriculture. The frequent emergence of new viral diseases is mainly due to international trade, climate change, and the ability of viruses for rapid evolution. Disease control is based on two strategies: i) immunization (genetic resistance obtained by plant breeding, plant transformation, cross-protection, or others), and ii) prophylaxis to restrain virus dispersion (using quarantine, certification, removal of infected plants, control of natural vectors, or other procedures). Disease management relies strongly on a fast and accurate identification of the causal agent. For known viruses, diagnosis consists in assigning a virus infecting a plant sample to a group of viruses sharing common characteristics, which is usually referred to as species. However, the specificity of diagnosis can also reach higher taxonomic levels, as genus or family, or lower levels, as strain or variant. Diagnostic procedures must be optimized for accuracy by detecting the maximum number of members within the group (sensitivity as the true positive rate) and distinguishing them from outgroup viruses (specificity as the true negative rate). This requires information on the genetic relationships within-group and with members of other groups. The influence of the genetic diversity of virus populations in diagnosis and disease management is well documented, but information on how to integrate the genetic diversity in the detection methods is still scarce. Here we review the techniques used for plant virus diagnosis and disease control, including characteristics such as accuracy, detection level, multiplexing, quantification, portability, and designability. The effect of genetic diversity and evolution of plant viruses in the design and performance of some detection and disease control techniques are also discussed. High-throughput or next-generation sequencing provides broad-spectrum and accurate identification of viruses enabling multiplex detection, quantification, and the discovery of new viruses. Likely, this technique will be the future standard in diagnostics as its cost will be dropping and becoming more affordable.
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Affiliation(s)
- Luis Rubio
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
- *Correspondence: Luis Rubio,
| | - Luis Galipienso
- Centro de Protección Vegetal y Biotecnology, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Inmaculada Ferriol
- Plant Responses to Stress Programme, Centre for Research in Agricultural Genomics (CRAG-CSIC_UAB-UB) Cerdanyola del Vallès, Barcelona, Spain
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Guerra JM, Hanes MA, Rasa C, Loganathan N, Innis-Whitehouse W, Gutierrez E, Nair S, Banu J. Modulation of bone turnover by Cissus quadrangularis after ovariectomy in rats. J Bone Miner Metab 2019; 37:780-795. [PMID: 30756174 DOI: 10.1007/s00774-018-0983-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/03/2018] [Indexed: 12/25/2022]
Abstract
In women, age-related bone loss is associated with increased risk of bone fracture. Existing therapies are associated with severe side effects; thus, there is a need to find alternative medicines with less or optimal side effects. Cissus quadrangularis (CQ), an Ayurvedic medicine used to enhance fracture healing, was tested for its bone protective properties and studied to discern the mechanism by which it is beneficial to bone. Female Sprague Dawley rats were either sham operated or ovariectomized and were fed CQ for 3 months. Several biochemical markers, cytokines and hormones were assayed. Femur, tibia and lumbar vertebrae were subjected to pQCT and µCT densitometry. MC3T3 cells were cultured, treated with CQ and used to analyze miRNA content and subjected to qPCR for gene expression analysis related to bone metabolism. CQO rats showed protected bone mass and microarchitecture of trabecular bone in the distal femoral metaphysis and the proximal tibial metaphysis. The lumbar vertebrae, however, showed no significant changes. Serum protein expression levels of P1NP increased and Trap5b and CTX levels decreased with in vivo CQ treatment. Some influence on the anti- and pro-inflammatory markers was also observed. Significantly high level of estradiol in the CQO rats was observed. In vitro expression of a few genes related to bone metabolism showed that osteocalcin increased significantly. The other genes-collagen I expression, SPP1, BMP2, DCAT1-decreased significantly. Certain miRNA that regulate bone turnover using the BMP pathway and Wnt signaling pathways were upregulated by CQ. qPCR after acute treatment with CQ showed significantly increased levels of osteocalcin and decreased levels of Wnt/β catenin antagonist DCAT1. Overall, CQ protected the microarchitecture of the long bones from ovariectomy-induced bone loss. This may be because of decreased inflammation and modulation through the BMP and Wnt signaling pathways. We conclude that CQ is a potential therapeutic agent to treat postmenopausal osteoporosis with no side effects.
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Affiliation(s)
- Juan M Guerra
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, 1201, W University Dr., Edinburg, TX, 78539, USA
- Department of Biology, University of Texas Rio Grande Valley, 1201, W University Dr., Edinburg, TX, 78539, USA
| | - Martha A Hanes
- Department of Lab Animal Resources, University of Texas Health at San Antonio, 7703 Floyd Curl Dr, San Antonio, TX 78229, USA
| | - Cordelia Rasa
- Department of Lab Animal Resources, University of Texas Rio Grande Valley, 1201, W University Dr, Edinburg, TX 78539, USA
| | | | - Wendy Innis-Whitehouse
- School of Medicine, University of Texas Rio Grande Valley, 1201 W University Dr, Edinburg, TX, 78539, USA
| | - Ednia Gutierrez
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, 1201, W University Dr., Edinburg, TX, 78539, USA
| | - Saraswathy Nair
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, 1201, W University Dr., Edinburg, TX, 78539, USA
| | - Jameela Banu
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, 1201, W University Dr., Edinburg, TX, 78539, USA.
- Department of Biology, University of Texas Rio Grande Valley, 1201, W University Dr., Edinburg, TX, 78539, USA.
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Alvarez-Díaz JC, Ortiz-Echeverry BA, Velásquez N. Duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemum. J Virol Methods 2018; 266:41-48. [PMID: 30578896 DOI: 10.1016/j.jviromet.2018.12.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 02/06/2023]
Abstract
A novel duplex RT-PCR assay for simultaneous detection of TSWV and CSVd in chrysanthemums was developed. Previous reported primers for amplification of TSWV and CSVd were used and a novel pair of primers for CSVd was designed to improve duplex amplification compatibility. Sensitivity and efficiency of the previous reported and novel primers for CSVd were assessed. Then, the sensitivity of the combined primers to amplify both TSWV and CSVd cDNA were also evaluated. Both TSWV and CSVd were detected in preparations diluted up to 10-4 and 10-5 respectively, from total RNA extracts. This duplex RT-PCR method showed an estimated diagnostic sensitivity (DSe) of 97% and diagnostic specificity (DSp) of 99%. For combination of the primers TSWV L1/ L2 and CSVd UCO-1 F/ UCO-1R, the protocol could detect pathogen RNA from naturally infected plants until 0.1 ng and 1 ng respectively. This novel protocol for detection of TSWV/CSVd represents a useful diagnostic tool without the need of expensive probes and less extensive laboratory work. This method could be helpful to assist the selection and further propagation of healthy chrysanthemums on the field as well as to understand the dynamics and the interaction of this virus and viroid within farms.
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Affiliation(s)
- Juan C Alvarez-Díaz
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia.
| | - Bianor A Ortiz-Echeverry
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
| | - Nubia Velásquez
- Departamento de Investigación y desarrollo, Universidad Católica de Oriente, Sector 3, cra. 46 No. 40B 50, Rionegro, Colombia
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Çevik B, Kıvrak H, Şahin-Çevik M. Development of a graft inoculation method and a real-time RT-PCR assay for monitoring Tomato chlorosis virus infection in tomato. J Virol Methods 2018; 265:1-8. [PMID: 30557574 DOI: 10.1016/j.jviromet.2018.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 12/13/2018] [Accepted: 12/14/2018] [Indexed: 01/10/2023]
Abstract
A graft inoculation method coupled with RT-qPCR was developed for monitoring ToCV infection in tomato plants. Ten seed-grown tomato seedlings were graft inoculated with phloem tissue-containing stem segments from a ToCV-infected tomato plants. Another group of tomato seedling were grafted with similar stem segments from a healthy tomato plant as mock inoculated control. The CP gene of ToCV was cloned under the control of T7 promoter and in vitro synthesized RNA was used as a standard for quantification. Total RNA was isolated from leaf samples of ToCV-inoculated and mock-inoculated control plants before the inoculation and 1-60 days post inoculation (dpi). The presence and the titer of ToCV were determined from all ToCV-inoculated or mock-inoculated control plants by RT-qPCR. After 15 dpi, ToCV was detected in 20-30% of graft-inoculated plants. The infection rate then increased progressively and reached to 70-80% by 60 dpi. Titer of ToCV was at the detectable level at 15 dpi and increased and reached to maximum level by 40 dpi and then started to decrease. The results showed that patch grafting is a simple and efficient method for experimental inoculation of ToCV and can be used as an alternative and/or complementary to vector transmission in the laboratories. The patch grafting could be combined with RT-qPCR and used for infecting and quantitative monitoring of ToCV or other phloem-limited viruses in tomato or in other plants.
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Affiliation(s)
- Bayram Çevik
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Plant Protection, 32260, Isparta, Turkey.
| | - Hatice Kıvrak
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Agricultural Biotechnology, 32260, Isparta, Turkey
| | - Mehtap Şahin-Çevik
- Applied Sciences University of Isparta, Faculty of Agricultural Sciences and Technologies, Department of Agricultural Biotechnology, 32260, Isparta, Turkey
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di Rienzo V, Bubici G, Montemurro C, Cillo F. Rapid identification of tomato Sw-5 resistance-breaking isolates of Tomato spotted wilt virus using high resolution melting and TaqMan SNP Genotyping assays as allelic discrimination techniques. PLoS One 2018; 13:e0196738. [PMID: 29709020 PMCID: PMC5927427 DOI: 10.1371/journal.pone.0196738] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 04/18/2018] [Indexed: 12/11/2022] Open
Abstract
In tomato, resistance to Tomato spotted wilt virus (TSWV) is conferred by the dominant gene, designated Sw-5. Virulent Sw-5 resistance breaking (SRB) mutants of TSWV have been reported on Sw-5 tomato cultivars. Two different PCR-based allelic discrimination techniques, namely Custom TaqMan™ SNP Genotyping and high-resolution melting (HRM) assays, were developed and compared for their ability to distinguish between avirulent (Sw-5 non-infecting, SNI) and SRB biotypes. TaqMan assays proved to be more sensitive (threshold of detection in a range of 50–70 TSWV RNA copies) and more reliable than HRM, assigning 25 TSWV isolates to their correct genotype with an accuracy of 100%. Moreover, the TaqMan SNP assays were further improved developing a rapid and simple protocol that included crude leaf extraction for RNA template preparations. On the other hand, HRM assays showed higher levels of sensitivity than TaqMan when used to co-detect both biotypes in different artificial mixtures. These diagnostic assays contributed to gain preliminary information on the epidemiology of TSWV isolates in open field conditions. In fact, the presented data suggest that SRB isolates are present as stable populations established year round, persisting on both winter (globe artichoke) and summer (tomato) crops, in the same cultivated areas of Southern Italy.
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Affiliation(s)
| | - Giovanni Bubici
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Cinzia Montemurro
- Spin off SINAGRI s.r.l., Bari, Italy
- Dipartimento di Scienze del Suolo, della Pianta e degli Alimenti, Università degli Studi di Bari "Aldo Moro", Bari, Italy
| | - Fabrizio Cillo
- Istituto per la Protezione Sostenibile delle Piante, Consiglio Nazionale delle Ricerche, Bari, Italy
- * E-mail:
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Simón A, Ruiz L, Velasco L, Janssen D. Absolute Quantification of Tomato leaf curl New Delhi virus Spain strain, ToLCNDV-ES: Virus Accumulation in a Host-Specific Manner. PLANT DISEASE 2018; 102:165-171. [PMID: 30673467 DOI: 10.1094/pdis-06-17-0840-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Tomato leaf curl New Delhi virus (ToLCNDV) (family Geminiviridae, genus Begomovirus) has recently been introduced in western Mediterranean countries. Isolates in Spain constitute a new strain, denominated ToLCNDV-ES, that is causing losses in commercial zucchini and melon crops; however, it is also, although less often, detected in commercial tomato crops. We developed a tissue-print hybridization test to detect the two genomic components of the virus and a TaqMan quantitative polymerase chain reaction (qPCR) test to estimate the number of genome copies in plants. qPCR was approximately 104 to 106 times more sensitive than tissue-print hybridization to detect viral genomic DNA-A and DNA-B, respectively. It also detected the virus in more experimentally and naturally ToLCNDV-ES-infected zucchini squash and tomato plants. ToLCNDV-ES DNA-A titers were significantly lower in tomato than in zucchini plants, often falling below the detection limits in the hybridization test. In addition, the DNA-B accumulation was impaired in tomato when compared with zucchini. According to the data obtained in this study, the differences in viral titers of both plant species contribute to explain the dissimilarities in symptom expression, capability of detection, and transmission of the virus.
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Affiliation(s)
- Almudena Simón
- IFAPA Centro La Mojonera, La Mojonera 04745, Almería, Spain
| | - Leticia Ruiz
- IFAPA Centro La Mojonera, La Mojonera 04745, Almería, Spain
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Rao X, Sun J. Development of SYBR Green I Based Real-Time RT-PCR Assay for Specific Detection of Watermelon silver mottle Virus. IRANIAN JOURNAL OF BIOTECHNOLOGY 2015; 13:20-24. [PMID: 28959295 DOI: 10.15171/ijb.1124] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Watermelon silver mottle virus (WSMoV), which belongs to the genus Tospovirus, causes significant loss in Cucurbitaceae plants. OBJECTIVES Development of a highly sensitive and reliable detection method for WSMoV. MATERIALS AND METHODS Recombinant plasmids for targeting the sequence of nucleocapsid protein gene of WSMoV were constructed. SYBR Green I real-time PCR was established and evaluated with standard recombinant plasmids and 27 watermelon samples showing WSMoV infection symptoms. RESULTS The recombinant plasmid was used as template for SYBR Green I real-time PCR to generate standard and melting curves. Melting curve analysis indicated no primer-dimers and non-specific products in the assay. No cross-reaction was observed with Capsicum chlorosis virus (genus Tospovirus) and Cucumber mosaic virus (genus Cucumovirus). Repeatability tests indicated that inter-assay variability of the Ct values was 1.6%. CONCLUSIONS A highly sensitive, reliable and rapid detection method of SYBR Green I real-time PCR for timely detection of WSMoV plants and vector thrips was established, which will facilitate disease forecast and control.
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Affiliation(s)
- Xueqin Rao
- Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
| | - Jie Sun
- Department of Plant Pathology, College of Agriculture, South China Agricultural University, Guangzhou 510642, China.,Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China
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Debreczeni DE, López C, Aramburu J, Darós JA, Soler S, Galipienso L, Falk BW, Rubio L. Complete sequence of three different biotypes of tomato spotted wilt virus (wild type, tomato Sw-5 resistance-breaking and pepper Tsw resistance-breaking) from Spain. Arch Virol 2015; 160:2117-23. [PMID: 26026956 DOI: 10.1007/s00705-015-2453-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 05/15/2015] [Indexed: 12/11/2022]
Abstract
Tomato spotted wilt virus (TSWV) occurs worldwide and causes production losses in many important horticultural crops such as tomato and pepper. Breeding resistant cultivars has been the most successful method so far for TSWV disease control, but only two genes have been found to confer resistance against a wide spectrum of TSWV isolates: Sw-5 in tomato and Tsw in pepper. However, TSWV resistance-breaking isolates have emerged in different countries a few years after using resistant cultivars. In this paper, we report the first complete nucleotide sequences of three Spanish TSWV isolates with different biotypes according to their abilities to overcome resistance: LL-N.05 (wild type, WT), Pujol1TL3 (Sw-5 resistance breaking, SBR) and PVR (Tsw resistance-breaking, TBR). The genome of these TSWV isolates consisted of three segments: L (8913-8914 nt), M (4752-4825 nt) and (S 2924-2961 nt). Variations in nucleotide sequences and genomic RNA lengths among the different virus biotypes are reported here. Phylogenetic analysis of the five TSWV open reading frames showed evidence of reassortment between genomic segments of LL-N.05 and Pujol1TL3, which was supported by analysis with different recombination-detecting algorithms.
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Affiliation(s)
- Diana E Debreczeni
- Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113, Moncada, Valencia, Spain
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13
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Peña EJ, Ferriol I, Sambade A, Buschmann H, Niehl A, Elena SF, Rubio L, Heinlein M. Experimental virus evolution reveals a role of plant microtubule dynamics and TORTIFOLIA1/SPIRAL2 in RNA trafficking. PLoS One 2014; 9:e105364. [PMID: 25133612 PMCID: PMC4136834 DOI: 10.1371/journal.pone.0105364] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/17/2014] [Indexed: 01/12/2023] Open
Abstract
The cytoskeleton is a dynamic network composed of filamentous polymers and regulatory proteins that provide a flexible structural scaffold to the cell and plays a fundamental role in developmental processes. Mutations that alter the spatial orientation of the cortical microtubule (MT) array of plants are known to cause important changes in the pattern of cell wall synthesis and developmental phenotypes; however, the consequences of such alterations on other MT-network-associated functions in the cytoplasm are not known. In vivo observations suggested a role of cortical MTs in the formation and movement of Tobacco mosaic virus (TMV) RNA complexes along the endoplasmic reticulum (ER). Thus, to probe the significance of dynamic MT behavior in the coordination of MT-network-associated functions related to TMV infection and, thus, in the formation and transport of RNA complexes in the cytoplasm, we performed an evolution experiment with TMV in Arabidopsis thaliana tor1/spr2 and tor2 mutants with specific defects in MT dynamics and asked whether TMV is sensitive to these changes. We show that the altered cytoskeleton induced genetic changes in TMV that were correlated with efficient spread of infection in the mutant hosts. These observations demonstrate a role of dynamic MT rearrangements and of the MT-associated protein TORTIFOLIA1/SPIRAL2 in cellular functions related to virus spread and indicate that MT dynamics and MT-associated proteins represent constraints for virus evolution and adaptation. The results highlight the importance of the dynamic plasticity of the MT network in directing cytoplasmic functions in macromolecular assembly and trafficking and illustrate the value of experimental virus evolution for addressing the cellular functions of dynamic, long-range order systems in multicellular organisms.
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Affiliation(s)
- Eduardo José Peña
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Strasbourg, France
| | - Inmaculada Ferriol
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
| | - Adrián Sambade
- Department of Comparative Neurobiology, Institut Cavanilles de Biodiversitat i Biologia Evolutiva CIBERNED, Universidad de Valencia, Valencia, Spain
| | - Henrik Buschmann
- Institute for Botany, University of Osnabrück, Osnabrück, Germany
| | - Annette Niehl
- Department of Environmental Sciences, Plant Physiology, University of Basel, Basel, Switzerland
| | - Santiago F. Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Valencia, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Luis Rubio
- Instituto Valenciano de Investigaciones Agrarias, Moncada, Valencia, Spain
- * E-mail: (LR); (MH)
| | - Manfred Heinlein
- Institut de Biologie Moléculaire des Plantes, UPR2357 CNRS, Strasbourg, France
- Department of Environmental Sciences, Plant Physiology, University of Basel, Basel, Switzerland
- * E-mail: (LR); (MH)
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Charoenvilaisiri S, Seepiban C, Bhunchoth A, Warin N, Luxananil P, Gajanandana O. Development of a multiplex RT-PCR-ELISA to identify four distinct species of tospovirus. J Virol Methods 2014; 202:54-63. [PMID: 24642237 DOI: 10.1016/j.jviromet.2014.03.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 03/05/2014] [Accepted: 03/07/2014] [Indexed: 11/26/2022]
Abstract
In this study, a multiplex RT-PCR-ELISA was developed to detect and differentiate four tospovirus species found in Thailand, namely Capsicum chlorosis virus (CaCV), Melon yellow spot virus (MYSV), Tomato necrotic ringspot virus (TNRV), and Watermelon silver mottle virus (WSMoV). In this system, nucleocapsid (N) gene fragments of four tospoviruses were simultaneously amplified and labeled with digoxigenin (DIG) in a single RT-PCR reaction using a pair of degenerate primers binding to the same conserved regions in all four tospovirus N genes. The DIG-labeled amplicons were distinguished into species by four parallel hybridizations to species-specific biotinylated probes in streptavidin-coated microtiter wells followed by ELISA detection using a peroxidase-conjugated anti-DIG antibody. Results indicated that the multiplex RT-PCR-ELISA assay could specifically identify each of these four tospoviruses without cross-reactivity between species or reactivity to healthy plant negative controls. Assay sensitivity was 10- to 1000-fold higher than conventional RT-PCR. When applied to naturally infected plants, all samples yielded concordant results between RT-PCR-ELISA and the reference RT-PCR. In conclusion, the multiplex RT-PCR-ELISA developed in this study has superior specificity, sensitivity, and high-throughput capacity compared to conventional RT-PCR and is an attractive alternative for the identification of different tospovirus species.
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Affiliation(s)
- Saengsoon Charoenvilaisiri
- Monoclonal Antibody Production Laboratory, Agricultural Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Pathumthani 12120, Thailand.
| | - Channarong Seepiban
- Monoclonal Antibody Production Laboratory, Agricultural Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Pathumthani 12120, Thailand
| | - Anjana Bhunchoth
- Plant Research Laboratory, Agricultural Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Kamphaengsaen, Nakornpathom, Thailand
| | - Nuchnard Warin
- Plant Research Laboratory, Agricultural Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Kamphaengsaen, Nakornpathom, Thailand
| | - Plearnpis Luxananil
- Microbial Cell Factory Laboratory, Bioresource Technology Unit, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Pathumthani 12120, Thailand
| | - Oraprapai Gajanandana
- Monoclonal Antibody Production Laboratory, Agricultural Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Pathumthani 12120, Thailand
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15
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Chen Y, Hu X. High-throughput detection of banana bunchy top virus in banana plants and aphids using real-time TaqMan® PCR. J Virol Methods 2013; 193:177-83. [DOI: 10.1016/j.jviromet.2013.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 05/31/2013] [Accepted: 06/06/2013] [Indexed: 10/26/2022]
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16
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Chen X, Xu X, Li Y, Liu Y. Development of a real-time fluorescent quantitative PCR assay for detection of Impatiens necrotic spot virus. J Virol Methods 2013; 189:299-304. [PMID: 23466630 DOI: 10.1016/j.jviromet.2013.02.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 02/15/2013] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
Impatiens necrotic spot virus (INSV) is an important plant virus that can cause severe disease in various ornamental and agricultural crops. Several species of thrips transmit INSV, of which the western flower thrip (Frankliniella occidentalis) is the most important. In this study, primers and TaqMan probes based on INSV non-structural protein gene sequences were designed, and a technique was developed for detecting INSV using fluorescent quantitative RT-PCR. The reproducibility, specificity and sensitivity for the RT-PCR were evaluated; and the RT-PCR method was developed to detect INSV in the host plants and western flower thrips. A standard curve constructed by a series of diluted plasmid DNA gave a good linear relationship between Ct value and concentration of plasmid DNA, a low coefficient of variation and good reproducibility. The detection method not only measured quantitatively the concentration of INSV in plant hosts and western flower thrips, but also measured accurately low concentrations of the virus. The measurable concentration fell to as low as 10⁰ copies/μl, while RT-PCR could detect only 10² copies/μl. The method had high specificity and could distinguish INSV from Tomato spotted wilt virus (TSWV) and Tomato zonate spot virus (TZSV), both from the same genus of viruses. This is the first report of the same method being used to detect INSV in both plant hosts and western flower thrips, and should be helpful in studies of INSV epidemiology.
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Affiliation(s)
- Xuejiao Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming 650201, China
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17
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Development of SYBR Green I based real-time PCR assays for quantitative detection of Rice tungro bacilliform virus and Rice tungro spherical virus. J Virol Methods 2012; 181:86-92. [DOI: 10.1016/j.jviromet.2012.01.018] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 01/16/2012] [Accepted: 01/24/2012] [Indexed: 11/24/2022]
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18
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Abstract
Lettuce is frequently attacked by several viruses causing disease epidemics and considerable yield losses along the Mediterranean basin. Aphids are key pests and the major vectors of plant viruses in lettuce fields. Lettuce mosaic virus (LMV) is probably the most important because it is seed-transmitted in addition to be transmissible by many aphid species that alight on the crop. Tomato spotted wilt virus (TSWV) is another virus that causes severe damage since the introduction of its major vector, the thrips Frankliniella occidentalis. In regions with heavy and humid soils, Lettuce Mirafiori big-vein virus (LMBVV) can also produce major yield losses.
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Affiliation(s)
- Aranzazu Moreno
- Department of Plant Protection, Instituto de Ciencias Agrarias, ICA-CSIC, Madrid, Spain
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19
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Ferriol I, Ruiz-Ruiz S, Rubio L. Detection and absolute quantitation of Broad bean wilt virus 1 (BBWV-1) and BBWV-2 by real time RT-PCR. J Virol Methods 2011; 177:202-5. [PMID: 21855578 DOI: 10.1016/j.jviromet.2011.08.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2011] [Revised: 07/25/2011] [Accepted: 08/01/2011] [Indexed: 01/01/2023]
Abstract
Broad bean wilt virus 1 (BBWV-1) and BBWV-2 are the two most significant viruses in the genus Fabavirus, causing damage to many economically important agricultural crops worldwide. A quantitative real-time reverse transcription-polymerase chain reaction (RT-qPCR) procedure using two TaqMan(®)MGB probes was developed for sensitive and specific detection and quantitation of BBWV-1 and BBWV-2. Primers and probes were designed from conserved sequence stretches to detect all isolates of each virus. Standard curves using RNA transcripts identical to both TaqMan(®)MGB probes enabled absolute quantitation, with a wide dynamic range and high sensitivity (10(3)-10(10) RNA molecules). RT-qPCR was assayed with genetically divergent BBWV-1 and BBWV-2 isolates from different plant hosts and countries, and was used to evaluate the temporal accumulation of BBWV-1 RNA in two plant hosts.
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Affiliation(s)
- I Ferriol
- Instituto Valenciano de Investigaciones Agrarias, 46113 Moncada, Valencia, Spain
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