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Lakshminarayana Reddy CN, Venkataravanappa V, Chowdappa A, Shridhar H, Mantesh M, Vinaykumar HD, Krishna Reddy M. Complete genome characterization of chilli veinal mottle virus associated with mosaic and mottling disease of tomato and development of LAMP assay for quick detection. 3 Biotech 2024; 14:139. [PMID: 38682094 PMCID: PMC11052978 DOI: 10.1007/s13205-024-03984-x] [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: 07/31/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024] Open
Abstract
Chilli veinal mottle virus (ChiVMV) is a potyvirus known to cause havoc in many solanaceous crops. Samples from tomato plants exhibiting typical mosaic and mottling symptoms in two locations from farmers' fields were collected and tested using DAC ELISA for the presence of ChiVMV and other viruses known to infect tomato. ChiVMV Gauribidanur isolate from infected tomato was mechanically inoculated to Datura metel, Nicotiana tabacum, Nicotiana benthamiana, Nicotiana glutinosa, chilli, and tomato plants which exhibited systemic mosaic and mottling symptoms 10 days post-inoculation. This results were further confirmed by RT-PCR and DAC ELISA using CP gene-specific primers and ChiVMV antisera, respectively. Transmission electron microscopy revealed the presence of long filamentous particles (800 × 11 nm) resembling viruses in the Potyviridae family. The complete genome of ChiVMV comprised 9716 nucleotides except for poly A tail, with a predicted open reading frame spanning 9270 nucleotides encoding polyproteins of 3089 amino acids. Comparative analysis revealed that ChiVMV-tomato isolates reported across the world shared maximum nucleotide identity (93-96.7%) with chilli isolates from India and Pakistan. These results were well supported by sequence demarcation analysis. Further, the Neibhor-Net network analysis of the complete genome of ChiVMV-tomato, along with other host isolates, formed a reticular network phylogenetic tree suggesting recombination events. Subsequently, RDP5 detected intra-specific recombination breakpoints at the positions 1656-5666 nucleotides with major parent ChiVMV (MN508960) Uravakonda and minor parent ChiVMV (MN508956) with a significant average p value of 1.905 × 10-22. The LAMP assay using ChiVMV-specific primers resulted in ladder-like amplified products on electrophoresed gel and a distinct red colour pattern with hydroxy naphthalene blue, indicating a positive reaction for the presence of ChiVMV in infected tomato samples. To validate LAMP-designed primers, RNA extracted from ChiVMV-infected tomato, chilli, datura, and tobacco samples were subjected to LAMP assay and it accurately detected the presence of ChiVMV in infected plant samples. Overall, this study provides holistic information of ChiVMV infecting tomato, spanning diagnosis, transmission, genetic characterization, and detection of recombination events, which collectively contribute to effective disease management, crop protection, and informed decision-making in agricultural practices.
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Affiliation(s)
- C. N. Lakshminarayana Reddy
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka 560065 India
| | - V. Venkataravanappa
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
| | - A. Chowdappa
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
| | - H. Shridhar
- CSIR- North East Institute of Science and Technology, Jorhat, Assam 785006 India
| | - M. Mantesh
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka 560065 India
| | - H. D. Vinaykumar
- Department of Plant Pathology, College of Agriculture, University of Agricultural Sciences, GKVK, Bangalore, Karnataka 560065 India
| | - M. Krishna Reddy
- Division of Plant Pathology, ICAR-Indian Institute of Horticultural Research, Hessaraghatta Lake PO, Bangalore, Karnataka 560089 India
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Bano H, Khan JA. Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) for rapid detection of viruses infecting patchouli (Pogostemon cablin). Arch Microbiol 2024; 206:75. [PMID: 38261081 DOI: 10.1007/s00203-023-03798-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 01/24/2024]
Abstract
Patchouli (Pogostemon cablin), a highly valued medicinal plant, suffers significant economic losses following infection with Broad bean wilt virus 2 (BBWV-2) and Peanut stripe virus (PStV). In this study, a field-based isothermal technique called reverse transcription loop-mediated isothermal amplification (RT-LAMP) was established for an early and specific detection of BBWV-2 and PStV. The oligo primers were designed to target the coat protein genes of PStV and BBWV-2. The reaction conditions, such as temperature and time duration, were optimized to 65 °C for 60 min. The LAMP amplicons positive for PStV and BBWV-2 revealed characteristic ladder-type bands following agarose gel electrophoresis. Further, a colorimetric assay using a metal ion-based indicator (Hydroxy-naphthol blue, HNB) was conducted to visualize the amplified products with the naked eye, thus facilitating accessibility to field practices. The assay developed in this study was found to be virus specific, and was 100 times more sensitive than RT-PCR. Thus, the RT-LAMP assay established in this study is quick, reliable, and cost-effective for the accurate identification of BBWV-2 and PStV. It will facilitate the screening of patchouli planting materials. Further, it may reduce the risk of virus spread and could be helpful in phytosanitary programs.
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Affiliation(s)
- Humaira Bano
- Plant Virus Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, 110025, India
| | - Jawaid A Khan
- Plant Virus Lab, Department of Biosciences, Jamia Millia Islamia (A Central University), New Delhi, 110025, India.
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Raigond B, Pathania S, Verma G, Bhardwaj P, Kochhar T, Chakrabarti SK. Development and application of reverse transcription-loop mediated isothermal amplification assay for sensitive detection of groundnut bud necrosis virus infecting potato. Virology 2023; 587:109872. [PMID: 37657354 DOI: 10.1016/j.virol.2023.109872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 07/28/2023] [Accepted: 08/18/2023] [Indexed: 09/03/2023]
Abstract
Reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of groundnut bud necrosis virus (GBNV) causing potato stem necrosis disease. The isothermal temperatures, reaction periods and concentrations of reaction mixture were optimized where, the assay worked well at 65 °C for 50 min, 6 U of WarmStart Bst 2.0 DNA polymerase, 1.4 mM dNTPs and 2.0 mM MgSO4. The optimized assay proved to be specific to GBNV with no cross reactivity to other viruses infecting potato in India. The specificity of RT-LAMP assay was found to be 100 fold more sensitive than that of RT-PCR. The developed assay was applied for the detection of GBNV from 80 potato leaf samples where 24 samples were found infected which was confirmed by RT-PCR. It was concluded that the RT-LAMP assay developed for detection of GBNV was specific, sensitive and suitable for its use in virus indexing under potato seed production programme.
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Affiliation(s)
- Baswaraj Raigond
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India; Center on Rabi Sorghum, ICAR-Indian Institute of Millets Research, Regional Station, Solapur, Maharashtra, 413006, India.
| | - Shruti Pathania
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Gaurav Verma
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Pooja Bhardwaj
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - Tarvinder Kochhar
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
| | - S K Chakrabarti
- Division of Plant Protection, ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India
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Johnmark O, Indieka S, Liu G, Gowda M, Suresh LM, Zhang W, Gao X. Fighting Death for Living: Recent Advances in Molecular and Genetic Mechanisms Underlying Maize Lethal Necrosis Disease Resistance. Viruses 2022; 14:v14122765. [PMID: 36560769 PMCID: PMC9784999 DOI: 10.3390/v14122765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/05/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Maize Lethal Necrosis (MLN) disease, caused by a synergistic co-infection of maize chlorotic mottle virus (MCMV) and any member of the Potyviridae family, was first reported in EasternAfrica (EA) a decade ago. It is one of the most devastating threats to maize production in these regions since it can lead up to 100% crop loss. Conventional counter-measures have yielded some success; however, they are becoming less effective in controlling MLN. In EA, the focus has been on the screening and identification of resistant germplasm, dissecting genetic and the molecular basis of the disease resistance, as well as employing modern breeding technologies to develop novel varieties with improved resistance. CIMMYT and scientists from NARS partner organizations have made tremendous progresses in the screening and identification of the MLN-resistant germplasm. Quantitative trait loci mapping and genome-wide association studies using diverse, yet large, populations and lines were conducted. These remarkable efforts have yielded notable outcomes, such as the successful identification of elite resistant donor lines KS23-5 and KS23-6 and their use in breeding, as well as the identification of multiple MLN-tolerance promising loci clustering on Chr 3 and Chr 6. Furthermore, with marker-assisted selection and genomic selection, the above-identified germplasms and loci have been incorporated into elite maize lines in a maize breeding program, thus generating novel varieties with improved MLN resistance levels. However, the underlying molecular mechanisms for MLN resistance require further elucidation. Due to third generation sequencing technologies as well functional genomics tools such as genome-editing and DH technology, it is expected that the breeding time for MLN resistance in farmer-preferred maize varieties in EA will be efficient and shortened.
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Affiliation(s)
- Onyino Johnmark
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- China and Kenya Belt and Road Joint Laboratory on Crop Molecular Biology, Nanjing Agricultural University, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Biochemistry and Molecular Biology Department, Egerton University, Njoro P.O. Box 536-20115, Kenya
| | - Stephen Indieka
- Biochemistry and Molecular Biology Department, Egerton University, Njoro P.O. Box 536-20115, Kenya
| | - Gaoqiong Liu
- Crops Soils and Horticulture Department, Egerton University, Njoro P.O. Box 536-20115, Kenya
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| | - L. M. Suresh
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, UN Avenue, Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| | - Wenli Zhang
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- China and Kenya Belt and Road Joint Laboratory on Crop Molecular Biology, Nanjing Agricultural University, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- China and Kenya Belt and Road Joint Laboratory on Crop Molecular Biology, Nanjing Agricultural University, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
- Correspondence:
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Nouri R, Dong M, Politza AJ, Guan W. Figure of Merit for CRISPR-Based Nucleic Acid-Sensing Systems: Improvement Strategies and Performance Comparison. ACS Sens 2022; 7:900-911. [PMID: 35238530 PMCID: PMC9191621 DOI: 10.1021/acssensors.2c00024] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-based nucleic acid-sensing systems have grown rapidly in the past few years. Nevertheless, an objective approach to benchmark the performances of different CRISPR sensing systems is lacking due to the heterogeneous experimental setup. Here, we developed a quantitative CRISPR sensing figure of merit (FOM) to compare different CRISPR methods and explore performance improvement strategies. The CRISPR sensing FOM is defined as the product of the limit of detection (LOD) and the associated CRISPR reaction time (T). A smaller FOM means that the method can detect smaller target quantities faster. We found that there is a tradeoff between the LOD of the assay and the required reaction time. With the proposed CRISPR sensing FOM, we evaluated five strategies to improve the CRISPR-based sensing: preamplification, enzymes of higher catalytic efficiency, multiple crRNAs, digitalization, and sensitive readout systems. We benchmarked the FOM performances of 57 existing studies and found that the effectiveness of these strategies on improving the FOM is consistent with the model prediction. In particular, we found that digitalization is the most promising amplification-free method for achieving comparable FOM performances (∼1 fM·min) as those using preamplification. The findings here would have broad implications for further optimization of the CRISPR-based sensing.
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Affiliation(s)
- Reza Nouri
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Ming Dong
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Anthony J. Politza
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
| | - Weihua Guan
- Department of Electrical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, United States
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Latent potential of current plant diagnostics for detection of sugarcane diseases. CURRENT RESEARCH IN BIOTECHNOLOGY 2022. [DOI: 10.1016/j.crbiot.2022.10.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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Salazar A, Ochoa-Corona FM, Olson JD, Babu B, Paret M. Probing Loop-Mediated Isothermal Amplification (LAMP) targeting two gene-fragments of rose rosette virus. PLoS One 2021; 16:e0256510. [PMID: 34843487 PMCID: PMC8629277 DOI: 10.1371/journal.pone.0256510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/12/2021] [Indexed: 01/13/2023] Open
Abstract
This study explores the development of Loop-mediated isothermal amplification (LAMP) for detection of rose rosette virus (RRV), a technique with the potential to be translated to rose nurseries. RRV is a negative-sense, single-stranded RNA virus which is a member of the genus Emaravirus (Family Fimoviridae) and the causal agent of the rose rosette disease (RRD). Although RRV symptoms are characteristics, early visual diagnosis of RRD can be misleading and confusing since it may appear like herbicide damage. Moreover, it may take incubation time for symptoms to appear after virus infection. Two sets of RRV gene sequences RNA3 and RNA4 were analyzed and two sets of four LAMP primers were designed. The direct antigen-capture method for direct trapping of RRV in plastic was used for RNA extraction followed by cDNA synthesis. RT-LAMP reactions were for 1 hour at 64°C (RRV-P3) and 66.5°C (RRV-P4) using either a thermocycler or a portable dry bath. RT-qLAMP was also optimized using DNA polymerase GspSSD LD using the same RRV sets of primers. RRV was detected in symptomatic and non-symptomatic RRD tissue from Oklahoma. The limit of detection (LoD) was 1pg/μL and 1 fg/μL using Bst 2.0 LAMP and GspSSD LD quantitative LAMP, respectively. In visual colorimetric pre- and post-reactions, the LoD was 10 pg/μL and 0.1 pg/μL using hydroxy naphthol blue (HNB, 120 μM) and SYBR green I (1:10 dilution), respectively. No cross-reactivity was detected in the RT-LAMP reaction testing cDNAs of eight commonly co-infecting rose viruses and one virus taxonomically related to RRV. Four different dyes were tested, and visible colorimetric reactions were obtained with RT-LAMP Bst 2.0 combined with SYBR I or HNB. RT-qLAMP with GspSSD2.0 offers LoD equal to RT-PCR and it is faster since it works with RNA directly.
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Affiliation(s)
- Andrea Salazar
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Institute for Biosecurity and Microbial Forensic, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
- Universidad de las Fuerzas Armadas- ESPE, Quito, Ecuador
| | - Francisco M. Ochoa-Corona
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Institute for Biosecurity and Microbial Forensic, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
- * E-mail:
| | - Jennifer D. Olson
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
| | - Binoy Babu
- North Florida Research and Education Center, University of Florida, Quincy, Florida, United States America
| | - Mathews Paret
- North Florida Research and Education Center, University of Florida, Quincy, Florida, United States America
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Lu G, Wang Z, Xu F, Pan YB, Grisham MP, Xu L. Sugarcane Mosaic Disease: Characteristics, Identification and Control. Microorganisms 2021; 9:microorganisms9091984. [PMID: 34576879 PMCID: PMC8468687 DOI: 10.3390/microorganisms9091984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 01/25/2023] Open
Abstract
Mosaic is one of the most important sugarcane diseases, caused by single or compound infection of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and/or Sugarcane streak mosaic virus (SCSMV). The compound infection of mosaic has become increasingly serious in the last few years. The disease directly affects the photosynthesis and growth of sugarcane, leading to a significant decrease in cane yield and sucrose content, and thus serious economic losses. This review covers four aspects of sugarcane mosaic disease management: first, the current situation of sugarcane mosaic disease and its epidemic characteristics; second, the pathogenicity and genetic diversity of the three viruses; third, the identification methods of mosaic and its pathogen species; and fourth, the prevention and control measures for sugarcane mosaic disease and potential future research focus. The review is expected to provide scientific literature and guidance for the effective prevention and control of mosaic through resistance breeding in sugarcane.
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Affiliation(s)
- Guilong Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
| | - Yong-Bao Pan
- USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA; (Y.-B.P.); (M.P.G.)
| | - Michael P. Grisham
- USDA-ARS, Sugarcane Research Unit, Houma, LA 70360, USA; (Y.-B.P.); (M.P.G.)
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (G.L.); (Z.W.); (F.X.)
- Correspondence:
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Li X, Li Y, Hu W, Li Y, Li Y, Chen S, Wang J. Simultaneous multiplex RT-PCR detection of four viruses associated with maize lethal necrosis disease. J Virol Methods 2021; 298:114286. [PMID: 34520808 DOI: 10.1016/j.jviromet.2021.114286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 04/28/2021] [Accepted: 09/08/2021] [Indexed: 11/19/2022]
Abstract
Maize lethal necrosis disease (MLND) is a serious disease of worldwide importance. It is caused by the co-infection of maize with maize chlorotic mottle virus (MCMV) and a potyvirus, such as sugarcane mosaic virus (SCMV), that acts synergistically to produce more severe symptoms and production losses. More recently, maize yellow mosaic virus (MaYMV) and maize-associated totivirus (MATV) were found to co-infect with MCMV and SCMV in maize plants. To facilitate the detection of these viruses in co-infected maize, a multiplex RT-PCR assay was developed in this study. The assay used five specific primer pairs and simultaneously amplified these four viruses as well as the elongation factor 1α (EF 1α) gene use as internal control in one tube. The concentration of the primers, annealing temperature, annealing time, extension time and amplification cycles were optimized for the multiplex RT-PCR. The detection limit of the assay was up to 100 pg of total cDNA template. This multiplex RT-PCR assay was shown to be a sensitive and effective tool for the screening of field samples for the presence of these viruses in co-infected maize.
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Affiliation(s)
- Xiaoqin Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, China
| | - Yu Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, China
| | - Wenli Hu
- School of Life Science, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, China
| | - Yingjuan Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, China
| | - Yan Li
- Yunnan Plant Protection and Quarantine Station, Kunming 650034, China
| | - Suiyun Chen
- School of Life Science, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, China.
| | - Jianguang Wang
- School of Life Science, Biocontrol Engineering Research Center of Crop Disease & Pest, Yunnan Province, Biocontrol Engineering Research Center of Plant Disease & Pest, Yunnan University, Kunming 650091, China.
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Rice JL, Hoy JW. Recovery from Mosaic Caused by Sorghum Mosaic Virus in Sugarcane and Impact on Yield. PLANT DISEASE 2020; 104:3166-3172. [PMID: 33079018 DOI: 10.1094/pdis-02-20-0376-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mosaic is a historically important viral disease of sugarcane in Louisiana caused by Sugarcane mosaic virus and, currently, by Sorghum mosaic virus (SrMV). Sugarcane clones can have variable responses to mosaic for different traits, including susceptibility to infection and yield loss. Disease incidence and rate of increase within a multiple-year crop cycle is affected by susceptibility and other epidemiological factors, possibly including recovery from symptom expression and virus infection. Recovery (defined as the emergence of asymptomatic plants from buds on planted symptomatic stalks) and the impact of mosaic on yield components were evaluated in two sugarcane cultivars, HoCP 09-804 and L 10-147. Recovery varied between the two cultivars. Across two experiments, L 10-147 had a higher frequency of recovery (range 9.4 to 19.8%) than HoCP 09-804 (range 0.9 to 2.3%). A reverse-transcription PCR assay did not detect SrMV in 96.5% of 143 L 10-147 leaf samples and 83.3% of 6 HoCP 09-804 leaf samples collected from recovered plants. When comparing symptomatic and asymptomatic plantings, mosaic reduced cane and sucrose yield in HoCP 09-804 but not L 10-147, suggesting a possible association between recovery and tolerance to virus infection.
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Affiliation(s)
- J L Rice
- Plant Pathology and Crop Physiology Department, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
| | - J W Hoy
- Plant Pathology and Crop Physiology Department, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, U.S.A
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Kumar R, Kaundal P, Arjunan J, Sharma S, Chakrabarti SK. Development of a visual detection method for Potato virus S by reverse transcription loop-mediated isothermal amplification. 3 Biotech 2020; 10:213. [PMID: 32351871 PMCID: PMC7182647 DOI: 10.1007/s13205-020-02214-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 04/16/2020] [Indexed: 12/12/2022] Open
Abstract
A reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay was developed to detect the Potato virus S (PVS) in potato. Two sets of six novel primers that recognize the coat protein gene sequence of the PVS were designed and RT-LAMP assay was optimized for the parameters such as different concentrations of primers, MgSO4, betaine, dNTPs, Bst DNA polymerase, temperature and duration. The RT-LAMP was carried out under isothermal conditions without the thermal cycler using PVS infected leaf and tuber samples, LAMP specific primers with amplification at 65 °C for 60 min, and 80 °C for 5 min. The results were assessed by gel electrophoresis and visual observation of colour change using SYBR Green I dye. The detection limit of the developed RT-LAMP assay was determined and compared with a conventional reverse transcription-polymerase chain reaction (RT-PCR). RT-LAMP was found 100 times more sensitive than RT-PCR. The optimized RT-LAMP assay is robust, reliable, sensitive and convenient for the detection of the PVS in infected potato tubers including asymptomatic plants. No cross-reactions were observed with healthy plants and other potato viruses. The assay is economical and can be employed in large scale testing of potato plants against PVS under healthy seed potato production programme.
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Affiliation(s)
- Ravinder Kumar
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
| | - Priyanka Kaundal
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
| | - Jeevalatha Arjunan
- 2ICAR-Indian Institute of Spices Research, Marikunnu P.O., Kozhikode, Kerala 673 012 India
| | - Sanjeev Sharma
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
| | - S K Chakrabarti
- 1ICAR-Central Potato Research Institute, Shimla, HP 171 001 India
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Zhang Y, Wang Y, Xie Z, Wang R, Guo Z, He Y. Rapid Detection of Lily mottle virus and Arabis mosaic virus Infecting Lily ( Lilium spp.) Using Reverse Transcription Loop-Mediated Isothermal Amplification. THE PLANT PATHOLOGY JOURNAL 2020; 36:170-178. [PMID: 32296296 PMCID: PMC7143516 DOI: 10.5423/ppj.oa.04.2019.0096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 11/28/2019] [Accepted: 02/03/2020] [Indexed: 05/17/2023]
Abstract
The Lily mottle virus (LMoV) impedes the growth and quality of lily crops in Lanzhou, China. Recently Arabis mosaic virus (ArMV) has been detected in LMoV-infected plants in this region, causing plant stunting as well as severe foliar symptoms, and likely posing a threat to lily production. Consequently, there is a need to develop simple, sensitive, and reliable detection methods for these two viruses to prevent them from spreading. Reverse transcription (RT) loop-mediated isothermal amplification (LAMP) assays have been developed to detect LMoV and ArMV using two primer pairs that match six conserved sequences of LMoV and ArMV coat proteins, respectively. RT-LAMP assay results were visually assessed in reaction tubes using green fluorescence and gel electrophoresis. Our assays successfully detected both LMoV and ArMV in lily plants without the occurrence of viral cross-reactivity from other lily viruses. Optimal conditions for LAMP reactions were 65°C and 60°C for 60 min for LMoV and ArMV, respectively. Detection sensitivity for both RT-LAMP assays was a hundredfold greater than that of our comparative RT-polymerase chain reaction assays. We have also found this relatively rapid, target specific and sensitive method can also be used for samples collected in the field and may be especially useful in regions with limited or no laboratory facilities.
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Affiliation(s)
- Yubao Zhang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yajun Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Zhongkui Xie
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
- Corresponding author. Phone) +86-931-4967204, FAX) +86-931-8273894, E-mail) ,
| | - Ruoyu Wang
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Zhihong Guo
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Yuhui He
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
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14
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Reverse transcription loop-mediated isothermal amplification based rapid detection of Sugarcane mosaic virus and Sugarcane streak mosaic virus associated with mosaic disease of sugarcane. INDIAN PHYTOPATHOLOGY 2020. [DOI: 10.1007/s42360-020-00219-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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15
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Tiberini A, Tomlinson J, Micali G, Fontana A, Albanese G, Tomassoli L. Development of a reverse transcription-loop- mediated isothermal amplification (LAMP) assay for the rapid detection of onion yellow dwarf virus. J Virol Methods 2019; 271:113680. [PMID: 31202851 DOI: 10.1016/j.jviromet.2019.113680] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/14/2019] [Accepted: 06/13/2019] [Indexed: 11/18/2022]
Abstract
Onion yellow dwarf virus (OYDV) is one of the most important viral pathogens of onion. In particular, on 'Rossa di Tropea' onion, granted with Protected Geographical Indication (PGI) trademarks, this pathogen represents the most limiting biotic stress in terms of spread, severity of symptoms and damage, and its detection is necessary to preserve high quality standards and avoid yield losses. A reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay was developed for detection of OYDV. The specificity, sensitivity, repeatability and reproducibility of the assay were validated according to EPPO standard PM7/98 (2). Diagnostic specificity, diagnostic sensitivity and diagnostic accuracy were determined in both leaf and bulb tissues. To enhance the feasibility of a LAMP-based method for field diagnosis, several nucleic acid extraction methods were compared to simplify sample preparation. The results showed the reliability of the method for OYDV detection, with a limit of detection (LOD) comparable to real time reverse transcription polymerase chain reaction (RT-qPCR). The ease of sample preparation, and the more than acceptable LOD, indicated that the RT-LAMP assay could be used in plant pathology laboratories with limited facilities and resources, as well as directly in the field. This work was carried out in the frame of "SI.ORTO" project.
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Affiliation(s)
- Antonio Tiberini
- Università degli Studi Mediterranea di Reggio Calabria, Dipartimento di AGRARIA, Località Feo di Vito, 89122 Reggio Calabria, Italy.
| | | | - Giuseppe Micali
- Università degli Studi Mediterranea di Reggio Calabria, Dipartimento di AGRARIA, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Anna Fontana
- Università degli Studi Mediterranea di Reggio Calabria, Dipartimento di AGRARIA, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Giuliana Albanese
- Università degli Studi Mediterranea di Reggio Calabria, Dipartimento di AGRARIA, Località Feo di Vito, 89122 Reggio Calabria, Italy
| | - Laura Tomassoli
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria, Centro di Ricerca Difesa e Certificazione, Via C.G. Bertero 22, 00156 Roma, Italy
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16
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Meena PN, Kharbikar LL, Rana RS, Satpathy S, Shanware A, Sivalingam PN, Nandanwar S. Detection of Mesta yellow vein mosaic virus (MeYVMV) in field samples by a loop-mediated isothermal amplification reaction. J Virol Methods 2018; 263:81-87. [PMID: 30359678 DOI: 10.1016/j.jviromet.2018.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 10/05/2018] [Accepted: 10/20/2018] [Indexed: 10/28/2022]
Abstract
A loop-mediated isothermal amplification (LAMP) assay was optimized for the detection of Mesta yellow vein mosaic virus (MeYVMV) in diseased plants of mesta (Hibiscus sabdariffa L.& H. cannabinus L.). The LAMP assay was optimized using a set of six primers targeting the MeYVMV genome and could be completed in 30-60 min at 63 °C. The LAMP amplification results were visualized by adding 1 μl of hydroxy naphthol blue (HNB) dye in a 25 μl LAMP reaction mixture prior to amplification as well as by electrophoresis. The LAMP assay, which detected MeYVMV in a 10-5-fold diluted total DNA, was more sensitive than the PCR assay (10-4-fold dilution). The optimized LAMP assay was able to detect MeYVMV in different parts of the kenaf and roselle plants. Similarly, the optimized PCR assay was also capable of detecting MeYVMV in all the different parts of the kenaf plant but failed to detect the virus in the stem and flower buds of the roselle plant. Validation of the LAMP and LAMP with HNB dye assays revealed that the optimized reactions can be used successfully for the in-situ detection of MeYVMV in field samples and in virus quarantine programs. This is the first report of the detection of the begomovirus species, MeYVMV, in the mucilaginous plant species, kenaf and roselle, using a LAMP assay.
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Affiliation(s)
- Prabhu Narayan Meena
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India.
| | - Lalit Laxman Kharbikar
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India; ICAR-National Institute of Biotic Stress Management, Baronda, Raipur, 493225, India.
| | - Rajeev Singh Rana
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India.
| | - Subrata Satpathy
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, Kolkata, 700120, India.
| | - Arti Shanware
- Rajiv Gandhi Biotechnology Centre, RTM Nagpur University, Nagpur, 440033, India.
| | | | - Shweta Nandanwar
- Harper Adams University, Newport, Shropshire, TF10 8NB, United Kingdom.
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17
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Anandakumar L, Bagyalakshmi K, Nithya K, Parameswari B, Viswanathan R. Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Assay for Rapid Diagnosis of Sugarcane yellow leaf virus in Sugarcane. SUGAR TECH 2018. [DOI: 10.1007/s12355-018-0606-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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18
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Chromogenic detection of yam mosaic virus by closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP). Arch Virol 2018; 163:1057-1061. [PMID: 29308543 PMCID: PMC5854734 DOI: 10.1007/s00705-018-3706-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 12/26/2017] [Indexed: 01/13/2023]
Abstract
A closed-tube reverse transcription loop-mediated isothermal amplification (CT-RT-LAMP) assay was developed for the detection of yam mosaic virus (YMV, genus Potyvirus) infecting yam (Dioscorea spp.). The assay uses a set of six oligonucleotide primers targeting the YMV coat protein region, and the amplification products in YMV-positive samples are visualized by chromogenic detection with SYBR Green I dye. The CT-RT-LAMP assay detected YMV in leaf and tuber tissues of infected plants. The assay is 100 times more sensitive in detecting YMV than standard RT-PCR, while maintaining the same specificity.
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19
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Lu Y, Yao B, Wang G, Hong N. The detection of ACLSV and ASPV in pear plants by RT-LAMP assays. J Virol Methods 2017; 252:80-85. [PMID: 29180245 DOI: 10.1016/j.jviromet.2017.11.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 11/20/2017] [Accepted: 11/21/2017] [Indexed: 10/18/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for the detection of Apple chlorotic leaf spot virus (ACLSV) and Apple stem pitting virus (ASPV), two important viruses frequently occurring in pear trees. A set of four RT-LAMP primers designed based on the highly conserved region of each CP gene of the two viruses showed high specificity and feasibility for ACLSV and ASPV detections. The RT-LAMP assays for ACLSV and ASPV in pear samples were 104 and 103 times more sensitive than that of conventional RT-PCR assays. The RT-LAMP under optimal reaction condition was subsequently utilized in the detection of the two viruses in-vitro cultures of pear and field pear samples. This study provides a rapid and sensitive tool to determine the infection statues of the two viruses in pear certification program.
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Affiliation(s)
- Yongcan Lu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Bingyu Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Guoping Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Ni Hong
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; The Key Laboratory of Plant Pathology of Hubei Province, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei 430070, China; National Indoor Conservation Center of Virus-free Germplasm of Fruit Crops, Huazhong Agricultural University, Wuhan, Hubei 430070, China.
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20
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Sengar GS, Deb R, Raja TV, Singh U, Kant R, Bhanuprakash V, Alyethodi RR, Kumar S, Verma P, Chakraborty S, Alex R, Singh R. RT-LAMP assay: an alternative approach for profiling of bovine heat shock protein 70 gene in PBMC cultured model. Mol Biol Rep 2017; 44:281-287. [PMID: 28551733 DOI: 10.1007/s11033-017-4108-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 05/22/2017] [Indexed: 11/29/2022]
Abstract
The purpose of this study is to develop a novel Reverse Transcriptase Loop-mediated isothermal amplification (RT-LAMP) based assay for in vitro profiling of heat shock protein 70 (Hsp70) in bovine peripheral blood mononuclear cell (PBMC) culture model utilizing the absorbance level of magnesium pyrophosphate-a by-product of LAMP reaction. A set of bovine Hsp70 specific RT-LAMP primers were designed to detect the differential absorbance level of magnesium pyrophosphate by-product which signifies the degree of Hsp70 amplification from cDNA of thermally induced cultured cells at different recovery periods. The study revealed significant (P < 0.05) correlation between absorbance level and the fold change of Hsp70 transcripts at different kinetic intervals of heat stress recovery in bovine PBMC cell culture models. RT-LAMP based absorbance assay can be used as an indicator to measure the degree of bovine Hsp70 transcripts produced during thermal stress and can be used as an alternative to the traditional Real time PCR assay. Developed RT-LAMP assay can be used as a cost-effective method for profiling of bovine HSP70 gene.
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Affiliation(s)
- Gyanendra Singh Sengar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India.,Department of Cellular & Molecular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, Uttar Pradesh, India
| | - Rajib Deb
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India.
| | - T V Raja
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Umesh Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Rajiv Kant
- Department of Cellular & Molecular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, Uttar Pradesh, India
| | - V Bhanuprakash
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - R R Alyethodi
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Sushil Kumar
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Preetam Verma
- Department of Cellular & Molecular Engineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Allahabad, 211007, Uttar Pradesh, India
| | - Soumendu Chakraborty
- ICAR-Indian Veterinary Research Institute, Izatnagar, 243122, Uttar Pradesh, India
| | - Rani Alex
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
| | - Rani Singh
- Molecular Genetics Laboratory, ICAR-Central Institute for Research on Cattle, Meerut, 250001, Uttar Pradesh, India
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21
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Chen L, Jiao Z, Liu D, Liu X, Xia Z, Deng C, Zhou T, Fan Z. One-step reverse transcription loop-mediated isothermal amplification for the detection of Maize chlorotic mottle virus in maize. J Virol Methods 2016; 240:49-53. [PMID: 27899288 DOI: 10.1016/j.jviromet.2016.11.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 10/02/2016] [Accepted: 11/26/2016] [Indexed: 10/20/2022]
Abstract
Maize chlorotic mottle virus (MCMV) is spreading in many regions worldwide, causing maize lethal necrosis when co-infected with a potyvirid. In this study, one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to detect MCMV in maize. A set of four specific primers was designed based on the conserved coat protein gene sequences of MCMV. The RT-LAMP could be completed within 60min under isothermal condition at 63°C. The sensitivity test showed that the RT-LAMP was about 10-fold more sensitive than RT-PCR and no cross-reactivity was detected with other viral pathogens infecting maize in China. Moreover, the results of RT-LAMP could be visually inspected by SYBR Green I staining in a closed-tube, facilitating high-throughput application of MCMV detection. This method was further verified by testing field-collected samples. These results suggested that the developed MCMV RT-LAMP technique is a rapid, efficient and sensitive method which could be used as a routine screen for MCMV infection.
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Affiliation(s)
- Ling Chen
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zhiyuan Jiao
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Dongmei Liu
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Xingliang Liu
- Beijing Entry-exit Inspection and Quarantine Bureau, Beijing 100016, China
| | - Zihao Xia
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Congliang Deng
- Beijing Entry-exit Inspection and Quarantine Bureau, Beijing 100016, China
| | - Tao Zhou
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Zaifeng Fan
- State Key Laboratory of Agro-biotechnology and Ministry of Agriculture Key Laboratory for Plant Pathology, China Agricultural University, Beijing 100193, China.
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22
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He X, Xue F, Xu S, Wang W. Rapid and sensitive detection of Lily symptomless virus by reverse transcription loop-mediated isothermal amplification. J Virol Methods 2016; 238:38-41. [PMID: 27737784 DOI: 10.1016/j.jviromet.2016.10.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 08/28/2016] [Accepted: 10/09/2016] [Indexed: 11/29/2022]
Abstract
Lily symptomless virus (LSV) is one of the most prevalent viruses that infect lily plants worldwide. A rapid and sensitive reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detection of LSV, using two primer pairs that specifically amplified the conserved sequence of LSV coat protein. The optimum reaction conditions were as follows: 4mM MgCl2 and 0.8M betaine with incubation at 64°C for 30min. The limit of detection of LSV from infected lily leaves was 10-fold higher for RT-LAMP than for conventional RT-PCR. Moreover, RT-LAMP detected LSV in not only symptomatic, but also in symptomless tissues of infected plants. These findings indicate that our RT-LAMP method for LSV can serve as a low-cost, simple, and rapid alternative to conventional detection assays.
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Affiliation(s)
- Xiangfeng He
- Beijing Engineering Research Center of Rural Landscape Planning and Design, College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing 102206, China.
| | - Fei Xue
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| | - Shufa Xu
- Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture, Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China.
| | - Wenhe Wang
- Beijing Engineering Research Center of Rural Landscape Planning and Design, College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing 102206, China.
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23
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Banerjee A, Roy S, Sharma SK, Dutta SK, Chandra S, Ngachan SV. Reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid diagnosis of chilli veinal mottle virus. Arch Virol 2016; 161:1957-61. [PMID: 27063408 DOI: 10.1007/s00705-016-2850-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 03/28/2016] [Indexed: 10/22/2022]
Abstract
Chilli veinal mottle virus (ChiVMV) causes significant economic loss to chilli cultivation in northeastern India, as well as in eastern Asia. In this study, we have developed a single-tube one-step reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid, sensitive and specific diagnosis of ChiVMV. Amplification could be visualized after adding SYBR Green I (1000×) dye within 60 min under isothermal conditions at 63 °C, with a set of four primers designed based on the large nuclear inclusion protein (NIb) domain of ChiVMV (isolate KC-ML1). The RT-LAMP method was 100 times more sensitive than one-step reverse transcription polymerase chain reaction (RT-PCR), with a detection limit of 0.0001 ng of total RNA per reaction.
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Affiliation(s)
- Amrita Banerjee
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India.
| | - Somnath Roy
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Umiam, Meghalaya, 793 103, India
| | - Susheel Kumar Sharma
- ICAR Research Complex for NEH Region, Manipur Centre, Lamphelpat, Manipur, 795 004, India
| | - Sudip Kumar Dutta
- ICAR Research Complex for NEH Region, Mizoram Centre, Kolasib, Mizoram, 796 081, India
| | - Satish Chandra
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India
| | - S V Ngachan
- ICAR Research Complex for North Eastern Hill Region, Umiam, Meghalaya, 793 103, India
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Su Y, Yang Y, Peng Q, Zhou D, Chen Y, Wang Z, Xu L, Que Y. Development and application of a rapid and visual loop-mediated isothermal amplification for the detection of Sporisorium scitamineum in sugarcane. Sci Rep 2016; 6:23994. [PMID: 27035751 PMCID: PMC4817513 DOI: 10.1038/srep23994] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 03/16/2016] [Indexed: 11/09/2022] Open
Abstract
Smut is a fungal disease with widespread prevalence in sugarcane planting areas. Early detection and proper identification of Sporisorium scitamineum are essential in smut management practices. In the present study, four specific primers targeting the core effector Pep1 gene of S. scitamineum were designed. Optimal concentrations of Mg(2+), primer and Bst DNA polymerase, the three important components of the loop-mediated isothermal amplification (LAMP) reaction system, were screened using a single factor experiment method and the L16(4(5)) orthogonal experimental design. Hence, a LAMP system suitable for detection of S. scitamineum was established. High specificity of the LAMP method was confirmed by the assay of S. scitamineum, Fusarium moniliforme, Pestalotia ginkgo, Helminthospcrium sacchari, Fusarium oxysporum and endophytes of Yacheng05-179 and ROC22. The sensitivity of the LAMP method was equal to that of the conventional PCR targeting Pep1 gene and was 100 times higher than that of the conventional PCR assay targeting bE gene in S. scitamineum. The results suggest that this novel LAMP system has strong specificity and high sensitivity. This method not only provides technological support for the epidemic monitoring of sugarcane smut, but also provides a good case for development of similar detection technology for other plant pathogens.
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Affiliation(s)
- Yachun Su
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Yuting Yang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Qiong Peng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Dinggang Zhou
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Yun Chen
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Zhuqing Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Fujian Agriculture and Forestry University, Ministry of Agriculture, Fuzhou 350002, China
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25
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Xie X, Chen W, Fu Q, Zhang P, An T, Cui A, An D. Molecular Variability and Distribution of Sugarcane Mosaic Virus in Shanxi, China. PLoS One 2016; 11:e0151549. [PMID: 26987060 PMCID: PMC4795778 DOI: 10.1371/journal.pone.0151549] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/01/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Sugarcane mosaic virus (SCMV) is responsible for large-scale economic losses in the global production of sugarcane, maize, sorghum, and some other graminaceous species. To understand the evolutionary mechanism of SCMV populations, this virus was studied in Shanxi, China. A total of 86 maize leaf samples (41 samples in 2012 and 45 samples in 2013) were collected from 4 regions of Shanxi. RESULTS Double-antibody sandwich (DAS)-ELISA and RT-PCR showed 59 samples (30 samples in 2012 and 29 samples in 2013) to be positive for SCMV, from which 10 new isolates of SCMV were isolated and sequenced. The complete genomes of these isolates are 9610 nt long, including the 5' and 3' non-coding regions, and encode a 3063-amino acid polyprotein. Phylogenetic analyses revealed that 24 SCMV isolates could be divided on the basis of the whole genome into 2 divergent evolutionary groups, which were associated with the host species. Among the populations, 15 potential recombination events were identified. The selection pressure on the genes of these SCMV isolates was also calculated. The results confirmed that all the genes were under negative selection. CONCLUSIONS Negative selection and recombination appear to be important evolutionary factors shaping the genetic structure of these SCMV isolates. SCMV is distributed widely in China and exists as numerous strains with distinct genetic diversity. Our findings will provide a foundation for evaluating the epidemiological characteristics of SCMV in China and will be useful in designing long-term, sustainable management strategies for SCMV.
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Affiliation(s)
- Xiansheng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi, China
| | - Wei Chen
- College of Life Science, Shanxi Normal University, Linfen, Shanxi, China
| | - Qiang Fu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Penghui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Tianci An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Aimin Cui
- Wheat Research Institute, Shanxi Academy of Agricultural Sciences, Linfen, Shanxi, China
| | - Derong An
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
- * E-mail:
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26
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Chandra A, Keizerweerd AT, Grisham MP. Detection of Puccinia kuehnii Causing Sugarcane Orange Rust with a Loop-Mediated Isothermal Amplification-Based Assay. Mol Biotechnol 2016; 58:188-96. [PMID: 26837389 DOI: 10.1007/s12033-016-9914-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Puccinia kuehnii is a fungal pathogen that causes orange rust in sugarcane, which is now prevalent in many countries. At the early stage of disease, it is almost indistinguishable from brown rust, which is caused by Puccinia melanocephala. Although several PCR assays are available to detect these diseases, the loop-mediated isothermal amplification (LAMP)-based assay has been reported to be more economical and easier to perform. Under isothermal conditions, DNA is amplified with high specificity and rapidity. Moreover, visual judgment of color change without further post-amplification processing makes the method convenient. The present study was undertaken to detect P. kuehnii genomic DNA using four primers corresponding to a unique DNA sequence of P. kuehnii. The LAMP assay was found to be optimal when 8 mM MgSO4 was used and the reaction was incubated at 63 °C for 90 min. Positive samples showed a color change from orange to green upon SYBR Green I dye addition. Specificity of the LAMP test was checked with DNA of P. melanocephala, which showed no reaction. Sensitivity of the LAMP method was observed to be the same as real-time PCR at 0.1 ng, thus providing a rapid and more affordable option for early disease detection.
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Affiliation(s)
- Amaresh Chandra
- Sugarcane Research Unit, USDA, ARS, 5883 USDA Road, Houma, LA, 70360, USA. .,Indian Institute of Sugarcane Research, Lucknow, 226 002, India.
| | | | - Michael P Grisham
- Sugarcane Research Unit, USDA, ARS, 5883 USDA Road, Houma, LA, 70360, USA.
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27
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Amata RL, Fernandez E, Filloux D, Martin DP, Rott P, Roumagnac P. Prevalence of Sugarcane yellow leaf virus in Sugarcane-Producing Regions in Kenya Revealed by Reverse-Transcription Loop-Mediated Isothermal Amplification Method. PLANT DISEASE 2016; 100:260-268. [PMID: 30694143 DOI: 10.1094/pdis-05-15-0602-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Yellow leaf (YL) is a disease of sugarcane that is currently widespread throughout most American and Asian sugarcane-producing countries. However, its actual distribution in Africa remains largely unknown. A reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed to facilitate and improve the detection of Sugarcane yellow leaf virus (SCYLV), the causal agent of YL. The RT-LAMP assay was found to be comparable with or superior to conventional RT-polymerase chain reaction (PCR) for the detection of SCYLV genotypes CUB and BRA in infected sugarcane 'C132-81' and 'SP71-6163', respectively. Additionally, 68 sugarcane samples that tested negative by RT-PCR were found positive by RT-LAMP, whereas the RT-LAMP assay failed to detect SCYLV in only 5 samples that tested positive by RT-PCR. Combining RT-PCR and RT-LAMP data enabled the detection of SCYLV in 86 of 183 Kenyan sugarcane plants, indicating high SCYLV prevalence throughout the country (ranging from 36 to 64% in individual counties). Seminested PCR assays were developed that enabled the amplification of a fragment encompassing the capsid protein coding region gene and its flanking 5' and 3' genomic regions. Sequences of this fragment for four Kenyan SCYLV isolates indicated that they shared 99.2 to 99.6% pairwise identity with one another and clearly clustered phylogenetically with SCYLV-BRA genotype isolates. To our knowledge, this is the first report of SCYLV in Kenya.
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Affiliation(s)
- Ruth L Amata
- Kenya Agricultural and Livestock Research Organization, Nairobi, 00200 Kenya
| | - Emmanuel Fernandez
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Denis Filloux
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
| | - Darren P Martin
- Computational Biology Group, Institute of Infectious Disease and Molecular Medicine, UCT Faculty of Health Sciences, Observatory 7925, South Africa
| | - Philippe Rott
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet; and Plant Pathology Department, Everglades Research and Education Center, University of Florida, IFAS, Belle Glade, 33430
| | - Philippe Roumagnac
- CIRAD-INRA-SupAgro, UMR BGPI, Campus International de Montferrier-Baillarguet, 34398 Montpellier Cedex-5, France
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28
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Hasiów-Jaroszewska B, Budzyńska D, Borodynko N, Pospieszny H. Rapid detection of genetically diverse tomato black ring virus isolates using reverse transcription loop-mediated isothermal amplification. Arch Virol 2015; 160:3075-8. [PMID: 26338092 DOI: 10.1007/s00705-015-2586-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 08/25/2015] [Indexed: 11/25/2022]
Abstract
A reverse transcription loop-mediated isothermal amplification assay (RT-LAMP) has been developed for detection of tomato black ring virus (TBRV) isolates collected from different hosts. One-step RT-LAMP was performed with a set of four primers, the design of which was based on the coat protein gene. Results of RT-LAMP were visualized by direct staining of products with fluorescent dyes, agarose gel electrophoresis, and analysis of amplification curves. The sensitivity of RT-LAMP was 100-fold greater than that of RT-PCR. The RT-LAMP assay developed here is a useful and practical method for diagnosis of TBRV.
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Affiliation(s)
- Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland.
| | - Daria Budzyńska
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland
| | - Natasza Borodynko
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland
| | - Henryk Pospieszny
- Department of Virology and Bacteriology, Institute of Plant Protection - National Research Institute, ul. Wł. Węgorka 20, 60-318, Poznan, Poland
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29
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Chandra A, Keizerweerd AT, Que Y, Grisham MP. Loop-mediated isothermal amplification (LAMP) based detection of Colletotrichum falcatum causing red rot in sugarcane. Mol Biol Rep 2015; 42:1309-16. [PMID: 25861736 DOI: 10.1007/s11033-015-3875-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 03/31/2015] [Indexed: 11/24/2022]
Abstract
Red rot, caused by Colletotrichum falcatum, is a destructive disease prevalent in most sugarcane-producing countries. Disease-free sugarcane planting materials (setts) are essential as the pathogen spreads primarily through infected setts. The present study was undertaken to develop a loop-mediated isothermal amplification (LAMP) assay for the detection of C. falcatum. C. falcatum genomic DNA was isolated from pure mycelium culture and infected tissues. Four sets of primers corresponding to a unique DNA sequence specific to C. falcatum were designed. Specificity of the LAMP test was checked with DNA of another fungal pathogen of sugarcane, Puccinia melanocephala, as well as two closely-related species, Colletotrichum fructivorum and Colletotrichum acutatum. No reaction was found with the three pathogens. When C. falcatum DNA from pure culture was used in a detection limit analysis, sensitivity of the LAMP method was observed to be ten times higher than that of conventional PCR; however, sensitivity was only 5 times higher when DNA from C. falcatum-infected tissues was used. Using the LAMP assay, C. falcatum DNA is amplified with high specificity, efficiency, and rapidity under isothermal conditions. Moreover, visual judgment of color change in <1 h without further post-amplification processing makes the LAMP method convenient, economical, and useful in diagnostic laboratories and the field.
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Affiliation(s)
- Amaresh Chandra
- USDA-ARS, MSA, Sugarcane Research Laboratory, Houma, LA, 70360, USA
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