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Yeni O, Şen M, Hasançebi S, Turgut Kara N. Optimization of loop-mediated isothermal amplification assay for sunflower mildew disease detection. Sci Rep 2024; 14:23224. [PMID: 39369029 PMCID: PMC11455944 DOI: 10.1038/s41598-024-72228-y] [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: 05/23/2024] [Accepted: 09/04/2024] [Indexed: 10/07/2024] Open
Abstract
Loop-Mediated Isothermal Amplification (LAMP) represents a valuable technique for DNA/RNA detection, known for its exceptional sensitivity, specificity, speed, accuracy, and affordability. This study focused on optimizing a LAMP-based method to detect early signs of Plasmopara halstedii, the casual pathogen of sunflower downy mildew, a severe threat to sunflower crops. Specifically, a set of six LAMP primers (two outer, two inner, and two loop) were designed from P. halstedii genomic DNA, targeting the ribosomal Large Subunit (LSU). These primers were verified by in silico analysis and experimental validation using both target and non-target species' DNAs. Optimizations encompassing reaction conditions (temperature, time) and component concentrations (magnesium, Bst DNA polymerase, primers, and dNTP) were determined. Validation of these optimizations was performed by agarose gel electrophoresis. Furthermore, various colorimetric chemicals (Neutral Red, Hydroxynaphthol Blue, SYBR Safe, Thiazole Green) were evaluated to facilitate method analysis, and the real-time analysis has been optimized, presenting multiple approaches for detecting sunflower downy mildew using the LAMP technique. The analytical sensitivity of the method was confirmed by detecting P. halstedii DNA concentrations as low as 0.5 pg/μl. This pioneering study, establishing P. halstedii detection through the LAMP method, stands as unique in its field. The precision, robustness, and practicality of the LAMP protocol make it an ideal choice for studies focusing on sunflower mildew, emphasizing its recommended use due to its operational ease and reliability.
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Affiliation(s)
- Oğuzhan Yeni
- Institute of Science, Program of Molecular Biotechnology and Genetics, Istanbul University, Istanbul, Turkey
| | - Mutlu Şen
- Institute of Science, Program of Biotechnology and Genetics, Trakya University, Edirne, Turkey
| | - Semra Hasançebi
- Faculty of Engineering, Department of Genetics and Bioengineering, Trakya University, Ahmet Karadeniz Yerleskesi, Edirne, Turkey
| | - Neslihan Turgut Kara
- Faculty of Science, Department of Molecular Biology and Genetics, Istanbul University, Vezneciler, 34134, Istanbul, Turkey.
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Akahori M, Miyazaki A, Koinuma H, Tokuda R, Iwabuchi N, Kitazawa Y, Maejima K, Namba S, Yamaji Y. Use of the 23S rRNA gene as a target template in the universal loop-mediated isothermal amplification (LAMP) of genomic DNA from phytoplasmas. Microbiol Spectr 2024; 12:e0010624. [PMID: 38534170 PMCID: PMC11064480 DOI: 10.1128/spectrum.00106-24] [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: 01/11/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
Plant-pathogenic bacteria cause numerous diseases in host plants and can result in serious damage. Timely and accurate diagnostic techniques are, therefore, crucial. While advances in molecular techniques have led to diagnostic systems able to distinguish known plant pathogens at the species or strain level, systems covering larger categories are mostly lacking. In this study, a specific and universal LAMP-based diagnostic system was developed for phytoplasmas, a large group of insect-borne plant-pathogenic bacteria that cause significant agricultural losses worldwide. Targeting the 23S rRNA gene of phytoplasma, the newly designed primer set CaPU23S-4 detected 31 'Candidatus Phytoplasma' tested within 30 min. This primer set also showed high specificity, without false-positive results for other bacteria (including close relatives of phytoplasmas) or healthy plants. The detection sensitivity was ~10,000 times higher than that of PCR methods for phytoplasma detection. A simple, rapid method of DNA extraction, by boiling phytoplasma-infected tissues, was developed as well. When used together with the universal LAMP assay, it enabled the prompt and accurate detection of phytoplasmas from plants and insects. The results demonstrate the potential of the 23S rRNA gene as a versatile target for the LAMP-based universal detection of bacteria at the genus level and provide a novel avenue for exploring this gene as molecular marker for phytoplasma presence detection.IMPORTANCEPhytoplasmas are associated with economically important diseases in crops worldwide, including lethal yellowing of coconut palm, "flavescence dorée" and "bois noir" of grapevine, X-disease in stone fruits, and white leaf and grassy shoot in sugarcane. Numerous LAMP-based diagnostic assays, mostly targeting the 16S rRNA gene, have been reported for phytoplasmas. However, these assays can only detect a limited number of 'Candidatus Phytoplasma' species, whereas the genus includes at least 50 of these species. In this study, a universal, specific, and rapid diagnostic system was developed that can detect all provisionally classified phytoplasmas within 1 h by combining the LAMP technique targeting the 23S rRNA gene with a simple method for DNA extraction. This diagnostic system will facilitate the on-site detection of phytoplasmas and may aid in the discovery of new phytoplasma-associated diseases and putative insect vectors, irrespective of the availability of infrastructure and experimental resources.
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Affiliation(s)
- Mako Akahori
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Akio Miyazaki
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Hiroaki Koinuma
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Ryosuke Tokuda
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Nozomu Iwabuchi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yugo Kitazawa
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kensaku Maejima
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Shigetou Namba
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Yasuyuki Yamaji
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo, Japan
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Meinecke CD, Vos LD, Yilmaz N, Steenkamp ET, Wingfield MJ, Wingfield BD, Villari C. A LAMP Assay for Rapid Detection of the Pitch Canker Pathogen Fusarium circinatum. PLANT DISEASE 2023; 107:2916-2923. [PMID: 36867583 DOI: 10.1094/pdis-04-22-0972-sr] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
The pine pitch canker pathogen Fusarium circinatum is endemic in the southeastern United States and Central America and represents an invasive threat globally. This ecologically adaptable fungus readily infects all parts of its pine hosts, leading to widespread mortality of nursery seedlings and decline in the health and productivity of forest stands. Because trees infected by F. circinatum can remain asymptomatic for long periods of time, accurate and rapid tools are needed for real-time diagnostics and surveillance at ports, in nurseries, and in plantations. To meet this need and to limit the spread and impact of the pathogen, we developed a molecular test using loop-mediated isothermal amplification (LAMP), a technology that allows for the rapid detection of pathogen DNA on portable, field-capable devices. LAMP primers were designed and validated to amplify a gene region unique to F. circinatum. Using a globally representative collection of F. circinatum isolates and other closely related species, we have demonstrated that the assay can be used to identify F. circinatum across its genetic diversity and that it is sensitive to as few as 10 cells from purified DNA extracts. The assay can also be used with a simple, pipette-free DNA extraction method and is compatible with testing symptomatic pine tissues in the field. This assay has the potential to facilitate diagnostic and surveillance efforts both in the laboratory and in the field and, thus, to reduce the spread and impact of pitch canker worldwide.
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Affiliation(s)
- Colton D Meinecke
- D. B. Warnell School of Forestry of Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
| | - Lieschen De Vos
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Neriman Yilmaz
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Emma T Steenkamp
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Michael J Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Brenda D Wingfield
- Forestry and Agricultural Biotechnology Institute (FABI), Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0028, South Africa
| | - Caterina Villari
- D. B. Warnell School of Forestry of Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
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Kogej Zwitter Z, Seljak G, Jakomin T, Brodarič J, Vučurović A, Pedemay S, Salar P, Malembic-Maher S, Foissac X, Mehle N. Epidemiology of flavescence dorée and hazelnut decline in Slovenia: geographical distribution and genetic diversity of the associated 16SrV phytoplasmas. FRONTIERS IN PLANT SCIENCE 2023; 14:1217425. [PMID: 37469777 PMCID: PMC10352807 DOI: 10.3389/fpls.2023.1217425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 06/13/2023] [Indexed: 07/21/2023]
Abstract
Flavescence dorée (FD) phytoplasma from 16SrV-C and -D subgroups cause severe damage to grapevines throughout Europe. This phytoplasma is transmitted from grapevine to grapevine by the sap-sucking leafhopper Scaphoideus titanus. European black alder and clematis serve as perennial plant reservoirs for 16SrV-C phytoplasma strains, and their host range has recently been extended to hazelnuts. In Slovenia, hazelnut orchards are declining due to 16SrV phytoplasma infections, where large populations of the non-autochthonous leafhopper Orientus ishidae have been observed. To better characterise the phytoplasma-induced decline of hazelnut and possible transmission fluxes between these orchards and grapevine, genetic diversity of 16SrV phytoplasmas in grapevine, hazelnut and leafhoppers was monitored from 2017 to 2022. The nucleotide sequence analysis was based on the map gene. The most prevalent map genotype in grapevine in all wine-growing regions of Slovenia was M54, which accounted for 84% of the 176 grapevines tested. Besides M54, other epidemic genotypes with lower frequency were M38 (6%), M51 (3%), M50 (2%) and M122 (1%). M38, M50 and M122 were also detected in infected cultivated hazelnuts and in specimens of O. ishidae leafhopper caught in declining hazelnut orchards. It suggests that this polyphagous vector could be responsible for phytoplasma infection in hazelnut orchards and possibly for some phytoplasma exchanges between hazelnuts and grapevine. We hereby describe new genotypes: M158 in grapevine as well as four never reported genotypes M159 to M162 in hazelnut. Of these four genotypes in hazelnut, one (M160) was also detected in O. ishidae. Analysis of additional genes of the new genotypes allowed us to assign them to the VmpA-III cluster, which corresponds to the 16SrV-C strains previously shown to be compatible with S. titanus transmission.
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Affiliation(s)
- Zala Kogej Zwitter
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
- Sensor Technologies, Jožef Stefan International Postgraduate School, Ljubljana, Slovenia
| | - Gabrijel Seljak
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Tjaša Jakomin
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Jakob Brodarič
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Ana Vučurović
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Sandra Pedemay
- National Research Institute for Agriculture, Food and Environment, Fruit Biology and Pathology, Bordeaux, France
| | - Pascal Salar
- National Research Institute for Agriculture, Food and Environment, Fruit Biology and Pathology, Bordeaux, France
| | - Sylvie Malembic-Maher
- National Research Institute for Agriculture, Food and Environment, Fruit Biology and Pathology, Bordeaux, France
| | - Xavier Foissac
- National Research Institute for Agriculture, Food and Environment, Fruit Biology and Pathology, Bordeaux, France
| | - Nataša Mehle
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
- School for Viticulture and Enology, University of Nova Gorica, Nova Gorica, Slovenia
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Raclariu-Manolică AC, Mauvisseau Q, de Boer HJ. Horizon scan of DNA-based methods for quality control and monitoring of herbal preparations. Front Pharmacol 2023; 14:1179099. [PMID: 37214460 PMCID: PMC10193163 DOI: 10.3389/fphar.2023.1179099] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/20/2023] [Indexed: 05/24/2023] Open
Abstract
Herbal medicines and preparations are widely used in healthcare systems globally, but concerns remain about their quality and safety. New herbal products are constantly being introduced to the market under varying regulatory frameworks, with no global consensus on their definition or characterization. These biologically active mixtures are sold through complex globalized value chains, which create concerns around contamination and profit-driven adulteration. Industry, academia, and regulatory bodies must collaborate to develop innovative strategies for the identification and authentication of botanicals and their preparations to ensure quality control. High-throughput sequencing (HTS) has significantly improved our understanding of the total species diversity within DNA mixtures. The standard concept of DNA barcoding has evolved over the last two decades to encompass genomic data more broadly. Recent research in DNA metabarcoding has focused on developing methods for quantifying herbal product ingredients, yielding meaningful results in a regulatory framework. Techniques, such as loop-mediated isothermal amplification (LAMP), DNA barcode-based Recombinase Polymerase Amplification (BAR-RPA), DNA barcoding coupled with High-Resolution Melting (Bar-HRM), and microfluidics-based methods, offer more affordable tests for the detection of target species. While target capture sequencing and genome skimming are considerably increasing the species identification resolution in challenging plant clades, ddPCR enables the quantification of DNA in samples and could be used to detect intended and unwanted ingredients in herbal medicines. Here, we explore the latest advances in emerging DNA-based technologies and the opportunities they provide as taxa detection tools for evaluating the safety and quality of dietary supplements and herbal medicines.
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Affiliation(s)
- Ancuța Cristina Raclariu-Manolică
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, Piatra Neamț, Romania
- Natural History Museum, University of Oslo, Oslo, Norway
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Jeseničnik T, Kaurin A, Grgič Z, Radišek S, Jakše J, Štajner N. Novel Identification of the Collection of Pathogenic Fungal Species Verticillium with the Development of Species-Specific SSR Markers. Pathogens 2023; 12:pathogens12040535. [PMID: 37111421 PMCID: PMC10143602 DOI: 10.3390/pathogens12040535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/29/2023] Open
Abstract
The genus Verticillium is a group of ascomycete fungi that includes several pathogenic plant species. In 2011, a new taxonomic classification, proposed by Inderbitzin and coworkers (2011), re-defined the genus as Verticillium sensu stricto. The objective of our study was the re-classification of the fungal species held in the culture collection in the Slovenian Institute of Hop Research and Brewing in accordance with the newly established taxonomy. With the PCR marker system proposed by Inderbitzin and coworkers in 2011, we re-classified 88 Verticillium isolates out of the 105 samples that are held in the institute's bank, which were obtained from different geographic locations in Europe, North America, and Japan, and from different host plants, including alfalfa, cotton, hop, olive, potato, and tomato. However, the PCR marker for the V. dahliae identification proved to be less specific, and it resulted in the positive amplification of Gibellulopsis nigrescens, V. isaacii, and V. longisporum. To enable the accurate distinction of the fungi, the SSR and LAMP markers were added to the analyses. The 12 newly identified SSR markers, which were used in simplex PCR reactions or in combination, enabled the accurate identification of all included Verticillium isolates and could potentially be used as biomarkers for rapid and easy species identification.
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Affiliation(s)
- Taja Jeseničnik
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Anela Kaurin
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Zarja Grgič
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Sebastjan Radišek
- Plant Protection Department, Slovenian Institute of Hop Research and Brewing, 3310 Žalec, Slovenia
| | - Jernej Jakše
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nataša Štajner
- Department of Agronomy, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
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Alič Š, Dermastia M, Burger J, Dickinson M, Pietersen G, Pietersen G, Dreo T. Genome-Informed Design of a LAMP Assay for the Specific Detection of the Strain of ' Candidatus Phytoplasma asteris' Phytoplasma Occurring in Grapevines in South Africa. PLANT DISEASE 2022; 106:2927-2939. [PMID: 35380469 DOI: 10.1094/pdis-10-21-2312-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Grapevine yellows is one of the most damaging phytoplasma-associated diseases worldwide. It is linked to several phytoplasma species, which can vary regionally due to phytoplasma and insect-vector diversity. Specific, rapid, and reliable detection of the grapevine yellows pathogen has an important role in phytoplasma control. The purpose of this study was to develop and validate a specific loop-mediated isothermal amplification (LAMP) assay for detection of a distinct strain of grapevine 'Candidatus Phytoplasma asteris' that is present in South Africa, through implementation of a genome-informed test design approach. Several freely available, user-friendly, web-based tools were coupled to design the specific LAMP assays. The criteria for selection of the assays were set for each step of the process, which resulted in four experimentally operative LAMP assays that targeted the ftsH/hflB gene region, specific to the aster yellows phytoplasma strain from South Africa. A real-time PCR was developed, targeting the same genetic region, to provide extensive validation of the LAMP assay. The validated molecular assays are highly specific to the targeted aster yellows phytoplasma strain from South Africa, with good sensitivity and reproducibility. We show a genome-informed molecular test design and an efficient validation approach for molecular tests if reference and sample materials are sparse and hard to obtain.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Špela Alič
- National Institute of Biology, 1000 Ljubljana, Slovenia
| | - Marina Dermastia
- National Institute of Biology, 1000 Ljubljana, Slovenia
- Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia
| | - Johan Burger
- Department of Genetics, Stellenbosch University, Matieland, 7602, South Africa
| | - Matthew Dickinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, LE12 5RD, United Kingdom
| | - Gerhard Pietersen
- Department of Microbiology and Plant Pathology, University of Pretoria, Hatfield 0028, South Africa
| | | | - Tanja Dreo
- National Institute of Biology, 1000 Ljubljana, Slovenia
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Vončina D, Diaz-Lara A, Preiner D, Al Rwahnih M, Stevens K, Jurić S, Malenica N, Šimon S, Meng B, Maletić E, Fulgosi H, Cvjetković B. Virus and Virus-like Pathogens in the Grapevine Virus Collection of Croatian Autochthonous Grapevine Cultivars. PLANTS (BASEL, SWITZERLAND) 2022; 11:1485. [PMID: 35684258 PMCID: PMC9182833 DOI: 10.3390/plants11111485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/17/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Grapevine collections play an important role, especially in the study of viruses and virus-like pathogens. In 2009, after an initial ELISA screening for eight viruses (arabis mosaic virus, grapevine fanleaf virus, grapevine fleck virus, grapevine leafroll-associated viruses 1, 2, and 3, and grapevine viruses A and B), a collection of 368 grapevine accessions representing 14 different Croatian autochthonous cultivars and containing single or mixed infection of viruses was established to further characterize the viral pathogens. Subsequently, Western blot, RT-PCR, cloning, and sequencing revealed that grapevine rupestris stem pitting-associated virus was frequently found in accessions of the collection, with isolates showing substantial genetic diversity in the helicase and coat protein regions. High-throughput sequencing of 22 grapevine accessions provides additional insight into the viruses and viroids present in the collection and confirms the fact that Croatian autochthonous grapevine cultivars have high infection rates and high virome diversity. The recent spread of "flavescence dorée" phytoplasma in Europe has not spared the collection. After the first symptoms observed in 2020 and 2021, the presence of phytoplasma was confirmed by LAMP in six grapevine accessions and some of them were lost. Single or multiple viruses and viroids, as well as own rooted grapevines in the collection, make the plants susceptible to various abiotic factors, which, together with the recent occurrence of "flavescence dorée", makes the maintenance of the collection a challenge. Future efforts will be directed towards renewing the collection, as 56% of the original collection has been lost in the last 13 years.
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Affiliation(s)
- Darko Vončina
- Department of Plant Pathology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), 10000 Zagreb, Croatia; (D.P.); (E.M.)
| | - Alfredo Diaz-Lara
- School of Engineering and Sciences, Tecnologico de Monterrey, Campus Queretaro, Queretaro 76130, Mexico;
| | - Darko Preiner
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), 10000 Zagreb, Croatia; (D.P.); (E.M.)
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
| | - Maher Al Rwahnih
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (M.A.R.); (K.S.)
| | - Kristian Stevens
- Foundation Plant Services, University of California-Davis, Davis, CA 95616, USA; (M.A.R.); (K.S.)
- Departments of Computer Science and Evolution and Ecology, University of California-Davis, Davis, CA 95616, USA
| | - Snježana Jurić
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (S.J.); (H.F.)
| | - Nenad Malenica
- Division of Molecular Biology, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia;
| | - Silvio Šimon
- Directorate for the Professional Support for the Development of Agriculture, Ministry of Agriculture, 10000 Zagreb, Croatia;
| | - Baozhong Meng
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Edi Maletić
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CroP-BioDiv), 10000 Zagreb, Croatia; (D.P.); (E.M.)
- Department of Viticulture and Enology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia
| | - Hrvoje Fulgosi
- Division of Molecular Biology, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (S.J.); (H.F.)
| | - Bogdan Cvjetković
- Department of Agricultural Zoology, Faculty of Agriculture, University of Zagreb, 10000 Zagreb, Croatia;
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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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10
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Development and Validation of a Loop-Mediated Isothermal Amplification Diagnostic Method to Detect the Quarantine Potato Pale Cyst Nematode, Globodera pallida. Pathogens 2021; 10:pathogens10060744. [PMID: 34204749 PMCID: PMC8231653 DOI: 10.3390/pathogens10060744] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 06/08/2021] [Accepted: 06/08/2021] [Indexed: 11/16/2022] Open
Abstract
The potato cyst nematode (PCN) Globodera pallida has acquired significant importance throughout Europe due to its nefarious effects on potato production. Rapid and reliable diagnosis of PCN is critical during the surveillance programs and for the implementation of control measures. Molecular DNA-based methods are available, but they require expensive laboratory facilities, equipment and trained technicians. Moreover, there is an additional need of time for sample shipment and testing. In this work, we have developed a new and simple assay which reliably discriminates G. pallida from other cyst nematodes in less than 40 min. This assay may be applied either on cysts or juveniles with the ability to detect a single juvenile of G. pallida in a sample of at least 40 juveniles of the non-target species G. rostochiensis. This test should be a tool to improve the performance of the laboratory and has the potential to be performed on-site.
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Rizzo D, Moricca S, Bracalini M, Benigno A, Bernardo U, Luchi N, Da Lio D, Nugnes F, Cappellini G, Salemi C, Cacciola SO, Panzavolta T. Rapid Detection of Pityophthorus juglandis (Blackman) (Coleoptera, Curculionidae) with the Loop-Mediated Isothermal Amplification (LAMP) Method. PLANTS 2021; 10:plants10061048. [PMID: 34067342 PMCID: PMC8224600 DOI: 10.3390/plants10061048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/14/2021] [Accepted: 05/20/2021] [Indexed: 11/16/2022]
Abstract
The walnut twig beetle Pityophthorus juglandis is a phloem-boring bark beetle responsible, in association with the ascomycete Geosmithia morbida, for the Thousand Cankers Disease (TCD) of walnut trees. The recent finding of TCD in Europe prompted the development of effective diagnostic protocols for the early detection of members of this insect/fungus complex. Here we report the development of a highly efficient, low-cost, and rapid method for detecting the beetle, or even just its biological traces, from environmental samples: the loop-mediated isothermal amplification (LAMP) assay. The method, designed on the 28S ribosomal RNA gene, showed high specificity and sensitivity, with no cross reactivity to other bark beetles and wood-boring insects. The test was successful even with very small amounts of the target insect’s nucleic acid, with limit values of 0.64 pg/µL and 3.2 pg/µL for WTB adults and frass, respectively. A comparison of the method (both in real time and visual) with conventional PCR did not display significant differences in terms of LoD. This LAMP protocol will enable quick, low-cost, and early detection of P. juglandis in areas with new infestations and for phytosanitary inspections at vulnerable sites (e.g., seaports, airports, loading stations, storage facilities, and wood processing companies).
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (G.C.)
| | - Salvatore Moricca
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
- Correspondence:
| | - Matteo Bracalini
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
| | - Alessandra Benigno
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
| | - Umberto Bernardo
- Portici Unit, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), P. le Enrico Fermi 1, 80055 Portici, Italy; (U.B.); (F.N.)
| | - Nicola Luchi
- Florence Unit, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, 50019 Sesto Fiorentino, Italy;
| | - Daniele Da Lio
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (D.D.L.); (C.S.)
| | - Francesco Nugnes
- Portici Unit, Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), P. le Enrico Fermi 1, 80055 Portici, Italy; (U.B.); (F.N.)
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy; (D.R.); (G.C.)
| | - Chiara Salemi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy; (D.D.L.); (C.S.)
| | - Santa Olga Cacciola
- Department of Agriculture, Food and Environment, University of Catania, 95123 Catania, Italy;
| | - Tiziana Panzavolta
- Department of Agricultural, Food, Environmental and Forestry Science and Technology (DAGRI), Plant Pathology and Entomology Section, University of Florence, Piazzale delle Cascine 28, 50144 Florence, Italy; (M.B.); (A.B.); (T.P.)
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12
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Phytoplasma diseases of plants: molecular diagnostics and way forward. World J Microbiol Biotechnol 2021; 37:102. [PMID: 34009500 DOI: 10.1007/s11274-021-03061-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Phytoplasmas are obligate phytopathogenic bacteria associated with devastating diseases in hundreds of crops across the world. They have been responsible for huge economic losses in many crop plants for decades now. Isolation and establishment of axenic culture of phytoplasma in complex media is a recent progress in phytoplasma research. Earlier methods for phytoplasma disease detection included symptom profiling, microscopy, serology and dodder transmission studies. With advancement in the field of molecular biology, phytoplasma diagnostics and characterisation witnessed radical improvement. Starting from PCR amplification which often necessities a nested PCR on account of low titre of phytoplasmas, to the closed tube quantitative PCR assays and then the ddPCR, an array of diagnostics have been developed for phytoplasma. The isothermal diagnostic platforms are the latest addition to this and the Loop Mediated Isothermal Amplification (LAMP) assay has been applied for the detection of phytoplasma from several hosts. The futuristic approach in phytoplasma detection will be very likely provided by an integration of nanotechnology and molecular diagnostics. Phytoplasma disease management majorly relies on early detection, vector control, use of disease free planting materials and cultivation of resistant varieties. Hence understanding the molecular mechanism of phytoplasma-host interaction is as important as timely and accurate detection, in the management of phytoplasma diseases. Further, the changing climatic scenario and global warming may lead to an upsurge in the phytoplasma diseases spread and severity across the world, making disease management even more challenging.
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Rizzo D, Da Lio D, Panattoni A, Salemi C, Cappellini G, Bartolini L, Parrella G. Rapid and Sensitive Detection of Tomato Brown Rugose Fruit Virus in Tomato and Pepper Seeds by Reverse Transcription Loop-Mediated Isothermal Amplification Assays (Real Time and Visual) and Comparison With RT-PCR End-Point and RT-qPCR Methods. Front Microbiol 2021; 12:640932. [PMID: 33967980 PMCID: PMC8096992 DOI: 10.3389/fmicb.2021.640932] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 03/15/2021] [Indexed: 11/13/2022] Open
Abstract
Tomato brown rugose fruit virus (ToBRFV) represents an emerging viral threat to the productivity of tomato and pepper protected cultivation worldwide. This virus has got the status of quarantine organism in the European Union (EU) countries. In particular, tomato and pepper seeds will need to be free of ToBRFV before entering the EU and before coming on the market. Thus, lab tests are needed. Here, we develop and validate a one-step reverse transcription LAMP platform for the detection of ToBRFV in tomato and pepper leaves, by real-time assay [reverse transcription loop-mediated isothermal amplification (RT-LAMP)] and visual screening (visual RT-LAMP). Moreover, these methods can also be applied successfully for ToBRFV detection in tomato and pepper seeds. The diagnostic specificity and sensitivity of both RT-LAMP and visual RT-LAMP are both 100%, with a detection limit of nearly 2.25 fg/μl, showing the same sensitivity as RT-qPCR Sybr Green, but 100 times more sensitive than end-point RT-PCR diagnostic methods. In artificially contaminated seeds, the proposed LAMP assays detected ToBRFV in 100% of contaminated seed lots, for up to 0.025–0.033% contamination rates in tomato and pepper, respectively. Our results demonstrate that the proposed LAMP assays are simple, inexpensive, and sensitive enough for the detection of ToBRFV, especially in seed health testing. Hence, these methods have great potential application in the routine detection of ToBRFV, both in seeds and plants, reducing the risk of epidemics.
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Daniele Da Lio
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Alessandra Panattoni
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Chiara Salemi
- Department of Agricultural, Food and Agro-Environmental Sciences, University of Pisa, Pisa, Italy
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Linda Bartolini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Pistoia, Italy
| | - Giuseppe Parrella
- Institute for Sustainable Plant Protection of National Research Council (IPSP-CNR), Portici, Italy
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14
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Dodhia KN, Cox BA, Oliver RP, Lopez-Ruiz FJ. Rapid in situ quantification of the strobilurin resistance mutation G143A in the wheat pathogen Blumeria graminis f. sp. tritici. Sci Rep 2021; 11:4526. [PMID: 33633193 PMCID: PMC7907364 DOI: 10.1038/s41598-021-83981-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 02/08/2021] [Indexed: 11/25/2022] Open
Abstract
As the incidence of fungicide resistance in plant pathogens continues to increase, control of diseases and the management of resistance would be greatly aided by rapid diagnostic methods. Quantitative allele-specific PCR (ASqPCR) is an ideal technique for the in-field analysis of fungicide resistance as it can quantify the frequency of mutations in fungicide targets. We have applied this technique to the fungal pathogen Blumeria graminis f. sp. tritici (Bgt), the causal agent of wheat powdery mildew. In Australia, strobilurin-resistant Bgt was first discovered in 2016. Molecular analysis revealed a nucleotide transversion in the cytochrome b (cytb) gene in the cytochrome bc1 enzyme complex, resulting in a substitution of alanine for glycine at position 143 (G143A). We have developed an in-field ASqPCR assay that can quantify both the resistant (A143) and sensitive (G143) cytb alleles down to 1.67% in host and Bgt DNA mixtures, within 90 min of sample collection. The in situ analysis of samples collected during a survey in Tasmania revealed A143 frequencies ranging between 9-100%. Validation of the analysis with a newly developed laboratory based digital PCR assay found no significant differences between the two methods. We have successfully developed an in-field quantification method, for a strobilurin-resistant allele, by pairing the ASqPCR assay on a lightweight qPCR instrument with a quick DNA extraction method. The deployment of these type of methodologies in the field can contribute to the effective in-season management of fungicide resistance.
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Affiliation(s)
- Kejal N Dodhia
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia
| | - Belinda A Cox
- Faculty of Science and Engineering, Curtin University, Perth, WA, 6102, Australia
| | | | - Francisco J Lopez-Ruiz
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, Perth, WA, 6102, Australia.
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15
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Rizzo D, Luchi N, Da Lio D, Bartolini L, Nugnes F, Cappellini G, Bruscoli T, Salemi C, Griffo RV, Garonna AP, Rossi E. Development of a loop-mediated isothermal amplification (LAMP) assay for the identification of the invasive wood borer Aromia bungii (Coleoptera: Cerambycidae) from frass. 3 Biotech 2021; 11:85. [PMID: 33500873 PMCID: PMC7815857 DOI: 10.1007/s13205-020-02602-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/17/2020] [Indexed: 11/24/2022] Open
Abstract
The red-necked longhorn beetle Aromia bungii (Faldermann, 1835) (Coleoptera: Cerambycidae) is native to east Asia, where it is a major pest of cultivated and ornamental species of the genus Prunus. Morphological or molecular discrimination of adults or larval specimens is required to identify this invasive wood borer. However, recovering larval stages of the pest from trunks and branches causes extensive damage to plants and is timewasting. An alternative approach consists in applying non-invasive molecular diagnostic tools to biological traces (i.e., fecal pellets, frass). In this way, infestations in host plants can be detected without destructive methods. This paper presents a protocol based on both real-time and visual loop-mediated isothermal amplification (LAMP), using DNA of A. bungii extracted from fecal particles in larval frass. Laboratory validations demonstrated the robustness of the protocols adopted and their reliability was confirmed performing an inter-lab blind panel. The LAMP assay and the qPCR SYBR Green method using the F3/B3 LAMP external primers were equally sensitive, and both were more sensitive than the conventional PCR (sensitivity > 103 to the same starting matrix). The visual LAMP protocol, due to the relatively easy performance of the method, could be a useful tool to apply in rapid monitoring of A. bungii and in the management of its outbreaks.
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Affiliation(s)
- Domenico Rizzo
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Nicola Luchi
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), Via Madonna del Piano 10, Sesto Fiorentino, 50019 Florence, Italy
| | - Daniele Da Lio
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Linda Bartolini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Francesco Nugnes
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), P.le Enrico Fermi 1, 80055 Portici, Italy
| | - Giovanni Cappellini
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Tommaso Bruscoli
- Laboratory of Phytopathological Diagnostics and Molecular Biology, Plant Protection Service of Tuscany, Via Ciliegiole 99, 51100 Pistoia, Italy
| | - Chiara Salemi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
| | - Raffaele V. Griffo
- Plant Protection Service of Campania, Centro Direzionale, Isola A6, 80124 Naples, Italy
| | - Antonio P. Garonna
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici, Italy
| | - Elisabetta Rossi
- Department of Agriculture, Food and Environment, University of Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Hamilton JL, Workman JN, Nairn CJ, Fraedrich SW, Villari C. Rapid Detection of Raffaelea lauricola Directly from Host Plant and Beetle Vector Tissues Using Loop-Mediated Isothermal Amplification. PLANT DISEASE 2020; 104:3151-3158. [PMID: 33079016 DOI: 10.1094/pdis-02-20-0422-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Since its introduction in 2002, laurel wilt disease has devastated indigenous lauraceous species in the southeastern United States. The causal agent is a fungal pathogen, Raffaelea lauricola, which, after being introduced into the xylem of trees by its vector beetle, Xyleborus glabratus, results in a fatal vascular wilt. Rapid detection and accurate diagnosis of infections is paramount to the successful implementation of disease management strategies. Current management operations to prevent the spread of laurel wilt disease are largely delayed by time-consuming laboratory procedures to confirm the diagnosis. In order to greatly speed up the operations, we developed a loop-mediated isothermal amplification (LAMP) species-specific assay that targets the β-tubulin gene region of R. lauricola, and allows for the rapid detection of the pathogen directly from host plant and beetle tissues. The assay is capable of amplifying as little as 0.5 pg of fungal DNA and as few as 50 conidia. The assay is also capable of detecting R. lauricola directly from wood tissue of artificially inoculated redbay saplings as early as 10 and 12 days postinoculation, when testing high-quality and crude DNA extracts, respectively. Finally, crude DNA extracts of individual adult female X. glabratus beetles were assayed and the pathogen was detected from all specimens. This assay greatly reduces the time required to confirm a laurel wilt diagnosis and, because LAMP technology is well suited to provide point-of-care testing, it has the potential to expedite and facilitate implementation of management operations in response to disease outbreaks.
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Affiliation(s)
- Jeffrey L Hamilton
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
| | - J Noah Workman
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
- Department of Genetics, Harvard Medical School, Boston, MA 02115, U.S.A
| | - Campbell J Nairn
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
| | - Stephen W Fraedrich
- United States Forest Service, Southern Research Station, Athens, GA 30602, U.S.A
| | - Caterina Villari
- Warnell School of Forestry & Natural Resources, University of Georgia, Athens, GA 30602, U.S.A
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17
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Si Ammour M, Castaldo E, Fedele G, Rossi V. Use of LAMP for Assessing Botrytis cinerea Colonization of Bunch Trash and Latent Infection of Berries in Grapevines. PLANTS 2020; 9:plants9111538. [PMID: 33187064 PMCID: PMC7696620 DOI: 10.3390/plants9111538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 11/07/2020] [Accepted: 11/09/2020] [Indexed: 11/16/2022]
Abstract
A real-time loop-mediated isothermal amplification (LAMP) assay was evaluated for the detection of Botrytis cinerea in grapevine bunch trash, immature berries, and ripening berries. A simple method for the preparation of crude extracts of grape tissue was also developed for on-site LAMP analysis. When tested with 14 other fungal species frequently found in grapevines, the LAMP assay was specific and sensitive to a B. cinerea DNA quantity of 0.1 ng/µL. The sensitivity was further tested using bunch trash samples with B. cinerea colonization levels between 6 and 100% and with bulk-berry samples composed of 4 pathogen-free berries or 4 berries among which 25 to 100% had been inoculated with B. cinerea. The LAMP assay detected the lowest B. cinerea colonization level tested in bunch trash and in immature and mature berries in less than 20 min. In single-berry experiments, LAMP amplified B. cinerea DNA from all artificially inoculated individual immature and mature berries. No amplification occurred in B. cinerea-free material. The real-time LAMP assay has the potential to be used as a rapid on-site diagnostic tool for assessing B. cinerea colonization in bunch trash and B. cinerea latent infections in berries, which represent critical stages for decision-making about disease management.
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Affiliation(s)
- Melissa Si Ammour
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Via E. Parmense 84, 29122 Piacenza, Italy; (M.S.A.); (G.F.)
| | | | - Giorgia Fedele
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Via E. Parmense 84, 29122 Piacenza, Italy; (M.S.A.); (G.F.)
| | - Vittorio Rossi
- Department of Sustainable Crop Production (DI.PRO.VES.), Università Cattolica del Sacro Cuore, Via E. Parmense 84, 29122 Piacenza, Italy; (M.S.A.); (G.F.)
- Correspondence:
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18
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Kyei-Poku G, Gauthier D, Quan G. Development of a Loop-Mediated Isothermal Amplification Assay as an Early-Warning Tool for Detecting Emerald Ash Borer (Coleoptera: Buprestidae) Incursions. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:2480-2494. [PMID: 32667637 DOI: 10.1093/jee/toaa135] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Indexed: 06/11/2023]
Abstract
The emerald ash borer (EAB), Agrilus planipennis (Fairmaire), is the most destructive invasive insect species of ash (Fraxinus spp.) in North America. An accurate method for early detection of this noxious insect pest is indispensable to providing adequate warning of A. planipennis infestation. A loop-mediated isothermal amplification (LAMP) assay (EAB-LAMP) was developed based on mitochondrial cytochrome c oxidase subunit I (COI) gene. The EAB-LAMP required only 30 min at 65°C to amplify A. planipennis DNA from specimens collected from geographically distinct locations. There was no cross-reactivity with other Agrilus and insect species. The developed EAB-LAMP differentially detected traces of A. planipennis genome (COI) within frass from various Fraxinus species. EAB-LAMP was also able to distinguish among A. planipennis DNA and other Agrilus species and nontarget insect species in trap captures. By detecting A. planipennis DNA in two additional trap captures (in situ), the EAB-LAMP was more sensitive and reliable than visual inspection. We tested the quantitative nature of the assay by evaluating pooled trap samples and demonstrated that the EAB-LAMP was capable of functioning optimally using a pool size of at least five individual trap samples. This potentially circumvents the need to perform large-scale individual analysis for processing trap samples. Considering its performance, specificity, sensitivity, and repeatability, the developed EAB-LAMP could be a valuable tool to support strategy and operation of large-scale surveillance for A. planipennis and could profitably be used in routine monitoring programs for effective management of A. planipennis.
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Affiliation(s)
- George Kyei-Poku
- Canadian Forest Service, Great Lakes Forestry Centre, East Sault Ste. Marie, ON, Canada
| | - Debbie Gauthier
- Canadian Forest Service, Great Lakes Forestry Centre, East Sault Ste. Marie, ON, Canada
| | - Guoxing Quan
- Canadian Forest Service, Great Lakes Forestry Centre, East Sault Ste. Marie, ON, Canada
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19
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Zou Y, Mason MG, Botella JR. Evaluation and improvement of isothermal amplification methods for point-of-need plant disease diagnostics. PLoS One 2020; 15:e0235216. [PMID: 32598374 PMCID: PMC7323990 DOI: 10.1371/journal.pone.0235216] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 06/10/2020] [Indexed: 01/01/2023] Open
Abstract
A number of isothermal DNA amplification technologies claim to be ideal for point-of-need (PON) applications as they enable reactions to be performed using a single-temperature heat source (e.g. water bath). Thus, we examined several isothermal amplification methods focusing on simplicity, cost, sensitivity and reproducibility to identify the most suitable method(s) for low resource PON applications. A number of methods were found unsuitable as they either involved multiple temperature incubations, were relatively expensive or required relatively large amounts target DNA for amplification. Among the methods examined, loop-mediated isothermal amplification (LAMP) and recombinase polymerase amplification (RPA) were found to be the most suitable for PON applications as they are both single step methods that provide highly sensitive and reproducible amplifications. The speed of LAMP reactions was greatly enhanced, up to 76%, with the addition of loop primers while the presence of swarm primers and the sequestration of free magnesium ions with nucleotides also enhanced the amplification speed. In contrast, we were unable to enhance RPA's performance from the original published literature. While both RPA and LAMP have some drawbacks, either isothermal technology can reliably be used for on-site diagnostics with minimal equipment.
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Affiliation(s)
- Yiping Zou
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Michael Glenn Mason
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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20
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Shrestha S, Neubauer J, Spanner R, Natwick M, Rios J, Metz N, Secor GA, Bolton MD. Rapid Detection of Cercospora beticola in Sugar Beet and Mutations Associated with Fungicide Resistance Using LAMP or Probe-Based qPCR. PLANT DISEASE 2020; 104:1654-1661. [PMID: 32282278 DOI: 10.1094/pdis-09-19-2023-re] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Cercospora leaf spot (CLS), caused by the fungal pathogen Cercospora beticola, is the most destructive disease of sugar beet worldwide. Although growing CLS-tolerant varieties is helpful, disease management currently requires timely application of fungicides. However, overreliance on fungicides has led to the emergence of fungicide resistance in many C. beticola populations, resulting in multiple epidemics in recent years. Therefore, this study focused on developing a fungicide resistance detection "toolbox" for early detection of C. beticola in sugar beet leaves and mutations associated with different fungicides in the pathogen population. A loop-mediated isothermal amplification (LAMP) method was developed for rapid detection of C. beticola in infected sugar beet leaves. The LAMP primers specific to C. beticola (Cb-LAMP) assay was able to detect C. beticola in inoculated sugar beet leaves as early as 1 day postinoculation. A quinone outside inhibitor (QoI)-LAMP assay was also developed to detect the G143A mutation in cytochrome b associated with QoI resistance in C. beticola. The assay detected the mutation in C. beticola both in vitro and in planta with 100% accuracy. We also developed a probe-based quantitative PCR (qPCR) assay for detecting an E198A mutation in β-tubulin associated with benzimidazole resistance and a probe-based qPCR assay for detection of mutations in cytochrome P450-dependent sterol 14α-demethylase (Cyp51) associated with resistance to sterol demethylation inhibitor fungicides. The primers and probes used in the assay were highly efficient and precise in differentiating the corresponding fungicide-resistant mutants from sensitive wild-type isolates.
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Affiliation(s)
- Subidhya Shrestha
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
| | - Jonathan Neubauer
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
| | - Rebecca Spanner
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
| | - Mari Natwick
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
| | - Joshua Rios
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
| | - Nicholas Metz
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
| | - Gary A Secor
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
| | - Melvin D Bolton
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58108, U.S.A
- United States Department of Agriculture-Agricultural Research Service, Northern Crop Science Laboratory, Fargo, ND 58102, U.S.A
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21
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Kaczmarek AM, King KM, West JS, Stevens M, Sparkes D, Dickinson MJ. A Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid and Specific Detection of Airborne Inoculum of Uromyces betae (Sugar Beet Rust). PLANT DISEASE 2019; 103:417-421. [PMID: 30652960 DOI: 10.1094/pdis-02-18-0337-re] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sugar beet rust disease (causal agent Uromyces betae) represents a serious threat to worldwide sugar beet (Beta vulgaris) crops, causing yield losses of up to 10% in the United Kingdom. Currently, the disease is managed mainly by application of fungicides after rust disease symptoms appear. Development of a future forecasting system, incorporating data on environmental factors and U. betae inoculum levels, would enable better disease control by more targeted application of fungicides. In this study, we developed a first molecular diagnostic, targeted to cytochrome b DNA sequences and based on loop-mediated isothermal amplification (LAMP) technology, for rapid (<30 min) and specific detection of U. betae. The new assay only detected U. betae strains (collected from across eastern England, the main sugar beet growing region in the United Kingdom) and Denmark; it did not detect other closely related pathogens (e.g., Puccinia sp., U. fabae) or others that are commonly found on sugar beet (Cercospora beticola, Erysiphe betae, Ramularia beticola). The assay could consistently detect down to small amounts of U. betae DNA (10 pg). Application of the new LAMP diagnostic to air spore tape samples collected between mid-June and mid-September from a single U.K. sugar beet field site revealed differences in temporal patterns of pathogen inoculum between the 2015 and 2016 seasons. The described LAMP assay could now be used as a component of a future automated inoculum-based forecasting system, enabling more targeted control of sugar beet rust disease.
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Affiliation(s)
- Agata M Kaczmarek
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, U.K.; and Rothamsted Research, Harpenden, Hertfordshire, U.K
| | - Kevin M King
- Rothamsted Research, Harpenden, Hertfordshire, U.K
| | | | - Mark Stevens
- British Beet Research Organisation (BBRO), Innovation Centre, Norwich Research Park, Norwich, U.K
| | - Debbie Sparkes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, U.K
| | - Matthew J Dickinson
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, U.K
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22
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Abstract
Loop-mediated isothermal AMPlification (LAMP) allows the rapid detection of pathogens by polymerase-mediated amplification of target nucleic acid sequences at a single incubation temperature. LAMP can be combined with very simple sample preparation/crude DNA extraction protocols, allowing the method to be used away from the laboratory for in-field detection. Equally, these benefits can also be leveraged to provide a rapid method suited to high-throughput diagnostic laboratories. In this chapter we described a crude DNA extraction protocol suitable for use in the field and provide a protocol for real-time detection using LAMP.
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Affiliation(s)
- Jennifer Hodgetts
- Fera, The National Agri-Food Innovation Campus, Sand Hutton, York, UK.
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23
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Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey B, Frey JE, Bühlmann A. A Loop-mediated Isothermal Amplification (LAMP) Assay for Rapid Identification of Bemisia tabaci. J Vis Exp 2018. [PMID: 30417877 PMCID: PMC6235616 DOI: 10.3791/58502] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The whitefly Bemisia tabaci (Gennadius) is an invasive pest of considerable importance, affecting the production of vegetable and ornamental crops in many countries around the world. Severe yield losses are caused by direct feeding, and even more importantly, also by the transmission of more than 100 harmful plant pathogenic viruses. As for other invasive pests, increased international trade facilitates the dispersal of B. tabaci to areas beyond its native range. Inspections of plant import products at points of entry such as seaports and airports are, therefore, seen as an important prevention measure. However, this last line of defense against pest invasions is only effective if rapid identification methods for suspicious insect specimens are readily available. Because the morphological differentiation between the regulated B. tabaci and close relatives without quarantine status is difficult for non-taxonomists, a rapid molecular identification assay based on the loop-mediated isothermal amplification (LAMP) technology has been developed. This publication reports the detailed protocol of the novel assay describing rapid DNA extraction, set-up of the LAMP reaction, as well as interpretation of its read-out, which allows identifying B. tabaci specimens within one hour. Compared to existing protocols for the detection of specific B. tabaci biotypes, the developed method targets the whole B. tabaci species complex in one assay. Moreover the assay is designed to be applied on-site by plant health inspectors with minimal laboratory training directly at points of entry. Thorough validation performed under laboratory and on-site conditions demonstrates that the reported LAMP assay is a rapid and reliable identification tool, improving the management of B. tabaci.
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Affiliation(s)
- Simon Blaser
- Department of Method Development and Analytics, Agroscope; Swiss Tropical and Public Health Institute; University of Basel;
| | - Hanspeter Diem
- Swiss Federal Plant Protection Service, Federal Office for Agriculture
| | | | | | | | - Neil Boonham
- Fera Science Limited; School of Natural and Environmental Sciences, Newcastle University
| | | | - Pie Müller
- Swiss Tropical and Public Health Institute; University of Basel
| | - Jürg Utzinger
- Swiss Tropical and Public Health Institute; University of Basel
| | - Beatrice Frey
- Department of Method Development and Analytics, Agroscope
| | - Jürg E Frey
- Department of Method Development and Analytics, Agroscope
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Blaser S, Diem H, von Felten A, Gueuning M, Andreou M, Boonham N, Tomlinson J, Müller P, Utzinger J, Frey JE, Bühlmann A. From laboratory to point of entry: development and implementation of a loop-mediated isothermal amplification (LAMP)-based genetic identification system to prevent introduction of quarantine insect species. PEST MANAGEMENT SCIENCE 2018; 74:1504-1512. [PMID: 29363271 PMCID: PMC5969315 DOI: 10.1002/ps.4866] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 01/12/2018] [Accepted: 01/12/2018] [Indexed: 05/07/2023]
Abstract
BACKGROUND Rapid genetic on-site identification methods at points of entry, such as seaports and airports, have the potential to become important tools to prevent the introduction and spread of economically harmful pest species that are unintentionally transported by the global trade of plant commodities. This paper reports the development and evaluation of a loop-mediated isothermal amplification (LAMP)-based identification system to prevent introduction of the three most frequently encountered regulated quarantine insect species groups at Swiss borders, Bemisia tabaci, Thrips palmi and several regulated fruit flies of the genera Bactrocera and Zeugodacus. RESULTS The LAMP primers were designed to target a fragment of the mitochondrial cytochrome c oxidase subunit I gene and were generated based on publicly available DNA sequences. Laboratory evaluations analysing 282 insect specimens suspected to be quarantine organisms revealed an overall test efficiency of 99%. Additional on-site evaluation at a point of entry using 37 specimens performed by plant health inspectors with minimal laboratory training resulted in an overall test efficiency of 95%. During both evaluation rounds, there were no false-positives and the observed false-negatives were attributable to human-induced manipulation errors. To overcome the possibility of accidental introduction of pests as a result of rare false-negative results, samples yielding negative results in the LAMP method were also subjected to DNA barcoding. CONCLUSION Our LAMP assays reliably differentiated between the tested regulated and non-regulated insect species within <1 h. Hence, LAMP assays represent suitable tools for rapid on-site identification of harmful pests, which might facilitate an accelerated import control process for plant commodities. © 2018 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Simon Blaser
- Agroscope, Department of Method Development and AnalyticsWädenswilSwitzerland
- Swiss Tropical and Public Health InstituteBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Hanspeter Diem
- Federal Office for AgricultureSwiss Federal Plant Protection Service, Zurich AirportZurichSwitzerland
| | - Andreas von Felten
- Federal Office for AgricultureSwiss Federal Plant Protection ServiceBernSwitzerland
| | - Morgan Gueuning
- Agroscope, Department of Method Development and AnalyticsWädenswilSwitzerland
| | | | - Neil Boonham
- The Food and Environment Research AgencyYorkUK
- Newcastle UniversityNewcastle upon TyneUK
| | | | - Pie Müller
- Swiss Tropical and Public Health InstituteBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Jürg Utzinger
- Swiss Tropical and Public Health InstituteBaselSwitzerland
- University of BaselBaselSwitzerland
| | - Jürg E Frey
- Agroscope, Department of Method Development and AnalyticsWädenswilSwitzerland
| | - Andreas Bühlmann
- Agroscope, Department of Plants and Plant ProductsWädenswilSwitzerland
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Lopez-Jimena B, Wehner S, Harold G, Bakheit M, Frischmann S, Bekaert M, Faye O, Sall AA, Weidmann M. Development of a single-tube one-step RT-LAMP assay to detect the Chikungunya virus genome. PLoS Negl Trop Dis 2018; 12:e0006448. [PMID: 29813065 PMCID: PMC5973553 DOI: 10.1371/journal.pntd.0006448] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 04/12/2018] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND A single-tube one-step real-time reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for rapid detection of chikungunya virus (CHIKV) targeting the conserved 6K-E1 target region was developed. The assay was validated with sera collected from a CHIKV outbreak in Senegal in 2015. METHODOLOGY/PRINCIPAL FINDINGS A novel design approach by combining Principal Component Analysis and phylogenetic analysis of 110 available CHIKV sequences and the LAMP oligonucleotide design software LAVA was used. The assay was evaluated with an External Quality Assessment panel from the European Network for Diagnostics of "Imported" Viral Diseases and was shown to be sensitive and specific and did not cross-detect other arboviruses. The limit of detection as determined by probit analysis, was 163 molecules, and 100% reproducibility in the assays was obtained for 103 molecules (7/8 repetitions were positive for 102 molecules). The assay was validated using 35 RNA samples extracted from sera, and results were compared with those obtained by quantitative RT-PCR carried out at the Institut Pasteur Dakar, demonstrating that the RT-LAMP is 100% sensitive and 80% specific, with a positive predictive value of 97% and negative predictive value of 100%. CONCLUSIONS/SIGNIFICANCE The RT-LAMP appeared to show superior performance with material stored for months compared to qRT-PCR and can be therefore recommended for use in infrastructures with poor settings.
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Affiliation(s)
- Benjamin Lopez-Jimena
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Stefanie Wehner
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Graham Harold
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | | | | | - Michaël Bekaert
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
| | - Oumar Faye
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Amadou Alpha Sall
- Arbovirus and viral haemorrhagic fever unit, Institut Pasteur de Dakar, Dakar, Senegal
| | - Manfred Weidmann
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, Scotland, United Kingdom
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Abstract
Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.
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Detection and Typing of "Candidatus Phytoplasma " spp. in Host DNA Extracts Using Oligonucleotide-Coupled Fluorescent Microspheres. Methods Mol Biol 2018. [PMID: 28600765 DOI: 10.1007/978-1-4939-7037-7_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The use of oligonucleotide-coupled fluorescent microspheres is a rapid, sequencing-independent, and reliable way to diagnose bacterial diseases. Previously described applications of oligonucleotide-coupled fluorescent microspheres for the detection and identification of bacteria in human clinical samples have been successfully adapted to detect and differentiate "Ca. Phytoplasma" species using as a target the chaperonin 60-encoding gene. In this chapter, we describe in detail the design and validation of oligonucleotide capture probes, and their application in the assay aiming to differentiate phytoplasma strains infecting Brassica napus and Camelina sativa plants grown in the same geographic location at the same time.
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28
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Li Y, Bai C, Yang L, Fu J, Yan M, Chen D, Zhang L. High flux isothermal assays on pathogenic, virulent and toxic genetics from various pathogens. Microb Pathog 2018; 116:68-72. [PMID: 29325863 DOI: 10.1016/j.micpath.2018.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2017] [Revised: 01/02/2018] [Accepted: 01/07/2018] [Indexed: 11/17/2022]
Abstract
Toxins, encoding by virulence factors, are significant cause of food-borne illnesses and death in the worldwide. Loop-mediated isothermal amplification (LAMP) is one of the widely used methodologies because of the high sensitivity, specificity and rapidity. Nowadays, LAMP has been regarded as an innovative gene amplification technology and emerged as an alternative to PCR-based methodologies in identification of the pathogenic virulent and toxic genetics. The high sensitivity of LAMP enables detection of the pathogens in sample materials even without time consuming and sample preparation. Therefore, we review the typical characteristics of LAMP assay, recent advance in detection of virulence factors and the application of LAMP assay on detection of four commonly virulence factors. As concluded, with the advantages of rapidity, simplicity, sensitivity, specificity and robustness, LAMP is capable of identification the virulence factors. Moreover, the main purpose of this review is to provide theory support for the application of LAMP assay on the virulence factors identification.
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Affiliation(s)
- Yanmei Li
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Caiying Bai
- Guangdong Women and Children Hospital, Guagzhou 510010, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China
| | - Jie Fu
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Muxia Yan
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Dingqiang Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Medical University, Guangzhou 510120, China.
| | - Li Zhang
- Department of Haematology, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China.
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29
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Bonney LC, Watson RJ, Afrough B, Mullojonova M, Dzhuraeva V, Tishkova F, Hewson R. A recombinase polymerase amplification assay for rapid detection of Crimean-Congo Haemorrhagic fever Virus infection. PLoS Negl Trop Dis 2017; 11:e0006013. [PMID: 29028804 PMCID: PMC5656326 DOI: 10.1371/journal.pntd.0006013] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 10/25/2017] [Accepted: 10/04/2017] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Crimean-Congo Haemorrhagic fever Virus (CCHFV) is a rapidly emerging vector-borne pathogen and the cause of a virulent haemorrhagic fever affecting large parts of Europe, Africa, the Middle East and Asia. METHODOLOGY/PRINCIPLE FINDINGS An isothermal recombinase polymerase amplification (RPA) assay was successfully developed for molecular detection of CCHFV. The assay showed rapid (under 10 minutes) detection of viral extracts/synthetic virus RNA of all 7 S-segment clades of CCHFV, with high target specificity. The assay was shown to tolerate the presence of inhibitors in crude preparations of mock field samples, indicating that this assay may be suitable for use in the field with minimal sample preparation. The CCHFV RPA was successfully used to screen and detect CCHFV positives from a panel of clinical samples from Tajikistan. CONCLUSIONS/SIGNIFICANCE The assay is a rapid, isothermal, simple-to-perform molecular diagnostic, which can be performed on a light, portable real-time detection device. It is ideally placed therefore for use as a field-diagnostic or in-low resource laboratories, for monitoring of CCHF outbreaks at the point-of-need, such as in remote rural regions in affected countries.
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Affiliation(s)
- Laura C. Bonney
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
- * E-mail:
| | - Robert J. Watson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Babak Afrough
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
| | - Manija Mullojonova
- Department of Virology, Tajik Research Institute of Preventive Medicine of the Ministry of Health of the Republic of Tajikistan, Dushanbe, Republic of Tajikistan
| | - Viktoriya Dzhuraeva
- Department of Virology, Tajik Research Institute of Preventive Medicine of the Ministry of Health of the Republic of Tajikistan, Dushanbe, Republic of Tajikistan
| | - Farida Tishkova
- Department of Virology, Tajik Research Institute of Preventive Medicine of the Ministry of Health of the Republic of Tajikistan, Dushanbe, Republic of Tajikistan
| | - Roger Hewson
- National Infection Service, Public Health England, Porton Down, Salisbury, United Kingdom
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Wambua L, Schneider B, Okwaro A, Wanga JO, Imali O, Wambua PN, Agutu L, Olds C, Jones CS, Masiga D, Midega C, Khan Z, Jores J, Fischer A. Development of field-applicable tests for rapid and sensitive detection of Candidatus Phytoplasma oryzae. Mol Cell Probes 2017. [PMID: 28647581 DOI: 10.1016/j.mcp.2017.06.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Napier grass Stunt Disease (NSD) is a severe disease of Napier grass (Pennisetum purpureum) in Eastern Africa, caused by the leafhopper-transmitted bacterium Candidatus Phytoplasma oryzae. The pathogen severely impairs the growth of Napier grass, the major fodder for dairy cattle in Eastern Africa. NSD is associated with biomass losses of up to 70% of infected plants. Diagnosis of NSD is done by nested PCR targeting the phytoplasma DNA, which is difficult to perform in developing countries with little infrastructure. We report the development of an easy to use, rapid, sensitive and specific molecular assay for field diagnosis of NSD. The procedure is based on recombinase polymerase amplification and targets the imp gene encoding a pathogen-specific immunodominant membrane protein. Therefore we followed a two-step process. First we developed an isothermal DNA amplification method for real time fluorescence application and then transferred this assay to a lateral flow format. The limit of detection for both procedures was estimated to be 10 organisms. We simplified the template preparation procedure by using freshly squeezed phloem sap from Napier grass. Additionally, we developed a laboratory serological assay with the potential to be converted to a lateral flow assay. Two murine monoclonal antibodies with high affinity and specificity to the immunodominant membrane protein IMP of Candidatus Phytoplasma oryzae were generated. Both antibodies specifically reacted with the denatured or native 17 kDa IMP protein. In dot blot experiments of extracts from infected plant, phytoplasmas were detected in as little as 12,5 μg of fresh plant material.
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Affiliation(s)
- Lillian Wambua
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya; School of Biological Sciences, University of Nairobi, P.O Box 30197, 00100 Nairobi, Kenya
| | - Bernd Schneider
- Julius Kühn Institute, Federal Research Centre for Cultivated Plants, Institute for Plant Protection in Fruit Crops and Viticulture, 69221 Dossenheim, Germany
| | - Allan Okwaro
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya; Department of Biochemistry & Biotechnology, Kenyatta University, P.O. Box 43844, 00100 Nairobi, Kenya
| | - Joseph Odhiambo Wanga
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya
| | - Olive Imali
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya
| | - Peninah Nduku Wambua
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya; School of Biological Sciences, University of Nairobi, P.O Box 30197, 00100 Nairobi, Kenya
| | - Lavender Agutu
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya
| | - Cassandra Olds
- Washington State University, Pullman, WA, USA; International Livestock Research Institute, P.O Box 30709, 00100 Nairobi, Kenya
| | - Chris Stephen Jones
- International Livestock Research Institute, P.O Box 30709, 00100 Nairobi, Kenya
| | - Daniel Masiga
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya
| | - Charles Midega
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya
| | - Zeyaur Khan
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya
| | - Joerg Jores
- International Livestock Research Institute, P.O Box 30709, 00100 Nairobi, Kenya; Institute of Veterinary Bacteriology, University of Bern, 3012 Bern, Switzerland
| | - Anne Fischer
- International Centre of Insect Physiology and Ecology, P.O Box 30772, 00100 Nairobi, Kenya.
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Liu J, Gopurenko D, Fletcher MJ, Johnson AC, Gurr GM. Phytoplasmas-The "Crouching Tiger" Threat of Australian Plant Pathology. FRONTIERS IN PLANT SCIENCE 2017; 8:599. [PMID: 28491068 PMCID: PMC5405143 DOI: 10.3389/fpls.2017.00599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 04/03/2017] [Indexed: 06/07/2023]
Abstract
Phytoplasmas are insect-vectored bacteria that cause disease in a wide range of plant species. The increasing availability of molecular DNA analyses, expertise and additional methods in recent years has led to a proliferation of discoveries of phytoplasma-plant host associations and in the numbers of taxonomic groupings for phytoplasmas. The widespread use of common names based on the diseases with which they are associated, as well as separate phenetic and taxonomic systems for classifying phytoplasmas based on variation at the 16S rRNA-encoding gene, complicates interpretation of the literature. We explore this issue and related trends through a focus on Australian pathosystems, providing the first comprehensive compilation of information for this continent, covering the phytoplasmas, host plants, vectors and diseases. Of the 33 16Sr groups reported internationally, only groups I, II, III, X, XI and XII have been recorded in Australia and this highlights the need for ongoing biosecurity measures to prevent the introduction of additional pathogen groups. Many of the phytoplasmas reported in Australia have not been sufficiently well studied to assign them to 16Sr groups so it is likely that unrecognized groups and sub-groups are present. Wide host plant ranges are apparent among well studied phytoplasmas, with multiple crop and non-crop species infected by some. Disease management is further complicated by the fact that putative vectors have been identified for few phytoplasmas, especially in Australia. Despite rapid progress in recent years using molecular approaches, phytoplasmas remain the least well studied group of plant pathogens, making them a "crouching tiger" disease threat.
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Affiliation(s)
- Jian Liu
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture & Forestry UniversityFuzhou, China
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
| | - David Gopurenko
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
- NSW Department of Primary Industries, Wagga Wagga Agricultural InstituteWagga Wagga, NSW, Australia
| | - Murray J. Fletcher
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
| | - Anne C. Johnson
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
| | - Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, Fujian Agriculture & Forestry UniversityFuzhou, China
- Graham Centre for Agricultural Innovation (Charles Sturt University & NSW Department of Primary Industries)Orange, NSW, Australia
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Chahar M, Mishra N, Anvikar A, Dixit R, Valecha N. Establishment and application of a novel isothermal amplification assay for rapid detection of chloroquine resistance (K76T) in Plasmodium falciparum. Sci Rep 2017; 7:41119. [PMID: 28134241 PMCID: PMC5278370 DOI: 10.1038/srep41119] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 12/14/2016] [Indexed: 02/08/2023] Open
Abstract
Chloroquine (CQ) resistance in Plasmodium falciparum is determined by the mutations in the chloroquine resistance transporter (Pfcrt) gene. The point mutation at codon 76 (K76T), which has been observed in more than 91% of P. falciparum isolates in India, is the major determinant of CQ resistance. To overcome the limitations and challenges of traditional methods, in this investigation we developed an easy to use loop mediated isothermal amplification (LAMP) protocol for rapid detection of the K76T mutation associated with CQ resistance in P. falciparum with naked eye visualization. In- house designed primers were synthesized and optimized to specifically distinguish the CQ resistant mutants of P. falciparum. The LAMP reaction was optimal at 61 °C for 60 min and calcein dye was added prior to amplification to enable visual detection. We demonstrate the detection limit of <2 ng/μl respectively, supporting the high sensitivity of this calcein based LAMP method. To the best of our knowledge this is the first report on the establishment of an easy, reliable and cost effective LAMP assay for rapid and specific detection of highly CQ resistance in P. falciparum malaria.
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Affiliation(s)
- Madhvi Chahar
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, 110077, India
| | - Neelima Mishra
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, 110077, India
| | - Anup Anvikar
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, 110077, India
| | - Rajnikant Dixit
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, 110077, India
| | - Neena Valecha
- Division of Epidemiology & Clinical Research, National Institute of Malaria Research, Sector-8 Dwarka, New Delhi, 110077, India
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Villari C, Mahaffee WF, Mitchell TK, Pedley KF, Pieck ML, Hand FP. Early Detection of Airborne Inoculum of Magnaporthe oryzae in Turfgrass Fields Using a Quantitative LAMP Assay. PLANT DISEASE 2017; 101:170-177. [PMID: 30682295 DOI: 10.1094/pdis-06-16-0834-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Gray leaf spot (GLS) is a destructive disease of perennial ryegrass caused by a host specific pathotype of the ascomycete Magnaporthe oryzae. Early diagnosis is crucial for effective disease management and the implementation of Integrated Pest Management practices. However, a rapid protocol for the detection of low levels of airborne inoculum is still missing. We developed a pathogen-specific quantitative loop-mediated isothermal amplification (qLAMP) assay coupled with a spore trap system for rapid detection and quantification of airborne inoculum of the M. oryzae perennial ryegrass pathotype, and tested its suitability for implementation in GLS-infected turfgrass fields. In summer 2015, two perennial ryegrass plots were artificially inoculated with the pathogen, with four continuously running custom impaction spore traps placed in each plot. Sampling units were replaced daily and tested with the developed qLAMP assay, while plots were monitored for symptom development. Results confirmed that the qLAMP assay-trap system was able to detect as few as 10 conidia up to 12 days before symptoms developed in the field. LAMP technology is particularly appropriate for field implementation by nontechnical users, and has the potential to be a powerful decision support tool to guide timing of fungicide applications for GLS management.
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Affiliation(s)
- Caterina Villari
- Department of Plant Pathology, The Ohio State University, Columbus 43210
| | - Walter F Mahaffee
- Horticultural Crops Research Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR 97330
| | | | - Kerry F Pedley
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, MD 21702
| | - Michael L Pieck
- Foreign Disease-Weed Science Research Unit, USDA-ARS, Fort Detrick, MD 21702
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Establishment and Evaluation of a Loop-Mediated Isothermal Amplification Assay for Detection of Raccoon Dog in Meat Mixtures. J FOOD QUALITY 2017. [DOI: 10.1155/2017/9319035] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Raccoon dog (Nyctereutes procyonoides) is an economically important animal used for fur production, but consuming its meat is injurious to human health. Currently, no rapid and sensitive method for detecting raccoon dog meat in meat mixtures is available. In this study, we developed an easily applicable, rapid, and economically feasible method for identifying the presence of raccoon dog in meat mixtures based on loop-mediated isothermal amplification (LAMP). Four sets of LAMP primers were tested at different temperatures, and the primers that worked best at 62°C (set 2) were determined. In the LAMP assay, there was no cross-reactivity with the meat procured from other species of animals and the detection limit of DNA concentration was 0.1 pg·μL−1, slightly higher than TaqMan real-time PCR (0.01 pg·μL−1), but sensitivity of 0.1 pg·μL−1 complies with most requirements of routine analysis. Moreover, by the LAMP method, the meat mixtures containing more than 0.5% of the raccoon dog component were directly detected (without DNA extraction) in the supernatant isolated from the meat mixtures after performing repeated cycles of thawing and freezing of minced meat mixtures. Our results show that LAMP assay is a valuable, straightforward, and sensitive detection tool for identification of raccoon dog meat in mixtures.
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Li JJ, Xiong C, Liu Y, Liang JS, Zhou XW. Loop-Mediated Isothermal Amplification (LAMP): Emergence As an Alternative Technology for Herbal Medicine Identification. FRONTIERS IN PLANT SCIENCE 2016; 7:1956. [PMID: 28082999 PMCID: PMC5183589 DOI: 10.3389/fpls.2016.01956] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 12/09/2016] [Indexed: 05/07/2023]
Abstract
Correct identification of medicinal plant ingredients is essential for their safe use and for the regulation of herbal drug supply chain. Loop-mediated isothermal amplification (LAMP) is a recently developed approach to identify herbal medicine species. This novel molecular biology technique enables timely and accurate testing, especially in settings where infrastructures to support polymerase chain reaction facilities are lacking. Studies that used this method have altered our view on the extent and complexity of herbal medicine identification. In this review, we give an introduction into LAMP analysis, covers the basic principles and important aspects in the development of LAMP analysis method. Then we presented a critical review of the application of LAMP-based methods in detecting and identifying raw medicinal plant materials and their processed products. We also provide a practical standard operating procedure (SOP) for the utilization of the LAMP protocol in herbal authentication, and consider the prospects of LAMP technology in the future developments of herbal medicine identification and the challenges associated with its application.
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Affiliation(s)
- Jing-jian Li
- College of Forestry and Landscape Architecture, South China Agricultural UniversityGuangzhou, China
| | - Chao Xiong
- College of Pharmacy, Hubei University of Chinese MedicineWuhan, China
| | - Yue Liu
- Sichuan Industrial Institute of Antibiotics, Chengdu UniversityChengdu, China
| | - Jun-song Liang
- College of Biology and Pharmacy, Yulin Normal UniversityYulin, China
| | - Xing-wen Zhou
- College of Biology and Pharmacy, Yulin Normal UniversityYulin, China
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Gurr GM, Johnson AC, Ash GJ, Wilson BAL, Ero MM, Pilotti CA, Dewhurst CF, You MS. Coconut Lethal Yellowing Diseases: A Phytoplasma Threat to Palms of Global Economic and Social Significance. FRONTIERS IN PLANT SCIENCE 2016; 7:1521. [PMID: 27833616 PMCID: PMC5080360 DOI: 10.3389/fpls.2016.01521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 09/26/2016] [Indexed: 05/25/2023]
Abstract
The recent discovery of Bogia coconut syndrome in Papua New Guinea (PNG) is the first report of a lethal yellowing disease (LYD) in Oceania. Numerous outbreaks of LYDs of coconut have been recorded in the Caribbean and Africa since the late Nineteenth century and have caused the death of millions of palms across several continents during the Twentieth century. Despite the severity of economic losses, it was only in the 1970s that the causes of LYDs were identified as phytoplasmas, a group of insect-transmitted bacteria associated with diseases in many other economically important crop species. Since the development of polymerase chain reaction (PCR) technology, knowledge of LYDs epidemiology, ecology and vectors has grown rapidly. There is no economically viable treatment for LYDs and vector-based management is hampered by the fact that vectors have been positively identified in very few cases despite many attempted transmission trials. Some varieties and hybrids of coconut palm are known to be less susceptible to LYD but none are completely resistant. Optimal and current management of LYD is through strict quarantine, prompt detection and destruction of symptomatic palms, and replanting with less susceptible varieties or crop species. Advances in technology such as loop mediated isothermal amplification (LAMP) for detection and tracking of phytoplasma DNA in plants and insects, remote sensing for identifying symptomatic palms, and the advent of clustered regularly interspaced short palindromic repeats (CRISPR)-based tools for gene editing and plant breeding are likely to allow rapid progress in taxonomy as well as understanding and managing LYD phytoplasma pathosystems.
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Affiliation(s)
- Geoff M. Gurr
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujain Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, College of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhou, China
- Graham Centre of Agricultural Innovation, Charles Sturt UniversityOrange, NSW, Australia
| | - Anne C. Johnson
- Graham Centre of Agricultural Innovation, Charles Sturt UniversityOrange, NSW, Australia
| | - Gavin J. Ash
- Research and Innovation Division, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern QueenslandToowoomba, QLD, Australia
| | - Bree A. L. Wilson
- Research and Innovation Division, Centre for Crop Health, Institute for Agriculture and the Environment, University of Southern QueenslandToowoomba, QLD, Australia
| | - Mark M. Ero
- PNG Oil Palm Research AssociationKimbe, Papua New Guinea
| | | | - Charles F. Dewhurst
- Formerly affiliated with the PNG Oil Palm Research AssociationKimbe, Papua New Guinea
| | - Minsheng S. You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujain Agriculture and Forestry UniversityFuzhou, China
- Institute of Applied Ecology, College of Plant Protection, Fujian Agriculture and Forestry UniversityFuzhou, China
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Nair S, Manimekalai R, Ganga Raj P, Hegde V. Loop mediated isothermal amplification (LAMP) assay for detection of coconut root wilt disease and arecanut yellow leaf disease phytoplasma. World J Microbiol Biotechnol 2016; 32:108. [PMID: 27263003 DOI: 10.1007/s11274-016-2078-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 04/27/2016] [Indexed: 11/28/2022]
Abstract
The coconut root wilt disease (RWD) and the arecanut yellow leaf disease (YLD) are two major phytoplasma associated diseases affecting palms in South India. Greatly debilitating the palm health, these diseases cause substantial yield reduction and economic loss to farmers. A rapid and robust diagnostic technique is crucial in efficient disease management. We established phytoplasma 16S rDNA targeted loop mediated isothermal amplification (LAMP) and real time LAMP based diagnostics for coconut RWD and arecanut YLD. The LAMP reaction was set at 65 °C and end point detection made using hydroxynaphthol blue (HNB) and agarose gel electrophoresis. Molecular typing of LAMP products were made with restriction enzyme HpyCH4 V. Conventional PCR with LAMP external primers and sequencing of amplicons was carried out. Real time LAMP was performed on the Genei II platform (Optigene Ltd., UK). An annealing curve analysis was programmed at the end of the incubation to check the fidelity of the amplicons. The phytoplasma positive samples produced typical ladder like bands on agarose gel, showed colour change from violet to blue with HNB and produced unique annealing peak at 85 ± 0.5 °C in the real time detection. Restriction digestion produced predicted size fragments. Sequencing and BLASTN analysis confirmed that the amplification corresponded to phytoplasma 16S rRNA gene. LAMP method devised here was found to be more robust compared to conventional nested PCR and hence has potential applications in detection of phytoplasma from symptomatic palm samples and in rapid screening of healthy seedlings.
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Affiliation(s)
- Smita Nair
- Central Plantation Crops Research Institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O, Kasaragod, 671124, Kerala, India
| | - Ramaswamy Manimekalai
- Department of Biotechnology, Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, 641007, Tamil Nadu, India.
| | - Palliyath Ganga Raj
- Central Plantation Crops Research Institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O, Kasaragod, 671124, Kerala, India
| | - Vinayaka Hegde
- Central Plantation Crops Research Institute, Indian Council of Agricultural Research (ICAR), Kudlu P.O, Kasaragod, 671124, Kerala, India
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Duan Y, Yang Y, Wang Y, Pan X, Wu J, Cai Y, Li T, Zhao D, Wang J, Zhou M. Loop-Mediated Isothermal Amplification for the Rapid Detection of the F200Y Mutant Genotype of Carbendazim-Resistant Isolates of Sclerotinia sclerotiorum. PLANT DISEASE 2016; 100:976-983. [PMID: 30686158 DOI: 10.1094/pdis-10-15-1185-re] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The point mutation at codon 200 (TTC→TAC, F200Y) confers moderate resistance to carbendazim in Sclerotinia sclerotiorum. This mutant genotype (F200Y) has been detected mainly by determining the minimum inhibitory concentration (MIC), which requires 3 to 5 days. Here, we developed a loop-mediated isothermal amplification (LAMP) assay for the rapid detection of the F200Y mutant genotype of carbendazim-resistant isolates of S. sclerotiorum. Specific LAMP primers were designed and concentrations of LAMP components were optimized. The optimal reaction conditions were 62 to 63°C for 45 min. The new LAMP assay requires no special equipment and is highly sensitive and specific (the i.e., it generated positive results with F200Y mutant genotype but generated negative results with other carbendazim-resistant mutants and with a variety of carbendazim-resistant mutants of Botrytis cinerea and Fusarium graminearum). Inclusion of the loop backward (LB) primer reduced the reaction time to 15 min. Results were identical with LAMP and MIC determinations. The advantages of the LB-accelerated LAMP assay for detection of the F200Y mutant genotype were demonstrated by assaying sclerotia produced on rape stems that were artificially inoculated in the field. The results indicated that the new LAMP assay represents an improved way to detect the F200Y mutant genotype of carbendazim-resistant isolates of S. sclerotiorum.
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Affiliation(s)
- Yabing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yong Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiayan Pan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Wu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yiqiang Cai
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tao Li
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Donglei Zhao
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianxin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingguo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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Kitamura M, Aragane M, Nakamura K, Watanabe K, Sasaki Y. Development of Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid Detection of Cannabis sativa. Biol Pharm Bull 2016; 39:1144-9. [DOI: 10.1248/bpb.b16-00090] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- Masashi Kitamura
- Laboratory of Molecular Pharmacognosy, Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University
- Forensic Science Laboratory, Ishikawa Prefectural Police H.Q
| | - Masako Aragane
- Medicinal Plant Garden, Tokyo Metropolitan Institute of Public Health
| | - Kou Nakamura
- Medicinal Plant Garden, Tokyo Metropolitan Institute of Public Health
| | | | - Yohei Sasaki
- Laboratory of Molecular Pharmacognosy, Division of Pharmaceutical Sciences, Graduate School of Medical Sciences, Kanazawa University
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Duan YB, Yang Y, Wang JX, Liu CC, He LL, Zhou MG. Development and application of loop-mediated isothermal amplification for detecting the highly benzimidazole-resistant isolates in Sclerotinia sclerotiorum. Sci Rep 2015; 5:17278. [PMID: 26606972 PMCID: PMC4660316 DOI: 10.1038/srep17278] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 10/28/2015] [Indexed: 01/22/2023] Open
Abstract
Resistance of benzimidazole fungicides is related to the point mutation of the β-tubulin gene in Sclerotinia sclerotiorum. The point mutation at codon 198 (GAG → GCG, E198A) occurs in more than 90% of field resistant populations in China. Traditional detection methods of benzimidazole-resistant mutants of S. sclerotiorum are time-consuming, tedious and inefficient. To establish a suitable and rapid detection of benzimidazole-resistant mutants of S. sclerotiorum, an efficient and simple method with high specificity was developed based on loop-mediated isothermal amplification (LAMP). Eight sets of LAMP primers were designed and four sets were optimized to specially distinguish benzimidazole-resistant mutants of S. sclerotiorum. With the optimal LAMP primers, the concentration of LAMP components was optimized and the reaction conditions were set as 60-64 °C for 60 min. This method had a good specificity, sensitivity, stability and repeatability. In the 1491 sclerotia, 614 (41.18%) were positive by LAMP, and 629 (42.19%) positive by MIC. Therefore, the LAMP assay is more feasible to detect benzimidazole-resistant mutants of S. sclerotiorum than traditional detection methods.
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Affiliation(s)
- Ya Bing Duan
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying Yang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jian Xin Wang
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cong Chao Liu
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ling Ling He
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ming Guo Zhou
- College of Plant Protection, State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing Agricultural University, Nanjing, 210095, China
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