1
|
Tu Y, Wang Y, Jiang H, Ren H, Wang X, Lv W. A Loop-Mediated Isothermal Amplification Assay for the Rapid Detection of Didymella segeticola Causing Tea Leaf Spot. J Fungi (Basel) 2024; 10:467. [PMID: 39057352 PMCID: PMC11278140 DOI: 10.3390/jof10070467] [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: 06/03/2024] [Revised: 07/01/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Tea leaf spot caused by Didymella segeticola is an important disease that threatens the healthy growth of tea plants (Camellia sinensis) and results in reductions in the productivity and quality of tea leaves. Early diagnosis of the disease is particularly important for managing the infection. Loop-mediated isothermal amplification (LAMP) assay is an efficient diagnostic technique with the advantages of simplicity, specificity, and sensitivity. In this study, we developed a rapid, visual, and high-sensitivity LAMP assay for D. segeticola detection based on sequence-characterized amplified regions. Two pairs of amplification primers (external primers F3 and B3 and internal primers FIP and BIP) were designed based on a specific sequence in D. segeticola (NCBI accession number: OR987684). Compared to common pathogens of other genera in tea plants and other species in the Didymella genus (Didymella coffeae-arabicae, Didymella pomorum, and Didymella sinensis), the LAMP method is specific for detecting the species D. segeticola. The assay was able to detect D. segeticola at a minimal concentration of 1 fg/μL genomic DNA at an optimal reaction temperature of 65 °C for 60 min. When healthy leaves were inoculated with D. segeticola in the laboratory, the LAMP method successfully detected D. segeticola in diseased tea leaves at 72 h post inoculation. The LAMP assays were negative when the DNA samples were extracted from healthy leaves. Leaf tissues with necrotic lesions from 18 germplasms of tea plants tested positive for the pathogen by the LAMP assay. In summary, this study established a specific, sensitive, and simple LAMP method to detect D. segeticola, which provides reliable technical support for estimating disease prevalence and facilitates sustainable management of tea leaf spot.
Collapse
Affiliation(s)
- Yiyi Tu
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
| | - Yuchun Wang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Biology, Genetics and breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Hong Jiang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
| | - Hengze Ren
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
| | - Xinchao Wang
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Biology, Genetics and breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| | - Wuyun Lv
- College of Tea Science and Tea Culture, Zhejiang A&F University, Hangzhou 311300, China; (Y.T.); (Y.W.); (H.J.); (H.R.)
- Tea Research Institute, Chinese Academy of Agricultural Sciences/National Center for Tea Improvement/Key Laboratory of Biology, Genetics and breeding of Special Economic Animals and Plants, Ministry of Agriculture and Rural Affairs, Hangzhou 310008, China
| |
Collapse
|
2
|
Liu J, Liang M, Lin T, Zhao Q, Wang H, Yang S, Guo Q, Wang X, Guo H, Cui L, Yan Y, Hieno A, Kageyama K, Suga H, Li M. A LAMP-Based Toolbox Developed for Detecting the Major Pathogens Affecting the Production and Quality of the Chinese Medicinal Crop Aconitum carmichaelii. PLANT DISEASE 2023; 107:658-666. [PMID: 35852903 DOI: 10.1094/pdis-05-22-1092-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Aconitum carmichaelii Debeaux is a traditional Chinese medicinal herb that has been utilized for approximately 2,000 years. However, as cultivation has increased, there have been more reports of A. carmichaelii infections caused by four major pathogenic fungal species, Fusarium oxysporum, F. solani, Mucor circinelloides, and Sclerotium rolfsii, resulting in increased disease incidences and limited production and quality. To detect these infections, we developed a LAMP-based toolbox in this study. The cytochrome c oxidase subunit 1 (cox1) gene, translation elongation factor-1α (EF-1α), internal transcribed spacer (ITS) regions of rDNA, and alcohol dehydrogenase 1 (ADH1) gene, respectively, were used to design species-specific LAMP primer sets for F. oxysporum, F. solani, S. rolfsii, and M. circinelloides. The results showed that the LAMP-based toolbox was effective at detecting pathogens in soil and plant materials. We also used this toolbox to investigate pathogen infection in the main planting regions of A. carmichaelii. Before harvesting, F. oxysporum, M. circinelloides, and S. rolfsii were commonly found in the planting fields and in infected A. carmichaelii plants. Therefore, the toolbox we developed will be useful for tracking these infections, as well as for disease control in A. carmichaelii.
Collapse
Affiliation(s)
- Jingzhe Liu
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Mengyi Liang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Tao Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qing Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Huiqin Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Shunyuan Yang
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Qian Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Xinyi Wang
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Hua Guo
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| | - Langjun Cui
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Yaping Yan
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
| | - Ayaka Hieno
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Koji Kageyama
- River Basin Research Center, Gifu University, Gifu 501-1193, Japan
| | - Haruhisa Suga
- Life Science Research Center, Gifu University, Gifu 501-1193, Japan
| | - Mingzhu Li
- The Key Laboratory of Medicinal Resources and Natural Pharmaceutical Chemistry, The Ministry of Education (Shaanxi Normal University), Xi'an, Shaanxi 710119, P.R. China
- College of Life Sciences, Shaanxi Normal University, Xi'an, Shaanxi 710119, P.R. China
| |
Collapse
|
3
|
Mourou M, Raimondo ML, Lops F, Carlucci A. Brassicaceae Fungi and Chromista Diseases: Molecular Detection and Host–Plant Interaction. PLANTS (BASEL, SWITZERLAND) 2023; 12:1033. [PMID: 36903895 PMCID: PMC10005080 DOI: 10.3390/plants12051033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
Brassicaceae plants cover a large number of species with great economic and nutritional importance around the world. The production of Brassica spp. is limited due to phytopathogenic fungal species causing enormous yield losses. In this scenario, precise and rapid detection and identification of plant-infecting fungi are essential to facilitate the effective management of diseases. DNA-based molecular methods have become popular methods for accurate plant disease diagnostics and have been used to detect Brassicaceae fungal pathogens. Polymerase chain reaction (PCR) assays including nested, multiplex, quantitative post, and isothermal amplification methods represent a powerful weapon for early detection of fungal pathogens and preventively counteract diseases on brassicas with the aim to drastically reduce the fungicides as inputs. It is noteworthy also that Brassicaceae plants can establish a wide variety of relationships with fungi, ranging from harmful interactions with pathogens to beneficial associations with endophytic fungi. Thus, understanding host and pathogen interaction in brassica crops prompts better disease management. The present review reports the main fungal diseases of Brassicaceae, molecular methods used for their detection, review studies on the interaction between fungi and brassicas plants, and the various mechanisms involved including the application of omics technologies.
Collapse
Affiliation(s)
- Marwa Mourou
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| | | | | | - Antonia Carlucci
- Department of Agricultural Sciences, Food, Natural Resources and Engineering, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
| |
Collapse
|
4
|
Niessen L, Fritze M, Wibbelt G, Puechmaille SJ. Development and Application of Loop-Mediated Isothermal Amplification (LAMP) Assays for Rapid Diagnosis of the Bat White-Nose Disease Fungus Pseudogymnoascus destructans. Mycopathologia 2022; 187:547-565. [PMID: 35931867 DOI: 10.1007/s11046-022-00650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 07/01/2022] [Indexed: 11/28/2022]
Abstract
Pseudogymnoascus destructans (= Geomyces destructans) is a psychrophilic filamentous fungus that causes White-Nose Disease (WND; the disease associated with White-Nose Syndrome, WNS) in hibernating bats. The disease has caused considerable reductions in bat populations in the USA and Canada since 2006. Identification and detection of the pathogen in pure cultures and environmental samples is routinely based on qPCR or PCR after DNA isolation and purification. Rapid and specific direct detection of the fungus in the field would strongly improve prompt surveillance, and support control measures. Based on the genes coding for ATP citrate lyase1 (acl1) and the 28S-18S ribosomal RNA intergenic spacer (IGS) in P. destructans, two independent LAMP assays were developed for the rapid and sensitive diagnosis of the fungus. Both assays could discriminate P. destructans from 159 tested species of filamentous fungi and yeasts. Sensitivity of the assays was 2.1 picogram per reaction (pg/rxn) and 21 femtogram per reaction (fg/rxn) for the acl1 and IGS based assays, respectively. Moreover, both assays also work with spores and mycelia of P. destructans that are directly added to the master mix without prior DNA extraction. For field-diagnostics, we developed and tested a field-applicable version of the IGS-based LAMP assay. Lastly, we also developed a protocol for preparation of fungal spores and mycelia from swabs and tape liftings of contaminated surfaces or infected bats. This protocol in combination with the highly sensitive IGS-based LAMP-assay enabled sensitive detection of P. destructans from various sources.
Collapse
Affiliation(s)
- Ludwig Niessen
- TUM School of Life Sciences, Technical University of Munich, Gregor-Mendel-Str. 4, 85354, Freising, Germany.
| | - Marcus Fritze
- Applied Zoology and Nature Conservation, University of Greifswald, Loitzer Str. 26, 17489, Greifswald, Germany.,German Bat Observatory, Am Juliusturm 64, 13599, Berlin, Germany
| | - Gudrun Wibbelt
- Leibniz Institute for Zoo and Wildlife Research, Alfred-Kowalke-Straße 17, 10315, Berlin, Germany
| | - Sebastien J Puechmaille
- Applied Zoology and Nature Conservation, University of Greifswald, Loitzer Str. 26, 17489, Greifswald, Germany.,ISEM, CNRS, EPHE, IRD, University of Montpellier, Montpellier, France.,Institut Universitaire de France, 75005, Paris, France
| |
Collapse
|
5
|
Xiao C, Li R. Detection and Control of Fusarium oxysporum from Soft Rot in Dendrobium officinale by Loop-Mediated Isothermal Amplification Assays. BIOLOGY 2021; 10:1136. [PMID: 34827129 PMCID: PMC8615024 DOI: 10.3390/biology10111136] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 01/15/2023]
Abstract
Soft rot causing Fusarium oxysporum is one of the most destructive diseases of Dendrobium officinale Kimura et Migo in China that reduces D. officinale yield and quality. A key challenge for an integrated management strategy for this disease is the rapid and accurate detection of F. oxysporum on D. officinale. Therefore, a new loop-mediated isothermal amplification (LAMP) assay was developed for this purpose. In this study, the primers were selected and designed using the translation elongation factor-1α (TEF-1α) gene region as the target DNA sequence in order to screen the best system of reaction of LAMP to detect F. oxysporum through optimizing different conditions of the LAMP reaction, including time, temperature, concentrations of MgSO4, and concentrations of inner and outer primers. The optimized system was able to efficiently amplify the target gene at 62 °C for 60 min with 1.2 μM internal primers, 0.4 μM external primers, 7 mM Mg2+, and 5 fg/µL minimum detection concentration of DNA for F. oxysporum. The amplified products could be detected with the naked eye after completion of the reaction with SYBR green I. We were better able to control the effect of soft rot in D. officinale using fungicides following a positive test result. Additionally, the control effect of synergism combinations against soft rot was higher than 75%. Thus, LAMP assays could detect F. oxysporum in infected tissues of D. officinale and soils in field, allowing for early diagnosis of the disease.
Collapse
Affiliation(s)
- Caiyun Xiao
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China;
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
| | - Rongyu Li
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China;
- The Provincial Key Laboratory for Agricultural Pest Management in Mountainous Region, Guiyang 550025, China
- College of Agriculture, Guizhou University, Guiyang 550025, China
| |
Collapse
|
6
|
Grabicoski EMG, Jaccoud-Filho DDS, Lee D, Henneberg L, Pileggi M. Real-Time Quantitative and Ion-Metal Indicator LAMP-Based Assays for Rapid Detection of Sclerotinia sclerotiorum. PLANT DISEASE 2020; 104:1514-1526. [PMID: 32105572 DOI: 10.1094/pdis-07-19-1455-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: 06/10/2023]
Abstract
Sclerotinia sclerotiorum is one of the most devastating and cosmopolitan plant pathogens. Rapid detection of S. sclerotiorum can provide growers an advantage in knowing what control measures should be taken to minimize crop damage and financial losses caused by it. Loop-mediated isothermal amplification (LAMP) is a fast, sensitive, and specific nucleic acid amplification method that does not require a thermal cycler. This study aimed to develop a LAMP-based assay for the specific detection of S. sclerotiorum (Ss-LAMP). A real-time quantitative LAMP reaction (Ss-qLAMP) and a calcein ion indicator-based LAMP reaction (Ss-cLAMP) were designed, optimized, and tested on fungi, plant, and soil samples. The Ss-LAMP reactions were very specific and sensitive. Applying the artificially inoculated soil samples with DNA purified by five protocols in the Ss-qLAMP reaction, it was possible to detect and quantify the pathogen DNA, regardless of the extraction protocol. Naturally infected soybean tissues had the pathogen detected by Ss-cLAMP directly in the reaction tube with no DNA extraction requirement. The assays should be applicable for many types of samples, such as soil, spore traps, and plant tissues from several crops, with no requirement for DNA extraction. The Ss-LAMP reactions took less than 1 h to complete, and they can be made directly in the field with real-time quantitative results (Ss-qLAMP) or qualitative naked-eye visual results (Ss-cLAMP). Results were obtained with 10 pg of DNA or 10 ng of crude mycelium, suggesting a detection limit close to a single DNA copy. Ss-LAMP reactions will allow rapid and accurate diagnosis of S. sclerotiorum and assist in pathogen management and control.
Collapse
Affiliation(s)
- Edilaine Mauricia Gelinski Grabicoski
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
- State University of Maringá, Department of Agronomy, Jardim Universitário, 87020-900, Maringá, PR, Brazil
| | - David de Souza Jaccoud-Filho
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| | - David Lee
- National Institute of Agricultural Botany, Cambridge CB3 0LE, United Kingdom
| | - Luciane Henneberg
- State University of Ponta Grossa, Department of Plant Science and Plant Protection, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| | - Marcos Pileggi
- State University of Ponta Grossa, Department of Structural, Molecular and Genetic Biology, Uvaranas, 84030-900, Ponta Grossa, PR, Brazil
| |
Collapse
|
7
|
Construction of Raman spectroscopic fingerprints for the detection of Fusarium wilt of banana in Taiwan. PLoS One 2020; 15:e0230330. [PMID: 32176731 PMCID: PMC7075571 DOI: 10.1371/journal.pone.0230330] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/27/2020] [Indexed: 01/15/2023] Open
Abstract
Banana (Musa sp.) is cultivated worldwide and is one of the most popular fruits. The soil-borne fungal disease Fusarium wilt of banana (FWB), commonly known as Panama disease, is caused by Fusarium oxysporum f. sp. cubense (Foc) and is a highly lethal vascular fungal disease in banana plants. Raman spectroscopy, an emerging laser-based technology based on Raman scattering, has been used for the qualitative characterization of biological tissues such as foodborne pathogens, cancer cells, and melamine. In this study, we describe a Raman spectroscopic technique that could potentially be used as a method for diagnosing FWB. To that end, the Raman fingerprints of Foc (including mycelia and conidia) and Foc-infected banana pseudostems with varying levels of symptoms were determined. Our results showed that eight, eleven, and eleven characteristic surface-enhanced Raman spectroscopy peaks were observed in the mycelia, microconidia, and macroconidia of Foc, respectively. In addition, we constructed the Raman spectroscopic fingerprints of banana pseudostem samples with varying levels of symptoms in order to be able to differentiate Foc-infected bananas from healthy bananas. The rate at which FWB was detected in asymptomatic Foc-infected samples by using the spectral method was 76.2%, which was comparable to the rates previously reported for other FWB detection methods based on real-time PCR assays, suggesting that the spectral method described herein could potentially serve as an alternative tool for detecting FWB in fields. As such, we hope that the developed spectral method will open up new possibilities for the on-site diagnosis of FWB.
Collapse
|
8
|
Magdama F, Monserrate-Maggi L, Serrano L, Sosa D, Geiser DM, Jiménez-Gasco MDM. Comparative analysis uncovers the limitations of current molecular detection methods for Fusarium oxysporum f. sp. cubense race 4 strains. PLoS One 2019; 14:e0222727. [PMID: 31545825 PMCID: PMC6756539 DOI: 10.1371/journal.pone.0222727] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/05/2019] [Indexed: 11/18/2022] Open
Abstract
Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4) is threatening banana production worldwide. Despite quarantine efforts, the pathogen continues to spread; thus, early diagnosis plays an essential role for the proper execution of contingency plans. Here, we assess the accuracy of four PCR-based molecular methods described in the literature for the identification and detection of race 4 strains, including Subtropical (Foc STR4) and Tropical Race 4 causing Fusarium wilt of banana. We screened a total of 302 isolates using these four markers, and performed phylogenetic analyses, Vegetative Compatibility Group (VCG) testing, sequence comparison, and pathogenicity tests for selected isolates. Our results show that three out of the four markers tested are not reliable for identification of Foc STR4 and TR4, as DNA from isolates from Ecuador, pathogenic and nonpathogenic to banana, obtained from different banana cultivars, displayed cross-reaction with these methods; that is, false positives can occur during the diagnostic process for race 4. Phylogenetic analyses, VCG testing, sequence comparison, and pathogenicity tests suggest the presence of non-target F. oxysporum isolates that share genomic regions with pathogenic strains but lack true pathogenicity to banana. The findings of this work are of foremost importance for international regulatory agencies performing surveillance tests in pathogen-free areas using the current diagnostic methods. We suggest the use of a genetic locus possibly related to virulence, previously identified by T-DNA, and amplified with primers W2987F/ W2987R, for diagnosis of Foc TR4 as the most reliable alternative. We urge the adoption of a more holistic view in the study of F. oxysporum as a plant pathogen that considers the biology and diversity of the species for the development of better diagnostic tools.
Collapse
Affiliation(s)
- Freddy Magdama
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, Guayaquil, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida, Campus Gustavo Galindo, Guayaquil, Ecuador
| | - Lorena Monserrate-Maggi
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, Guayaquil, Ecuador
| | - Lizette Serrano
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, Guayaquil, Ecuador
| | - Daynet Sosa
- Escuela Superior Politécnica del Litoral, ESPOL, Centro de Investigaciones Biotecnológicas del Ecuador, Campus Gustavo Galindo, Guayaquil, Ecuador
- Escuela Superior Politécnica del Litoral, ESPOL, Facultad de Ciencias de la Vida, Campus Gustavo Galindo, Guayaquil, Ecuador
| | - David M. Geiser
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - María del Mar Jiménez-Gasco
- Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, University Park, Pennsylvania, United States of America
- * E-mail:
| |
Collapse
|
9
|
Dong H, Fan H, Lei Z, Wu C, Zhou D, Li H. Histological and Gene Expression Analyses in Banana Reveals the Pathogenic Differences between Races 1 and 4 of Banana Fusarium Wilt Pathogen. PHYTOPATHOLOGY 2019; 109:1029-1042. [PMID: 30829554 DOI: 10.1094/phyto-10-18-0384-r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Fusarium oxysporum f. sp. cubense, the causative agent of Panama disease, is classified into three races: Foc1, Foc2, and Foc4. However, the histological characteristics, the accumulation of fusaric acid (FA), and resistant gene expression in banana infected with different races remain unclear. In this study, we compared the infection processes, FA contents, and gene expression levels in a Cavendish banana cultivar (Musa AAA Brazilian) inoculated with Foc1 and Foc4. Results showed that Foc4 can rapidly extend from the roots to the leaves, whereas Foc1 expands slowly from the roots to the rhizomes but cannot expand further upward. In addition, the colonization of plants by Foc4 was significantly higher compared with Foc1, as was the content of FA in those infected plant tissues. We observed that a large amount of starch granules was produced in the rhizomes and the number of starch granules was significantly higher after infection with Foc1 than after infection with Foc4. We further found that starch has an important inhibitory effect on the phytotoxicity induced by FA, thus leading to more resistance to the pathogens in the plants with high amounts of starch accumulation than in those with a low amount of starch accumulation. Moreover, the expression levels of 10 defense-related genes were analyzed and the results showed that the induction levels of those genes were higher after infection with Foc1 than after infection with Foc4. These results suggest that the observed differences in the invasion of host tissues and FA accumulation, and the number of starch granules and expression of defense-related genes, may contribute to a difference in virulence between the two races and the resulting difference in host resistance response, respectively.
Collapse
Affiliation(s)
- Honghong Dong
- 1 State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Huiyun Fan
- 1 State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Zhaoxi Lei
- 1 State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| | - Chao Wu
- 1 State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
- 2 Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou, Guangdong 510405, China
| | - Dengbo Zhou
- 3 Institute of Tropical Bioscience and Biotechnology, China Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
| | - Huaping Li
- 1 State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou 510642, China
| |
Collapse
|
10
|
Fan H, Dong H, Xu C, Liu J, Hu B, Ye J, Mai G, Li H. Pectin methylesterases contribute the pathogenic differences between races 1 and 4 of Fusarium oxysporum f. sp. cubense. Sci Rep 2017; 7:13140. [PMID: 29030626 PMCID: PMC5640671 DOI: 10.1038/s41598-017-13625-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 09/27/2017] [Indexed: 02/08/2023] Open
Abstract
Plant cell walls, which are mainly composed of pectin, play important roles in plant defence responses to pathogens. Pectin is synthesised in a highly esterified form and then de-esterified by pectin methylesterases (PMEs). Because of this, PMEs are directly involved in plant defence. However, the molecular mechanisms of their interactions with pectins remain unclear. In this study, we compared the expression level and enzyme activities of PMEs in a banana Cavendish cultivar (Musa AAA 'Brazilian') inoculated with Fusarium oxysporum f. sp. cubense pathogenic races 1 (Foc1) and 4 (Foc4). We further examined the spatial distribution of PMEs and five individual homogalacturonans (HGs) with different degree of pectin methylesterification (DM). Results suggested that the banana roots infected with Foc1 showed lower PME activity than those infected with Foc4, which was consisted with observed higher level of pectin DM. The level of HGs crosslinked with Ca2+ was significantly higher in roots infected with Foc1 compared with those infected with Foc4. Therefore, banana exhibited significantly different responses to Foc1 and Foc4 infection, and these results suggest differences in PME activities, DM of pectin and Ca2+-bridged HG production. These differences could have resulted in observed differences in virulence between Foc1 and Foc4.
Collapse
Affiliation(s)
- Huiyun Fan
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Honghong Dong
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Chunxiang Xu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jing Liu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Bei Hu
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Jingwen Ye
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Guiwan Mai
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China
| | - Huaping Li
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, College of Agriculture, South China Agricultural University, Guangzhou, 510642, China.
| |
Collapse
|
11
|
Development of a hydrolysis probe-based real-time assay for the detection of tropical strains of Fusarium oxysporum f. sp. cubense race 4. PLoS One 2017; 12:e0171767. [PMID: 28178348 PMCID: PMC5298334 DOI: 10.1371/journal.pone.0171767] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/25/2017] [Indexed: 11/19/2022] Open
Abstract
Fusarium oxysporum f. sp. cubense (Foc) is one of the most important threats to global banana production. Strategies to control the pathogen are lacking, with plant resistance offering the only long-term solution, if sources of resistance are available. Prevention of introduction of Foc into disease-free areas thus remains a key strategy to continue sustainable banana production. In recent years, strains of Foc affecting Cavendish bananas have destroyed plantations in a number of countries in Asia and in the Middle East, and one African country. One vegetative compatibility group (VCG), 01213/16, is considered the major threat to bananas in tropical and subtropical climatic conditions. However, other genetically related VCGs, such as 0121, may potentially jeopardize banana cultures if they were introduced into disease-free areas. To prevent the introduction of these VCGs into disease-free Cavendish banana-growing countries, a real-time PCR test was developed to accurately detect both VCGs. A previously described putative virulence gene was used to develop a specific combination of hydrolysis probe/primers for the detection of tropical Foc race 4 strains. The real-time PCR parameters were optimized by following a statistical approach relying on orthogonal arrays and the Taguchi method in an attempt to enhance sensitivity and ensure high specificity of the assay. This study also assessed critical performance criteria, such as repeatability, reproducibility, robustness, and specificity, with a large including set of 136 F. oxysporum isolates, including 73 Foc pathogenic strains representing 24 VCGs. The validation data demonstrated that the new assay could be used for regulatory testing applications on banana plant material and can contribute to preventing the introduction and spread of Foc strains affecting Cavendish bananas in the tropics.
Collapse
|
12
|
Real-Time Polymerase Chain Reaction (PCR) Based Identification and Detection of Fungi Belongs to Genus Fusarium. Fungal Biol 2017. [DOI: 10.1007/978-3-319-34106-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
13
|
Lin YH, Lin YJ, Chang TD, Hong LL, Chen TY, Chang PFL. Development of a TaqMan Probe-Based Insulated Isothermal Polymerase Chain Reaction (iiPCR) Assay for Detection of Fusarium oxysporum f. sp. cubense Race 4. PLoS One 2016; 11:e0159681. [PMID: 27448242 PMCID: PMC4957775 DOI: 10.1371/journal.pone.0159681] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 07/05/2016] [Indexed: 01/08/2023] Open
Abstract
This study developed a novel and inexpensive detection method based on a TaqMan probe-based insulated isothermal polymerase chain reaction (iiPCR) method for the rapid detection of Panama disease caused by Fusarium oxysporum f. sp. cubense (Foc) race 4, which is currently among the most serious fungal vascular diseases worldwide. By using the portable POCKIT™ device with the novel primer set iiFoc-1/iiFoc-2, the Foc race 4 iiPCR assay (including DNA amplification and signal monitoring) could be completed within one hour. The developed Foc race 4 iiPCR assay is thus a user-friendly and efficient platform designed specifically for the detection of Foc race 4. The detection limit of this optimized Foc iiPCR system was estimated to be 1 copy of the target standard DNA as well as 1 fg of the Foc genomic DNA. This approach can serve as a rapid detection method for in planta detection of Foc race 4 in field-infected banana. It was concluded that this molecular detection procedure based on iiPCR has good potential for use as an efficient detection method.
Collapse
Affiliation(s)
- Ying-Hong Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Yi-Jia Lin
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Tsai-De Chang
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Li-Ling Hong
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Tzu-Yu Chen
- Department of Plant Medicine, National Pingtung University of Science and Technology, Pingtung, Taiwan
| | - Pi-Fang Linda Chang
- Department of Plant Pathology, National Chung Hsing University, Taichung, Taiwan
- Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- NCHU-UCD Plant and Food Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
| |
Collapse
|
14
|
Qiao B, Cui JY, Sun L, Yang S, Zhao YL. Cross-priming amplification targeting the coagulase gene for rapid detection of coagulase-positive Staphylococci. J Appl Microbiol 2015; 119:188-95. [PMID: 25913490 DOI: 10.1111/jam.12836] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 04/07/2015] [Accepted: 04/15/2015] [Indexed: 11/26/2022]
Abstract
AIMS To develop and evaluate cross-priming amplification (CPA) combined with immuno-blotting for the detection of coagulase-positive Staphylococci including Staphylococcus aureus. METHODS AND RESULTS Twenty-four sets of cross and detection primers were designed according to four sequences of coagulase gene in Staph. aureus. The most specific primer pair was screened out for the next amplification and interaction. The specificity was evaluated in a total of 53 species of Staph. aureus and non-Staph. aureus. Two red lines indicating positive were always observed on the BioHelix Express strip for 12 subspecies of Staph. aureus. In contrast, only one signal line showing negative results was detected in all of non-Staph. aureus samples. The limit of detection (LOD) of CPA was 3·6 ± 2·7 fg for the genomic DNA, which is about 100 and 10 times sensitive than those of PCR and loop-mediated isothermal amplification respectively. For the pure culture of Staph. aureus and milk powders, the LODs of CPA were about 1·34 CFU per reaction and 5·2 ± 3·7 CFU per 100 g of milk powder respectively. The CPA method was also successfully applied to evaluate the contamination of Staph. aureus in 318 samples of daily food. CONCLUSIONS CPA is a very sensitive and rapid method to detect Staph. aureus by simple laboratory instrument. SIGNIFICANCE AND IMPACT OF THE STUDY It is the first report on the application of the CPA with immuno-blotting for detection of coagulase-positive Staphylococci including Staph. aureus.
Collapse
Affiliation(s)
- B Qiao
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, China
| | - J-Y Cui
- School of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China
| | - L Sun
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - S Yang
- School of Life Science, Shandong Province Key Laboratory of Applied Mycology, Qingdao International Center on Microbes Utilizing Biogas, Qingdao Agricultural University, Qingdao, Shandong Province, China.,Key Laboratory of Systems Bioengineering, Ministry of Education, Tianjin University, Tianjin, China
| | - Y-L Zhao
- Department of Medical Microbiology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| |
Collapse
|
15
|
Howard RL, French DJ, Richardson JA, O'Neill CE, Andreou MP, Brown T, Clark D, Clarke IN, Holloway JW, Marsh P, Debenham PG. Rapid detection of diagnostic targets using isothermal amplification and HyBeacon probes--a homogenous system for sequence-specific detection. Mol Cell Probes 2014; 29:92-8. [PMID: 25542839 DOI: 10.1016/j.mcp.2014.12.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Revised: 12/16/2014] [Accepted: 12/17/2014] [Indexed: 01/17/2023]
Abstract
Isothermal amplification is a rapid, simple alternative to PCR, with amplification commonly detected using fluorescently labelled oligonucleotide probes, intercalating dyes or increased turbidity as a result of magnesium pyrophosphate generation. SNP identification is possible but requires either allele-specific primers or multiple dye-labelled probes, but further downstream processing is often required for allelic identification. Here we demonstrate that modification of common isothermal amplification methods by the addition of HyBeacon probes permits homogeneous sequence detection and discrimination by melting or annealing curve analysis. Furthermore, we demonstrate that isothermal amplification and sequence discrimination is possible directly from a crude sample such as an expressed buccal swab.
Collapse
Affiliation(s)
| | | | - James A Richardson
- University of Southampton School of Chemistry, Highfield, Southampton SO17 1BJ, UK
| | - Colette E O'Neill
- University of Southampton Faculty of Medicine, Clinical and Experimental Sciences, Southampton General Hospital, Southampton SO16 6YD, UK
| | | | - Tom Brown
- University of Southampton School of Chemistry, Highfield, Southampton SO17 1BJ, UK
| | - Duncan Clark
- OptiGene Ltd., Unit 5, Blatchford Road, Horsham, RH13 5QR, UK
| | - Ian N Clarke
- University of Southampton Faculty of Medicine, Clinical and Experimental Sciences, Southampton General Hospital, Southampton SO16 6YD, UK
| | - John W Holloway
- University of Southampton Faculty of Medicine, Clinical and Experimental Sciences, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Peter Marsh
- Health Protection Agency, Southampton General Hospital, Southampton SO16 6YD, UK
| | | |
Collapse
|