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Li Z, Feng W, Zhu Z, Lu S, Lin M, Dong J, Wang Z, Liu F, Chen Q. Cas-OPRAD: a one-pot RPA/PCR CRISPR/Cas12 assay for on-site Phytophthora root rot detection. Front Microbiol 2024; 15:1390422. [PMID: 38903797 PMCID: PMC11188302 DOI: 10.3389/fmicb.2024.1390422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Accepted: 05/21/2024] [Indexed: 06/22/2024] Open
Abstract
Phytophthora sojae is a devastating plant pathogen that causes soybean Phytophthora root rot worldwide. Early on-site and accurate detection of the causal pathogen is critical for successful management. In this study, we have developed a novel and specific one-pot RPA/PCR-CRISPR/Cas12 assay for on-site detection (Cas-OPRAD) of Phytophthora root rot (P. sojae). Compared to the traditional RPA/PCR detection methods, the Cas-OPRAD assay has significant detection performance. The Cas-OPRAD platform has excellent specificity to distinguish 33 P. sojae from closely related oomycetes or fungal species. The PCR-Cas12a assay had a consistent detection limit of 100 pg. μL-1, while the RPA-Cas12a assay achieved a detection limit of 10 pg. μL-1. Furthermore, the Cas-OPRAD assay was equipped with a lateral flow assay for on-site diagnosis and enabled the visual detection of P. sojae on the infected field soybean samples. This assay provides a simple, efficient, rapid (<1 h), and visual detection platform for diagnosing Phytophthora root rot based on the one-pot CRISPR/Cas12a assay. Our work provides important methods for early and accurate on-site detection of Phytophthora root rot in the field or customs fields.
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Affiliation(s)
- Zhiting Li
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Wanzhen Feng
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Zaobing Zhu
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Shengdan Lu
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Mingze Lin
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
| | - Jiali Dong
- Sanya Institute of China Agricultural University, Sanya, China
| | - Zhixin Wang
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Post-Entry Quarantine Center for Tropical Plant, Haikou, China
| | - Fuxiu Liu
- Post-Entry Quarantine Center for Tropical Plant, Haikou, China
| | - Qinghe Chen
- School of Breeding and Multiplication, School of Tropical Agriculture and Forestry, Hainan University, Sanya, China
- Key Laboratory of Green Prevention and Control of Tropical Plant Diseases and Pests, Ministry of Education, Hainan University, Haikou, China
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Qiao N, Jiang M, Chen Y, Wang X, Chi W, Li S, Zhu X, Sun X. A Sequencing-Based Phylogenetic Analysis of Various Strains of Watermelon Silver Mottle Virus in Northern China and Their One-Step Detection Using Reverse Transcription Loop-Mediated Isothermal Amplification. PLANT DISEASE 2024; 108:1769-1775. [PMID: 38240655 DOI: 10.1094/pdis-09-23-1952-re] [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: 05/31/2024]
Abstract
Watermelon silver mottle virus (WSMoV), a potentially invasive virus, is known to reduce the yield and degrade the quality of infected crops in Cucurbitaceae and Solanaceae families, resulting in significant economic losses in limited areas of several Asian countries. WSMoV, previously detected on various crops in southern China, has now become more prevalent on watermelon and sweet pepper in the northern cities of China for the first time. A sequencing-based phylogenetic analysis has confirmed that the viral strains infecting cucumber, watermelon, and sweet pepper plants in Shandong Province are most closely related to those isolated from Guangdong, Guangxi, and Taiwan, suggesting a farther and continuous spread of WSMoV throughout China. To develop a fast, accurate, and practical protocol for WSMoV detection, we designed a set of primers from the conserved sequence of the WSMoV nucleocapsid protein (N) gene for a one-step assay based on reverse transcription loop-mediated isothermal amplification (RT-LAMP). The RT-LAMP assay was performed successfully for 50 min at 61°C and exhibited a highly specific result without cross-reactions with other similar viruses and a sensitivity that is 100-fold higher than that of the traditional RT-PCR. The confirmation of 26 WSMoV suspect samples collected from various regions in Shandong through the RT-LAMP testing has demonstrated that the assay is suitable and practical for detection of WSMoV in both laboratory and field settings.
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Affiliation(s)
- Ning Qiao
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Miao Jiang
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Yuxing Chen
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Xingcui Wang
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Wenjuan Chi
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Shoujie Li
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
| | - Xiaoping Zhu
- College of Plant Protection, Shandong Agricultural University, Taian, Shandong, China
| | - Xiaoan Sun
- Facility Horticulture Laboratory of Universities in Shandong, Weifang University of Science and Technology, Shouguang, Shandong, China
- Division of Plant Industry, Florida Department of Agriculture and Consumer Services, Gainesville, FL, U.S.A. (Retired)
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Ren WC, Wang SJ, Wang ZQ, Zhu MQ, Zhang YH, Lian S, Li BH, Dong XL, Liu N. Detection of Cytb Point Mutation (G143A) that Confers High-Level Resistance to Pyraclostrobin in Glomerella cingulata Using LAMP Method. PLANT DISEASE 2023; 107:1166-1171. [PMID: 36205690 DOI: 10.1094/pdis-08-22-1992-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Glomerella leaf spot (GLS) caused by Glomerella cingulata is a newly emerging disease that results in severe defoliation and fruit spots in apples. In China, the compound of pyraclostrobin and tebuconazole was registered to control GLS in 2018 and has achieved excellent control efficiency. In this study, we showed that the high-level resistant isolates of G. cingulata to pyraclostrobin, caused by the point mutation at codon 143 (GGT→GCT, G143A) in the cytochrome b gene, has appeared in apple orchards in Shandong Province in 2020, and the resistance frequency was 4.8%. Based on the genotype of the resistant isolates, we developed a loop-mediated isothermal amplification (LAMP) assay for detection of the pyraclostrobin resistance. The LAMP assay was demonstrated to have good specificity, sensitivity, and repeatability, and it exhibited high accuracy in detecting pyraclostrobin resistance in the field. This study reported the resistance status of GLS to pyraclostrobin in Shandong Province and developed a molecular tool for the detection of pyraclostrobin resistance, which is of practical significance for the scientific control of GLS.
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Affiliation(s)
- Wei-Chao Ren
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Si-Jia Wang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Zhong-Qiang Wang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Mei-Qi Zhu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yi-Han Zhang
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Sen Lian
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Bao-Hua Li
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Xiang-Li Dong
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Na Liu
- Key Laboratory of Integrated Crop Pest Management of Shandong Province, College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong 266109, China
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Molecular Approaches for Detection of Trichoderma Green Mold Disease in Edible Mushroom Production. BIOLOGY 2023; 12:biology12020299. [PMID: 36829575 PMCID: PMC9953464 DOI: 10.3390/biology12020299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/16/2023]
Abstract
Due to the evident aggressive nature of green mold and the consequently huge economic damage it causes for producers of edible mushrooms, there is an urgent need for prevention and infection control measures, which should be based on the early detection of various Trichoderma spp. as green mold causative agents. The most promising current diagnostic tools are based on molecular methods, although additional optimization for real-time, in-field detection is still required. In the first part of this review, we briefly discuss cultivation-based methods and continue with the secondary metabolite-based methods. Furthermore, we present an overview of the commonly used molecular methods for Trichoderma species/strain detection. Additionally, we also comment on the potential of genomic approaches for green mold detection. In the last part, we discuss fast screening molecular methods for the early detection of Trichoderma infestation with the potential for in-field, point-of-need (PON) application, focusing on isothermal amplification methods. Finally, current challenges and future perspectives in Trichoderma diagnostics are summarized in the conclusions.
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Wang L, Tu H, Hou H, Zhou Z, Yuan H, Luo C, Gu Q. Occurrence and Detection of Carbendazim Resistance in Botryosphaeria dothidea from Apple Orchards in China. PLANT DISEASE 2022; 106:207-214. [PMID: 34227835 DOI: 10.1094/pdis-06-20-1204-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Botryosphaeria dothidea causes white rot, which is among the most devastating diseases affecting apple crops globally. In this study, we assessed B. dothidea resistance to carbendazim by collecting samples from warts on the infected branches of apple trees or from fruits exhibiting evidence of white rot. All samples were collected from different orchards in nine provinces of China in 2018 and 2019. In total, 440 B. dothidea isolates were evaluated, of which 19 isolates from three provinces were found to exhibit carbendazim resistance. We additionally explored the fitness and resistance stability of these isolates, revealing that they were no less fit than carbendazim-sensitive isolates in terms of pathogenicity, sporulation, and mycelial growth and that the observed carbendazim resistance was stable. Sequencing of the β-tubulin gene in carbendazim-resistant isolates showed the presence of a substitution at codon 198 (GAG to GCG) that results in an alanine substitution in place of glutamic acid (E198A) in all 19 resistant isolates. A loop-mediated isothermal amplification (LAMP) method was then developed to rapidly and specifically identify this E198A mutation. This LAMP method offers value as a tool for rapidly detecting carbendazim-resistant isolates bearing this E198A mutation and can thus be used for the widespread monitoring of apple crops to detect and control the development of such resistance.
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Affiliation(s)
- Li Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongtao Tu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Hui Hou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Zengqiang Zhou
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Hongbo Yuan
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Chaoxi Luo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, and College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Qinsheng Gu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
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Shao W, Zhao Y, Ma Z. Advances in Understanding Fungicide Resistance in Botrytis cinerea in China. PHYTOPATHOLOGY 2021; 111:455-463. [PMID: 33174825 DOI: 10.1094/phyto-07-20-0313-ia] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Gray mold, caused by Botrytis cinerea, is a devastating disease that causes significant yield losses in various economically important plants. Fungicide application is one of the main strategies for management of gray mold; however, B. cinerea has developed resistance to various groups of fungicide. In China, benzimidazole-, dicarboximide-, and quinone outside inhibitor-resistant populations of B. cinerea have become dominant. Substitute mutations in fungicide target genes are responsible for resistance in B. cinerea. Based on known resistance mechanisms, molecular methods including loop-mediated isothermal amplification have been developed for rapid detection of resistant isolates of B. cinerea. Because B. cinerea is able to quickly develop resistance to various fungicides, various integrated strategies have been implemented in the last decade, including biological and agricultural practices, to manage fungicide resistance in B. cinerea.
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Affiliation(s)
- Wenyong Shao
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Youfu Zhao
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, U.S.A
| | - Zhonghua Ma
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou, China
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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] [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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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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Enicks DA, Bomberger RA, Amiri A. Development of a Portable LAMP Assay for Detection of Neofabraea perennans in Commercial Apple Fruit. PLANT DISEASE 2020; 104:2346-2353. [PMID: 32697656 DOI: 10.1094/pdis-09-19-2036-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
Bull's eye rot (BER) is a major economic postharvest disease of apple and pear that can be caused by four Neofabraea species: N. perennans, N. alba, N. malicorticis, and N. kienholzii. In Central Washington, BER is predominantly caused by N. perennans. The fungus infects fruit preharvest, and because of the dry growing season in the region, infections remain latent with symptoms expressed only after 3 to 4 months of storage, when BER incidences as high as 20% can been seen, especially in rainy seasons and on susceptible cultivars. To ensure early and efficient infection detections before BER symptoms become visible at point-of-care locations, a portable diagnostic tool based on loop-mediated isothermal amplification (LAMP) was developed using the β-tubulin gene. The LAMP assay was optimized and tested for specificity and sensitivity using DNA extracted from pure cultures of N. perennans and seven other fungal species. The results showed that the selected LAMP primer set was specific to N. perennans and highly sensitive as it detected DNA concentrations as low as 0.001 ng/µl after only 10 min. The assay was validated for N. perennans detection on artificially inoculated apples using a portable thermocycler, Genie II, without the need for DNA extraction. The LAMP assay detected N. perennans on apples inoculated with spore suspensions 3 weeks prior to harvest at concentrations of 103 spores/ml or higher. The assay was further validated using commercial Piñata apples from organic and conventional orchards, demonstrating the ability of this technique to amplify N. perennans from asymptomatic fruit in a commercial setting 3 months before commercial maturity. The LAMP assay developed for N. perennans detection can be easily expanded to detect the other BER causal species. LAMP has potential to be used in orchards and at point-of-care facilities to better inform on BER management at different fruit growth stages, and it has potential to be utilized to better understand the epidemiology of Neofabraea spp.
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Affiliation(s)
- David A Enicks
- Washington State University, Tree Fruit Research and Education Center, Wenatchee, WA 98801
| | - Rachel A Bomberger
- Washington State University, Department of Plant Pathology, Pullman, WA 99164
| | - Achour Amiri
- Washington State University, Tree Fruit Research and Education Center, Wenatchee, WA 98801
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Zhang M, Ye J, He JS, Zhang F, Ping J, Qian C, Wu J. Visual detection for nucleic acid-based techniques as potential on-site detection methods. A review. Anal Chim Acta 2019; 1099:1-15. [PMID: 31986265 DOI: 10.1016/j.aca.2019.11.056] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 11/21/2019] [Accepted: 11/22/2019] [Indexed: 12/15/2022]
Abstract
Nucleic acid-based techniques could achieve highly sensitive detection by amplifying template molecules to millions of folds. It has been one of the most valued analytical methods and is applied in many detection fields, such as diagnosis of infectious diseases, food safety assurance and so on. Nucleic acid-based techniques consist of three steps: nucleic acid extraction, amplification, and product detection. Among them, the detection step plays a vital role because it shows the results directly. As the trend of detection is simple, rapid and instrument-free, it is of necessity to carry out visual detection, where the result read-out could be visible and distinguished by the naked eye. In this critical review, advanced visual detection methods are summarized and discussed in detail, aiming to promote the potential application in on-site detection.
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Affiliation(s)
- Mengyao Zhang
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jing Ye
- Zhijiangnan Think Tank, Zhejiang Institute of Science and Technology Information, Hangzhou, 310006, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China.
| | - Fang Zhang
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, 350108, China
| | - Jianfeng Ping
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Cheng Qian
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058, China; Key Laboratory of on Site Processing Equipment for Agricultural Products, Ministry of Agriculture, Hangzhou, 310058, China.
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Vielba-Fernández A, de Vicente A, Pérez-García A, Fernández-Ortuño D. Monitoring Methyl Benzimidazole Carbamate-Resistant Isolates of the Cucurbit Powdery Mildew Pathogen, Podosphaera xanthii, Using Loop-Mediated Isothermal Amplification. PLANT DISEASE 2019; 103:1515-1524. [PMID: 31059385 DOI: 10.1094/pdis-12-18-2256-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
Powdery mildew, caused by the fungus Podosphaera xanthii, is one of the most economically important diseases affecting cucurbit crops in Spain. Currently, chemical control offers the most efficient management of the disease; however, P. xanthii isolates resistant to multiple classes of site-specific fungicides have been reported in the Spanish cucurbit powdery mildew population. In previous studies, resistance to the fungicides known as methyl benzimidazole carbamates (MBCs) was found to be caused by the amino acid substitution E198A on β-tubulin. To detect MBC-resistant isolates in a faster, more efficient, and more specific way than the traditional methods used to date, a loop-mediated isothermal amplification (LAMP) system was developed. In this study, three sets of LAMP primers were designed. One set was designed for the detection of the wild-type allele and two sets were designed for the E198A amino acid change. Positive results were only obtained with both mutant sets; however, LAMP reaction conditions were only optimized with primer set 2, which was selected for optimal detection of the E198A amino acid change in P. xanthii-resistant isolates, along with the optimal temperature and duration parameters of 65°C for 75 min, respectively. The hydroxynaphthol blue (HNB) metal indicator was used for quick visualization of results through the color change from violet to sky blue when the amplification was positive. HNB was added before the amplification to avoid opening the lids, thus decreasing the probability of contamination. To confirm that the amplified product corresponded to the β-tubulin gene, the LAMP product was digested with the enzyme LweI and sequenced. Our results show that the LAMP technique is a specific and reproducible method that could be used for monitoring MBC resistance of P. xanthii directly in the field.
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Affiliation(s)
- Alejandra Vielba-Fernández
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea, "La Mayora" Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain
| | - Antonio de Vicente
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea, "La Mayora" Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain
| | - Alejandro Pérez-García
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea, "La Mayora" Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain
| | - Dolores Fernández-Ortuño
- Departamento de Microbiología, Facultad de Ciencias, Universidad de Málaga, 29071 Málaga, Spain; and Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea, "La Mayora" Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Campus de Teatinos, 29071 Málaga, Spain
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Wu JY, Hu XR, Zhang CQ. Molecular Detection of QoI Resistance in Colletotrichum gloeosporioides Causing Strawberry Anthracnose Based on Loop-Mediated Isothermal Amplification Assay. PLANT DISEASE 2019; 103:1319-1325. [PMID: 30998417 DOI: 10.1094/pdis-09-18-1593-re] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Anthracnose is one of the most common diseases in strawberry plants. Colletotrichum gloeosporioides is the major cause of anthracnose in China, including Zhejiang Province. Early, specific, reliable, and time-saving detection is urgently needed to prevent the further spread of C. gloeosporioides, guiding farmers to utilize chemicals to control anthracnose. In this study, we showed that the high resistance to pyraclostrobin, caused by a point mutation at codon 143 (GGT→GCT) in the cytochrome b gene of C. gloeosporioides was prevalent in the strawberry growing regions, and we developed a loop-mediated isothermal amplification (LAMP) assay as a detection method. Primer sets S0 and S4 could be used to specifically detect C. gloeosporioides isolates and the G143A mutations, respectively. A detection limit of 10-2 ng (10 pg), which is at least 10-fold more sensitive than conventional polymerase chain reaction, was achieved by the LAMP assay. Here, we utilized lateral-flow devices (LFDs), nitrocellulose membranes that can absorb nucleic acids, to acquire the total genomic DNA of strawberry plants within 2 min. The LFD membranes were used as DNA templates for the LAMP assays to accurately detect strawberry plants infected with C. gloeosporioides. This diagnostic method for strawberry anthracnose was accomplished within 1 h, including the sample preparation and LAMP assays. Collectively, we developed a sensitive and practical method for monitoring C. gloeosporioides and its quinone outside inhibitor-resistant mutants. The LAMP assay for detection of C. gloeosporioides in strawberry plants has great potential for rapid strawberry anthracnose surveillance and will provide farmers with advice on preventing C gloeosporioides at the early stages of strawberry development.
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Affiliation(s)
- J Y Wu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, P.R. China
| | - X R Hu
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, P.R. China
| | - C Q Zhang
- College of Agriculture and Food Science, Zhejiang A&F University, Lin'an, Zhejiang, 311300, P.R. China
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Malarczyk D, Panek J, Frąc M. Alternative Molecular-Based Diagnostic Methods of Plant Pathogenic Fungi Affecting Berry Crops-A Review. Molecules 2019; 24:molecules24071200. [PMID: 30934757 PMCID: PMC6479758 DOI: 10.3390/molecules24071200] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/14/2019] [Accepted: 03/23/2019] [Indexed: 01/01/2023] Open
Abstract
Increasing consumer awareness of potentially harmful pesticides used in conventional agriculture has prompted organic farming to become notably more prevalent in recent decades. Central European countries are some of the most important producers of blueberries, raspberries and strawberries in the world and organic cultivation methods for these fruits have a significant market share. Fungal pathogens are considered to be the most significant threat to organic crops of berries, causing serious economic losses and reducing yields. In order to ameliorate the harmful effects of pathogenic fungi on cultivations, the application of rapid and effective identification methods is essential. At present, various molecular methods are applied for fungal species recognition, such as PCR, qPCR, LAMP and NGS.
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Affiliation(s)
- Dominika Malarczyk
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
| | - Jacek Panek
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
| | - Magdalena Frąc
- Institute of Agrophysics, Polish Academy of Sciences, 20-290 Lublin, Poland.
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