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Yang C, Nguyen VA, Nulu NPC, Kalaipandian S, Beveridge FC, Biddle J, Young A, Adkins SW. Towards Pathogen-Free Coconut Germplasm Exchange. PLANTS (BASEL, SWITZERLAND) 2024; 13:1809. [PMID: 38999649 PMCID: PMC11244555 DOI: 10.3390/plants13131809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 06/18/2024] [Accepted: 06/24/2024] [Indexed: 07/14/2024]
Abstract
Coconut (Cocos nucifera L.) is an important palm species that serves as the mainstay of several industries and contributes to the livelihoods of millions of smallholder farmers. International exchange of coconut germplasm has been undertaken for several decades to facilitate the conservation of selected varieties within global genebanks and for the distribution to farmers and scientists. In vitro systems are a convenient and an efficient method for the exchange of coconut germplasm. However, it is possible that these tissue culture systems can transfer lethal pathogens causing a threat to the importing countries. In this review, the following topics are discussed: the major disease-causing agents of concern, the various tissues that could be used for coconut germplasm exchange, and the techniques available for the detection and elimination of disease-causing agents from various transmission systems. Additionally, the lack of clear, science-backed guidelines to facilitate the exchange of in vitro coconut materials is raised, along with recommendations for future studies to ensure the safe movement of coconut germplasm without biosecurity risks.
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Affiliation(s)
- Chongxi Yang
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, QLD 4343, Australia
| | - Van Anh Nguyen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - Sundaravelpandian Kalaipandian
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, QLD 4343, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
- Department of Bioengineering, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha School of Engineering, Chennai 602105, India
| | - Fernanda Caro Beveridge
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, QLD 4343, Australia
| | - Julianne Biddle
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, QLD 4343, Australia
| | - Anthony Young
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, QLD 4343, Australia
| | - Steve W Adkins
- School of Agriculture and Food Sustainability, The University of Queensland, Gatton, QLD 4343, Australia
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4072, Australia
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2
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Gupta N, Kumar R, Kishan G, Sharma SK, Srivastava N, Kumar A, Baranwal VK. Development of Simplified Recombinase Polymerase Amplification Assay for Rapid and Robust Detection of Citrus Yellow Vein Clearing Virus. Curr Microbiol 2024; 81:103. [PMID: 38386082 DOI: 10.1007/s00284-024-03614-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/06/2024] [Indexed: 02/23/2024]
Abstract
Citrus is an economically important fruit crop, belongs to family Rutaceae, cultivated commercially in over 130 countries, which holds a leading profitable position in the international market. The most important citrus varieties are mandarins, oranges, lemons, sweet limes, grapefruits and pomelos. Citrus yellow vein clearing virus (CYVCV) is an important graft transmissible plant pathogen known to reduce productivity of citrus fruits due to its predominant association and widespread occurrence. Requirement of fast, reliable, efficient & economical CYVCV indexing assay is a prerequisite for production of healthy planting material. Currently, nucleic acid isolation and thermal cycler-based assay available for CYVCV indexing is a cumbersome lab intensive method. The present study was undertaken to develop and validate reverse transcription-recombinase polymerase amplification (RT-RPA) assay requiring no tedious RNA isolation, separate cDNA synthesis and costlier instrument like thermo-cycler. Optimized RT-RPA assay was able to amplify CYVCV up to 10-7 dilution (equivalent to 0.1 pg/μl) with the prepared templates of both RNA and crude saps and showed higher sensitivity in detection of CYVCV infection in field samples as compared to the conventional RT-PCR. Developed RT-RPA assay showed high specificity without any cross-reaction with other citrus pathogens (Indian citrus ringspot virus, citrus yellow mosaic virus, citrus tristeza virus, citrus exocortis viroid and huanglongbing). RT-RPA using crude leaf sap as template is quite simple, robust, highly sensitive, time and cost effective; therefore, it can be used in resource constrained laboratories as screening tool, for field surveys and on-site testing programs in farms, nurseries and biosecurity. Present study, first time reports the development, optimization and validation of crude sap-based RT-RPA assay for the detection of CYVCV infection in citrus plants namely; Kinnow mandarin, Mosambi and Grape fruit.
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Affiliation(s)
- Nitika Gupta
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Rakesh Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Gopi Kishan
- ICAR-Indian Institute of Seed Science, Uttar Pradesh, Kushmaur, Mau, India
| | - Susheel Kumar Sharma
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Nishant Srivastava
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Ashwini Kumar
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Virendra Kumar Baranwal
- Advanced Centre for Plant Virology, Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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3
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Trippa D, Scalenghe R, Basso MF, Panno S, Davino S, Morone C, Giovino A, Oufensou S, Luchi N, Yousefi S, Martinelli F. Next-generation methods for early disease detection in crops. PEST MANAGEMENT SCIENCE 2024; 80:245-261. [PMID: 37599270 DOI: 10.1002/ps.7733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/21/2023] [Indexed: 08/22/2023]
Abstract
Plant pathogens are commonly identified in the field by the typical disease symptoms that they can cause. The efficient early detection and identification of pathogens are essential procedures to adopt effective management practices that reduce or prevent their spread in order to mitigate the negative impacts of the disease. In this review, the traditional and innovative methods for early detection of the plant pathogens highlighting their major advantages and limitations are presented and discussed. Traditional techniques of diagnosis used for plant pathogen identification are focused typically on the DNA, RNA (when molecular methods), and proteins or peptides (when serological methods) of the pathogens. Serological methods based on mainly enzyme-linked immunosorbent assay (ELISA) are the most common method used for pathogen detection due to their high-throughput potential and low cost. This technique is not particularly reliable and sufficiently sensitive for many pathogens detection during the asymptomatic stage of infection. For non-cultivable pathogens in the laboratory, nucleic acid-based technology is the best choice for consistent pathogen detection or identification. Lateral flow systems are innovative tools that allow fast and accurate results even in field conditions, but they have sensitivity issues to be overcome. PCR assays performed on last-generation portable thermocyclers may provide rapid detection results in situ. The advent of portable instruments can speed pathogen detection, reduce commercial costs, and potentially revolutionize plant pathology. This review provides information on current methodologies and procedures for the effective detection of different plant pathogens. © 2023 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Daniela Trippa
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Riccardo Scalenghe
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | | | - Stefano Panno
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Salvatore Davino
- Dipartimento di Scienze Agrarie Alimentari e Forestali, Università degli Studi di Palermo, Palermo, Italy
| | - Chiara Morone
- Regione Piemonte - Phytosanitary Division, Torino, Italy
| | - Antonio Giovino
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Palermo, Italy
| | - Safa Oufensou
- Dipartimento di Agraria, Università degli Studi di Sassari, Sassari, Italy
| | - Nicola Luchi
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Federico Martinelli
- Department of Biology, University of Florence, Florence, Italy
- National Research Council, Institute for Sustainable Plant Protection, (CNR-IPSP), Florence, Italy
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4
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Sun Y, Yokomi R. Whole genome sequence of Citrus yellow vein clearing virus CA1 isolate. BMC Res Notes 2023; 16:166. [PMID: 37563684 PMCID: PMC10416512 DOI: 10.1186/s13104-023-06443-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023] Open
Abstract
OBJECTIVES Citrus yellow vein clearing virus (CYVCV) is an emerging disease that poses a significant threat to the citrus industry in California. In this study, the viral genomic RNA was isolated from Eureka lemon plants in the greenhouse exhibiting CYVCV symptoms. Subsequently, the corresponding DNA genome amplicon was sequenced and annotated. These efforts expand the genotype database of CYVCV, which aims to enhance detection assays, promote understanding of the virus's genetics and evolution, and support the management of this disease. DATA DESCRIPTION In this report, we present the complete genome sequence of the CYVCV California isolate (CA1). The genome was found to be 7,530 bp in length, with a G + C content of 51.7%. The 5' and 3' termini were determined using 5' and 3' termini rapid amplification of cDNA ends (RACE) systems. Furthermore, our analysis revealed the presence of six open reading frames (ORFs) potentially encoding proteins. All sequence data and annotation have been deposited in GenBank under the accession number OR037276.1.
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Affiliation(s)
- Yongduo Sun
- Department of Agriculture - Agricultural Research Service, United States, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA.
| | - Raymond Yokomi
- Department of Agriculture - Agricultural Research Service, United States, San Joaquin Valley Agricultural Sciences Center, Parlier, CA, 93648, USA.
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5
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Luigi M, Manglli A, Corrado CL, Tiberini A, Costantini E, Ferretti L, Tomassoli L, Bertin S. Development, Validation, and Application of Reverse Transcription Real-Time and Droplet Digital PCR Assays for the Detection of the Potyviruses Watermelon Mosaic Virus and Zucchini Yellow Mosaic Virus in Cucurbits. PLANTS (BASEL, SWITZERLAND) 2023; 12:2364. [PMID: 37375989 DOI: 10.3390/plants12122364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 05/29/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023]
Abstract
Among the cucurbit-infecting viruses, watermelon mosaic virus (WMV) and zucchini yellow mosaic virus (ZYMV) (Potyvirus: Potyviridae) are responsible for severe symptoms on cucumber, melon, watermelon, and zucchini cultivations worldwide. In this study, reverse transcription real-time PCR (real-time RT-PCR) and droplet-digital PCR (RT-ddPCR) assays targeting the coat protein (CP) genes of WMV and ZYMV were developed and validated according to the international standards of plant pest diagnosis (EPPO PM 7/98 (5)). First, the diagnostic performance of WMV-CP and ZYMV-CP real-time RT-PCRs was evaluated, and the assays displayed an analytical sensitivity of 10-5 and 10-3, respectively. The tests also showed an optimal repeatability, reproducibility and analytical specificity, and were reliable for the virus detection in naturally infected samples and across a wide range of cucurbit hosts. Based on these results, the real-time RT-PCR reactions were adapted to set up RT-ddPCR assays. These were the first RT-ddPCR assays aiming at the detection and quantification of WMV and ZYMV and showed a high sensitivity, being able to detect until 9 and 8 copies/µL of WMV or ZYMV, respectively. The RT-ddPCRs allowed the direct estimation of the virus concentrations and opened to a broad range of applications in disease management, such as the evaluation of partial resistance in breeding processes, identification of antagonistic/synergistic events, and studies on the implementation of natural compounds in the integrated management strategies.
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Affiliation(s)
- Marta Luigi
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Ariana Manglli
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Carla Libia Corrado
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Antonio Tiberini
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Elisa Costantini
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Luca Ferretti
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Laura Tomassoli
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Sabrina Bertin
- Research Centre for Plant Protection and Certification, Council for Agricultural Research and Economics, 00156 Rome, Italy
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6
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Huang Q, Wang N, Liu J, Liao H, Zeng Z, Hu C, Wei C, Tan S, Liu F, Li G, Huang H, Chen D, Wei S, Qin Z. Soil bacterial communities associated with marbled fruit in Citrus reticulata Blanco 'Orah'. FRONTIERS IN PLANT SCIENCE 2023; 14:1098042. [PMID: 37223817 PMCID: PMC10200933 DOI: 10.3389/fpls.2023.1098042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 04/03/2023] [Indexed: 05/25/2023]
Abstract
Citrus reticulata Blanco 'Orah' is grown throughout southern China and provides enormous economic value. However, the agricultural industry has suffered substantial losses during recent years due to marbled fruit disease. The present study focuses on the soil bacterial communities associated with marbled fruit in 'Orah'. The agronomic traits and microbiomes of plants with normal and marbled fruit from three different orchards were compared. No significant differences were found in agronomic traits between the groups, except for higher fruit yields and higher quality of fruits in normal fruit group. Additionally, a total of 2,106,050 16S rRNA gene sequences were generated via the NovoSeq 6000. The alpha diversity index (including the Shannon and Simpson indices), Bray-Curtis similarity, and principal component analyses indicated no significant differences in microbiome diversity between normal and marbled fruit groups. For the healthy 'Orah', the most abundant associated phyla were Bacteroidetes, Firmicutes, and Proteobacteria. In comparison, Burkholderiaceae and Acidobacteria were the most abundant taxa with the marbled fruit group. In addition, the family Xanthomonadaceae and the genus Candidatus Nitrosotalea were prevalent with this group. Analysis using the Kyoto Encyclopedia of Genes and Genomes pathways showed that several pathways related to metabolism significantly differed between the groups. Thus, the present study provides valuable information regarding soil bacterial communities associated with marbled fruit in 'Orah'.
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Affiliation(s)
- Qichun Huang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Nina Wang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Jimin Liu
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, Nanning, China
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Huihong Liao
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zhikang Zeng
- Institute of Agricultural Science and Technology Information, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Chengxiao Hu
- College of Resources and Environment, Huazhong Agricultural University, Wuhan, China
| | - Chizhang Wei
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Songyue Tan
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Fuping Liu
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Guoguo Li
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hongming Huang
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Dongkui Chen
- Horticulture Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Shaolong Wei
- Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Zelin Qin
- Institute of Agricultural Science and Technology Information, Guangxi Academy of Agricultural Sciences, Nanning, China
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7
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Raguseo C, Gerin D, Pollastro S, Rotolo C, Rotondo PR, Faretra F, De Miccolis Angelini RM. A Duplex-Droplet Digital PCR Assay for Simultaneous Quantitative Detection of Monilinia fructicola and Monilinia laxa on Stone Fruits. Front Microbiol 2021; 12:747560. [PMID: 34912308 PMCID: PMC8667764 DOI: 10.3389/fmicb.2021.747560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 11/04/2021] [Indexed: 11/28/2022] Open
Abstract
Brown rot, caused by different Monilinia species, is a most economically important disease of pome and stone fruits worldwide. In Europe and in Italy, the quarantine pathogen M. fructicola was recently introduced and rapidly spread and, by competing with the main indigenous species Monilinia fructigena and Monilinia laxa, caused relevant changes in Monilinia populations. As a result, in most areas, the pathogen almost replaced M. fructigena and now coexists with M. laxa. The availability of specific and easy-of-use quantification methods is essential to study the population dynamics, and in this work, a new method for the simultaneous quantification of M. fructicola and M. laxa based on droplet digital PCR (ddPCR) technique was established. Under the optimized reaction conditions, consisting of 250/500 nM of primers/probe sets concentration, 58°C as annealing temperature and 50 PCR cycles, the duplex-ddPCR assay was 200-fold more sensitive than duplex-real-time quantitative PCR (qPCR) assay, quantifying < 1 copy μL–1 of target DNA in the PCR mixture. The results obtained with the validation assay performed on apricot and peach fruits, artificially inoculated with conidial suspensions containing different ratios of M. fructicola and M. laxa, showed a high correlation (R2 = 0.98) between the relative quantity of DNA of the two species quantified by ddPCR and qPCR and a more accurate quantification by ddPCR compared to qPCR at higher concentrations of M. fructicola. The herein described method represents a useful tool for the early detection of Monilinia spp. on stone fruits and for the improving knowledge on the epidemiology of brow rot and interactions between the two prevalent Monilinia species.
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Affiliation(s)
- Celeste Raguseo
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Donato Gerin
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Stefania Pollastro
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Caterina Rotolo
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Palma Rosa Rotondo
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
| | - Francesco Faretra
- Department of Soil, Plant and Food Sciences, University of Bari, Bari, Italy
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8
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Cui X, Abd El-Aty AM, Zhang C, Xu L, Liu H, Jia H, Wang Y, Cao Z, Salvador JP, She Y, Jin F, Wang J, Jin M, Hammock BD. Enhanced Bio-Barcode Immunoassay Using Droplet Digital PCR for Multiplex Detection of Organophosphate Pesticides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:11131-11141. [PMID: 34494438 DOI: 10.1021/acs.jafc.1c03216] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
A bio-barcode immunoassay based on droplet digital polymerase chain reaction (ddPCR) was developed to simultaneously quantify triazophos, parathion, and chlorpyrifos in apple, cucumber, cabbage, and pear. Three gold nanoparticle (AuNP) probes and magnetic nanoparticle (MNP) probes were prepared, binding through their antibodies with the three pesticides in the same tube. Three groups of primers, probes, templates, and three antibodies were designed to ensure the specificity of the method. Under the optimal conditions, the detection limits (expressed as IC10) of triazophos, parathion, and chlorpyrifos were 0.22, 0.45, and 4.49 ng mL-1, respectively. The linear ranges were 0.01-20, 0.1-100, and 0.1-500 ng mL-1, and the correlation coefficients (R2) were 0.9661, 0.9834, and 0.9612, respectively. The recoveries and relative standard deviations (RSDs) were in the ranges of 75.5-98.9 and 8.3-16.7%. This study provides the first insights into the ddPCR for the determination of organophosphate pesticides. It also laid the foundation for high-throughput detection of other small molecules.
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Affiliation(s)
- Xueyan Cui
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - A M Abd El-Aty
- State Key Laboratory of Biobased Material and Green Papermaking, College of Food Science and Engineering, Qilu University of Technology, Shandong Academy of Science, Jinan 250353, P. R. China
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt
- Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Chan Zhang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Lingyuan Xu
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Haijin Liu
- Inspection and Testing Center of Agricultural and Livestock Products of Tibet, Lhasa 850000, P. R. China
| | - Huiyan Jia
- Ningbo Academy of Agricultural Sciences, Ningbo 315040, Zhengjiang, P. R. China
| | - Yuanshang Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Zhen Cao
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - J-Pablo Salvador
- Nanobiotechnology for Diagnostics Group, Instituto de Química Avanzada de Cataluña, IQAC-CSIC, C/ Jordi Girona, 18-26, 08034 Barcelona, Spain
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Avenida Monforte de Lemos, 3-5, Pavillion 11, Floor 0, 28029 Madrid, Spain
| | - Yongxin She
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Fen Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Jing Wang
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Maojun Jin
- Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Science, Beijing 100081, P. R. China
| | - Bruce D Hammock
- Department of Entomology & Nematology and the UC Davis Comprehensive Cancer Center, University of California, Davis, Davis, California 95616, United States
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9
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Lee HJ, Cho IS, Ju HJ, Jeong RD. Development of a reverse transcription droplet digital PCR assay for sensitive detection of peach latent mosaic viroid. Mol Cell Probes 2021; 58:101746. [PMID: 34102255 DOI: 10.1016/j.mcp.2021.101746] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/24/2021] [Accepted: 06/02/2021] [Indexed: 10/21/2022]
Abstract
Peach latent mosaic viroid (PLMVd) represents a continuing threat to peach tree production worldwide. In this study, a sensitive and accurate quantification of PLMVd in peach leaves was established using a reverse transcription droplet digital polymerase chain reaction (RT-ddPCR) assay. The quantitative linearity, accuracy, and sensitivity of RT-ddPCR for the detection of PLMVd were comparatively assessed to those of reverse-transcription real-time quantitative polymerase chain reaction (RT-qPCR) assay. The specificity assay shows no amplification in major peach viruses, apple chlorotic leaf spot virus and prunus necrotic ring spot virus and negative control. Furthermore, the levels of PLMVd transcripts determined using RT-ddPCR and RT-qPCR showed a high degree of linearity and quantitative correlation. Our results also indicated that the RT-ddPCR assay is at least two-fold more sensitive than qPCR and could therefore, be used to detect PLMVd in field samples. Moreover, optimization of RT-ddPCR was found to enhance the sensitivity of PLMVd detection in the peach leaf samples with low viral loads. In summary, the established RT-ddPCR assay represents a promising alternative method for the precise quantitative detection of PLMVd; it would be particularly applicable for diagnosing PLMVd infections in plant quarantine inspection and PLMVd-free certification program.
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Affiliation(s)
- Hyo-Jeong Lee
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea
| | - In-Sook Cho
- Horticultural and Herbal Crop Environment Division, National Institute of Horticultural and Herbal Science, RDA, Wanju, 55365, Republic of Korea
| | - Ho-Jong Ju
- Department of Agricultural Biology, College of Agriculture & Life Sciences, Jeonbuk National University, Jeonju-si, 54896, Republic of Korea
| | - Rae-Dong Jeong
- Department of Applied Biology, Institute of Environmentally Friendly Agriculture, Chonnam National University, Gwangju, 61185, Republic of Korea.
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10
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Digital PCR: What Relevance to Plant Studies? BIOLOGY 2020; 9:biology9120433. [PMID: 33266157 PMCID: PMC7760125 DOI: 10.3390/biology9120433] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 01/01/2023]
Abstract
Simple Summary Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics. Abstract Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.
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11
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Hou W, Li S, Massart S. Is There a "Biological Desert" With the Discovery of New Plant Viruses? A Retrospective Analysis for New Fruit Tree Viruses. Front Microbiol 2020; 11:592816. [PMID: 33329473 PMCID: PMC7710903 DOI: 10.3389/fmicb.2020.592816] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/29/2020] [Indexed: 12/13/2022] Open
Abstract
High throughput sequencing technologies accelerated the pace of discovery and identification of new viral species. Nevertheless, biological characterization of a new virus is a complex and long process, which can hardly follow the current pace of virus discovery. This review has analyzed 78 publications of new viruses and viroids discovered from 32 fruit tree species since 2011. The scientific biological information useful for a pest risk assessment and published together with the discovery of a new fruit tree virus or viroid has been analyzed. In addition, the 933 publications citing at least one of these original publications were reviewed, focusing on the biology-related information provided. In the original publications, the scientific information provided was the development of a detection test (94%), whole-genome sequence including UTRs (92%), local and large-scale epidemiological surveys (68%), infectivity and indicators experiments (50%), association with symptoms (25%), host range infection (23%), and natural vector identification (8%). The publication of a new virus is cited 2.8 times per year on average. Only 18% of the citations reported information on the biology or geographical repartition of the new viruses. These citing publications improved the new virus characterization by identifying the virus in a new country or continent, determining a new host, developing a new diagnostic test, studying genome or gene diversity, or by studying the transmission. Based on the gathered scientific information on the virus biology, the fulfillment of a recently proposed framework has been evaluated. A baseline prioritization approach for publishing a new plant virus is proposed for proper assessment of the potential risks caused by a newly identified fruit tree virus.
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Affiliation(s)
- Wanying Hou
- Key Laboratory of Tobacco Pest Monitoring Controlling and Integrated Management, Institute of Tobacco Research, Chinese Academy of Agricultural Sciences, Qingdao, China
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Shifang Li
- Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sebastien Massart
- Plant Pathology Laboratory, TERRA, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Leichtfried T, Reisenzein H, Steinkellner S, Gottsberger RA. Transmission studies of the newly described apple chlorotic fruit spot viroid using a combined RT-qPCR and droplet digital PCR approach. Arch Virol 2020; 165:2665-2671. [PMID: 32638117 PMCID: PMC7547948 DOI: 10.1007/s00705-020-04704-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/15/2020] [Indexed: 01/17/2023]
Abstract
The transmission of the apscaviroid tentatively named apple chlorotic fruit spot viroid (ACFSVd) was investigated using a one-step reverse-transcription (RT) droplet digital PCR assay for absolute quantification of the viroid, followed by quantification of relative standard curves by RT-qPCR. Our results indicate that ACFSVd is effectively transmitted by grafting, budding and seeds. No transmission has yet been observed to the viroid-inoculated pome fruit species Pyrus sp. and Cydonia sp. ACFSVd was detected in viruliferous aphids (Myzus persicae, Dysaphis plantaginea) and in codling moths (Cydia pomonella). The viroid was also detected systemically in the infected hemiparasitic plant Viscum album subsp. album (mistletoe).
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Affiliation(s)
- Thomas Leichtfried
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
| | - Helga Reisenzein
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
| | - Siegrid Steinkellner
- Institute of Plant Protection, University of Natural Resources and Life Sciences, 3430, Tulln an der Donau, Austria.
| | - Richard A Gottsberger
- Institute for Sustainable Plant Protection, Austrian Agency for Health and Food Safety, 1220, Vienna, Austria
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Baldi P, La Porta N. Molecular Approaches for Low-Cost Point-of-Care Pathogen Detection in Agriculture and Forestry. FRONTIERS IN PLANT SCIENCE 2020; 11:570862. [PMID: 33193502 PMCID: PMC7655913 DOI: 10.3389/fpls.2020.570862] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 09/29/2020] [Indexed: 05/14/2023]
Abstract
Early detection of plant diseases is a crucial factor to prevent or limit the spread of a rising infection that could cause significant economic loss. Detection test on plant diseases in the laboratory can be laborious, time consuming, expensive, and normally requires specific technical expertise. Moreover, in the developing countries, it is often difficult to find laboratories equipped for this kind of analysis. Therefore, in the past years, a high effort has been made for the development of fast, specific, sensitive, and cost-effective tests that can be successfully used in plant pathology directly in the field by low-specialized personnel using minimal equipment. Nucleic acid-based methods have proven to be a good choice for the development of detection tools in several fields, such as human/animal health, food safety, and water analysis, and their application in plant pathogen detection is becoming more and more common. In the present review, the more recent nucleic acid-based protocols for point-of-care (POC) plant pathogen detection and identification are described and analyzed. All these methods have a high potential for early detection of destructive diseases in agriculture and forestry, they should help make molecular detection for plant pathogens accessible to anyone, anywhere, and at any time. We do not suggest that on-site methods should replace lab testing completely, which remains crucial for more complex researches, such as identification and classification of new pathogens or the study of plant defense mechanisms. Instead, POC analysis can provide a useful, fast, and efficient preliminary on-site screening that is crucial in the struggle against plant pathogens.
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Affiliation(s)
- Paolo Baldi
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- *Correspondence: Paolo Baldi,
| | - Nicola La Porta
- IASMA Research and Innovation Centre, Fondazione Edmund Mach, Trento, Italy
- The EFI Project Centre on Mountain Forests (MOUNTFOR), San Michele a/Adige, Trento, Italy
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