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Greer SF, Surendran A, Grant M, Lillywhite R. The current status, challenges, and future perspectives for managing diseases of brassicas. Front Microbiol 2023; 14:1209258. [PMID: 37533829 PMCID: PMC10392840 DOI: 10.3389/fmicb.2023.1209258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/23/2023] [Indexed: 08/04/2023] Open
Abstract
The Brassica genus comprises the greatest diversity of agriculturally important crops. Several species from this genus are grown as vegetable and oil crops for food, animal feed and industrial purposes. In particular, B. oleracea has been extensively bred to give rise to several familiar vegetables (cabbage, broccoli, cauliflower, kale and Brussels Sprouts, etc.) that are grouped under seven major cultivars. In 2020, 96.4 million tonnes of vegetable brassicas were produced globally with a 10.6% increase over the past decade. Yet, like other crops, the production of brassicas is challenged by diseases among which, black rot, clubroot, downy mildew and turnip yellows virus have been identified by growers as the most damaging to UK production. In some cases, yield losses can reach 90% depending upon the geographic location of cultivation. This review aims to provide an overview of the key diseases of brassicas and their management practices, with respect to the biology and lifecycle of the causal pathogens. In addition, the existing controls on the market as well as those that are currently in the research and development phases were critically reviewed. There is not one specific control method that is effective against all the diseases. Generally, cultural practices prevent disease rather than reduce or eliminate disease. Chemical controls are limited, have broad-spectrum activity, are damaging to the environment and are rapidly becoming ineffective due to the evolution of resistance mechanisms by the pathogens. It is therefore important to develop integrated pest management (IPM) strategies that are tailored to geographic locations. Several knowledge gaps have been identified and listed in this review along with the future recommendations to control these four major diseases of brassicas. As such, this review paper will act as a guide to sustainably tackle pre-harvest diseases in Brassica crops to reduce food loss.
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Affiliation(s)
- Shannon F. Greer
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Arthy Surendran
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Carbon, Crop and Soils Group, SRUC, Edinburgh, United Kingdom
| | - Murray Grant
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Robert Lillywhite
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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2
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Botella JR. Point-of-Care DNA Amplification for Disease Diagnosis and Management. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:1-20. [PMID: 36027938 DOI: 10.1146/annurev-phyto-021621-115027] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Early detection of pests and pathogens is of paramount importance in reducing agricultural losses. One approach to early detection is point-of-care (POC) diagnostics, which can provide early warning and therefore allow fast deployment of preventive measures to slow down the establishment of crop diseases. Among the available diagnostic technologies, nucleic acid amplification-based diagnostics provide the highest sensitivity and specificity, and those technologies that forego the requirement for thermocycling show the most potential for use at POC. In this review, I discuss the progress, advantages, and disadvantages of the established and most promising POC amplification technologies. The success and usefulness of POC amplification are ultimately dependent on the availability of POC-friendly nucleic acid extraction methods and amplification readouts, which are also briefly discussed in the review.
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Affiliation(s)
- José R Botella
- Plant Genetic Engineering Laboratory, School of Agriculture and Food Sciences, University of Queensland, Brisbane, Australia;
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Sun K, Cai JF, Zhang Y, Mu YN, A SH, Shen YL, Yang LJ, Li HL. Heterogeneous Nitrogen Supply With High Frequency and Ramet Damage Increases the Benefits of Clonal Integration in Invasive Hydrocotyle vulgaris. FRONTIERS IN PLANT SCIENCE 2022; 13:825492. [PMID: 35574144 PMCID: PMC9100825 DOI: 10.3389/fpls.2022.825492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/29/2022] [Indexed: 05/14/2023]
Abstract
Nitrogen (N) deposition significantly affects the growth and the function of invasive clonal plants. However, the effects of heterogeneous N supply with different frequencies on the growth and the potential contribution of clonal integration in invasion plants are still unclear, especially in the complex environment considering ramet damage. To address this question, apical and basal ramets of the clonal invader Hydrocotyle vulgaris were connected or disconnected, N was added to the basal ramets with a high frequency, a low frequency, or no supply, and the total N quantity was the same for the different frequency. Furthermore, 8 aphids were placed on the apical ramets, and 30% of each leaf was cut off to cause damage. The connection between ramets significantly increased the biomass, total carbon (C), and total N of the basal and apical ramets. Higher frequency N supply significantly increased the biomass, total C, and total N of the basal ramets and the entire clonal fragment biomass. The damage had no significant effect on the growth of basal and apical ramets. Especially, under the high N frequency and ramet damage condition, the connection between ramets more significantly increased the biomass, total C, and total N of the apical ramets and the entire clonal fragment biomass. In addition, the uptake rates of 15 NH 4 + and 15 NO 3 - in H. vulgaris had no significant difference, and N supply increased the uptake rates of 15 NH 4 + and 15 NO 3 - of the basal ramets. Our results suggest that both higher frequency N supply and clonal integration are beneficial to the growth of H. vulgaris. Moreover, the heterogeneous N supply with high frequency and ramet damage increases the benefits of clonal integration in H. vulgaris. These findings improve our understanding of the response of clonal invader H. vulgaris to nitrogen deposition and ramet damage.
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Congdon BS, Webster CG, Severtson D, Spafford H. In-Field Capable Loop-Mediated Isothermal Amplification Detection of Spodoptera frugiperda (Lepidoptera: Noctuidae) Larvae Using a Rapid and Simple Crude Extraction Technique. JOURNAL OF ECONOMIC ENTOMOLOGY 2021; 114:2610-2614. [PMID: 34516635 DOI: 10.1093/jee/toab168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Indexed: 06/13/2023]
Abstract
Fall armyworm, Spodoptera frugiperda J.E. Smith (Lepidoptera: Noctuidae), is an economically important pest worldwide and has recently been identified in Australia. Morphological identification of S. frugiperda at early larval stages can be difficult often requiring expert microscopy analysis. Rapid and accurate in-field diagnosis is vital for management decision support and there are no tools currently available for this purpose. In this study, a sensitive, specific, and in-field capable loop-mediated isothermal amplification (LAMP) assay was developed to detect S. frugiperda larvae. A primer set based on a highly conserved region of the S. frugiperda cytochrome oxidase subunit 1 (COX1) gene provided detection within 30 min from both total DNA and crude extractions. The crude extraction technique of crushing 10 mg of S. frugiperda material in 50 µl ddH2O and further diluting the homogenate in ddH2O is rapid, simple, and does not require heat blocks, centrifuges, or special buffers increasing its utility as a field-based technique. The primer set detected as little as 24 pg of S. frugiperda DNA and did not cross-react with any other of the lepidopteran species tested that are easily confused with S. frugiperda in Australia. Therefore, this assay could be used in-field to correctly identify the presence of S. frugiperda and thereby greatly assist with timely management decisions.
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Affiliation(s)
- B S Congdon
- Primary Industries Development, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
| | - C G Webster
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
| | - D Severtson
- Primary Industries Development, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
| | - H Spafford
- Primary Industries Development, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
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Li X, Hu W, Li Y, Li Y, Chen S, Wang J. Development of an RT-LAMP assay for the detection of maize yellow mosaic virus in maize. J Virol Methods 2021; 300:114384. [PMID: 34856307 DOI: 10.1016/j.jviromet.2021.114384] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/12/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Maize is one of the most widely cultivated cereal crops worldwide. Maize yellow mosaic virus (MaYMV) (species Maize yellow mosaic virus, genus Polerovirus and family Luteoviridae) was first reported in maize from China. In this study, a one-step reverse-transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting MaYMV. The optimal concentrations of betaine, Mg2+ and dNTPs for the assay were 0 M, 1.4 mM and 6 mM, respectively, and the optimal reaction time was 50 min. Using total plant RNA as the template, the detection limit of the RT-LAMP assay for MaYMV was 1 pg, while that of RT-PCR was 100 pg, indicating that the RT-LAMP assay developed was 100 times more sensitive than RT-PCR. Importantly, the RT-LAMP assay successfully detected MaYMV using rapidly extracted crude RNA from infected maize as a template. In conclusion, the RT-LAMP assay developed was a rapid, specific, sensitive and low-cost method for the detection of MaYMV in field samples of maize.
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Affiliation(s)
- Xiaoqin Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Wenli Hu
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Yu Li
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Yan Li
- Yunnan Plant Protection and Quarantine Station, Kunming, 650034, China
| | - Suiyun Chen
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China
| | - Jianguang Wang
- School of Life Science, Biocontrol Engineering Research Center of Crop Diseases & Pests, Yunnan Province, Biocontrol Engineering Research Center of Plant Diseases & Pests, Yunnan University, Kunming, 650091, China.
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Salazar A, Ochoa-Corona FM, Olson JD, Babu B, Paret M. Probing Loop-Mediated Isothermal Amplification (LAMP) targeting two gene-fragments of rose rosette virus. PLoS One 2021; 16:e0256510. [PMID: 34843487 PMCID: PMC8629277 DOI: 10.1371/journal.pone.0256510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 11/12/2021] [Indexed: 01/13/2023] Open
Abstract
This study explores the development of Loop-mediated isothermal amplification (LAMP) for detection of rose rosette virus (RRV), a technique with the potential to be translated to rose nurseries. RRV is a negative-sense, single-stranded RNA virus which is a member of the genus Emaravirus (Family Fimoviridae) and the causal agent of the rose rosette disease (RRD). Although RRV symptoms are characteristics, early visual diagnosis of RRD can be misleading and confusing since it may appear like herbicide damage. Moreover, it may take incubation time for symptoms to appear after virus infection. Two sets of RRV gene sequences RNA3 and RNA4 were analyzed and two sets of four LAMP primers were designed. The direct antigen-capture method for direct trapping of RRV in plastic was used for RNA extraction followed by cDNA synthesis. RT-LAMP reactions were for 1 hour at 64°C (RRV-P3) and 66.5°C (RRV-P4) using either a thermocycler or a portable dry bath. RT-qLAMP was also optimized using DNA polymerase GspSSD LD using the same RRV sets of primers. RRV was detected in symptomatic and non-symptomatic RRD tissue from Oklahoma. The limit of detection (LoD) was 1pg/μL and 1 fg/μL using Bst 2.0 LAMP and GspSSD LD quantitative LAMP, respectively. In visual colorimetric pre- and post-reactions, the LoD was 10 pg/μL and 0.1 pg/μL using hydroxy naphthol blue (HNB, 120 μM) and SYBR green I (1:10 dilution), respectively. No cross-reactivity was detected in the RT-LAMP reaction testing cDNAs of eight commonly co-infecting rose viruses and one virus taxonomically related to RRV. Four different dyes were tested, and visible colorimetric reactions were obtained with RT-LAMP Bst 2.0 combined with SYBR I or HNB. RT-qLAMP with GspSSD2.0 offers LoD equal to RT-PCR and it is faster since it works with RNA directly.
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Affiliation(s)
- Andrea Salazar
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Institute for Biosecurity and Microbial Forensic, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
- Universidad de las Fuerzas Armadas- ESPE, Quito, Ecuador
| | - Francisco M. Ochoa-Corona
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Institute for Biosecurity and Microbial Forensic, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
- * E-mail:
| | - Jennifer D. Olson
- Oklahoma State University, Stillwater, Oklahoma, United States of America
- Department of Entomology and Plant Pathology, Stillwater, Oklahoma, United States of America
| | - Binoy Babu
- North Florida Research and Education Center, University of Florida, Quincy, Florida, United States America
| | - Mathews Paret
- North Florida Research and Education Center, University of Florida, Quincy, Florida, United States America
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Jones RAC, Sharman M, Trębicki P, Maina S, Congdon BS. Virus Diseases of Cereal and Oilseed Crops in Australia: Current Position and Future Challenges. Viruses 2021; 13:2051. [PMID: 34696481 PMCID: PMC8539440 DOI: 10.3390/v13102051] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/22/2022] Open
Abstract
This review summarizes research on virus diseases of cereals and oilseeds in Australia since the 1950s. All viruses known to infect the diverse range of cereal and oilseed crops grown in the continent's temperate, Mediterranean, subtropical and tropical cropping regions are included. Viruses that occur commonly and have potential to cause the greatest seed yield and quality losses are described in detail, focusing on their biology, epidemiology and management. These are: barley yellow dwarf virus, cereal yellow dwarf virus and wheat streak mosaic virus in wheat, barley, oats, triticale and rye; Johnsongrass mosaic virus in sorghum, maize, sweet corn and pearl millet; turnip yellows virus and turnip mosaic virus in canola and Indian mustard; tobacco streak virus in sunflower; and cotton bunchy top virus in cotton. The currently less important viruses covered number nine infecting nine cereal crops and 14 infecting eight oilseed crops (none recorded for rice or linseed). Brief background information on the scope of the Australian cereal and oilseed industries, virus epidemiology and management and yield loss quantification is provided. Major future threats to managing virus diseases effectively include damaging viruses and virus vector species spreading from elsewhere, the increasing spectrum of insecticide resistance in insect and mite vectors, resistance-breaking virus strains, changes in epidemiology, virus and vectors impacts arising from climate instability and extreme weather events, and insufficient industry awareness of virus diseases. The pressing need for more resources to focus on addressing these threats is emphasized and recommendations over future research priorities provided.
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Affiliation(s)
- Roger A. C. Jones
- UWA Institute of Agriculture, University of Western Australia, Crawley, WA 6009, Australia
| | - Murray Sharman
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, P.O. Box 267, Brisbane, QLD 4001, Australia;
| | - Piotr Trębicki
- Grains Innovation Park, Agriculture Victoria, Department of Jobs, Precincts and Regions, Horsham, VIC 3400, Australia; (P.T.); (S.M.)
| | - Solomon Maina
- Grains Innovation Park, Agriculture Victoria, Department of Jobs, Precincts and Regions, Horsham, VIC 3400, Australia; (P.T.); (S.M.)
| | - Benjamin S. Congdon
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia;
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Barton M, Parry H, Ward S, Hoffmann AA, Umina PA, van Helden M, Macfadyen S. Forecasting impacts of biological control under future climates: mechanistic modelling of an aphid pest and a parasitic wasp. Ecol Modell 2021. [DOI: 10.1016/j.ecolmodel.2021.109679] [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]
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9
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Congdon BS, Baulch JR, Coutts BA. Novel Sources of Turnip Yellows Virus Resistance in Brassica and Impacts of Temperature on Their Durability. PLANT DISEASE 2021; 105:2484-2493. [PMID: 33487015 DOI: 10.1094/pdis-10-20-2312-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Turnip yellows virus (TuYV; family Solemoviridae, genus Polerovirus) is the most widespread and economically damaging virus of canola (Brassica napus L.) production in Australia. However, no Australian commercial seed companies market TuYV-resistant canola cultivars, and little information is available on the susceptibility of those available. To identify potential sources of TuYV resistance, 100 B. napus accessions from the ERANET ASSYST diversity set were screened in the field and five of these were selected for further phenotyping via aphid inoculation. Furthermore, 43 Australian canola cultivars, six B. napus genotypes with previously reported resistance, and 33 B. oleracea and B. rapa cultivars were phenotyped. All Australian cultivars were susceptible except for 'ATR Stingray'. Stronger resistance to systemic TuYV infection (IR) was identified in diversity set accessions 'Liraspa-A', 'SWU Chinese 3', and 'SWU Chinese 5'. As indicated by lower relative enzyme-linked immunosorbent assay absorbance values (R-E405) in infected plants, resistance to TuYV accumulation (AR) often accompanied IR. Moderate IR was identified in four B. oleracea cultivars and one B. rapa cultivar. Very strong AR was identified in four B. oleracea cultivars and AR of some degree was common across many cultivars of this species tested. The impact of temperature during the inoculation access period or post-inoculation incubation on the resistance identified was examined. Infection rates were significantly higher in resistant B. napus genotypes when inoculated at 16°C than at 26°C, suggesting an increase in aphid transmission efficiency. IR in B. napus genotypes was strong when incubated at 16°C, but weakened at elevated temperatures with almost total breakdown in most genotypes at 30°C. However, infected plants of B. napus and B. oleracea genotypes with AR maintained lower R-E405 values than susceptible controls at all temperatures tested. Novel sources of resistance identified in this study offer potential as breeding material in Australia and abroad.
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Affiliation(s)
- Benjamin S Congdon
- Primary Industries Development, Department of Primary Industries and Regional Development, Kensington, Western Australia 6151, Australia
| | - Jonathan R Baulch
- Primary Industries Development, Department of Primary Industries and Regional Development, Kensington, Western Australia 6151, Australia
| | - Brenda A Coutts
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, Kensington, Western Australia 6151, Australia
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Genetic diversity and recombination between turnip yellows virus strains in Australia. Arch Virol 2021; 166:813-829. [PMID: 33481112 DOI: 10.1007/s00705-020-04931-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/06/2020] [Indexed: 01/24/2023]
Abstract
Disease outbreaks caused by turnip yellows virus (TuYV), a member of the genus Polerovirus, family Luteoviridae, regularly occur in canola and pulse crops throughout Australia. To understand the genetic diversity of TuYV for resistance breeding and management, genome sequences of 28 TuYV isolates from different hosts and locations were determined using high-throughput sequencing (HTS). We aimed to identify the parts of the genome that were most variable and clarify the taxonomy of viruses related to TuYV. Poleroviruses contain seven open reading frames (ORFs): ORF 0-2, 3a, and 3-5. Phylogenetic analysis based on the genome sequences, including isolates of TuYV and brassica yellows virus (BrYV) from the GenBank database, showed that most genetic variation among isolates occurred in ORF 5, followed by ORF 0 and ORF 3a. Phylogenetic analysis of ORF 5 revealed three TuYV groups; P5 group 1 and group 3 shared 45-49% amino acid sequence identity, and group 2 is a recombinant between the other two. Phylogenomic analysis of the concatenated ORFs showed that TuYV is paraphyletic with respect to BrYV, and together these taxa form a well-supported monophyletic group. Our results support the hypothesis that TuYV and BrYV belong to the same species and that the phylogenetic topologies of ORF 0, 3a and 5 are incongruent and may not be informative for species demarcation. A number of beet western yellow virus (BWYV)- and TuYV-associated RNAs (aRNA) were also identified by HTS for the first time in Australia.
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Reverse transcriptase loop-mediated isothermal amplification and reverse transcriptase recombinase amplification assays for rapid and sensitive detection of cardamom vein clearing virus. 3 Biotech 2020; 10:250. [PMID: 32420009 DOI: 10.1007/s13205-020-02238-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/28/2020] [Indexed: 10/24/2022] Open
Abstract
In the present study, two isothermal molecular assays viz. reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) and reverse transcriptase recombinase amplification (RT-RPA) were developed to detect the cardamom vein clearing virus (CdVCV) infecting cardamom. Assays were optimized for parameters like duration, temperature and concentration of magnesium sulfate, and betaine in the case of RT-LAMP and magnesium acetate in the case of RT-RPA. Detection limits of both assays were determined and compared with conventional RT-PCR and SYBR Green-based real-time RT-PCR. RT-LAMP was found 10,000 times additional sensitive than RT-PCR and one-tenth that of real-time RT-PCR. RT-RPA was found 1000 times additional sensitive than RT-PCR and one-hundredth that of real-time RT-PCR. Both assays were specific, rapid, and sensitive for detecting CdVCV. Compared to real-time RT-PCR, these assays are economical and can be employed in large scale screening of cardamom plants against CdVCV for the selection of virus-free plants.
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Naveen KP, Bhat AI. Development of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays for the detection of two novel viruses infecting ginger. J Virol Methods 2020; 282:113884. [PMID: 32442456 DOI: 10.1016/j.jviromet.2020.113884] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/14/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022]
Abstract
Our recent studies have shown the association of two novel viruses namely, ginger chlorotic fleck-associated virus 1 (GCFaV-1) and ginger chlorotic fleck-associated virus 2 (GCFaV-2) with chlorotic fleck disease of ginger. As ginger is propagated through vegetative means, the development of diagnostics would aid in the identification of virus-free plants. In the present study, reverse transcription loop-mediated isothermal amplification (RT-LAMP) and reverse transcription recombinase polymerase amplification (RT-RPA) assays were developed and validated for the quick detection of GCFaV-1 and GCFaV-2. The detection limits of viruses by these assays, when compared with conventional and real-time RT-PCR, showed that RT-LAMP was up to 1000 times more sensitive than conventional RT-PCR and one-hundredth that of real-time RT-PCR for both the viruses. The detection limit of RT-RPA for GCFaV-1 was up to 100 times more than that of RT-PCR and one-thousandth that of real-time RT-PCR. On the other hand, for detecting GCFaV-2, RT-RPA was found up to 1000 times more sensitive than conventional RT-PCR and one hundredth that of real-time RT-PCR. Based on the cost-effectiveness and duration, RT-LAMP and RT-RPA assays can be suggested for the rapid detection of both viruses.
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Affiliation(s)
- K P Naveen
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu, Kozhikode 673012, India
| | - A I Bhat
- Division of Crop Protection, ICAR-Indian Institute of Spices Research, Marikunnu, Kozhikode 673012, India.
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Panno S, Matić S, Tiberini A, Caruso AG, Bella P, Torta L, Stassi R, Davino S. Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology. PLANTS (BASEL, SWITZERLAND) 2020; 9:E461. [PMID: 32268586 PMCID: PMC7238132 DOI: 10.3390/plants9040461] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 04/02/2020] [Accepted: 04/02/2020] [Indexed: 01/14/2023]
Abstract
In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.
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Affiliation(s)
- Stefano Panno
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Slavica Matić
- Department of Agricultural, Forestry and Food Sciences, University of Turin, 10095 Turin, Italy;
| | - Antonio Tiberini
- Council for Agricultural Research and Economics, Research Center for Plant Protection and Certification, 00156 Rome, Italy;
| | - Andrea Giovanni Caruso
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Patrizia Bella
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Livio Torta
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Raffaele Stassi
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
| | - Salvatore Davino
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy; (A.G.C.); (P.B.); (L.T.); (R.S.)
- Institute for Sustainable Plant Protection, National Research Council (IPSP-CNR), 10135 Turin, Italy
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Congdon BS, Baulch JR, Coutts BA. Impact of Turnip yellows virus infection on seed yield of an open-pollinated and hybrid canola cultivar when inoculated at different growth stages. Virus Res 2019; 277:197847. [PMID: 31887329 DOI: 10.1016/j.virusres.2019.197847] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 11/18/2019] [Accepted: 12/20/2019] [Indexed: 10/25/2022]
Abstract
Turnip yellows virus (TuYV; family Luteoviridae, genus Polerovirus) is the most economically damaging virus infecting canola (Brassica napus) in the south-west Australian grainbelt. However, the impact of TuYV infection at different growth stages on canola seed yield has not been examined. This information is vital for implementing targeted management strategies. Four glasshouse experiments were conducted to examine seed yield losses incurred by an open-pollinated (ATR Bonito) and hybrid (Hyola® 404RR) canola cultivar when aphid-inoculated with TuYV at GS12 (two leaves unfolded), GS17 (seven leaves unfolded), GS30 (beginning of stem elongation) and GS65 (full flowering). When inoculated at GS12 and GS17, cv. Bonito plants incurred 30 % and 36 % seed yield losses, respectively, compared to healthy plants. Similarly, cv. 404RR incurred 41 % and 26 % seed yield losses at GS12 and GS17, respectively. However, when inoculated at GS30, whilst cv. Bonito plants incurred a 26 % seed yield loss, cv. 404RR incurred no significant loss. Neither cultivar incurred seed yield losses from inoculation at GS65. Additional information was collected from these experiments to improve sampling protocols to enhance TuYV detection, with a molecular and serological technique. When canola plants were at pre-flowering growth stages, TuYV was reliably detected 7-14 days after inoculation (DAI) in the youngest leaf. Once flowering had begun, TuYV was consistently detected 7-14 DAI in petals and flower buds. In contrast, regardless of growth stage, testing the oldest leaf regularly resulted in delayed detection or false negatives. Information generated in this study helps to quantify the value of management strategies targeted at preventing TuYV spread in pre-flowering canola crops and ultimately increase the efficiency of resource use.
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Affiliation(s)
- B S Congdon
- Industry and Economic Development, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia.
| | - J R Baulch
- Industry and Economic Development, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
| | - B A Coutts
- Sustainability and Biosecurity, Department of Primary Industries and Regional Development, 3 Baron-Hay Court, Kensington, Western Australia, 6151, Australia
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Qin Y, Chen G, Zhang C, Wang Y, Zhou J. Development of loop-mediated isothermal amplification combined with a chromatographic lateral-flow dipstick for rapid detection of Chattonella marina. HARMFUL ALGAE 2019; 89:101666. [PMID: 31672231 DOI: 10.1016/j.hal.2019.101666] [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: 05/19/2019] [Revised: 09/10/2019] [Accepted: 09/14/2019] [Indexed: 06/10/2023]
Abstract
Harmful algal blooms caused by Chattonella marina recently have caused severe negative effect on coastal economy worldwide, with increased occurrence frequency and scale. It is therefore vital to establish new methods for rapid detection of this alga. In this study, the internal transcribed spacer (ITS) sequence was used as the target gene for molecular detection of C. marina. First, four loop-mediated isothermal amplification (LAMP) primers were designed based on the six regions of ITS, and the LAMP reaction system was established using these primers. Next, a probe was designed to detect the LAMP products by lateral-flow dipstick (LFD). Finally, a new method for rapid and sensitive detection of C. marina that is referred to as LAMP-LFD was established. The LAMP reaction system, amplification time, and amplification temperature were particularly optimized. The optimal parameters are as follows: Mg2+ concentration, 10 mM;dNTP concentration, 1.2 mM;ratio of internal primer concentration to outer primer concentration, 8:1;reaction time, 60 min;and reaction temperature, 60 °C. Both specificity and sensitivity were tested using the optimized LAMP reaction system in combination with LFD (LAMP-LFD). The established LAMP-LFD displayed good specificity and no cross reaction was detected with non-target algal species. The detection limit of LAMP-LFD was 3.4 × 10-4 ng μL-1 (3.4 × 10-4 ng per reaction) for the genomic DNA of target algae, and 1.3 copies μL-1 (1.3 copies per reaction) for the plasmid DNA containing the target ITS. Sensitivity tests using genomic DNA and plasmid DNA as templates consistently revealed that LAMP-LFD is 100 times more sensitive than regular PCR. The established LAMP-LFD was applied to analyze the simulated samples and the results showed that the detection limit of LAMP-LFD could reach 1 cell mL-1. LAMP-LFD also demonstrated good specificity and sensitivity in the analysis of natural samples. The whole procedure of LAMP-LFD could be completed within 1.5 h. Taken together, the LAMP-LFD assay developed here is characterized by simplicity, high specificity and sensitivity, and rapidity and therefore is promising for rapid detection of C. marina.
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Affiliation(s)
- Yue Qin
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Weihai, 264209, PR China
| | - Jin Zhou
- Division of Ocean Science and Technology, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, PR China
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16
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Application of Loop-Mediated Isothermal Amplification in an Early Warning System for Epidemics of an Externally Sourced Plant Virus. PLANTS 2019; 8:plants8050139. [PMID: 31137835 PMCID: PMC6572431 DOI: 10.3390/plants8050139] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 05/16/2019] [Accepted: 05/22/2019] [Indexed: 11/18/2022]
Abstract
Restricting Turnip yellows virus (TuYV) spread in canola (Brassica napus) crops often relies upon the application of systemic insecticides to protect young vulnerable plants from wide-scale green-peach aphid (GPA; Myzus persicae) colonization and subsequent virus infection. For these to be applied at the optimal time to ensure they prevent epidemics, growers would need to be forewarned of incoming viruliferous aphid migration and colonization. This study was conducted to field validate a loop-mediated isothermal amplification (LAMP) protocol designed to detect TuYV in aphids caught on traps and develop an early warning system for TuYV epidemics. Double-sided yellow sticky traps were deployed at 30 sites sown with canola over a two-year period in the south-west Australian grainbelt. Using LAMP, the percentage (%) of trap sides with TuYV-carrying aphids was measured and related to TuYV infection incidence in the adjacent crop. When TuYV was detected in aphids on >30% trap sides in a six-week period from pre-emergence to GS15 (five-leaf stage), TuYV reached >60% crop incidence by GS30 (beginning of stem elongation). Whereas, TuYV detection in aphids on ≤15% trap sides during this period was associated with ≤6% TuYV incidence by GS30. Furthermore, when large numbers of aphids, including GPA, were caught during this period but no TuYV was detected in them, minimal TuYV spread (≤5%) occurred in the crop by GS30. Therefore, the LAMP TuYV protocol can be used in an early warning system for TuYV epidemics by providing detection of initial viruliferous aphid migration into a canola crop before they establish colonies throughout the crop and spread virus. This would enable proactive, non-prophylactic, and thereby more effective systemic insecticide applications to minimize seed yield and quality losses due to early season TuYV infection.
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Filardo FF, Thomas JE, Webb M, Sharman M. Faba bean polerovirus 1 (FBPV-1); a new polerovirus infecting legume crops in Australia. Arch Virol 2019; 164:1915-1921. [PMID: 30993462 DOI: 10.1007/s00705-019-04233-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/08/2019] [Indexed: 11/28/2022]
Abstract
A new polerovirus species with the proposed name faba bean polerovirus 1 (FBPV-1) was found in winter legume crops and weeds in New South Wales, Australia. We describe the complete genome sequence of 5,631 nucleotides, containing all putative open reading frames, from two isolates, one from faba bean (Vicia faba) and one from chickpea (Cicer arietinum). FBPV-1 has a genome organization typical of poleroviruses with six open reading frames. However, recombination analysis strongly supports a recombination event in which the 5' portion of FBPV-1, which encodes for proteins P0, P1 and P1-P2, appears to be from a novel parent with a closest nucleotide identity of only 66% to chickpea chlorotic stunt virus. The 3' portion of FBPV-1 encodes for proteins P3, P4 and P3-P5 and shares 94% nucleotide identity to a turnip yellows virus isolate from Western Australia.
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Affiliation(s)
- Fiona F Filardo
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia.
| | - John E Thomas
- The University of Queensland, Queensland Alliance for Agriculture and Food Innovation, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Matthew Webb
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia
| | - Murray Sharman
- Queensland Department of Agriculture and Fisheries, Ecosciences Precinct, GPO Box 267, Brisbane, QLD, 4001, Australia
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