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Fernandez I Marti A, Parungao M, Hollin J, Selimotic B, Farrar G, Seyler T, Anand A, Ahmad R. A Novel, Precise and High-Throughput Technology for Viroid Detection in Cannabis (MFDetect TM). Viruses 2023; 15:1487. [PMID: 37515174 PMCID: PMC10385567 DOI: 10.3390/v15071487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Hop latent viroid (HLVd) is a severe disease of cannabis, causing substantial economic losses in plant yield and crop value for growers worldwide. The best way to control the disease is early detection to limit the spread of the viroid in grow facilities. This study describes MFDetectTM as a rapid, highly sensitive, and high-throughput tool for detecting HLVd in the early stages of plant development. Furthermore, in the largest research study conducted so far for HLVd detection in cannabis, we compared MFDetectTM with quantitative RT-PCR in a time course experiment using different plant tissues, leaves, petioles, and roots at different plant developmental stages to demonstrate both technologies are comparable. Our study found leaf tissue is a suitable plant material for HLVd detection, with the viroid titer increasing in the infected leaf tissue with the age of plants. The study showed that other tissue types, including petiole and roots, were equally sensitive to detection via MFDetectTM. The assay developed in this research allows the screening of thousands of plants in a week. The assay can be scaled easily to provide growers with a quick turnaround and a cost-effective diagnostic tool for screening many plants and tissue types at different stages of development.
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Affiliation(s)
- Angel Fernandez I Marti
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Marcus Parungao
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Jonathan Hollin
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Berin Selimotic
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Graham Farrar
- Glass House Farms, 645 W Laguna Road, Camarillo, CA 93012, USA
| | - Tristan Seyler
- Glass House Farms, 645 W Laguna Road, Camarillo, CA 93012, USA
| | - Ajith Anand
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
| | - Riaz Ahmad
- MyFloraDNA, Inc., 1451 River Park Dr., Sacramento, CA 95815, USA
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Uchiyama S, Imamura Y, Matsuura T. A thermal cycler-based, homogenization-free plant total nucleic acid extraction method for plant viruses and viroids assay. J Virol Methods 2023; 313:114666. [PMID: 36539042 DOI: 10.1016/j.jviromet.2022.114666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/13/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022]
Abstract
In this study, we report a plant total nucleic acid (TNA) extraction method for nucleic acid (NA)-based assays of plant viruses and viroids. This method combines NA release by incubating sliced plant tissue in solution and NA purification using silica spin column. The method is performed using a thermal cycler and microcentrifuge and does not involve tissue homogenization. For a wide range of plant species, TNA can be extracted from petioles, midribs, and stems, in 30 min. PCR/RT-PCR assays using extracts from this method detected all three DNA viruses, 14 RNA viruses, and 4 viroids tested and plant internal controls were also available. This method does not involve hazardous chemicals, is cost-effective. The method is readily implemented in various laboratories, a simple, rapid, and labor-saving option for NA-based assays of plant viruses and viroids.
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Affiliation(s)
- Shuichi Uchiyama
- Narita Sub-station, Yokohama Plant Protection Station, 2159, Aza Tennamino, Komaino, Narita 282-0021, Japan.
| | - Yuya Imamura
- Tsukuba Farm, Yokohama Plant Protection Station, 1-7, Nagamine, Tsukuba 305-0052, Japan
| | - Takayuki Matsuura
- Research Division, Yokohama Plant Protection Station, 1-16-10, Shin Yamashita, Naka-ku, Yokohama 231-0801, Japan
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PCR-DGGE Analysis Proves the Suppression of Rhizoctonia and Sclerotium Root Rot Due to Successive Inoculations. J Fungi (Basel) 2022; 8:jof8020133. [PMID: 35205888 PMCID: PMC8876646 DOI: 10.3390/jof8020133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/23/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
The soil-borne pathogens Rhizoctonia solani and Sclerotium rolfsii have emerged as major pathogens of radish (Raphanus sativus) worldwide. The induction of soil suppressive of radish root rot disease was evaluated in soil repeatedly inoculated with R. solani, nonpathogenic binucleate Rhizoctonia sp. AG-A W1 (BNR) and S. rolfsii. The repeated inoculations of soil with R. solani and BNR significantly suppressed the disease severity of R. solani and S. rolfsii compared to the control. In contrast, the repeated inoculation of soil with S. rolfsii significantly suppressed only the pathogen, S. rolfsii. The community structure was examined using PCR-DGGE (polymerase chain reaction denaturing gradient gel electrophoresis) method. The bands of Trichoderma sp. were observed in the first, second and third inoculations of the soil with BNR. Similarly, bands of Trichoderma sp. were observed in the second and third inoculations of the soil with S. rolfsii and R. solani. Compared to the control, disease severity was significantly reduced in the soil repeatedly inoculated with S. rolfsii and R. solani . In conclusion, Trichoderma species were accumulated in specific patterns depending on the applied fungal inoculum in the suppressive soil.
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Hataya T. An Improved Method for the Extraction of Nucleic Acids from Plant Tissue without Grinding to Detect Plant Viruses and Viroids. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122683. [PMID: 34961154 PMCID: PMC8708111 DOI: 10.3390/plants10122683] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 06/14/2023]
Abstract
Gene amplification techniques such as polymerase chain reaction (PCR) are widely used for the diagnosis of plant diseases caused by viruses and viroids. It is preferable that sample preparation methods for PCR or reverse transcription (RT) PCR are rapid, straightforward, and inexpensive. We previously reported a method for the extraction of nucleic acids without mechanical tissue grinding using a buffer containing potassium ethyl xanthogenate (PEX) to detect viroid RNAs. In the present report, the previous PEX method was improved and simplified. In the simplified PEX (SPEX) method, the process of PEX buffer treatment for plant cell wall disruption is improved to one step of incubation at 80 °C for 10 min, instead of three steps that took more than 26 min at 65 °C in the previous method. Total nucleic acids could be extracted from fresh, frozen, or dried leaves of a cultivar or wild species of tobacco, tomato, citron, hop plants, and pericarps of persimmon fruits by the SPEX method. Several RNA viruses and viroids were successfully detected from the extracted nucleic acids together with an internal mRNA by RT-PCR. The SPEX method may be useful for detecting not only viruses and viroids, but also other plant pathogens.
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Affiliation(s)
- Tatsuji Hataya
- Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
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Molecular and biological characterization of citrus bent leaf viroid from Malaysia. Mol Biol Rep 2021; 49:1581-1586. [PMID: 34773552 DOI: 10.1007/s11033-021-06930-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/02/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND A 328-nucleotide variant of citrus bent leaf viroid (CBLVd) was characterized by citrus varieties in Malaysia. After the first report in Malaysia, the emerging CBLVd was detected in five citrus species, namely Citrofortunella microcarpa, Citrus aurantifolia, Citrus hystrix, Citrus maxima, and Citrus sinensis. METHODS AND RESULTS CBLVd was detected in 23 out of 133 symptomatic samples through RT-PCR. Sequence analysis of the RT-PCR amplicons from this study showed 99-100% sequence identity to the reference CBLVd Jp isolate and CBLVd isolates reported in Malaysia. Inoculation of sap, obtained from a CBLVd positive sample, into 6-month old healthy C. microcarpa seedlings showed symptoms of slight leaf bending, reduced leaf size of matured leaves, and mild mosaic between 4 to 6 months after inoculation. Moreover, the observed symptoms of chlorosis, midvein necrosis, leaf rolling, and smalling of leaves in calamondin, C. microcarpa (Bunge) Wijnands, were not reported in earlier studies and opened a new avenue for the study of symptomology. The mechanical transmissibility of CBLVd in the inoculated seedlings was reconfirmed by RT-PCR assay and sequencing. CONCLUSIONS Based on the results, the sequence similarity of CBLVd isolates from different areas of Malaysia showed no significant difference among each other and the reference isolate. The CBLVd is mechanically transmissible and could produce variable symptoms in different hosts.
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Hataya T, Naoi T. Precisely Monomeric Linear RNAs of Viroids Belonging to Pospiviroid and Hostuviroid Genera Are Infectious Regardless of Transcription Initiation Site and 5'-Terminal Structure. Cells 2021; 10:cells10112971. [PMID: 34831194 PMCID: PMC8616387 DOI: 10.3390/cells10112971] [Citation(s) in RCA: 3] [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: 09/13/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/16/2022] Open
Abstract
Infectious dimeric RNA transcripts are a powerful tool for reverse genetic analyses in viroid studies. However, the construction of dimeric cDNA clones is laborious and time consuming, especially in mutational analyses by in vitro mutagenesis. In this study, we developed a system to synthesize a precisely monomeric linear RNA that could be transcribed in vitro directly from the cDNA clones of four viroid species. The cDNA clones were constructed such that RNA transcription was initiated at the guanine nucleotide of a predicted processing and ligation site in the viroid replication process. Although the transcribed RNAs were considered to possess 5′-triphosphate and 3′-hydroxyl termini, the RNA transcripts were infectious even without in vitro modifications. Additionally, infectivity was detected in the monomeric RNA transcripts, in which transcription was initiated at guanine nucleotides distinct from the predicted processing/ligation site. Moreover, monomeric viroid RNAs bearing 5′-monophosphate, 5′-hydroxyl, or 5′-capped termini were found to be infectious. Northern blot analysis of the pooled total RNA of the plants inoculated with the 5′-terminal modified RNA of potato spindle tuber viroid (PSTVd) indicated that maximum PSTVd accumulation occurred in plants with 5′-monophosphate RNA inoculation, followed by the plants with 5′-triphosphate RNA inoculation. Our system for synthesizing an infectious monomeric linear viroid RNA from a cDNA clone will facilitate mutational analyses by in vitro mutagenesis in viroid research.
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Affiliation(s)
- Tatsuji Hataya
- Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan;
- Correspondence:
| | - Takashi Naoi
- Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan;
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Naoi T, Hataya T. Tolerance Even to Lethal Strain of Potato Spindle Tuber Viroid Found in Wild Tomato Species Can Be Introduced by Crossing. PLANTS 2021; 10:plants10030575. [PMID: 33803660 PMCID: PMC8003082 DOI: 10.3390/plants10030575] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]
Abstract
To date, natural resistance or tolerance, which can be introduced into crops by crossing, to potato spindle tuber viroid (PSTVd) has not been reported. Additionally, responses to PSTVd infection in many wild tomato species, including some species that can be crossed with PSTVd-susceptible cultivated tomatoes (Solanum lycopersicum var. lycoperaicum), have not been ascertained. The aim of this study was to evaluate responses to PSTVd infection including resistance and tolerance. Accordingly, we inoculated several cultivated and wild tomato species with intermediate and lethal strains of PSTVd. None of the host plants exhibited sufficient resistance to PSTVd to render systemic infection impossible; however, these plants displayed other responses, including tolerance. Further analysis of PSTVd accumulation revealed low accumulation of PSTVd in two wild species, exhibiting high tolerance, even to the lethal strain. Additionally, F1 hybrids generated by crossing a PSTVd-sensitive wild tomato (Solanum lycopersicum var. cerasiforme) with these wild relatives also exhibited tolerance to the lethal PSTVd strain, which is accompanied by low PSTVd accumulation during early infection. These results indicate that the tolerance toward PSTVd in wild species is a dominant trait and can be utilized for tomato breeding by crossing.
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Affiliation(s)
- Takashi Naoi
- Pathogen-Plant Interactions, Graduate School of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan;
| | - Tatsuji Hataya
- Pathogen-Plant Interactions, Research Faculty of Agriculture, Hokkaido University, Kita 9, Nishi 9, Kita-ku, Sapporo 060-8589, Japan
- Correspondence:
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Toda T, Hanesaka S, Shishido K, Fuji SI, Furuya H. Development of specific primers for Fusarium oxysporum causing damping off of Lilium formolongi. J Genet Eng Biotechnol 2020; 18:1. [PMID: 31903514 PMCID: PMC6943095 DOI: 10.1186/s43141-019-0015-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/21/2019] [Indexed: 11/10/2022]
Abstract
Primers specific for the hypothetical forma specialis of Fusarium oxysporum were designed to amplify DNA from this pathogenic fungus that infects plants including lilies. The F. oxysporum sequence between the transposal elements han and hop was used for primer design. Three primer pairs designed from this region were confirmed as specific for 24 isolates of F. oxysporum pathogenic to lilies, except for one pathogenic isolates as extraordinary. No amplification was observed from F. oxysporum non-pathogenic to lily, from 12 forma specialis, and 14 fungi and oomycetes concerned with Liliaceae plants. We propose that specific primers designed from this region will be useful to detect isolates of F. oxysporum that are pathogenic to lilies.
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Affiliation(s)
- Takeshi Toda
- Department of Bioproduction Science, Faculty of Bioresource Science, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan.
| | - Shun Hanesaka
- Department of Bioproduction Science, Faculty of Bioresource Science, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
| | - Kuniaki Shishido
- Fukushima Prefecture Office, 2-16 Sugitsuma-cho, Fukushima, 960-8670, Japan
| | - Shin-Ichi Fuji
- Department of Bioproduction Science, Faculty of Bioresource Science, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
| | - Hiromitsu Furuya
- Department of Bioproduction Science, Faculty of Bioresource Science, Akita Prefectural University, 241-438 Kaidobata-Nishi, Shimoshinjo-Nakano, Akita, 010-0195, Japan
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Molecular diversity among viroids infecting chrysanthemum in India. Virus Genes 2017; 53:636-642. [PMID: 28527099 DOI: 10.1007/s11262-017-1468-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 05/16/2017] [Indexed: 10/19/2022]
Abstract
Association of Chrysanthemum stunt viroid (CSVd) and Chrysanthemum chlorotic mottle viroid (CChMVd) with the Chrysanthemum plants exhibiting severe stunting, distinct yellow leaf mottling, and chlorosis was detected in the main chrysanthemum-growing regions of India. Sequence analysis of 90 cDNA clones obtained for CSVd and CChMVd, representing the chrysanthemum-growing regions of India, revealed the high degree of sequence variation throughout the genome under natural conditions. Additionally, all the analyzed CChMVd clones revealed the presence of UUUC in the tetraloop, a signature of symptomatic variants in susceptible cultivars. Phylogenetic analysis revealed that Indian CSVd is closely related to European isolates from ornamentals, whereas CChMVd clustered along with the isolates reported from the East Asian countries.
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Toda T, Iwasa A, Fuji S, Furuya H. Widespread Occurrence of Pythium arrhenomanes Pathogenic to Rice Seedlings Around Japanese Rice Fields. PLANT DISEASE 2015; 99:1823-1831. [PMID: 30699504 DOI: 10.1094/pdis-01-15-0124-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In Japan, rice seedlings grown in nurseries and used for transplanting are subject to a damping-off disease caused by Pythium spp. In this study, 148 isolates of Pythium spp. were obtained from rice seedlings in 39 locations of northern Japan. Among the isolates, 137 were identified as Pythium arrhenomanes using polymerase chain reaction (PCR) with species-specific primers, DNA sequencing analyses of the internal transcribed regions of ribosomal DNA, and the morphologies of oogonia, antheridia, oospores, and zoosporangia. Inoculation tests showed that the isolates identified as P. arrhenomanes were pathogenic to rice seedlings and parasitic to southern crabgrass with only minor damage. P. arrhenomanes was reisolated from the roots of both rice seedlings and southern crabgrass. Poaceae weeds, hosts of Pythium spp., grow in and around nurseries and in ridges surrounding rice fields. To detect Pythium spp., 188 Poaceae weeds were collected from 37 locations in Akita Prefecture. P. arrhenomanes was frequently detected in 164 weed roots from all locations by PCR using species-specific primers. Thus, we determined that P. arrhenomanes exists in and around rice seedling nurseries and rice fields, and that it is much more widely distributed than previously recognized in northern Japan.
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Affiliation(s)
- Takeshi Toda
- Faculty of Biological Resources, Akita Prefectural University, Shimo-shinjo, Akita 010-0195, Japan
| | - Akinori Iwasa
- Faculty of Biological Resources, Akita Prefectural University, Shimo-shinjo, Akita 010-0195, Japan
| | - Shinichi Fuji
- Faculty of Biological Resources, Akita Prefectural University, Shimo-shinjo, Akita 010-0195, Japan
| | - Hiromitsu Furuya
- Faculty of Biological Resources, Akita Prefectural University, Shimo-shinjo, Akita 010-0195, Japan
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Cho WK, Jo Y, Jo KM, Kim KH. A current overview of two viroids that infect chrysanthemums: Chrysanthemum stunt viroid and Chrysanthemum chlorotic mottle viroid. Viruses 2013; 5:1099-113. [PMID: 23594461 PMCID: PMC3705267 DOI: 10.3390/v5041099] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 04/08/2013] [Accepted: 04/08/2013] [Indexed: 11/17/2022] Open
Abstract
The chrysanthemum (Dendranthema X grandiflorum) belongs to the family Asteraceae and it is one of the most popular flowers in the world. Viroids are the smallest known plant pathogens. They consist of a circular, single-stranded RNA, which does not encode a protein. Chrysanthemums are a common host for two different viroids, the Chrysanthemum stunt viroid (CSVd) and the Chrysanthemum chlorotic mottle viroid (CChMVd). These viroids are quite different from each other in structure and function. Here, we reviewed research associated with CSVd and CChMVd that covered disease symptoms, identification, host range, nucleotide sequences, phylogenetic relationships, structures, replication mechanisms, symptom determinants, detection methods, viroid elimination, and development of viroid resistant chrysanthemums, among other studies. We propose that the chrysanthemum and these two viroids represent convenient genetic resources for host-viroid interaction studies.
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Affiliation(s)
- Won Kyong Cho
- Department of Agricultural Biotechnology, Plant Genomics and Breeding Institute, Institute for Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul 151-921, Korea.
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SUZUKI F, FUJI S, KOBA A, NAKAJIMA T, ARAI M. Analysis of genetic diversity and population structure in Pyricularia oryzae collected from western Japan using SSR markers. ACTA ACUST UNITED AC 2012. [DOI: 10.3186/jjphytopath.78.10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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Murcia N, Serra P, Olmos A, Duran-Vila N. A novel hybridization approach for detection of citrus viroids. Mol Cell Probes 2008; 23:95-102. [PMID: 19162174 DOI: 10.1016/j.mcp.2008.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Revised: 12/17/2008] [Accepted: 12/24/2008] [Indexed: 10/21/2022]
Abstract
Citrus plants are natural hosts of several viroid species all belonging to the family Pospiviroidae. Previous attempts to detect viroids from field-grown species and cultivars yielded erratic results unless analyses were performed using Etrog citron a secondary bio-amplification host. To overcome the use of Etrog citron a number of RT-PCR approaches have been proposed with different degrees of success. Here we report the suitability of an easy to handle northern hybridization protocol for viroid detection of samples collected from field-grown citrus species and cultivars. The protocol involves: (i) Nucleic acid preparations from bark tissue samples collected from field-grown trees regardless of the growing season and storage conditions; (ii) Separation in 5% PAGE or 1% agarose, blotting to membrane and fixing; (iii) Hybridization with viroid-specific DIG-labelled probes and detection with anti-DIG-alkaline phosphatase conjugate and autoradiography with the CSPD substrate. The method has been tested with viroid-infected trees of sweet orange, lemon, mandarin, grapefruit, sour orange, Swingle citrumello, Tahiti lime and Mexican lime. This novel hybridization approach is extremely sensitive, easy to handle and shortens the time needed for reliable viroid indexing tests. The suitability of PCR generated DIG-labelled probes and the sensitivity achieved when the samples are separated and blotted from non-denaturing gels are discussed.
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Affiliation(s)
- N Murcia
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, 46113 Moncada, Valencia, Spain
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Aldaghi M, Massart S, Dutrecq O, Bertaccini A, Jijakli MH, Lepoivre P. A simple and rapid protocol of crude DNA extraction from apple trees for PCR and real-time PCR detection of 'Candidatus Phytoplasma mali'. J Virol Methods 2008; 156:96-101. [PMID: 19010357 DOI: 10.1016/j.jviromet.2008.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 10/01/2008] [Accepted: 10/07/2008] [Indexed: 11/16/2022]
Abstract
Different PCR protocols have been established for detection of European fruit trees phytoplasmas; however the majority of the procedures for extracting phytoplasma DNA are complex, time consuming, and expensive, with a risk of contamination or loss of target DNA. In present study, a crude extract preparation method previously used to detect other plant pathogens was adapted to samples from apple trees infected by 'Candidatus Phytoplasma mali'. End-point and real-time PCR detection of 'Ca. P. mali' were used to compare this extraction procedure with an established method for efficient extraction of purified DNA. The crude extract proved fully adequate for phytoplasma detection in samples from 86 in vitro and 35 in vivo apple shoots or plants and 10 periwinkle plants. High inter- and intra-run reproducibility was obtained for phytoplasma detection with different TaqMan MGB- or SYBR Green-based real-time PCR protocols applied to the crude extracts. Real-time PCR applied to serially diluted crude and purified extracts revealed the same phytoplasma detection limit (dilution up to 10(5)). All results confirm the suitability of this simple, quick, efficient extraction technique for accurate detection of 'Ca. P. mali' in different types of apple and periwinkle samples.
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Affiliation(s)
- M Aldaghi
- Plant Pathology Unit, Gembloux Agricultural University (FUSAGx), Passage des déportés 2, 5030 Gembloux, Belgium
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Pest risk assessment made by France on Hop stunt viroid (HSVd) considered by France as harmful in the French overseas department of Réunion - Scientific Opinion of the Panel on Plant Health. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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17
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Pest risk assessment made by France on Citrus exocortis viroid (CEVd) considered by France as harmful in French overseas department of Réunion - Scientific Opinion of the Panel on Plant Health. EFSA J 2008. [DOI: 10.2903/j.efsa.2008.685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Suga H, Karugia GW, Ward T, Gale LR, Tomimura K, Nakajima T, Miyasaka A, Koizumi S, Kageyama K, Hyakumachi M. Molecular characterization of the Fusarium graminearum species complex in Japan. PHYTOPATHOLOGY 2008; 98:159-66. [PMID: 18943192 DOI: 10.1094/phyto-98-2-0159] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Members of the Fusarium graminearum species complex are important cereal pathogens worldwide and belong to one of at least nine phylogenetically distinct species. We examined 298 strains of the F. graminearum species complex collected from wheat or barley in Japan to determine the species and trichothecene chemotype. Phylogenetic analyses and species-diagnostic polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLPs) revealed the presence and differential distribution of F. graminearum sensu stricto (s. str.) and F. asiaticum in Japan. F. graminearum s. str. is predominant in the north, especially in the Hokkaido area, while F. asiaticum is predominant in southern regions. In the Tohoku area, these species co-occurred. Trichothecene chemotyping of all strains by multiplex PCR revealed significantly different chemotype compositions of these species. All 50 strains of F. graminearum s. str. were of a 15- or 3-acetyl deoxynivalenol type, while 173 (70%) out of 246 strains of F. asiaticum were of a nivalenol type. The possibility of gene flow between the two species was investigated by use of 15 PCR-RFLP markers developed in this study. However, no obvious hybrids were detected from 98 strains examined, including strains collected from regions where both species co-occur.
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Affiliation(s)
- H Suga
- Life Science Research Center, Gifu University, Yanagido, Gifu, Japan.
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19
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Garmaroodi HS, Taga M. Duplication of a conditionally dispensable chromosome carrying pea pathogenicity (PEP) gene clusters in Nectria haematococca. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2007; 20:1495-504. [PMID: 17990957 DOI: 10.1094/mpmi-20-12-1495] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
A supernumerary chromosome called a conditionally dispensable chromosome (CDC) is essential for pathogenicity of Nectria haematococca on pea. Among several CDCs discovered in N. haematococca, the PDA1 CDC that harbors the pisatin demethylation gene PDA1 is one of the best-studied CDCs and serves as a model for plant-pathogenic fungi. Although the presence of multiple copies is usual for supernumerary chromosomes in other eukaryotes, this possibility has not been examined well for any CDCs in N. haematococca. In this study, we produced strains with multiple copies of the PDA1 CDC by protoplast fusion and analyzed dosage effects of this chromosome. Using multiple methods, including cytological chromosome counting and fluorescence in situ hybridization, the fusion products between two transformants derived from the same strain that bears a single PDA1 CDC were shown to contain two PDA1 CDCs from both transformants and estimated to be haploid resulting from the deletion of an extra set or sets of A chromosomes in the fused nuclei. In phenotype assays, dosage effects of PDA1 CDC in the fusion products were evident as increased virulence and homoserine-utilizing ability compared with the parents. In a separate fusion experiment, PDA1 CDC accumulated up to four copies in a haploid genome.
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Affiliation(s)
- Hamid S Garmaroodi
- Graduate School of Natural Science and Technology, Okayama University, Japan.
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20
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Du Z, Jin B, Liu W, Chen L, Chen J. Highly sensitive fluorescent-labeled probes and glass slide hybridization for the detection of plant RNA viruses and a viroid. Acta Biochim Biophys Sin (Shanghai) 2007; 39:326-34. [PMID: 17492129 DOI: 10.1111/j.1745-7270.2007.00290.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
In this study, a modified method of the conventional RNA dot-blot hybridization was established, by replacing (32)P labels with CY5 labels and replacing nylon membranes with positive-charged glass slides, for detecting plant RNA viruses and a viroid. The modified RNA dot-blot hybridization method was named glass slide hybridization. The optimum efficiency of RNA binding onto the surfaces of activated glass slide was achieved using aminosilane-coated glass slide as a solid matrix and 5xsaline sodium citrate (SSC) as a spotting solution. Using a CY5-labeled DNA probe prepared through PCR amplification, the optimized glass slide hybridization could detect as little as 1.71 pg of tobacco mosaic virus (TMV) RNA. The sensitivity of the modified method was four times that of dot-blot hybridization on nylon membrane with a (32)P-labeled probe. The absence of false positive within the genus Potyvirus [potato virus A, potato virus Y (PVY) and zucchini yellow mosaic virus] showed that this method was highly specific. Furthermore, potato spindle tuber viroid (PSTVd) was also detected specifically. A test of 40 field potato samples showed that this method was equivalent to the conventional dot-blot hybridization for detecting PVY and PSTVd. To our knowledge, this is the first report of using dot-blot hybridization on glass slides with fluorescent-labeled probes for detecting plant RNA viruses and a viroid.
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Affiliation(s)
- Zhiyou Du
- College of Life Sciences, Zhejiang University, Hangzhou 310029, China
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21
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Hosokawa M, Shiba H, Kawabe T, Nakashima A, Yazawa S. A Simple and Simultaneous Detection Method for Two Different Viroids Infecting Chrysanthemum by Multiplex Direct RT-PCR. ACTA ACUST UNITED AC 2007. [DOI: 10.2503/jjshs.76.60] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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22
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Bernad L, Duran-Vila N. A novel RT-PCR approach for detection and characterization of citrus viroids. Mol Cell Probes 2006; 20:105-13. [PMID: 16464560 DOI: 10.1016/j.mcp.2005.11.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2005] [Accepted: 11/02/2005] [Indexed: 11/28/2022]
Abstract
Citrus plants are natural hosts of five viroid species and a large number of sequence variants. Because of their small size, viroids lend themselves to various RT-PCR approaches for their detection and further characterization. The one-step RT-PCR approach proposed here is based on the synthesis of viroid-cDNA by reverse transcription at 60 degrees C using a viroid specific 27-mer primer followed by standard second strand synthesis plus PCR amplification with various primer pairs. According to the primers used, full or partial length viroid-DNA is obtained. The technique avoids amplicon contamination in routine diagnosis. The suitability of the technique has been demonstrated using several nucleic acid extraction procedures and different viroid infected host species. The homogenization of tissue inside sealed plastic bags followed by nucleic acid extraction using a SDS/potassium acetate method is recommended because of its efficiency, simplicity and low cost. This extraction procedure, when coupled to the one-step RT-PCR approach, can be useful to avoid cross-contamination during routine diagnosis. A PCR strategy capable of discriminating between mild and severe strains of CEVd and identifying cachexia-inducing isolates of HSVd, is also described.
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Affiliation(s)
- L Bernad
- Departamento de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), Apartado Oficial, Moncada (Valencia), Spain
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23
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Hosokawa M, Matsushita Y, Uchida H, Yazawa S. Direct RT-PCR method for detecting two chrysanthemum viroids using minimal amounts of plant tissue. J Virol Methods 2006; 131:28-33. [PMID: 16102850 DOI: 10.1016/j.jviromet.2005.07.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2005] [Revised: 07/05/2005] [Accepted: 07/05/2005] [Indexed: 11/30/2022]
Abstract
A direct reverse transcription-polymerase chain reaction (RT-PCR) method for detecting the chrysanthemum stunt viroid (CSVd) and chrysanthemum chlorotic mottle viroid (CChMVd) to screen for a viroid-free chrysanthemum plant at a small plant size was established and named microtissue direct RT-PCR. A razor or syringe needle was used for RNA template preparations. Under a stereoscopic microscope, a razor or syringe needle was used to pierce, a tissue sample to a depth of 0.1-0.2mm, and the sample was directly transferred to the RT mixtures. Methods using razors or needles for the preparation of templates could detect CSVd and CChMVd with a high sensitivity. The most sensitive method used a razor or syringe needle to acquire template from the shoot tips. Using the microtissue direct RT-PCR method, both viroids could be detected from the high- and low-viroid-concentration plants. The microtissue direct RT-PCR method was more sensitive than a conventional template preparation method. Using the microtissue direct RT-PCR method established in this study, the laborious subculture step could be omitted because detecting viroids and screening for viroid-free plants even at a small plant size before the subculture could be possible. In addition, the microtissue direct RT-PCR method could also be a powerful tool for clarifing the viroid distribution among microtissues, such as shoot apical meristems.
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Affiliation(s)
- M Hosokawa
- Laboratory of Vegetable and Ornamental Horticulture, Department of Agronomy and Horticultural Science, Graduate School of Agriculture, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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24
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Singh RP, Dilworth AD, Singh M, Babcock KM. An alkaline solution simplifies nucleic acid preparation for RT-PCR and infectivity assays of viroids from crude sap and spotted membrane. J Virol Methods 2005; 132:204-11. [PMID: 16297455 DOI: 10.1016/j.jviromet.2005.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2005] [Revised: 09/22/2005] [Accepted: 09/30/2005] [Indexed: 11/16/2022]
Abstract
Formats of a simple protocol for the preparation of nucleic acids for infectivity and RT-PCR detection of viroids from minute amounts of plant material are described. The method consists of preparing crude extracts in a NaOH-EDTA solution and then testing the supernatant. The NaOH-EDTA extract can be used at four distinct stages of preparation depending upon the accuracy desired, namely: (1) incubation of extract for 15 min at room temperature and the use of the supernatant for RT-PCR; (2) the supernatant can be spotted onto a nitrocellulose membrane (NCM) without vacuum, and the water-eluted liquid is used for RT-PCR; (3) centrifugation of the extract and use of supernatant in RT-PCR; (4) for quantitative accuracy, spotting the centrifuged supernatant on NCM using a vacuum device and then using the water-eluted liquid for RT-PCR. The protocols are rapid, inexpensive and applicable to large-scale epidemiological survey of ornamental plants or crops. The membranes are easily transported long distances and can be stored at room temperature for several months while retaining the ability to detect viroids by RT-PCR and by infectivity assays.
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Affiliation(s)
- Rudra P Singh
- Potato Research Centre, Agriculture and Agri-Food Canada, 850 Lincoln Road, P.O. Box 20280, Fredericton, New Brunswick, Canada E3B 4Z7.
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25
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Yi G, Choi JH, Lee JH, Jeong U, Nam MH, Yun DW, Eun MY. Rapid and simple procedure for homogenizing leaf tissues suitable for mini-midi-scale DNA extraction in rice. Prep Biochem Biotechnol 2005; 35:257-61. [PMID: 16109637 DOI: 10.1081/pb-200065652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
We describe a rapid and simple procedure for homogenizing leaf samples suitable for mini/midi-scale DNA preparation in rice. The methods used tungsten carbide beads and general vortexer for homogenizing leaf samples. In general, two samples can be ground completely within 11.3+/-1.5 sec at one time. Up to 20 samples can be ground at a time using a vortexer attachment. The yields of the DNA ranged from 2.2 to 7.6 microg from 25-150 mg of young fresh leaf tissue. The quality and quantity of DNA was compatible for most of PCR work and RFLP analysis.
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Affiliation(s)
- Gihwan Yi
- Rice Division, Yeongnam Agricultural Research Institute, Milyang, Korea.
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26
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Thompson JR, Jelkmann W. The Detection and Variation of Strawberry mottle virus. PLANT DISEASE 2003; 87:385-390. [PMID: 30831833 DOI: 10.1094/pdis.2003.87.4.385] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Strawberry mottle virus (SMoV) is probably the most important virus to infect strawberry (Fragaria spp.). All species of strawberry are susceptible to SMoV, resulting in severe losses both in fruit and runner yield. However, due to the absence of definitive symptoms in commercial varieties, the only effective means of detecting SMoV is by transmission to susceptible indicator plants. In this study, we describe a reverse transcription-polymerase chain reaction (RT-PCR) method for the detection of SMoV in Fragaria spp. with the use of primers specific for the noncoding regions (NCR) of both RNA1 and RNA2 of the virus. Using this method, all of 16 isolates from various geographical origins were positive for SMoV. Partial sequences of a 327-nt long coding region were obtained for the putative large coat protein of all isolates by RT-PCR using degenerate primers. Nucleotide identities between isolates ranged from 72.8 to 99.7%. A 546-nt sequence of the putative polymerase gene of nine isolates was obtained by RT-PCR and compared. Nucleotide identities ranged from 73.4 to 100%. There was a clear tendency for isolates to group according to their geographical origin. Sequence data obtained of the NCR show four completely conserved regions of 20 or more bases.
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Affiliation(s)
- J R Thompson
- BBA, Institut für Pflanzenschutz im Obstbau, Schwabenheimer Straße 101, D- 69221, Dossenheim, Germany
| | - W Jelkmann
- BBA, Institut für Pflanzenschutz im Obstbau, Schwabenheimer Straße 101, D- 69221, Dossenheim, Germany
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27
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Ito T, Ieki H, Ozaki K. Simultaneous detection of six citrus viroids and Apple stem grooving virus from citrus plants by multiplex reverse transcription polymerase chain reaction. J Virol Methods 2002; 106:235-9. [PMID: 12393154 DOI: 10.1016/s0166-0934(02)00147-7] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We developed a multiplex reverse transcription polymerase chain reaction (RT-PCR) to detect six citrus viroids: Citrus exocortis viroid (CEVd), Citrus bent leaf viroid (CBLVd), Hop stunt viroid (HSVd), Citrus viroid III (CVd-III), Citrus viroid IV (CVd-IV) and Citrus viroid OS (CVd-OS) and Apple stem grooving virus (ASGV, synonym: Citrus tatter leaf virus (CTLV)) from citrus plants. The multiplex RT-PCR was also designed to distinguish CVd-I-LSS (a distinct variant of CBLVd) from CBLVd. By the multiplex RT-PCR, one to eight fragments specific to the pathogens were simultaneously amplified from one sample and identified by their specific molecular sizes in 6% polyacrylamide gel electrophoresis. The results of the multiplex RT-PCR were consistent with those of other diagnoses, such as uniplex RT-PCR, to detect each of the pathogens. The multiplex RT-PCR provides a simple and rapid method for detecting various viroids and ASGV in citrus plants, which will help diagnose many citrus plants at a time.
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Affiliation(s)
- Takao Ito
- Department of Citrus Research, National Institute of Fruit Tree Science, Kuchinotsu, Nagasaki 859-2501, Japan.
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28
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Ito T, Ieki H, Ozaki K, Iwanami T, Nakahara K, Hataya T, Ito T, Isaka M, Kano T. Multiple citrus viroids in citrus from Japan and their ability to produce exocortis-like symptoms in citron. PHYTOPATHOLOGY 2002; 92:542-547. [PMID: 18943029 DOI: 10.1094/phyto.2002.92.5.542] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
ABSTRACT Sequential polyacrylamide gel electrophoresis analyses showed many viroid-like RNAs in samples collected from citrus trees in Japan. Reverse transcription polymerase chain reaction and sequencing analyses of the amplified fragments verified that they were derived from variants of six citrus viroids, Citrus exocortis viroid (CEVd), Citrus bent leaf viroid (CBLVd) including CVd-I-LSS (a distinct variant of CBLVd), Hop stunt viroid, Citrus viroid III, Citrus viroid IV, and Citrus viroid OS. The samples induced symptoms with variable severity in Arizona 861-S1 'Etrog' citrons (Citrus medica L.) likely due to the varying accumulation patterns produced by the different viroids. Some of the symptoms caused by the samples harboring the citrus viroids other than CEVd were as severe as those caused by CEVd. Some source citrus trees showing the severe bark scaling characteristic of exocortis disease in trifoliate orange (Poncirus trifoliata (L.) Raf.) rootstocks contained only citrus viroids other than CEVd in complex. This indicates that certain exocortis-like diseases in Japan were caused by some combination of citrus viroids not including CEVd.
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29
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Chandelier A, Dubois N, Baelen F, De Leener F, Warnon S, Remacle J, Lepoivre P. RT-PCR-ELOSA tests on pooled sample units for the detection of virus Y in potato tubers. J Virol Methods 2001; 91:99-108. [PMID: 11164491 DOI: 10.1016/s0166-0934(00)00238-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
A highly sensitive RT-PCR protocol able to detect potato virus Y (PVY) in pooled sample units (tubers) was developed. PVY-specific primers selected in the coat protein gene were found to amplify a 359 bp fragment from diluted crude extract of infected tubers. For the detection of the amplification products, a colorimetric detection procedure in microtiter plates was established. The amplicons are hybridized between a covalently linked capture probe and a specific biotinylated detection probe ELOSA tests. This detection method detects at least 50 pg of virus per reaction for the four cultivars tested. The RT-PCR-ELOSA assay was adapted to pooled units in order to increase the sample size while reducing the number of tests.
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Affiliation(s)
- A Chandelier
- Faculté Universitaire des Sciences Agronomiques de Gembloux, Unité de Phytopathologie, Passage des Déportés, 2 B-5030 Gembloux, Belgium
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30
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Choi SK, Choi JK, Park WM, Ryu KH. RT-PCR detection and identification of three species of cucumoviruses with a genus-specific single pair of primers. J Virol Methods 1999; 83:67-73. [PMID: 10598084 DOI: 10.1016/s0166-0934(99)00106-8] [Citation(s) in RCA: 101] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Reverse transcription and polymerase chain reaction (RT-PCR) was used for detection and identification of three cucumoviruses (cucumber mosaic virus, CMV; peanut stunt virus, PSV; tomato aspermy virus, TAV) in various plants sources with a single pair of primers, designed as CPTALL-3 and CPTALL-5. The pair of cucumovirus genus-specific primers that flank the coat protein gene were designed and used to amplify a DNA fragment of approximately ranging from 938 to 966 bp. The RT-PCR with the set of primers specifically amplified the target size of DNA fragment in all the tested cucumoviruses (CMV S-IA, S-IB and S-II, PSV and TAV). No DNA product of any length was produced when brome mosaic virus or tobacco mosaic virus RNA was used as templates. The cucumoviruses examined were differentiated by PCR-restriction fragment length polymorphism with different enzymes. This indicates that the designed primers are only specific for the cucumoviruses and useful for reliable information of identification of members of the Cucumovirus genus.
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Affiliation(s)
- S K Choi
- Graduate School of Biotechnology, Korea University, Seoul, South Korea
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