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Rahman MM, Jarugula S, Bagewadi B, Fayad A, Karasev AV, Naidu RA. Characterization of a New, Country Bean ( Lablab purpureus) Lineage of Bean Common Mosaic Necrosis Virus. PLANT DISEASE 2024; 108:434-441. [PMID: 37709726 DOI: 10.1094/pdis-04-23-0822-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/16/2023]
Abstract
Country bean (Lablab purpureus, family Fabaceae) is grown in subsistence agriculture in Bangladesh as a multipurpose crop for food, animal feed, and green manure. This study was undertaken to investigate the genetic diversity of bean common mosaic necrosis virus (BCMNV, genus Potyvirus, family Potyviridae) in country beans. Leaf samples from country beans showing yellowing, vein banding, and mosaic symptoms were collected during field surveys between 2015 and 2019 cropping seasons from farmers' fields in different geographic regions. These samples were tested by serological and molecular diagnostic assays for the presence of BCMNV. Virus-positive samples were subjected to high-throughput Illumina sequencing to generate near-complete genomes of BCMNV isolates. In pairwise comparisons, the polyprotein sequences of BCMNV isolates from Bangladesh showed greater than 98% identities among themselves and shared less than 84% sequence identity at the nucleotide level with virus isolates reported from other countries. In the phylogenetic analysis, BCMNV isolates from Bangladeshi country beans formed a separate clade from virus isolates reported from common beans in other countries in the Americas, Africa, Europe, and from East Timor. Grow-out studies showed seed-to-seedling transmission of BCMNV, implying a possible seedborne nature of the virus in country beans.
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Affiliation(s)
- Mohammad M Rahman
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
| | - Sridhar Jarugula
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
| | - Basavaraj Bagewadi
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Amer Fayad
- Center for International Research, Education, and Development, Virginia Polytechnic Institute and State University, Blacksburg, VA, U.S.A
| | - Alexander V Karasev
- Department of Entomology, Plant Pathology, and Nematology, University of Idaho, Moscow, ID, U.S.A
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350, U.S.A
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Shirima RR, Wosula EN, Hamza AA, Mohammed NA, Mouigni H, Nouhou S, Mchinda NM, Ceasar G, Amour M, Njukwe E, Legg JP. Epidemiological Analysis of Cassava Mosaic and Brown Streak Diseases, and Bemisia tabaci in the Comoros Islands. Viruses 2022; 14:v14102165. [PMID: 36298720 PMCID: PMC9608219 DOI: 10.3390/v14102165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/15/2022] [Accepted: 09/28/2022] [Indexed: 01/20/2023] Open
Abstract
A comprehensive assessment of cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) was carried out in Comoros where cassava yield (5.7 t/ha) is significantly below the African average (8.6 t/ha) largely due to virus diseases. Observations from 66 sites across the Comoros Islands of Mwali, Ngazidja, and Ndzwani revealed that 83.3% of cassava fields had foliar symptoms of CBSD compared with 95.5% for CMD. Molecular diagnostics confirmed the presence of both cassava brown streak ipomoviruses (CBSIs) and cassava mosaic begomoviruses (CMBs). Although real-time RT-PCR only detected the presence of one CBSI species (Cassava brown streak virus, CBSV) the second species (Ugandan cassava brown streak virus, UCBSV) was identified using next-generation high-throughput sequencing. Both PCR and HTS detected the presence of East African cassava mosaic virus (EACMV). African cassava mosaic virus was not detected in any of the samples. Four whitefly species were identified from a sample of 131 specimens: Bemisia tabaci, B. afer, Aleurodicus dispersus, and Paraleyrodes bondari. Cassava B. tabaci comprised two mitotypes: SSA1-SG2 (89%) and SSA1-SG3 (11%). KASP SNP genotyping categorized 82% of cassava B. tabaci as haplogroup SSA-ESA. This knowledge will provide an important base for developing and deploying effective management strategies for cassava viruses and their vectors.
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Affiliation(s)
- Rudolph Rufini Shirima
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
- Correspondence: ; Tel.: +25-52-2270-0092
| | - Everlyne Nafula Wosula
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
| | - Abdou Azali Hamza
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Nobataine Ali Mohammed
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Hadji Mouigni
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Salima Nouhou
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Naima Mmadi Mchinda
- Institut National de Recherche pour L’Agriculture, La Pêche et L’Environnement (INRAPE), Moroni BP 1406, Comoros
| | - Gloria Ceasar
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
| | - Massoud Amour
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
| | - Emmanuel Njukwe
- West and Central African Council for Agricultural Research and Development (CORAF), Dakar CP 18523, Senegal
| | - James Peter Legg
- International Institute of Tropical Agriculture (IITA-Tanzania), P.O. Box 34441, Dar es Salaam 14112, Tanzania
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Kinship networks of seed exchange shape spatial patterns of plant virus diversity. Nat Commun 2021; 12:4505. [PMID: 34301941 PMCID: PMC8302746 DOI: 10.1038/s41467-021-24720-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 06/28/2021] [Indexed: 12/02/2022] Open
Abstract
By structuring farmers’ informal networks of seed exchange, kinship systems play a key role in the dynamics of crop genetic diversity in smallholder farming systems. However, because many crop diseases are propagated through infected germplasm, local seed systems can also facilitate the dissemination of seedborne pathogens. Here, we investigate how the interplay of kinship systems and local networks of germplasm exchange influences the metapopulation dynamics of viruses responsible for the cassava mosaic disease (CMD), a major threat to food security in Africa. Combining anthropological, genetic and plant epidemiological data, we analyzed the genetic structure of local populations of the African cassava mosaic virus (ACMV), one of the main causal agents of CMD. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with local modes of seed exchange. Our results demonstrate that plant virus ecosystems have also a cultural component and that social factors that shape regional seed exchange networks influence the genetic structure of plant virus populations. This study combines ethnobotanical and epidemiological data to understand how social networks of seed exchange influence the genetic structure of the African cassava mosaic virus in Gabon. Results reveal contrasted patterns of viral diversity in patrilineal and matrilineal communities, consistent with cultural differences in modes of seed exchange.
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4
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Igwe DO, Anyanwu CB, Afiukwa CA, Nnamani CV, Nweke FN, Ude GN, Ubi BE. Phenotypic and molecular screenings for determination of cassava mosaic disease (CMD) status in farmers' fields in Ebonyi State, Nigeria. Mol Biol Rep 2021; 48:227-240. [PMID: 33301051 PMCID: PMC7727096 DOI: 10.1007/s11033-020-06039-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 11/27/2020] [Indexed: 12/02/2022]
Abstract
African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV) are among the major constraints to cassava productivity within tropical and sub-tropical regions, including Ebonyi State, Nigeria. Thus, virus indexing has become imperative to determine the status of cassava mosaic disease (CMD) in Ebonyi State, to implement appropriate preventive and control strategies. Seventy-eight cassava accessions obtained from different locations of Ebonyi State were phenotypically scored, using scales 1-5 depending on CMD symptomatic expressions, followed by multiplex-PCR and sequencing for validation. 11% of cassava accessions cultivated in Afikpo were resistant (RE) to ACMV compared to 8% of moderately-resistant (MR) accessions in Izzi and 55% of tolerant (TO) ACMV accessions in Ebonyi. 100% of cassava accessions in Onicha and 66% in Afikpo South were susceptible (SU) and highly susceptible (HS) to ACMV, respectively. With multiplex-PCR, 97.4% (ACMV) and 2.6% (EACMV) were positive. Dunn's multiple comparison tests of CMD mean incidence demonstrated differences (P < 0.05), except between RE and MR, and TO and MR. More transitions (A/G, C/T) compared to transversions (A/T, G/T), were detected, with nonsynonymous mutations (Leucine/Isoleucine; Valine/Isoleucine; Arginine/Lysine; Methionine/Isoleucine), and good bit-scores (91.13-99.07% identites; e-values of 7.00e-148-0.00e+00). Phylogeny resolved the sequences into five major groups. DNA sequencing validated the detected ACMV and EACMV species. This study revealed variants of ACMV and low adoption of RE and MR cassava accessions in the farmers' fields. The findings will guide in getting disease-free and resistant varieties as planting materials to significantly mitigate the CMD spread in Ebonyi State, Nigeria.
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Affiliation(s)
- David Okeh Igwe
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi, Nigeria.
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | | | | | - Catherine Veronica Nnamani
- Plant Taxonomy and Conservation Biology Research Unit, Department of Applied Biology, Presco Campus, Ebonyi State University, Abakaliki, Nigeria
| | - Friday Nwalo Nweke
- Biology/Microbiology/Biotechnology, Faculty Science, Federal University, Ndufu-Alike Ikwo (FUNAI), Ikwo, Ebonyi, Nigeria
| | - George Nkem Ude
- Department of Natural Sciences, Bowie State University, Bowie, USA
| | - Benjamin Ewa Ubi
- Department of Biotechnology, Ebonyi State University, Abakaliki, Ebonyi, Nigeria
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5
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Tembo M, Adediji AO, Bouvaine S, Chikoti PC, Seal SE, Silva G. A quick and sensitive diagnostic tool for detection of Maize streak virus. Sci Rep 2020; 10:19633. [PMID: 33184360 PMCID: PMC7661706 DOI: 10.1038/s41598-020-76612-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 10/29/2020] [Indexed: 11/09/2022] Open
Abstract
Maize streak virus disease (MSVD), caused by Maize streak virus (MSV; genus Mastrevirus), is one of the most severe and widespread viral diseases that adversely reduces maize yield and threatens food security in Africa. An effective control and management of MSVD requires robust and sensitive diagnostic tests capable of rapid detection of MSV. In this study, a loop-mediated isothermal amplification (LAMP) assay was designed for the specific detection of MSV. This test has shown to be highly specific and reproducible and able to detect MSV in as little as 10 fg/µl of purified genomic DNA obtained from a MSV-infected maize plant, a sensitivity 105 times higher to that obtained with polymerase chain reaction (PCR) in current general use. The high degree of sequence identity between Zambian and other African MSV isolates indicate that this LAMP assay can be used for detecting MSV in maize samples from any region in Africa. Furthermore, this assay can be adopted in minimally equipped laboratories and with potential use in plant clinic laboratories across Africa strengthening diagnostic capacity in countries dealing with MSD.
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Affiliation(s)
- Mathias Tembo
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia.
| | - Adedapo O Adediji
- Department of Crop Protection and Environmental Biology, Faculty of Agriculture, University of Ibadan, Ibadan, Oyo State, Nigeria
| | - Sophie Bouvaine
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Patrick C Chikoti
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/Bag 7, Lusaka, Zambia
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
| | - Gonҫalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, ME4 4TB, Kent, UK
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6
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Siriwan W, Jimenez J, Hemniam N, Saokham K, Lopez-Alvarez D, Leiva AM, Martinez A, Mwanzia L, Becerra Lopez-Lavalle LA, Cuellar WJ. Surveillance and diagnostics of the emergent Sri Lankan cassava mosaic virus (Fam. Geminiviridae) in Southeast Asia. Virus Res 2020; 285:197959. [PMID: 32407870 DOI: 10.1016/j.virusres.2020.197959] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/17/2022]
Abstract
Emergent agricultural pathogens cause severe damage worldwide and their invasive potential is significantly increased by global trade, crop intensification and climate change. Standard surveillance and diagnostic protocols need to be evaluated and implemented, particularly with diseases caused by a wide range of pathogens that induce similar symptoms. Such is the case with Cassava Mosaic Disease (CMD) present in Africa and Asia, and associated with mixed virus infections and recombinant and re-assorted virus strains. CMD has been recently reported in Southeast Asia (SEA) and is already widely spread throughout this region. This communication offers an update on protocols and tools used to track the distribution of CMD and to characterize the pathogen associated with it in SEA.
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Affiliation(s)
| | - Jenyfer Jimenez
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Kingkan Saokham
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, 10900, Thailand
| | - Diana Lopez-Alvarez
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Ana M Leiva
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Andres Martinez
- Data Management Group, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Leroy Mwanzia
- Data Management Group, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | | | - Wilmer J Cuellar
- Virology Laboratory, International Center for Tropical Agriculture (CIAT), Cali, Colombia.
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7
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Maruthi M, Whitfield EC, Otti G, Tumwegamire S, Kanju E, Legg JP, Mkamilo G, Kawuki R, Benesi I, Zacarias A, Munga T, Mwatuni F, Mbugua E. A method for generating virus-free cassava plants to combat viral disease epidemics in Africa. PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY 2019; 105:77-87. [PMID: 31007376 PMCID: PMC6472600 DOI: 10.1016/j.pmpp.2018.09.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 07/25/2018] [Accepted: 09/13/2018] [Indexed: 06/09/2023]
Abstract
Here, we report a method to clean cassava plants from viral infections that cause cassava mosaic and brown streak diseases in Africa. Infected plants of resistant or tolerant varieties from Malawi, Mozambique, Kenya, Tanzania and Uganda were cleaned in the UK using a combination of tissue culture, chemotherapy and thermotherapy. In the first cycle of our virus-indexing procedure, we successfully cleaned 27 of the 31 varieties (87%), and after an additional three cleaning cycles, all plants were virus-free. Virus-free tissue-cultured plants were shipped back to Africa for distribution to farmers. This first cross-boundary effort provides important lessons for mitigating the two-major cassava viral diseases.
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Key Words
- ACMV, African cassava mosaic virus
- CBSD, Cassava brown streak disease
- CBSV, Cassava brown streak virus
- CMD, Cassava mosaic disease
- CTAB, Cetyl trimethylammonium bromide
- Cassava brown streak disease
- Cassava mosaic disease
- EACMV, East African cassava mosaic virus
- EACMV-Ug, East African cassava mosaic virus-Uganda
- LFC, Laminar flow cabinet
- MS, Murashige and Skoog
- Manihot esculenta
- PPM, Plant Preservation Mixture
- RH, Relative humidity
- SDW, Sterilised deionised water
- UCBSV, Ugandan cassava brown streak virus
- UIC, Unique identifying code
- Virus diagnosis
- Virus indexing
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Affiliation(s)
- M.N. Maruthi
- Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - E. Charles Whitfield
- Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Gerald Otti
- Natural Resources Institute (NRI), University of Greenwich, Chatham Maritime, Kent, United Kingdom
| | - Silver Tumwegamire
- International Institute of Agriculture (IITA), P.O Box 34441, Dar es Salaam, Tanzania
| | - Edward Kanju
- International Institute of Agriculture (IITA), P.O Box 34441, Dar es Salaam, Tanzania
| | - James P. Legg
- International Institute of Agriculture (IITA), P.O Box 34441, Dar es Salaam, Tanzania
| | - Geoffrey Mkamilo
- Department of Agricultural Research and Development (DRD), P.O Box 2066, Dar es Salaam, Tanzania
| | - Robert Kawuki
- National Agricultural Research Organization (NARO), P.O Box 295, Entebbe, Uganda
| | - Ibrahim Benesi
- Department for Agricultural Research Services (DARS), Chitedze Research Station, P. O. Box 158, Lilongwe, Malawi
| | - Anabela Zacarias
- National Institute of Agricultural Research (IIAM), P.O Box 3658, Maputo, Mozambique
| | - Therezia Munga
- Kenya Agricultural and Livestock Research Organization (KALRO), Kenya
| | - Francis Mwatuni
- Kenya Plant Inspectorate Services (KEPHIS), Plant Quarantine and Biosecurity Station, Muguga, P.O. Box 49592 00100, Nairobi, Kenya
| | - Edward Mbugua
- Genetic Technologies International Limited (GTIL), P.O. Box 47430-00100, Nairobi, Kenya
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8
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Adiputra J, Kesoju SR, Naidu RA. The Relative Occurrence of Grapevine leafroll-associated virus 3 and Grapevine red blotch virus in Washington State Vineyards. PLANT DISEASE 2018; 102:2129-2135. [PMID: 30226418 DOI: 10.1094/pdis-12-17-1962-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Vineyard surveys were conducted for three consecutive seasons in eastern Washington State, the major grapevine-growing region in the state, to document the occurrence of Grapevine leafroll-associated virus 3 (GLRaV-3) and Grapevine red blotch virus (GRBV). The majority of samples were collected from red-berried wine grape (Vitis vinifera) cultivars exhibiting symptoms of or suspected for grapevine leafroll (GLD) and red blotch (GRBD) diseases. A limited number of samples from white-berried cultivars were collected randomly due to the lack of visual symptoms. Samples were collected from a total of 2,063 grapevines from 18 red-berried cultivars and seven white-berried cultivars planted in eight American Viticultural Areas and tested for GLRaV-3 and GRBV using RT-PCR and PCR, respectively. The results showed 67.77% and 6.01% of total samples positive for GLRaV-3 and GRBV, respectively, and 9.06% of samples positive for both viruses. About 17% of samples tested negative for the two viruses, but some of these samples were positive for GLRaV-2 and GLRaV-4. Overall results indicated that GLRaV-3 was more common than GRBV, independent of cultivars and the geographic origin of samples. Due to variability in symptoms in red-berried cultivars, virus-specific diagnostic assays were deemed necessary for reliable identification of GLRaV-3 and GRBV and to differentiate GLD and GRBD symptoms from those induced by biotic and abiotic stresses in vineyards. A multiplex PCR protocol was developed for simultaneous detection of GLRaV-3 and GRBV in grapevine samples. A global phylogenetic analysis of GRBV genome sequences revealed segregation of virus isolates from Washington State vineyards into two distinct clades, with the majority of isolates belonging to clade II.
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Affiliation(s)
- Jati Adiputra
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350
| | - Sandya R Kesoju
- Department of Agriculture, Columbia Basin College, Pasco, WA 99301
| | - Rayapati A Naidu
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA 99350
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Mulenga RM, Legg JP, Ndunguru J, Miano DW, Mutitu EW, Chikoti PC, Alabi OJ. Survey, Molecular Detection, and Characterization of Geminiviruses Associated with Cassava Mosaic Disease in Zambia. PLANT DISEASE 2016; 100:1379-1387. [PMID: 30686191 DOI: 10.1094/pdis-10-15-1170-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
A survey was conducted from April to May 2014 in 214 farmers' fields located across six major cassava-producing provinces (Western, Northwestern, Northern, Luapula, Lusaka, and Eastern) of Zambia to determine the status of cassava mosaic disease (CMD) and the species diversity of associated cassava mosaic geminiviruses (CMG). Mean CMD incidence varied across all six provinces but was greatest in Lusaka Province (81%) and least in Northern Province (44%). Mean CMD severity varied slightly between provinces, ranging from 2.78 in Eastern Province to 3.00 in Northwestern Province. Polymerase chain reaction discrimination of 226 survey samples, coupled with complete DNA-A genome sequence analysis, revealed the presence of African cassava mosaic virus (ACMV), East African cassava mosaic virus (EACMV), and East African cassava mosaic Malawi virus (EACMMV) as single or mixed infections of different proportions. Single-virus infections were predominant, occurring in 62.8% (ACMV), 5.8% (EACMMV), and 2.2% (EACMV) of samples relative to mixed-virus infections, which occurred in 19.5% (ACMV + EACMMV), 0.4% (ACMV + EACMV), and 0.9% (ACMV + EACMV + EACMMV) of samples. Phylogenetic analysis revealed the segregation of virus isolates from Zambia into clades specific to ACMV, EACMV, and EACMMV, further confirming the presence of all three viruses in Zambia. The results point to a greater diversity of CMG across major cassava-growing provinces of Zambia and implicate contaminated cassava cuttings in disease spread.
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Affiliation(s)
- Rabson M Mulenga
- Zambia Agriculture Research Institute, Mount Makulu Central Research Station, Chilanga, Lusaka, Zambia
| | - James P Legg
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
| | - Joseph Ndunguru
- Mikocheni Agriculture Research Institute, Dar es Salaam, Tanzania
| | - Douglas W Miano
- University of Nairobi, College of Agriculture and Veterinary Sciences, Department of Plant Sciences and Crop Protection, Kangemi, Nairobi, Kenya
| | - Eunice W Mutitu
- University of Nairobi, College of Agriculture and Veterinary Sciences, Department of Plant Sciences and Crop Protection, Kangemi, Nairobi, Kenya
| | - Patrick C Chikoti
- Zambia Agriculture Research Institute, Mount Makulu Central Research Station
| | - O J Alabi
- Department of Plant Pathology & Microbiology, Texas A&M AgriLife Research and Extension Center, Weslaco 78596
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10
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Otti G, Bouvaine S, Kimata B, Mkamillo G, Kumar PL, Tomlins K, Maruthi MN. High-throughput multiplex real-time PCR assay for the simultaneous quantification of DNA and RNA viruses infecting cassava plants. J Appl Microbiol 2016; 120:1346-56. [PMID: 26743662 DOI: 10.1111/jam.13043] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 01/04/2016] [Accepted: 01/04/2016] [Indexed: 11/30/2022]
Abstract
AIMS To develop a multiplex TaqMan-based real-time PCR assay (qPCR) for the simultaneous detection and quantification of both RNA and DNA viruses affecting cassava (Manihot esculenta) in eastern Africa. METHODS AND RESULTS The diagnostic assay was developed for two RNA viruses; Cassava brown streak virus (CBSV) and Uganda cassava brown streak virus (UCBSV) and two predominant DNA viruses; African cassava mosaic virus (ACMV) and East African cassava mosaic virus (EACMV), which cause the economically important cassava brown streak disease (CBSD) and cassava mosaic disease (CMD) respectively. Our method, developed by analysing PCR products of viruses, was highly sensitive to detect target viruses from very low quantities of 4-10 femtograms. Multiplexing did not diminish sensitivity or accuracy compared to uniplex alternatives. The assay reliably detected and quantified four cassava viruses in field samples where CBSV and UCBSV synergy was observed in majority of mixed-infected varieties. CONCLUSIONS We have developed a high-throughput qPCR diagnostic assay capable of specific and sensitive quantification of predominant DNA and RNA viruses of cassava in eastern Africa. SIGNIFICANCE AND IMPACT OF THE STUDY The qPCR methods are a great improvement on the existing methods and can be used for monitoring virus spread as well as for accurate evaluation of the cassava varieties for virus resistance.
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Affiliation(s)
- G Otti
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, UK
| | - S Bouvaine
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, UK
| | - B Kimata
- Naliendele Agricultural Research Institute, Naliendele, Tanzania
| | - G Mkamillo
- Naliendele Agricultural Research Institute, Naliendele, Tanzania
| | - P L Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - K Tomlins
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, UK
| | - M N Maruthi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent, UK
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11
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Legg JP, Lava Kumar P, Makeshkumar T, Tripathi L, Ferguson M, Kanju E, Ntawuruhunga P, Cuellar W. Cassava virus diseases: biology, epidemiology, and management. Adv Virus Res 2015; 91:85-142. [PMID: 25591878 DOI: 10.1016/bs.aivir.2014.10.001] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cassava (Manihot esculenta Crantz.) is the most important vegetatively propagated food staple in Africa and a prominent industrial crop in Latin America and Asia. Its vegetative propagation through stem cuttings has many advantages, but deleteriously it means that pathogens are passed from one generation to the next and can easily accumulate, threatening cassava production. Cassava-growing continents are characterized by specific suites of viruses that affect cassava and pose particular threats. Of major concern, causing large and increasing economic impact in Africa and Asia are the cassava mosaic geminiviruses that cause cassava mosaic disease in Africa and Asia and cassava brown streak viruses causing cassava brown streak disease in Africa. Latin America, the center of origin and domestication of the crop, hosts a diverse set of virus species, of which the most economically important give rise to cassava frog skin disease syndrome. Here, we review current knowledge on the biology, epidemiology, and control of the most economically important groups of viruses in relation to both farming and cultural practices. Components of virus control strategies examined include: diagnostics and surveillance, prevention and control of infection using phytosanitation, and control of disease through the breeding and promotion of varieties that inhibit virus replication and/or movement. We highlight areas that need further research attention and conclude by examining the likely future global outlook for virus disease management in cassava.
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Affiliation(s)
- James P Legg
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania.
| | - P Lava Kumar
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - T Makeshkumar
- Central Tuber Crops Research Institute (CTCRI), Thiruvananthapuram, India
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Morag Ferguson
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Edward Kanju
- International Institute of Tropical Agriculture (IITA), Dar es Salaam, Tanzania
| | | | - Wilmer Cuellar
- Centro Internacional de Agricultura Tropical (CIAT), Cali, Colombia
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12
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High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding. Virus Res 2014; 186:87-96. [DOI: 10.1016/j.virusres.2013.12.028] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2013] [Revised: 12/18/2013] [Accepted: 12/20/2013] [Indexed: 11/20/2022]
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13
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Kumar S, Singh L, Ram R, Zaidi AA, Hallan V. Simultaneous detection of major pome fruit viruses and a viroid. Indian J Microbiol 2014; 54:203-10. [PMID: 25320423 PMCID: PMC4188501 DOI: 10.1007/s12088-013-0431-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Accepted: 10/13/2013] [Indexed: 11/29/2022] Open
Abstract
A rapid and sensitive two-step RT-PCR protocol for simultaneous detection of major apple viruses, namely Apple mosaic virus (ApMV), Apple stem pitting virus (ASPV), Apple stem grooving virus (ASGV), Apple chlorotic leaf spot virus (ACLSV) and Apple scar skin viroid (ASSVd), was developed. Five specific primer pairs were tested and confirmed for these viruses and viroid together in a single tube, giving amplicons of ~198, ~330, ~370, ~547 and ~645 bp corresponding to ASGV, ASSVd, ASPV, ApMV and ACLSV, respectively. Using a guanidinium-based extraction buffer along with a commercial kit resulted in better quality RNA as compared to kit, suited for multiplex RT-PCR. A rapid CTAB method for RNA isolation from apple tissue was developed, which produce good yield and saves time. To the best of our knowledge, this is the first report on the simultaneous detection of five pathogens (four viruses and a viroid) from apple with NADH dehydrogenase subunit 5 (nad5) as an internal control.
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Affiliation(s)
- Surender Kumar
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Lakhmir Singh
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Raja Ram
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Aijaz A. Zaidi
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
| | - Vipin Hallan
- Plant Virology Lab, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061 HP India
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14
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Aloyce RC, Tairo F, Sseruwagi P, Rey MEC, Ndunguru J. A single-tube duplex and multiplex PCR for simultaneous detection of four cassava mosaic begomovirus species in cassava plants. J Virol Methods 2012; 189:148-56. [PMID: 23174160 DOI: 10.1016/j.jviromet.2012.10.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2012] [Revised: 09/26/2012] [Accepted: 10/22/2012] [Indexed: 11/29/2022]
Abstract
A single-tube duplex and multiplex PCR was developed for the simultaneous detection of African cassava mosaic virus (ACMV), East African cassava mosaic Cameroon virus (EACMCV), East African cassava mosaic Malawi virus (EACMMV) and East African cassava mosaic Zanzibar virus (EACMZV), four cassava mosaic begomoviruses (CMBs) affecting cassava in sub-Saharan Africa. Co-occurrence of the CMBs in cassava synergistically enhances disease symptoms and complicates their detection and diagnostics. Four primer pairs were designed to target DNA-A component sequences of cassava begomoviruses in a single tube PCR amplification using DNA extracted from dry-stored cassava leaves. Duplex and multiplex PCR enabled the simultaneous detection and differentiation of the four CMBs, namely ACMV (940bp), EACMCV (435bp), EACMMV (504bp) and EACMZV (260bp) in single and mixed infections, and sequencing results confirmed virus identities according to the respective published sequences of begomovirus species. In addition, we report here a modified Dellapotra et al. (1983) protocol, which was used to extract DNA from dry and fresh cassava leaves with comparable results. Using the duplex and multiplex techniques, time was saved and amount of reagents used were reduced, which translated into reduced cost of the diagnostics. This tool can be used by cassava breeders screening for disease resistance; scientists doing virus diagnostic studies; phytosanitary officers checking movement of diseased planting materials, and seed certification and multipliers for virus indexing.
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Affiliation(s)
- R C Aloyce
- Mikocheni Agriculture Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania.
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15
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Abarshi MM, Mohammed IU, Jeremiah SC, Legg JP, Kumar PL, Hillocks RJ, Maruthi MN. Multiplex RT-PCR assays for the simultaneous detection of both RNA and DNA viruses infecting cassava and the common occurrence of mixed infections by two cassava brown streak viruses in East Africa. J Virol Methods 2011; 179:176-84. [PMID: 22080852 DOI: 10.1016/j.jviromet.2011.10.020] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2011] [Revised: 10/20/2011] [Accepted: 10/27/2011] [Indexed: 11/18/2022]
Abstract
Uniplex and multiplex reverse transcription-polymerase chain reaction (RT-PCR) protocols were developed for the detection of cassava brown streak viruses (CBSVs) in single and mixed infections with cassava mosaic begomoviruses (CMBs) in a tropical crop plant, cassava (Manihot esculenta). CMBs contain ssDNA as their genome (genus Begomovirus, family Geminiviridae) while CBSVs are made up of positive sense ssRNA (genus Ipomovirus, family Potyviridae), and they cause the economically important cassava mosaic and cassava brown streak diseases, respectively, in sub-Saharan Africa. Diagnostic methodologies have long been available for CMBs but they are limited for CBSVs especially in mixed infections. In this study, the two CBSVs, Cassava brown streak virus (CBSV) and Cassava brown streak Uganda virus (CBSUV) occurring singly or in mixed infection with CMBs, African cassava mosaic virus and East African cassava mosaic virus were detected in a single RT-PCR using both previously described and newly designed virus-specific primers. These protocols were highly efficient for detecting CBSVs compared to the existing methods and have great potential to minimize sample handling and contamination. As well as improving the diagnosis of cassava viruses, the development of multiplex RT-PCR protocols have revealed the common occurrence of mixed infections by CBSV and CBSUV in cassava fields of Tanzania and Kenya, which was contrary to the common belief until recently that these two viruses have existed separately. These protocols have implications for diagnosis and epidemiological studies on cassava virus diseases in Eastern Africa.
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Affiliation(s)
- M M Abarshi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, United Kingdom
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16
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Akinbade S, Hanna R, Nguenkam A, Njukwe E, Fotso A, Doumtsop A, Ngeve J, Tenku S, Kumar PL. First report of the
East African cassava mosaic virus
‐Uganda (EACMV‐UG) infecting cassava (
Manihot esculenta
) in Cameroon. ACTA ACUST UNITED AC 2010. [DOI: 10.5197/j.2044-0588.2010.021.022] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- S.A. Akinbade
- International Institute of Tropical Agriculture (IITA)PMB 5320IbadanNigeria
| | | | | | | | | | | | - J. Ngeve
- Institut de Recherche Agricole pour le DéveloppementBP 2123YaoundéCameroon
| | - S.T.N. Tenku
- Institut de Recherche Agricole pour le DéveloppementBP 2123YaoundéCameroon
| | - P. Lava Kumar
- International Institute of Tropical Agriculture (IITA)PMB 5320IbadanNigeria
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17
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Alabi OJ, Kumar PL, Mgbechi-Ezeri JU, Naidu RA. Two new 'legumoviruses' (genus Begomovirus) naturally infecting soybean in Nigeria. Arch Virol 2010; 155:643-56. [PMID: 20229118 DOI: 10.1007/s00705-010-0630-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2009] [Accepted: 02/08/2010] [Indexed: 11/26/2022]
Abstract
Two new 'legumoviruses' (genus Begomovirus; family Geminiviridae) naturally infecting soybean (Glycine max L. Merr.) in Nigeria were molecularly characterized. Based on characteristic symptoms in soybean, the two viruses are provisionally designated as Soybean mild mottle virus (SbMMV) and Soybean chlorotic blotch virus (SbCBV). SbCBV has a bipartite genome, whereas SbMMV has only a DNA A component. The DNA A component of SbMMV is 2,768 nucleotides (nt) long and the DNA A and DNA B components of SbCBV are 2,708 and 2,647 nt long, respectively. In pairwise comparisons, the DNA A component of SbMMV and SbCBV showed 62% nt sequence identity, indicating that these two viruses are distinct. Whereas the DNA A of SbMMV contains two virion- and four complementary-sense open reading frames, that of SbCBV lacks the virus-sense AV2, a signature gene present in 'Old World' begomoviruses. A pairwise comparison with the corresponding nucleotide sequence of other begomoviruses in the databases indicated that SbCBV had a maximum of 74% identity with cowpea golden mosaic virus and SbMMV had a maximum of 65% identity with mungbean yellow mosaic India virus and kudzu mosaic virus. Phylogenetic analysis of the DNA A component of SbCBV and SbMMV together with those of other begomoviruses available in the databases showed clustering of the two viruses within the 'legumovirus' clade of the begomovirus phylogenetic tree. In addition, the DNA A and B components of SbCBV from Centrosema pubescens Benth were found to be identical to those from soybean, indicating that leguminous wild species are a potential alternative host for the virus. Since soybean is an introduced crop, the identification of two distinct begomoviruses naturally infecting soybean in Nigeria suggests the occurrence of 'legumoviruses' in plant species indigenous to Africa and underscores their potential threat to sustainable cultivation of soybean on the African continent.
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Affiliation(s)
- Olufemi J Alabi
- Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, 24106 North Bunn Road, Prosser, WA 99350, USA
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18
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Improvement of Multiplex PCR Efficiency by Using The MPprimer to Design Primers and Optimizing The Amplification Conditions*. PROG BIOCHEM BIOPHYS 2010. [DOI: 10.3724/sp.j.1206.2009.00552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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19
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Abarshi MM, Mohammed IU, Wasswa P, Hillocks RJ, Holt J, Legg JP, Seal SE, Maruthi MN. Optimization of diagnostic RT-PCR protocols and sampling procedures for the reliable and cost-effective detection of Cassava brown streak virus. J Virol Methods 2009; 163:353-9. [PMID: 19879299 DOI: 10.1016/j.jviromet.2009.10.023] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 10/19/2009] [Accepted: 10/22/2009] [Indexed: 12/01/2022]
Abstract
Sampling procedures and diagnostic protocols were optimized for accurate diagnosis of Cassava brown streak virus (CBSV) (genus Ipomovirus, family Potyviridae). A cetyl trimethyl ammonium bromide (CTAB) method was optimized for sample preparation from infected cassava plants and compared with the RNeasy plant mini kit (Qiagen) for sensitivity, reproducibility and costs. CBSV was detectable readily in total RNAs extracted using either method. The major difference between the two methods was in the cost of consumables, with the CTAB 10x cheaper (0.53 pounds sterling=US$0.80 per sample) than the RNeasy method (5.91 pounds sterling=US$8.86 per sample). A two-step RT-PCR (1.34 pounds sterling=US$2.01 per sample), although less sensitive, was at least 3-times cheaper than a one-step RT-PCR (4.48 pounds sterling=US$6.72). The two RT-PCR tests revealed consistently the presence of CBSV both in symptomatic and asymptomatic leaves and indicated that asymptomatic leaves can be used reliably for virus diagnosis. Depending on the accuracy required, sampling 100-400 plants per field is an appropriate recommendation for CBSD diagnosis, giving a 99.9% probability of detecting a disease incidence of 6.7-1.7%, respectively. CBSV was detected at 10(-4)-fold dilutions in composite sampling, indicating that the most efficient way to index many samples for CBSV will be to screen pooled samples. The diagnostic protocols described below are reliable and the most cost-effective methods available currently for detecting CBSV.
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Affiliation(s)
- M M Abarshi
- Natural Resources Institute, University of Greenwich, Chatham Maritime, Kent ME4 4TB, United Kingdom
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20
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DAMAYANTI TRIASMIRA, ALABI OLUFEMIJOSEPH, NAIDU RAYAPATIADIKESAVULU, RAUF AUNU. Severe Outbreak of a Yellow Mosaic Disease on the Yard Long Bean in Bogor, West Java. HAYATI JOURNAL OF BIOSCIENCES 2009. [DOI: 10.4308/hjb.16.2.78] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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