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Amelework AB, Bairu MW. Advances in Genetic Analysis and Breeding of Cassava ( Manihot esculenta Crantz): A Review. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11121617. [PMID: 35736768 PMCID: PMC9228751 DOI: 10.3390/plants11121617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/08/2022] [Indexed: 05/30/2023]
Abstract
Cassava (Manihot esculenta Crantz) is the sixth most important food crop and consumed by 800 million people worldwide. In Africa, cassava is the second most important food crop after maize and Africa is the worlds' largest producer. Though cassava is not one of the main commodity crops in South Africa, it is becoming a popular crop among farming communities in frost-free areas, due to its climate-resilient nature. This necessitated the establishment of a multi-disciplinary research program at the Agricultural Research Council of South Africa. The objective of this review is to highlight progress made in cassava breeding and genetic analysis. This review highlights the progress of cassava research worldwide and discusses research findings on yield, quality, and adaptability traits in cassava. It also discusses the limitations and the prospects of the cassava R&D program towards development of the cassava industry in South Africa.
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Affiliation(s)
- Assefa B. Amelework
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa;
| | - Michael W. Bairu
- Agricultural Research Council, Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa;
- Faculty of Natural & Agricultural Sciences, School of Agricultural Sciences, Food Security and Safety Focus Area, North-West University, Private Bag X2046, Mmabatho 2735, South Africa
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Soro M, Tiendrébéogo F, Pita JS, Traoré ET, Somé K, Tibiri EB, Néya JB, Mutuku JM, Simporé J, Koné D. Epidemiological assessment of cassava mosaic disease in Burkina Faso. PLANT PATHOLOGY 2021; 70:2207-2216. [PMID: 35873883 PMCID: PMC9291739 DOI: 10.1111/ppa.13459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 08/05/2021] [Indexed: 05/11/2023]
Abstract
Surveys were conducted in 2016 and 2017 across the main cassava-growing regions of Burkina Faso to assess the status of cassava mosaic disease (CMD) and to determine the virus strains causing the disease, using field observation and phylogenetic analysis. CMD incidence varied between regions and across years but was lowest in Hauts-Bassins (6.0%, 2016 and 5.4%, 2017) and highest in Centre-Sud (18.5%, 2016) and in Boucle du Mouhoun (51.7%, 2017). The lowest CMD severity was found in Est region (2.0) for both years and the highest in Sud-Ouest region (3.3, 2016) and Centre-Sud region (2.8, 2017). The CMD infection was primarily associated with contaminated cuttings in all regions except in Hauts-Bassins, where whitefly-borne infection was higher than cuttings-borne infection in 2016. PCR screening of 687 samples coupled with sequence analysis revealed the presence of African cassava mosaic-like (ACMV-like) viruses and East African cassava mosaic-like (EACMV-like) viruses as single infections at 79.5% and 1.1%, respectively. Co-infections of ACMV-like and EACMV-like viruses were detected in 19.4% of the tested samples. In addition, 86.7% of the samples positive for EACMV-like virus were found to be positive for East African cassava mosaic Cameroon virus (EACMCMV). Phylogenetic analysis revealed the segregation of cassava mosaic geminiviruses (CMGs) from Burkina Faso into three clades specific to ACMV, African cassava mosaic Burkina Faso virus (ACMBFV), and EACMCMV, confirming the presence of these viruses. The results of this study show that EACMCMV occurrence may be more prevalent in Burkina Faso than previously thought.
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Affiliation(s)
- Monique Soro
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanIvory Coast
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Fidèle Tiendrébéogo
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - Justin S. Pita
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanIvory Coast
| | - Edwig T. Traoré
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE)Université Joseph Ki‐ZerboOuagadougouBurkina Faso
| | - Koussao Somé
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
- Laboratoire de Génétique et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
| | - Ezechiel B. Tibiri
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - James B. Néya
- Laboratoire de Virologie et de Biotechnologies VégétalesInstitut de l’Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
- Laboratoire Mixte International Patho‐BiosIRD‐INERAOuagadougouBurkina Faso
| | - J. Musembi Mutuku
- Central and West African Virus Epidemiology (WAVE)Pôle scientifique et d’innovation de BingervilleUniversité Félix Houphouët‐Boigny (UFHB)BingervilleIvory Coast
| | - Jacques Simporé
- Laboratoire de Biologie Moléculaire et de Génétique (LABIOGENE)Université Joseph Ki‐ZerboOuagadougouBurkina Faso
| | - Daouda Koné
- Laboratoire de Biotechnologie, Agriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët‐BoignyAbidjanIvory Coast
- Centre d’Excellence Africain sur le Changement Climatique, la Biodiversité et l’Agriculture Durable (WASCAL/CEA‐CCBAD, Université Félix Houphouët‐Boigny)PSI‐Université Félix Houphouët‐BoignyAbidjanIvory Coast
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Crespo-Bellido A, Hoyer JS, Dubey D, Jeannot RB, Duffy S. Interspecies Recombination Has Driven the Macroevolution of Cassava Mosaic Begomoviruses. J Virol 2021; 95:e0054121. [PMID: 34106000 PMCID: PMC8354330 DOI: 10.1128/jvi.00541-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/01/2021] [Indexed: 11/20/2022] Open
Abstract
Begomoviruses (family Geminiviridae, genus Begomovirus) significantly hamper crop production and threaten food security around the world. The frequent emergence of new begomovirus genotypes is facilitated by high mutation frequencies and the propensity to recombine and reassort. Homologous recombination has been especially implicated in the emergence of novel cassava mosaic begomovirus (CMB) genotypes, which cause cassava mosaic disease (CMD). Cassava (Manihot esculenta) is a staple food crop throughout Africa and an important industrial crop in Asia, two continents where production is severely constrained by CMD. The CMD species complex is comprised of 11 bipartite begomovirus species with ample distribution throughout Africa and the Indian subcontinent. While recombination is regarded as a frequent occurrence for CMBs, a revised, systematic assessment of recombination and its impact on CMB phylogeny is currently lacking. We assembled data sets of all publicly available, full-length DNA-A (n = 880) and DNA-B (n = 369) nucleotide sequences from the 11 recognized CMB species. Phylogenetic networks and complementary recombination detection methods revealed extensive recombination among the CMB sequences. Six out of the 11 species descended from unique interspecies recombination events. Estimates of recombination and mutation rates revealed that all species experience mutation more frequently than recombination, but measures of population divergence indicate that recombination is largely responsible for the genetic differences between species. Our results support that recombination has significantly impacted the CMB phylogeny and has driven speciation in the CMD species complex. IMPORTANCE Cassava mosaic disease (CMD) is a significant threat to cassava production throughout Africa and Asia. CMD is caused by a complex comprised of 11 recognized virus species exhibiting accelerated rates of evolution, driven by high frequencies of mutation and genetic exchange. Here, we present a systematic analysis of the contribution of genetic exchange to cassava mosaic virus species-level diversity. Most of these species emerged as a result of genetic exchange. This is the first study to report the significant impact of genetic exchange on speciation in a group of viruses.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Divya Dubey
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Ronica B. Jeannot
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers State University of New Jersey, New Brunswick, New Jersey, USA
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Chikoti PC, Mulenga RM, Tembo M, Sseruwagi P. Cassava mosaic disease: a review of a threat to cassava production in Zambia. JOURNAL OF PLANT PATHOLOGY : AN INTERNATIONAL JOURNAL OF THE ITALIAN PHYTOPATHOLOGICAL SOCIETY 2019; 101:467-477. [PMID: 31983872 PMCID: PMC6951474 DOI: 10.1007/s42161-019-00255-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 01/30/2019] [Indexed: 05/18/2023]
Abstract
Cassava (Manihot esculenta Crantz) is one of the most important root staple crops in Zambia. An estimated 30% of Zambians, over 4 million people, consume cassava as part of their daily diet. Cassava is mostly grown by subsistence farmers on fields of less than 1 ha. Cultivation of cassava is hampered by several biotic constraints, of which cassava mosaic disease (CMD) is currently the most important factor limiting cassava production in Zambia. CMD occurs in all the cassava-growing provinces and accounts for 50% to 70% of yield losses countrywide. Strategies to counter CMD were initiated in the early 1990s and included the release of CMD-resistant cassava cultivars. However, efforts to control CMD are limited because few growers plant these cultivars. More recently, to address the CMD problem, regular disease monitoring and diagnostic capabilities have been strengthened, and there is increased support for screening breeders materials. CMD is a rising threat to cassava production in Zambia. This review of CMD research on disease surveillance, CMD spread, yield losses, awareness campaigns and control options in Zambia over the past 25 years informs future control efforts and management strategies.
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Affiliation(s)
- Patrick Chiza Chikoti
- Zambia Agriculture Research Institute, Mt. Makulu Central Research Station, P/B 7, Chilanga, Zambia
| | - Rabson Mpundu Mulenga
- Zambia Agriculture Research Institute, Mt. Makulu Central Research Station, P/B 7, Chilanga, Zambia
| | - Mathias Tembo
- Zambia Agriculture Research Institute, Mt. Makulu Central Research Station, P/B 7, Chilanga, Zambia
| | - Peter Sseruwagi
- Mikocheni Agricultural Research Institute, P.O. Box 6226, Dar es Salaam, Tanzania
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Fondong VN. The Search for Resistance to Cassava Mosaic Geminiviruses: How Much We Have Accomplished, and What Lies Ahead. FRONTIERS IN PLANT SCIENCE 2017; 8:408. [PMID: 28392798 PMCID: PMC5365051 DOI: 10.3389/fpls.2017.00408] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Accepted: 03/09/2017] [Indexed: 05/23/2023]
Abstract
The cassava mosaic disease (CMD), which occurs in all cassava growing regions of Africa and the Indian subcontinent, is caused by cassava mosaic geminiviruses (CMGs). CMGs are considered to be the most damaging vector-borne plant pathogens. So far, the most successful approach used to control these viruses has been the transfer of a polygenic recessive resistance locus, designated CMD1, from wild cassava to cassava cultivars. Further progress in harnessing natural resistance to contain CMGs has come from the discovery of the dominant monogenic resistance locus, CMD2, in some West African cassava cultivars. CMD2 has been combined with CMD1 through genetic crosses. Because of the limitations of the cassava breeding approach, especially with regard to time required to produce a variety and the loss of preferred agronomic attributes, efforts have been directed toward the deployment of genetic engineering approaches. Most of these approaches have been centered on RNA silencing strategies, developed mainly in the model plant Nicotiana benthamiana. Early RNA silencing platforms assessed for CMG resistance have been use of viral genes for co-suppression, antisense suppression or for hairpin RNAs-mediated gene silencing. Here, progress and challenges in the deployment of these approaches in the control of CMGs are discussed. Novel functional genomics approaches with potential to overcome some of the drawbacks of the current strategies are also discussed.
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Affiliation(s)
- Vincent N. Fondong
- Department of Biological Sciences, Delaware State UniversityDover, DE, USA
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6
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De Bruyn A, Harimalala M, Zinga I, Mabvakure BM, Hoareau M, Ravigné V, Walters M, Reynaud B, Varsani A, Harkins GW, Martin DP, Lett JM, Lefeuvre P. Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar. BMC Evol Biol 2016; 16:182. [PMID: 27600545 PMCID: PMC5012068 DOI: 10.1186/s12862-016-0749-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 08/18/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. RESULTS The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. CONCLUSIONS Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region of the world, the risks of recombinant CMG variants emerging on this island are likely to be higher than elsewhere. Evidence of an epidemiological link between Madagascan and mainland African CMGs suggests that the consequences of such emergence events could reach far beyond the shores of this island.
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Affiliation(s)
- Alexandre De Bruyn
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- Université de la Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Mireille Harimalala
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- Université de la Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- FOFIFA, Laboratoire de Pathologie Végétale, BP 1444 Ambatobe, Madagascar
| | - Innocent Zinga
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- LSBAD, Université de Bangui, BP908 Bangui, Centrafrique France
| | - Batsirai M. Mabvakure
- South African National Bioinformatics Institute, Medical Research Council Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Murielle Hoareau
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Virginie Ravigné
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- CIRAD, UMR BGPI, Campus International de Baillarguet, Montpellier, 34398 France
| | - Matthew Walters
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
| | - Bernard Reynaud
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
- Université de la Réunion, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Arvind Varsani
- School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Private Bag 4800, Christchurch, New Zealand
- Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, FL 32611 USA
- Structural Biology Research Unit, University of Cape Town, Rondebosch, 7701 Cape Town, South Africa
| | - Gordon W. Harkins
- South African National Bioinformatics Institute, Medical Research Council Bioinformatics Unit, University of the Western Cape, Cape Town, South Africa
| | - Darren P. Martin
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Observatory 7925, Cape Town, South Africa
| | - Jean-Michel Lett
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
| | - Pierre Lefeuvre
- CIRAD, UMR PVBMT, Pôle de Protection des Plantes, 7 chemin de l’IRAT, Saint-Pierre, Ile de la Réunion 97410 France
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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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Khan AJ, Akhtar S, Al-Matrushi AM, Fauquet CM, Briddon RW. Introduction of East African cassava mosaic Zanzibar virus to Oman harks back to "Zanzibar, the capital of Oman". Virus Genes 2012; 46:195-8. [PMID: 23085885 DOI: 10.1007/s11262-012-0838-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 10/11/2012] [Indexed: 11/27/2022]
Abstract
Cassava mosaic disease (CMD) is the most devastating disease of the subsistence crop cassava (Manihot esculenta) across Africa and the Indian subcontinent. The disease is caused by viruses of the genus Begomovirus (family Geminiviridae)-seven species have been identified so far. The Sultanate of Oman is unusual among countries in Arabia in growing cassava on a small scale for local consumption. During a recent survey in A'Seeb wilayat of Muscat governorate, Oman, cassava plants were identified with symptoms typical of CMD. A begomovirus, East African cassava mosaic Zanzibar virus (EACMZV), was isolated from symptomatic plants. This virus was previously only known to occur in Zanzibar and Kenya. During the 19th Century, Zanzibar was governed by Oman and was so important that the Sultan of Oman moved his capital there from Muscat. After a period of colonial rule, the governing Arab elite was overthrown, following independence in the 1960s, and many expatriate Omanis returned to their homeland. Having gained a liking for the local Zanzibar cuisine, it appears that returning Omanis did not wish to do without dishes made from one particular favorite, cassava. Consequently, they carried planting material back to Oman for cultivation in their kitchen gardens. The evidence suggests that this material harbored EACMZV. Recently, Oman has been shown to be a nexus for geminiviruses and their associated satellites from diverse geographic origins. With their propensity to recombine, a major mechanism for evolution of geminiviruses, and the fact that Oman (and several other Arabian countries) is a major hub for trade and travel by air and sea, the possibility of onward spread is worrying.
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Affiliation(s)
- Akhtar J Khan
- Department of Crop Sciences, College of Agricultural & Marine Sciences, Sultan Qaboos University, Al-Khod 123, Muscat, Oman.
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Threats to cassava production: known and potential geographic distribution of four key biotic constraints. Food Secur 2011. [DOI: 10.1007/s12571-011-0141-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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10
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Ramkat RC, Calari A, Maghuly F, Laimer M. Biotechnological approaches to determine the impact of viruses in the energy crop plant Jatropha curcas. Virol J 2011; 8:386. [PMID: 21812981 PMCID: PMC3163225 DOI: 10.1186/1743-422x-8-386] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 08/03/2011] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Geminiviruses infect a wide range of plant species including Jatropha and cassava both belonging to family Euphorbiaceae. Cassava is traditionally an important food crop in Sub - Saharan countries, while Jatropha is considered as valuable biofuel plant with great perspectives in the future. RESULTS A total of 127 Jatropha samples from Ethiopia and Kenya and 124 cassava samples from Kenya were tested by Enzyme-Linked Immunosorbent Assay (ELISA) for RNA viruses and polymerase chain reaction for geminiviruses. Jatropha samples from 4 different districts in Kenya and Ethiopia (analyzed by ELISA) were negative for all three RNA viruses tested: Cassava brown streak virus (CBSV), Cassava common mosaic virus, Cucumber mosaic virus, Three cassava samples from Busia district (Kenya) contained CBSV. Efforts to develop diagnostic approaches allowing reliable pathogen detection in Jatropha, involved the amplification and sequencing of the entire DNA A molecules of 40 Kenyan isolates belonging to African cassava mosaic virus (ACMV) and East African cassava mosaic virus - Uganda. This information enabled the design of novel primers to address different questions: a) primers amplifying longer sequences led to a phylogenetic tree of isolates, allowing some predictions on the evolutionary aspects of Begomoviruses in Jatrophia; b) primers amplifying shorter sequences represent a reliable diagnostic tool. This is the first report of the two Begomoviruses in J. curcas. Two cassava samples were co - infected with cassava mosaic geminivirus and CBSV. A Defective DNA A of ACMV was found for the first time in Jatropha. CONCLUSION Cassava geminiviruses occurring in Jatropha might be spread wider than anticipated. If not taken care of, this virus infection might negatively impact large scale plantations for biofuel production. Being hosts for similar pathogens, the planting vicinity of the two crop plants needs to be handled carefully.
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Affiliation(s)
- Rose C Ramkat
- Plant Biotechnology Unit, IAM, VIBT, BOKU, Muthgasse 18, A - 1190 Vienna, Austria
| | - Alberto Calari
- Plant Biotechnology Unit, IAM, VIBT, BOKU, Muthgasse 18, A - 1190 Vienna, Austria
| | - Fatemeh Maghuly
- Plant Biotechnology Unit, IAM, VIBT, BOKU, Muthgasse 18, A - 1190 Vienna, Austria
| | - Margit Laimer
- Plant Biotechnology Unit, IAM, VIBT, BOKU, Muthgasse 18, A - 1190 Vienna, Austria
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De Barro PJ, Liu SS, Boykin LM, Dinsdale AB. Bemisia tabaci: a statement of species status. ANNUAL REVIEW OF ENTOMOLOGY 2011; 56:1-19. [PMID: 20690829 DOI: 10.1146/annurev-ento-112408-085504] [Citation(s) in RCA: 736] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Bemisia tabaci has long been considered a complex species. It rose to global prominence in the 1980s owing to the global invasion by the commonly named B biotype. Since then, the concomitant eruption of a group of plant viruses known as begomoviruses has created considerable management problems in many countries. However, an enduring set of questions remains: Is B. tabaci a complex species or a species complex, what are Bemisia biotypes, and how did all the genetic variability arise? This review considers these issues and concludes that there is now sufficient evidence to state that B. tabaci is not made up of biotypes and that the use of biotype in this context is erroneous and misleading. Instead, B. tabaci is a complex of 11 well-defined high-level groups containing at least 24 morphologically indistinguishable species.
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Patil BL, Fauquet CM. Differential interaction between cassava mosaic geminiviruses and geminivirus satellites. J Gen Virol 2010; 91:1871-82. [PMID: 20335493 DOI: 10.1099/vir.0.019513-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Geminiviruses are often associated with subviral agents called DNA satellites that require proteins encoded by the helper virus for their replication, movement and encapsidation. Hitherto, most of the single-stranded DNA satellites reported to be associated with members of the family Geminiviridae have been associated with monopartite begomoviruses. Cassava mosaic disease is known to be caused by viruses belonging to nine different begomovirus species in the African continent and the Indian subcontinent. In addition to these species, several strains have been recognized that exhibit contrasting phenotypes and infection dynamics. It is established that Sri Lankan cassava mosaic virus can trans-replicate betasatellites and can cross host barriers. To extend these studies further, we carried out an exhaustive investigation of the ability of geminiviruses, selected to represent all cassava-infecting geminivirus species, to trans-replicate betasatellites (DNA-beta) and to interact with alphasatellites (nanovirus-like components; previously called DNA-1). Each of the cassava-infecting geminiviruses showed a contrasting and differential interaction with the DNA satellites, not only in the capacity to interact with these molecules but also in the modulation of symptom phenotypes by the satellites. These observations could be extrapolated to field situations in order to hypothesize about the possibility of acquisition of such DNA satellites currently associated with other begomoviruses. These results call for more detailed analyses of these subviral components and an investigation of their possible interaction with the cassava mosaic disease complex.
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Affiliation(s)
- Basavaprabhu L Patil
- International Laboratory for Tropical Agricultural Biotechnology (ILTAB), Danforth Plant Science Center, 975 North Warson Road, St Louis, MO 63132, USA
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13
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Duffy S, Holmes EC. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol 2009; 90:1539-1547. [PMID: 19264617 PMCID: PMC4091138 DOI: 10.1099/vir.0.009266-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Accepted: 02/17/2009] [Indexed: 12/16/2022] Open
Abstract
Whitefly-transmitted geminiviruses are major pathogens of the important crop cassava in Africa. The intensive sampling and sequencing of cassava mosaic disease-causing viruses that occurred in the wake of a severe outbreak in Central Africa (1997-2002) allowed us to estimate the rate of evolution of this virus. East African cassava mosaic virus and related species are obligately bipartite (DNA-A and DNA-B segments), and these two genome segments have different evolutionary histories. Despite these phylogenetic differences, we inferred high rates of nucleotide substitution in both segments: mean rates of 1.60x10(-3) and 1.33x10(-4) substitutions site(-1) year(-1) for DNA-A and DNA-B, respectively. While similarly high substitution rates were found in datasets free of detectable recombination, only that estimated for the coat protein gene (AV1), for which an additional DNA-A sequence isolated in 1995 was available, was statistically robust. These high substitution rates also confirm that those previously estimated for the monopartite tomato yellow leaf curl virus (TYLCV) are representative of multiple begomoviruses. We also validated our rate estimates by comparing them with those depicting the emergence of TYLCV in North America. These results further support the notion that geminiviruses evolve as rapidly as many RNA viruses.
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Affiliation(s)
- Siobain Duffy
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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Bull SE, Briddon RW, Sserubombwe WS, Ngugi K, Markham PG, Stanley J. Infectivity, pseudorecombination and mutagenesis of Kenyan cassava mosaic begomoviruses. J Gen Virol 2007; 88:1624-1633. [PMID: 17412996 DOI: 10.1099/vir.0.82662-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cloned DNA-A and DNA-B components of Kenyan isolates of East African cassava mosaic virus (EACMV, EACMV-UG and EACMV-KE2), East African cassava mosaic Kenya virus (EACMKV) and East African cassava mosaic Zanzibar virus (EACMZV) are shown to be infectious in cassava. EACMV and EACMKV genomic components have the same iteron sequence (GGGGG) and can form viable pseudorecombinants, while EACMZV components have a different sequence (GGAGA) and are incompatible with EACMV and EACMKV. Mutagenesis of EACMZV has demonstrated that open reading frames (ORFs) AV1 (encoding the coat protein), AV2 and AC4 are not essential for a symptomatic infection of cassava, although mutants of both ORF AV1 and AV2 produce attenuated symptoms in this host. Furthermore, ORF AV1 and AV2 mutants were compromised for coat protein production, suggesting a close structural and/or functional relationship between these coding regions or their protein products.
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Affiliation(s)
- Simon E Bull
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
| | - Rob W Briddon
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
| | - William S Sserubombwe
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
| | - Kahiu Ngugi
- Kenya Agricultural Research Institute, Katumani Applied Biotechnology Laboratory, PO Box 340, Machakos, Kenya
| | - Peter G Markham
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
| | - John Stanley
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney Lane, Norwich NR4 7UH, UK
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15
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Legg JP, Owor B, Sseruwagi P, Ndunguru J. Cassava mosaic virus disease in East and Central Africa: epidemiology and management of a regional pandemic. Adv Virus Res 2006; 67:355-418. [PMID: 17027685 DOI: 10.1016/s0065-3527(06)67010-3] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- J P Legg
- International Institute of Tropical Agriculture, Dar es Salaam, Tanzania
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16
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Bull SE, Briddon RW, Sserubombwe WS, Ngugi K, Markham PG, Stanley J. Genetic diversity and phylogeography of cassava mosaic viruses in Kenya. J Gen Virol 2006; 87:3053-3065. [PMID: 16963765 DOI: 10.1099/vir.0.82013-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cassava is a major factor in food security across sub-Saharan Africa. However, the crop is susceptible to losses due to biotic stresses, in particular to viruses of the genus Begomovirus (family Geminiviridae) that cause cassava mosaic disease (CMD). During the 1990s, an epidemic of CMD severely hindered cassava production across eastern and central Africa. A significant influence on the appearance of virus epidemics is virus diversity. Here, a survey of the genetic diversity of CMD-associated begomoviruses across the major cassava-growing areas of Kenya is described. Because an initial PCR-restriction fragment-length polymorphism analysis identified a much greater diversity of viruses than assumed previously, representative members of the population were characterized by sequence analysis. The full-length sequences of 109 components (68 DNA-A and 41 DNA-B) were determined, representing isolates of East African cassava mosaic virus and East African cassava mosaic Zanzibar virus, as well as a novel begomovirus species for which the name East African cassava mosaic Kenya virus is proposed. The DNA-B components were much less diverse than their corresponding DNA-A components, but nonetheless segregated into western and eastern (coastal) groups. All virus species and strains encountered showed distinct geographical distributions, highlighting the importance of preventing both the movement of viruses between these regions and the importation of the disease from adjacent countries and islands in the Indian Ocean that would undoubtedly encourage further diversification.
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Affiliation(s)
- Simon E Bull
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney, Norwich NR4 7UH, UK
| | - Rob W Briddon
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney, Norwich NR4 7UH, UK
| | - William S Sserubombwe
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney, Norwich NR4 7UH, UK
| | - Kahiu Ngugi
- Kenya Agricultural Research Institute, Katumani Applied Biotechnology Laboratory, PO Box 340, Machakos, Kenya
| | - Peter G Markham
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney, Norwich NR4 7UH, UK
| | - John Stanley
- Department of Disease and Stress Biology, John Innes Centre (JIC), Colney, Norwich NR4 7UH, UK
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