1
|
Gogile A, Kebede M, Kidanemariam D, Abraham A. Identification of yam mosaic virus as the main cause of yam mosaic diseases in Ethiopia. Heliyon 2024; 10:e26387. [PMID: 38449648 PMCID: PMC10915350 DOI: 10.1016/j.heliyon.2024.e26387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 01/18/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
Yam (Dioscorea spp.) is a staple food crop with cultural, nutritional and economic significance for millions of small-scale farmers in sub-Saharan Africa. While various virus-like symptoms such as mosaic and chlorosis are frequently observed in yam fields in Ethiopia, little information is available on the prevalence, distribution, and molecular characteristics of viruses causing these symptoms. The aim of this study was to investigate the incidence and distribution of yam viruses and determine the primary cause of yam mosaic diseases (YMD) in Ethiopia. Both symptomatic (n = 280) and asymptomatic (n = 110) yam leaf samples were collected and tested for potyviruses using ACP-ELISA. In addition, the symptomatic leaf samples were screened for yam mosaic virus (YMV), yam mild mosaic virus (YMMV), and cucumber mosaic virus (CMV) by DAS-ELISA. Subsequently, total RNA was extracted from 130 leaf samples comprising 94 symptomatic and 36 asymptomatic samples representing the different study areas. The representative RT-PCR amplicons (n = 6) were Sanger sequenced. The ACP-ELISA and DAS-ELISA results showed 9.2%, and 12.9% YMV infection, respectively, while the RT-PCR analysis showed 28.5% YMV positivity rate. Both CMV and YMMV were not detected in any of the samples tested. Thus, YMV is confirmed as the primary cause of YMD in Ethiopia. YMV isolates from Ethiopia shared 92-93% nucleotide identity among themselves and 85-99% with other YMV isolates from the GenBank. Phylogenetic analysis revealed that YMV isolates from Ethiopia, South America, and west-central Africa have the most recent common ancestor, while isolates from China and Japan are clustered as sister groups. This study enhances our understanding of YMV's genetic diversity and provides valuable information regarding the first report of YMV in Ethiopia.
Collapse
Affiliation(s)
- Ashebir Gogile
- Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, P.O.Box 16417, Addis Ababa, Ethiopia
- Department of Biology, College of Natural and Computational Sciences, Wolaita Sodo University, P.O.Box 138, Wolaita Sodo, Ethiopia
| | - Misrak Kebede
- Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, P.O.Box 16417, Addis Ababa, Ethiopia
| | - Dawit Kidanemariam
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria, South Africa
| | - Adane Abraham
- Department of Biotechnology, College of Natural and Applied Sciences, Addis Ababa Science and Technology University, P.O.Box 16417, Addis Ababa, Ethiopia
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Palapye, Botswana
| |
Collapse
|
2
|
Festus RO, Seal SE, Prempeh R, Quain MD, Silva G. Improved Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) for the Rapid and Sensitive Detection of Yam mosaic virus. Viruses 2023; 15:1592. [PMID: 37515278 PMCID: PMC10383231 DOI: 10.3390/v15071592] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/14/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
Yam (Dioscorea spp.) productivity is constrained significantly by the lack of a formal seed system. Vegetative propagation, through tuber setts as 'seed' yams, encourages the recycling of virus-infected planting materials, contributing to high virus incidence and yield losses. Efforts are ongoing to increase the production of high-quality seed yams in a formal seed system to reduce virus-induced yield losses and enhance the crop's productivity and food security. Specific and sensitive diagnostic tests are imperative to prevent the multiplication of virus-infected materials contributing to a sustainable seed yam certification system. During routine indexing of yam accessions, discrepancies were observed between the results obtained from the reverse transcription loop-mediated isothermal amplification (RT-LAMP) test and those from reverse transcription polymerase chain reaction (RT-PCR); RT-LAMP failed to detect Yam mosaic virus (YMV) in some samples that tested positive by RT-PCR. This prompted the design of a new set of LAMP primers, YMV1-OPT primers. These primers detected as little as 0.1 fg/µL of purified RNA obtained from a YMV-infected plant, a sensitivity equivalent to that obtained with RT-PCR. RT-LAMP using YMV1-OPT primers is recommended for all future virus-indexing of seed yams for YMV, offering a rapid, sensitive, and cost-effective approach.
Collapse
Affiliation(s)
- Ruth O Festus
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Susan E Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Ruth Prempeh
- Council for Scientific and Industrial Research-Crops Research Institute, Fumesua, Kumasi P.O. Box 3785, Ghana
| | - Marian D Quain
- Council for Scientific and Industrial Research-Crops Research Institute, Fumesua, Kumasi P.O. Box 3785, Ghana
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| |
Collapse
|
3
|
Diouf MB, Guyader S, Nopoly MM, Gaspard O, Filloux D, Candresse T, Marais A, Teycheney PY, Umber M. Molecular diversity of yam virus Y and identification of banana mild mosaic virus isolates infecting yam (Dioscorea spp.). Arch Virol 2023; 168:180. [PMID: 37311875 DOI: 10.1007/s00705-023-05809-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/02/2023] [Indexed: 06/15/2023]
Abstract
Two members of the family Betaflexiviridae associated with yam (Dioscorea spp.) have been described so far: yam latent virus (YLV) and yam virus Y (YVY). However, their geographical distribution and molecular diversity remain poorly documented. Using a nested RT-PCR assay, we detected YVY in D. alata, D. bulbifera, D. cayenensis, D. rotundata, and D. trifida in Guadeloupe, and in D. rotundata in Côte d'Ivoire, thus extending the known host range of this virus and geographical distribution. Using amplicon sequencing, we determined that the molecular diversity of YVY in the yam samples analyzed in this work ranged between 0.0 and 29.1% and that this diversity is partially geographically structured. We also identified three isolates of banana mild mosaic virus (BanMMV) infecting D. alata in Guadeloupe, providing the first evidence for BanMMV infection in yam.
Collapse
Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France
- CIRAD, UMR AGAP Institut, 97130, Capesterre Belle Eau, France
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle Eau, France
| | | | | | | | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France
- PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, 34090, Montpellier, France
| | - Thierry Candresse
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Armelle Marais
- INRAE, Univ. Bordeaux, UMR BFP, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMT, 97410, Saint-Pierre, La Réunion, France
- UMR PVBMT, Université de la Réunion, 97410, Saint-Pierre, La Réunion, France
| | - Marie Umber
- INRAE, UR ASTRO, 97170, Petit‑Bourg, Guadeloupe, France.
| |
Collapse
|
4
|
Epidemiology of Yam Viruses in Guadeloupe: Role of Cropping Practices and Seed-Tuber Supply. Viruses 2022; 14:v14112366. [PMID: 36366464 PMCID: PMC9692558 DOI: 10.3390/v14112366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 10/20/2022] [Accepted: 10/24/2022] [Indexed: 01/31/2023] Open
Abstract
The epidemiology of yam viruses remains largely unexplored. We present a large-scale epidemiological study of yam viruses in Guadeloupe based on the analysis of 1124 leaf samples collected from yams and weeds. We addressed the prevalence of cucumber mosaic virus (CMV), Cordyline virus 1 (CoV1), Dioscorea mosaic associated virus (DMaV), yam asymptomatic virus 1 (YaV1), yam mosaic virus (YMV), yam mild mosaic virus (YMMV), badnaviruses, macluraviruses and potexviruses, and the key epidemiological drivers of these viruses. We provide evidence that several weeds are reservoirs of YMMV and that YMMV isolates infecting weeds cluster together with those infecting yams, pointing to the role of weeds in the epidemiology of YMMV. We report the occurrence of yam chlorotic necrosis virus (YCNV) in Guadeloupe, the introduction of YMMV isolates through the importation of yam tubers, and the absence of vertical transmission of YaV1. We identified specific effects on some cropping practices, such as weed management and the use of chemical pesticides, on the occurrence of a few viruses, but no crop-related factor had a strong or general effect on the overall epidemiology of the targeted viruses. Overall, our work provides insights into the epidemiology of yam viruses that will help design more efficient control strategies.
Collapse
|
5
|
Diouf MB, Festus R, Silva G, Guyader S, Umber M, Seal S, Teycheney PY. Viruses of Yams (Dioscorea spp.): Current Gaps in Knowledge and Future Research Directions to Improve Disease Management. Viruses 2022; 14:v14091884. [PMID: 36146691 PMCID: PMC9501508 DOI: 10.3390/v14091884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 08/19/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
Viruses are a major constraint for yam production worldwide. They hamper the conservation, movement, and exchange of yam germplasm and are a threat to food security in tropical and subtropical areas of Africa and the Pacific where yam is a staple food and a source of income. However, the biology and impact of yam viruses remains largely unknown. This review summarizes current knowledge on yam viruses and emphasizes gaps that exist in the knowledge of the biology of these viruses, their diagnosis, and their impact on production. It provides essential information to inform the implementation of more effective virus control strategies.
Collapse
Affiliation(s)
- Mame Boucar Diouf
- INRAE, UR ASTRO, F-97170 Petit-Bourg, France
- CIRAD, UMR AGAP Institut, F-97130 Capesterre-Belle-Eau, France
- UMR AGAP Institut, University Montpellier, CIRAD, INRAE, Institut Agro, F-97130 Capesterre-Belle-Eau, France
| | - Ruth Festus
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Gonçalo Silva
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | | | - Marie Umber
- INRAE, UR ASTRO, F-97170 Petit-Bourg, France
| | - Susan Seal
- Natural Resources Institute, University of Greenwich, Central Avenue, Chatham Maritime, Kent ME4 4TB, UK
| | - Pierre Yves Teycheney
- CIRAD, UMR PVBMT, F-97410 Saint Pierre, France
- UMR PVBMT, Université de la Réunion, F-97410 Saint-Pierre, France
- Correspondence: ; Tel.: +33-262-492-819
| |
Collapse
|
6
|
Mendoza AR, Margaria P, Nagata T, Winter S, Blawid R. Characterization of yam mosaic viruses from Brazil reveals a new phylogenetic group and possible incursion from the African continent. Virus Genes 2022; 58:294-307. [PMID: 35538384 DOI: 10.1007/s11262-022-01903-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/31/2022] [Indexed: 11/29/2022]
Abstract
Yam (Dioscorea spp.) is an important crop for smallholder farmers in the Northeast region of Brazil. Wherever yam is grown, diseases caused by yam mosaic virus (YMV) are prevalent. In the present study, the diversity of YMV infecting Dioscorea cayennensis-rotundata was analyzed. In addition, five species of Dioscorea (D. alata, D. altissima, D. bulbifera, D. subhastata, and D. trifida) commonly found in Brazil were analyzed using ELISA and high-throughput sequencing (HTS). YMV was detected only in D. cayennensis-rotundata, of which 66.7% of the samples tested positive in ELISA. Three YMV genome sequences were assembled from HTS and one by Sanger sequencing to group the sequences in a clade phylogenetically distinct from YMV from other origins. Temporal phylogenetic analyses estimated the mean evolutionary rate for the CP gene of YMV as 1.76 × 10-3 substitutions per site per year, and the time to the most recent common ancestor as 168.68 years (95% Highest Posterior Density, HPD: 48.56-363.28 years), with a most likely geographic origin in the African continent. The data presented in this study contribute to reveal key aspects of the probable epidemiological history of YMV in Brazil.
Collapse
Affiliation(s)
- Alejandro Risco Mendoza
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil. .,Department of Plant Pathology, Agronomy Faculty, Universidad Nacional Agraria La Molina, Lima, Peru.
| | - Paolo Margaria
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Tatsuya Nagata
- Department of Cell Biology, Laboratory of Electron Microscopy and Virology, University of Brasília, Distrito Federal, Brasília, Brazil
| | - Stephan Winter
- Plant Virus Department, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures GmbH, Brunswick, Germany
| | - Rosana Blawid
- Department of Agronomy, Fitossanidade, Laboratory of Phytovirology, Federal Rural University of Pernambuco, Recife, Brazil
| |
Collapse
|
7
|
A Review of Viruses Infecting Yam ( Dioscorea spp.). Viruses 2022; 14:v14040662. [PMID: 35458392 PMCID: PMC9033002 DOI: 10.3390/v14040662] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/19/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Yam is an important food staple for millions of people globally, particularly those in the developing countries of West Africa and the Pacific Islands. To sustain the growing population, yam production must be increased amidst the many biotic and abiotic stresses. Plant viruses are among the most detrimental of plant pathogens and have caused great losses of crop yield and quality, including those of yam. Knowledge and understanding of virus biology and ecology are important for the development of diagnostic tools and disease management strategies to combat the spread of yam-infecting viruses. This review aims to highlight current knowledge on key yam-infecting viruses by examining their characteristics, genetic diversity, disease symptoms, diagnostics, and elimination to provide a synopsis for consideration in developing diagnostic strategy and disease management for yam.
Collapse
|
8
|
Umber M, Filloux D, Svanella-Dumas L, Bonheur L, Acina-Mambole I, Gomez RM, Faure C, Anzala F, Pavis C, Roumagnac P, Marais A, Theil S, Candresse T, Teycheney PY. Host range and molecular variability of the sadwavirus dioscorea mosaic associated virus. Arch Virol 2022; 167:917-922. [PMID: 35107668 DOI: 10.1007/s00705-022-05379-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 01/20/2022] [Indexed: 11/02/2022]
Abstract
Dioscorea mosaic associated virus (DMaV) is a member of the genus Sadwavirus, family Secoviridae, that is associated with mosaic symptoms in Dioscorea rotundata in Brazil. The genome of a DMaV isolate detected in D. trifida in Guadeloupe was sequenced by high-throughput sequencing. Using an RT-PCR-based detection assay, we found that DMaV infects D. alata, D. bulbifera, D. cayenensis-rotundata, D. esculenta, and D. trifida accessions conserved in Guadeloupe and Côte d'Ivoire and displays a very high level of molecular diversity in a relatively small region of the genome targeted by the assay. We also provide evidence that DMaV is also present in D. rotundata in Benin and in D. alata in Nigeria.
Collapse
Affiliation(s)
- Marie Umber
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Denis Filloux
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Laurence Svanella-Dumas
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Lydiane Bonheur
- CIRAD, UMR AGAP Institut, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle-Eau, France
| | - Isabelle Acina-Mambole
- CIRAD, UMR AGAP Institut, Station de Neufchâteau, Sainte-Marie, 97130, Capesterre Belle-Eau, France.,UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 97130, Capesterre Belle-Eau, France
| | - Rose-Marie Gomez
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Chantal Faure
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Fabiola Anzala
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Claudie Pavis
- INRAE, UR1321 ASTRO Agrosystèmes tropicaux, 97170, Petit-Bourg, Guadeloupe, France
| | - Philippe Roumagnac
- CIRAD, UMR PHIM, 34090, Montpellier, France.,PHIM Plant Health Institute, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
| | - Armelle Marais
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Sébastien Theil
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Thierry Candresse
- Univ. Bordeaux, INRAE, UMR 1332 Biologie du Fruit et Pathologie, CS20032, 33882, Villenave d'Ornon Cedex, France
| | - Pierre-Yves Teycheney
- CIRAD, UMR PVBMY, F-97410, Saint Pierre, La Réunion, France. .,UMR PVBMT, Université de la Réunion, F-97410, Saint Pierre, La Réunion, France.
| |
Collapse
|