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Dossou L, Pinel-Galzi A, Aribi J, Poulicard N, Albar L, Fatogoma S, Ndjiondjop MN, Koné D, Hébrard E. Molecular Tools to Infer Resistance-Breaking Abilities of Rice Yellow Mottle Virus Isolates. Viruses 2023; 15:v15040959. [PMID: 37112939 PMCID: PMC10144094 DOI: 10.3390/v15040959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.
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Affiliation(s)
- Laurence Dossou
- AfricaRice Center, M'bé Research Station, Bouaké 01 BP 2551, Côte d'Ivoire
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Jamel Aribi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Laurence Albar
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Sorho Fatogoma
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | | | - Daouda Koné
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
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Farooq T, Hussain MD, Shakeel MT, Riaz H, Waheed U, Siddique M, Shahzadi I, Aslam MN, Tang Y, She X, He Z. Global genetic diversity and evolutionary patterns among Potato leafroll virus populations. Front Microbiol 2022; 13:1022016. [PMID: 36590416 PMCID: PMC9801716 DOI: 10.3389/fmicb.2022.1022016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 01/04/2023] Open
Abstract
Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world.
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Affiliation(s)
- Tahir Farooq
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Muhammad Dilshad Hussain
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Muhammad Taimoor Shakeel
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hasan Riaz
- Institute of Plant Protection, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Ummara Waheed
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Maria Siddique
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Irum Shahzadi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Muhammad Naveed Aslam
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yafei Tang
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Xiaoman She
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
| | - Zifu He
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
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LaTourrette K, Holste NM, Garcia-Ruiz H. Polerovirus genomic variation. Virus Evol 2021; 7:veab102. [PMID: 35299789 PMCID: PMC8923251 DOI: 10.1093/ve/veab102] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/21/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Abstract
The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single-, positive-strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3), and a read-through domain (ORF5) that is fused to the CP to form a CP-read-through (RT) protein. The genus Polerovirus contains twenty-six virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and by the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single-nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and virus protein genome-linked (VPg) contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. The results described here suggest that using contrasting mechanisms, P0, VPg, and CP-RT mediate adaptation to host plants and to vectors and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, and identification of susceptibility genes and contributes to our understanding of virus interactions with their host, vectors, and environment.
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Affiliation(s)
- Katherine LaTourrette
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
- Complex Biosystems Interdisciplinary Life Sciences Program, Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln, 2200 Vine Street, Lincoln, NE 68583, USA
| | - Natalie M Holste
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
| | - Hernan Garcia-Ruiz
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
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Odongo PJ, Onaga G, Ricardo O, Natsuaki KT, Alicai T, Geuten K. Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:671355. [PMID: 34267770 PMCID: PMC8276079 DOI: 10.3389/fpls.2021.671355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.
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Affiliation(s)
- Patrick J. Odongo
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Geoffrey Onaga
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
- M’bé Research Station, Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
| | - Oliver Ricardo
- Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Keiko T. Natsuaki
- Graduate School of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Titus Alicai
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Koen Geuten
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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Rakotomalala M, Vrancken B, Pinel-Galzi A, Ramavovololona P, Hébrard E, Randrianangaly JS, Dellicour S, Lemey P, Fargette D. Comparing patterns and scales of plant virus phylogeography: Rice yellow mottle virus in Madagascar and in continental Africa. Virus Evol 2019; 5:vez023. [PMID: 31384483 PMCID: PMC6671560 DOI: 10.1093/ve/vez023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Rice yellow mottle virus (RYMV) in Madagascar Island provides an opportunity to study the spread of a plant virus disease after a relatively recent introduction in a large and isolated country with a heterogeneous host landscape ecology. Here, we take advantage of field survey data on the occurrence of RYMV disease throughout Madagascar dating back to the 1970s, and of virus genetic data from ninety-four isolates collected since 1989 in most regions of the country to reconstruct the epidemic history. We find that the Malagasy isolates belong to a unique recombinant strain that most likely entered Madagascar through a long-distance introduction from the most eastern part of mainland Africa. We infer the spread of RYMV as a continuous process using a Bayesian statistical framework. In order to calibrate the time scale in calendar time units in this analysis, we pool the information about the RYMV evolutionary rate from several geographical partitions. Whereas the field surveys and the phylogeographic reconstructions both point to a rapid southward invasion across hundreds of kilometers throughout Madagascar within three to four decades, they differ on the inferred origin location and time of the epidemic. The phylogeographic reconstructions suggest a lineage displacement and unveil a re-invasion of the northern regions that may have remained unnoticed otherwise. Despite ecological differences that could affect the transmission potential of RYMV in Madagascar and in mainland Africa, we estimate similar invasion and dispersal rates. We could not identify environmental factors that have a relevant impact on the lineage dispersal velocity of RYMV in Madagascar. This study highlights the value and complementarity of (historical) nongenetic and (more contemporaneous) genetic surveillance data for reconstructing the history of spread of plant viruses.
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Affiliation(s)
- Mbolarinosy Rakotomalala
- Centre Régional de Recherche du Nord-Ouest du FOFIFA, BP 289, Mahavoky Avaratra, Mahajanga 401, Madagascar
| | - Bram Vrancken
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Agnès Pinel-Galzi
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | - Perle Ramavovololona
- Département de Biologie et d'Ecologie Végétales, Faculté des Sciences, Université d'Antananarivo, BP 906
| | - Eugénie Hébrard
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
| | | | - Simon Dellicour
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium.,Spatial Epidemiology Lab, Université Libre de Bruxelles, CP 264 / 3,50 av FD Roosevelt, B-1050 Brussels, Belgium
| | - Philippe Lemey
- Department of Microbiology and Immunology, Laboratory for Clinical and Epidemiological Virology, Rega Institute, KU Leuven, Herestraat 49 box 1040, 3000 Leuven, Belgium
| | - Denis Fargette
- IRD, Cirad, Université Montpellier, IPME, 911 avenue Agropolis, BP 64501 34934 Montpellier cedex 5, France
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Complete Genome Sequences of Rice Yellow Mottle Virus Isolates from the Federal Democratic Republic of Ethiopia. Microbiol Resour Announc 2019; 8:8/30/e00589-19. [PMID: 31346021 PMCID: PMC6658691 DOI: 10.1128/mra.00589-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The full-length genomes of two isolates of Rice yellow mottle virus from Ethiopia were sequenced. A comparison with 28 sequences from East Africa showed that they clustered within a new strain named S4et, related to the S4mg and S4ug strains found in the Lake Victoria Basin and Madagascar, respectively.
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Full-Length Genome Sequences of Recombinant and Nonrecombinant Sympatric Strains of Rice yellow mottle virus from Western Kenya. GENOME ANNOUNCEMENTS 2018; 6:6/8/e01508-17. [PMID: 29472342 PMCID: PMC5824002 DOI: 10.1128/genomea.01508-17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Five isolates of Rice yellow mottle virus from western Kenya were fully sequenced. One isolate of strain S4lv had been collected in 1966. Two isolates belonged to the emerging strain S4ug recently described in Uganda. Two isolates collected in 2012 are putative recombinants between the S4lv and S4ug strains.
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