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Obonyo D, Ouma G, Ikawa R, Odeny DA. Meta-transcriptomic identification of groundnut RNA viruses in western Kenya and the novel detection of groundnut as a host for Cauliflower mosaic virus. Virology 2024; 593:110011. [PMID: 38367474 DOI: 10.1016/j.virol.2024.110011] [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: 10/16/2023] [Revised: 01/22/2024] [Accepted: 01/29/2024] [Indexed: 02/19/2024]
Abstract
BACKGROUND Groundnut (Arachis hypogaea L.) is the 13th most important global crop grown throughout the tropical and subtropical regions of the world. One of the major constraints to groundnut production is viruses, which are also the most economically important and most abundant pathogens among cultivated legumes. Only a few studies have reported the characterization of RNA viruses in cultivated groundnuts in western Kenya, most of which deployed classical methods of detecting known viruses. METHODS We sampled twenty-one symptomatic and three asymptomatic groundnut leaf samples from farmers' fields in western Kenya. Total RNA was extracted from the samples followed by First-strand cDNA synthesis and sequencing on the Illumina HiSeq 2500 platform. After removing host and rRNA sequences, high-quality viral RNA sequences were de novo assembled and viral genomes annotated using the publicly available NCBI virus database. Multiple sequence alignment and phylogenetic analysis were done using MEGA X. RESULTS Bioinformatics analyses using as low as ∼3.5 million reads yielded complete and partial genomes for Cauliflower mosaic virus (CaMV), Cowpea polerovirus 2 (CPPV2), Groundnut rosette assistor virus (GRAV), Groundnut rosette virus (GRV), Groundnut rosette virus satellite RNA (satRNA) and Peanut mottle virus (PeMoV) falling within the species demarcation criteria. This is the first report of CaMV and the second report of CPPV2 on groundnut hosts in the world. Confirmation of the detected viruses was further verified through phylogenetic analyses alongside reported publicly available highly similar viruses. PeMoV was the only seed-borne virus reported. CONCLUSION Our findings demonstrate the power of Next Generation Sequencing in the discovery and identification of novel viruses in groundnuts. The detection of the new viruses indicates the complexity of virus diseases in groundnuts and would require more focus in future studies to establish the effect of the viruses as sole or mixed infections on the crop. The detection of PeMoV with potential origin from Malawi indicates the importance of seed certification and cross-boundary seed health testing.
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Affiliation(s)
- Dennis Obonyo
- Department of Biotechnology, University of Eldoret, Kenya, P.O Box 1125-30100, Eldoret, Kenya; Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - George Ouma
- Institute for Climate Change and Adaptation, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Rachel Ikawa
- Centre for Biotechnology and Bioinformatics, University of Nairobi, P.O Box 30197-00100, Nairobi, Kenya
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, Eastern and Southern Africa, P.O Box 39063-00623, Nairobi, Kenya.
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Achola E, Wasswa P, Fonceka D, Clevenger JP, Bajaj P, Ozias-Akins P, Rami JF, Deom CM, Hoisington DA, Edema R, Odeny DA, Okello DK. Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:35. [PMID: 36897398 PMCID: PMC10006280 DOI: 10.1007/s00122-023-04259-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/21/2022] [Indexed: 06/18/2023]
Abstract
We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523 high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1 on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.
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Affiliation(s)
- Esther Achola
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Daniel Fonceka
- Regional Study Center for the Improvement of Drought Adaptation, Senegalese Institute for Agricultural Research, BP 3320, Thiès, Senegal
- UMR AGAP, CIRAD, 34398, Montpellier, France
- UMR AGAP, CIRAD, BP 3320, Thies, Senegal
| | | | - Prasad Bajaj
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, 502324, India
| | - Peggy Ozias-Akins
- Center for Applied Genetic Technologies, University of Georgia, Tifton, GA, 31793, USA
| | - Jean-François Rami
- UMR AGAP, CIRAD, 34398, Montpellier, France
- UMR AGAP, CIRAD, BP 3320, Thies, Senegal
- CIRAD, INRAE, AGAP, Univ Montpellier, Institut Agro, 34398, Montpellier, France
| | - Carl Michael Deom
- Department of Pathology, The University of Georgia, Athens, GA, 30602, USA
| | - David A Hoisington
- Feed the Future Innovation Lab for Peanut, University of Georgia, Athens, GA, 30602, USA
| | - Richard Edema
- Makerere University Regional Center for Crop Improvement Kampala, P.O. Box 7062, Kampala, Uganda
| | - Damaris Achieng Odeny
- International Crops Research Institute for the Semi-Arid Tropics, PO Box, Nairobi, 39063-00623, Kenya.
| | - David Kalule Okello
- National Semi-Arid Resources Research Institute-Serere, P.O. Box 56, Kampala, Uganda.
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Jones S, Cowan G, MacFarlane S, Mukoye B, Mangeni BC, Were H, Torrance L. RNA sequence analysis of diseased groundnut (Arachis hypogaea) reveals the full genome of groundnut rosette assistor virus (GRAV). Virus Res 2019; 277:197837. [PMID: 31836513 DOI: 10.1016/j.virusres.2019.197837] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/05/2019] [Accepted: 12/09/2019] [Indexed: 10/25/2022]
Abstract
The complete genome sequences for two variant isolates of groundnut rosette assistor virus (GRAV) have been determined from symptomatic groundnut plants in western Kenya. The sequences of the two GRAV isolates (sc7.1 and sc7.2) are 84.2% identical at the nucleotide level and 98.5% identical at the coat protein level. The variants sc7.1 and sc7.2 comprise 5850 and 5879 nucleotides respectively, and show similar genome organizations with 7 predicted ORFs (P0, P1, P2, P3a, P3 (coat protein, CP), P4 (movement protein, MP) and P5 (coat protein-readthrough protein, CP-RT). Currently, GRAV is an unassigned virus in the Luteoviridae family, due to the fact that only the sequence of the coat protein was previously obtained. The presence of both ORF0 and ORF 4 within the genome sequence determined in the current work suggest that GRAV should be classified as a member of the genus Polerovirus.
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Affiliation(s)
- Susan Jones
- Information and Computational Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK.
| | - Graham Cowan
- Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Stuart MacFarlane
- Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK
| | - Benard Mukoye
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Bonphace Collins Mangeni
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Hassan Were
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Lesley Torrance
- Cell and Molecular Sciences Group, The James Hutton Institute, Dundee, DD2 5DA, UK; The School of Biology, University of St Andrews, Biomedical Sciences Research Complex, St Andrews, KY16 9ST, UK
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Hema M, Sreenivasulu P, Patil BL, Kumar PL, Reddy DVR. Tropical food legumes: virus diseases of economic importance and their control. Adv Virus Res 2015; 90:431-505. [PMID: 25410108 DOI: 10.1016/b978-0-12-801246-8.00009-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Diverse array of food legume crops (Fabaceae: Papilionoideae) have been adopted worldwide for their protein-rich seed. Choice of legumes and their importance vary in different parts of the world. The economically important legumes are severely affected by a range of virus diseases causing significant economic losses due to reduction in grain production, poor quality seed, and costs incurred in phytosanitation and disease control. The majority of the viruses infecting legumes are vectored by insects, and several of them are also seed transmitted, thus assuming importance in the quarantine and in the epidemiology. This review is focused on the economically important viruses of soybean, groundnut, common bean, cowpea, pigeonpea, mungbean, urdbean, chickpea, pea, faba bean, and lentil and begomovirus diseases of three minor tropical food legumes (hyacinth bean, horse gram, and lima bean). Aspects included are geographic distribution, impact on crop growth and yields, virus characteristics, diagnosis of causal viruses, disease epidemiology, and options for control. Effectiveness of selection and planting with virus-free seed, phytosanitation, manipulation of crop cultural and agronomic practices, control of virus vectors and host plant resistance, and potential of transgenic resistance for legume virus disease control are discussed.
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Affiliation(s)
- Masarapu Hema
- Department of Virology, Sri Venkateswara University, Tirupati, India
| | - Pothur Sreenivasulu
- Formerly Professor of Virology, Sri Venkateswara University, Tirupati, India
| | - Basavaprabhu L Patil
- National Research Centre on Plant Biotechnology, IARI, Pusa Campus, New Delhi, India
| | - P Lava Kumar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Dodla V R Reddy
- Formerly Principal Virologist, ICRISAT, Patancheru, Hyderabad, India.
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García-Arenal F, McDonald BA. An analysis of the durability of resistance to plant viruses. PHYTOPATHOLOGY 2003; 93:941-52. [PMID: 18943860 DOI: 10.1094/phyto.2003.93.8.941] [Citation(s) in RCA: 115] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
ABSTRACT Genetic resistance often fails because a resistance-breaking (RB) pathogen genotype increases in frequency. On the basis of an analysis of cellular plant pathogens, it was recently proposed that the evolutionary potential of a pathogen is a major determinant of the durability of resistance. We test this hypothesis for plant viruses, which differ substantially from cellular pathogens in the nature, size, and expression of their genomes. Our analysis was based on 29 plant virus species that provide a good representation of the genetic and biological diversity of plant viruses. These 29 viruses were involved in 35 pathosystems, and 50 resistance factors deployed against them were analyzed. Resistance was found to be durable more often than not, in contrast with resistance to cellular plant pathogens. In a third of the analyzed pathosystems RB strains have not been reported, and in another third RB strains have been reported but have not become prevalent in the virus population. The evolutionary potential of the viruses in the 35 pathosystems was evaluated with a compound risk index based on three evolutionary factors: the population of the pathogen, the degree of recombination, and the amount of gene and genotype flow. Our analysis indicates that evolutionary potential may be an important determinant of the durability of resistance against plant viruses.
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de Assis Filho FM, Paguio OR, Sherwood JL, Deom CM. Symptom induction by Cowpea chlorotic mottle virus on Vigna unguiculata is determined by amino acid residue 151 in the coat protein. J Gen Virol 2002; 83:879-883. [PMID: 11907338 DOI: 10.1099/0022-1317-83-4-879] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The type strain of Cowpea chlorotic mottle virus (CCMV-T) produces a bright chlorosis in cowpea (Vigna unguiculata cv. California Blackeye). The attenuated variant (CCMV-M) induces mild green mottle symptoms that were previously mapped to RNA 3. Restriction fragment exchanges between RNA 3 cDNA clones of CCMV-T and CCMV-M that generate infectious transcripts and site-directed mutagenesis indicated that the codon encoding amino acid residue 151 of the coat protein determines the symptom phenotypes of CCMV-T and CCMV-M. Amino acid 151 is within an alpha-helical structure required for calcium ion binding and virus particle stability. No differences in virion stability or accumulation were detected between CCMV-T and CCMV-M. Mutational analysis suggested that the amino acid at position 151 and not the nucleotide sequence induce the symptom phenotype. Thus, it is likely that subtle influences by amino acid residue 151 in coat protein-host interactions result in chlorotic and mild green mottle symptoms.
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Affiliation(s)
- F M de Assis Filho
- Department of Plant Pathology, The University of Georgia, Athens, GA 30602, USA1
| | - O R Paguio
- Department of Plant Pathology, The University of Georgia, Athens, GA 30602, USA1
| | - J L Sherwood
- Department of Plant Pathology, The University of Georgia, Athens, GA 30602, USA1
| | - C M Deom
- Department of Plant Pathology, The University of Georgia, Athens, GA 30602, USA1
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Wangai AW, Pappu SS, Pappu HR, Deom CM, Naidu RA. Distribution and Characteristics of Groundnut Rosette Disease in Kenya. PLANT DISEASE 2001; 85:470-474. [PMID: 30823121 DOI: 10.1094/pdis.2001.85.5.470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Groundnut rosette is a major virus disease of peanut in sub-Saharan Africa. The disease is caused by a complex of three agents: GRAV (groundnut rosette assistor luteovirus), GRV (groundnut rosette umbravirus), and the associated satellite RNA (Sat-RNA). During the 1997 to 1998 crop season, the incidence of rosette in farmers' fields was estimated at 24 to 40% in western Kenya and 30% in the Rift Valley. Sequence analysis of Kenyan isolates revealed that GRAV-CP sequences shared 97 to 100% and 95 to 98% sequence homology at nucleotide and amino acid levels, respectively, amongst themselves and with the Malawian and Nigerian isolates. The ORFs 3 and 4 of GRV were similar, with a homology of 99% at the nucleotide and amino acid levels among Kenyan isolates. The GRV sequences of Kenyan isolates were closer to the Malawian (95 to 96%) than to the Nigerian (87 to 88%) isolates. Sat-RNA shared 89 to 94% nucleotide identity with those from Malawi and Nigeria. A closer sequence relationship was observed between Kenyan and Malawian isolates in all regions compared. This is the first report on the distribution and molecular characterization of groundnut rosette disease complex in East Africa.
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Affiliation(s)
| | | | - H R Pappu
- Department of Plant Pathology, University of Georgia, Coastal Plain Experiment Station, Tifton 31793
| | - C M Deom
- Department of Plant Pathology, University of Georgia, Miller Plant Sciences Building, Athens 30602
| | - R A Naidu
- Department of Plant Pathology, University of Georgia, Miller Plant Sciences Building, Athens 30602
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García-Arenal F, Fraile A, Malpica JM. Variability and genetic structure of plant virus populations. ANNUAL REVIEW OF PHYTOPATHOLOGY 2001; 39:157-86. [PMID: 11701863 DOI: 10.1146/annurev.phyto.39.1.157] [Citation(s) in RCA: 372] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Populations of plant viruses, like all other living beings, are genetically heterogeneous, a property long recognized in plant virology. Only recently have the processes resulting in genetic variation and diversity in virus populations and genetic structure been analyzed quantitatively. The subject of this review is the analysis of genetic variation, its quantification in plant virus populations, and what factors and processes determine the genetic structure of these populations and its temporal change. The high potential for genetic variation in plant viruses, through either mutation or genetic exchange by recombination or reassortment of genomic segments, need not necessarily result in high diversity of virus populations. Selection by factors such as the interaction of the virus with host plants and vectors and random genetic drift may in fact reduce genetic diversity in populations. There is evidence that negative selection results in virus-encoded proteins being not more variable than those of their hosts and vectors. Evidence suggests that small population diversity, and genetic stability, is the rule. Populations of plant viruses often consist of a few genetic variants and many infrequent variants. Their distribution may provide evidence of a population that is undifferentiated, differentiated by factors such as location, host plant, or time, or that fluctuates randomly in composition, depending on the virus.
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Affiliation(s)
- F García-Arenal
- Departamento de Biotecnología, E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, 28040 Madrid, Spain.
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