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Chaowongdee S, Vannatim N, Malichan S, Kuncharoen N, Tongyoo P, Siriwan W. Comparative transcriptomics analysis reveals defense mechanisms of Manihot esculenta Crantz against Sri Lanka Cassava MosaicVirus. BMC Genomics 2024; 25:436. [PMID: 38698332 PMCID: PMC11067156 DOI: 10.1186/s12864-024-10315-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Cassava mosaic disease (CMD), caused by Sri Lankan cassava mosaic virus (SLCMV) infection, has been identified as a major pernicious disease in Manihot esculenta Crantz (cassava) plantations. It is widespread in Southeast Asia, especially in Thailand, which is one of the main cassava supplier countries. With the aim of restricting the spread of SLCMV, we explored the gene expression of a tolerant cassava cultivar vs. a susceptible cassava cultivar from the perspective of transcriptional regulation and the mechanisms underlying plant immunity and adaptation. RESULTS Transcriptomic analysis of SLCMV-infected tolerant (Kasetsart 50 [KU 50]) and susceptible (Rayong 11 [R 11]) cultivars at three infection stages-that is, at 21 days post-inoculation (dpi) (early/asymptomatic), 32 dpi (middle/recovery), and 67 dpi (late infection/late recovery)-identified 55,699 expressed genes. Differentially expressed genes (DEGs) between SLCMV-infected KU 50 and R 11 cultivars at (i) 21 dpi to 32 dpi (the early to middle stage), and (ii) 32 dpi to 67 dpi (the middle stage to late stage) were then identified and validated by real-time quantitative PCR (RT-qPCR). DEGs among different infection stages represent genes that respond to and regulate the viral infection during specific stages. The transcriptomic comparison between the tolerant and susceptible cultivars highlighted the role of gene expression regulation in tolerant and susceptible phenotypes. CONCLUSIONS This study identified genes involved in epigenetic modification, transcription and transcription factor activities, plant defense and oxidative stress response, gene expression, hormone- and metabolite-related pathways, and translation and translational initiation activities, particularly in KU 50 which represented the tolerant cultivar in this study.
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Affiliation(s)
- Somruthai Chaowongdee
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Nattachai Vannatim
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Nattakorn Kuncharoen
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Pumipat Tongyoo
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, Nakhon Pathom, 73140, Thailand
| | - Wanwisa Siriwan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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Ibrahim E, Rychlá A, Alquicer G, Slavíková L, Peng Q, Klíma M, Vrbovský V, Trebicki P, Kundu JK. Evaluation of Resistance of Oilseed Rape Genotypes to Turnip Yellows Virus. PLANTS (BASEL, SWITZERLAND) 2023; 12:2501. [PMID: 37447062 DOI: 10.3390/plants12132501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/15/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023]
Abstract
Turnip yellows virus (TuYV), is one of the most important pathogens of oilseed rape, which has caused enormous yield losses in all growing regions of the world in recent years. Therefore, there is a need for resistant varieties for sustainable crop protection. We have investigated the resistance of known varieties and newly developed advanced-breeding lines of oilseed rape to TuYV in greenhouse and field trials. We have analysed the TuYV titre of individual genotypes inoculated with the virus using viruliferous aphids Myzus persicae. The genotypes 'DK Temptation' and 'Rescator' had the lowest and highest virus titres, respectively, and were used as resistant and susceptible models for comparative analyses with other genotypes. In the greenhouse, the best results were obtained with the genotypes 'OP-8143 DH' (2.94 × 105 copies), OP-BN-72 (3.29 × 105 copies), 'Navajo' (3.58 × 105 copies) and 'SG-C 21215' (4.09 × 105 copies), which reached virus titres about 2 times higher than the minimum virus concentration measured in 'DK Temptation' (1.80 × 105 copies). In the field trials, the genotypes 'Navajo' (3.39 × 105 copies), 'OP-8148 DH' (4.44 × 105 copies), 'SG-C 21215' (6.80 × 105 copies) and OP-8480 (7.19 × 105 copies) had the lowest virus titres and reached about 3 times the virus titre of DK Temptation (2.54 × 105 copies). Both trials showed that at least two commercial varieties (e.g., DK Temptation, Navajo) and three advanced breeding lines (e.g., OP-8143 DH, OP-BN-72, SG-C 21215) had low titres of the virus after TuYV infection. This indicates a high level of resistance to TuYV in 'Navajo' or the newly developed breeding lines and the basis of resistance is probably different from R54 (as in 'DK Temptation'). Furthermore, the greenhouse trials together with RT -qPCR-based virus titre analysis could be a cost-effective and efficient method to assess the level of resistance of a given genotype to TuYV infection compared to the field trials. However, further research is needed to identify the underlying mechanisms causing this difference in susceptibility.
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Affiliation(s)
- Emad Ibrahim
- Crop Research Institute, 16106 Prague, Czech Republic
| | - Andrea Rychlá
- OSEVA Development and Research Ltd., Oilseed Research Institute, 74601 Opava, Czech Republic
| | | | | | - Qi Peng
- Crop Research Institute, 16106 Prague, Czech Republic
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | | | - Viktor Vrbovský
- OSEVA Development and Research Ltd., Oilseed Research Institute, 74601 Opava, Czech Republic
| | - Piotr Trebicki
- Applied BioSciences, Macquarie University, Sydney 2109, Australia
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Chaowongdee S, Malichan S, Pongpamorn P, Paemanee A, Siriwan W. Metabolic profiles of Sri Lankan cassava mosaic virus-infected and healthy cassava (Manihot esculenta Crantz) cultivars with tolerance and susceptibility phenotypes. BMC PLANT BIOLOGY 2023; 23:178. [PMID: 37020181 PMCID: PMC10074701 DOI: 10.1186/s12870-023-04181-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND Cassava mosaic disease (CMD) of cassava (Manihot esculenta Crantz) has expanded across many continents. Sri Lankan cassava mosaic virus (SLCMV; family Geminiviridae), which is the predominant cause of CMD in Thailand, has caused agricultural and economic damage in many Southeast Asia countries such as Vietnam, Loas, and Cambodia. The recent SLCMV epidemic in Thailand was commonly found in cassava plantations. Current understanding of plant-virus interactions for SLCMV and cassava is limited. Accordingly, this study explored the metabolic profiles of SLCMV-infected and healthy groups of tolerant (TME3 and KU50) and susceptible (R11) cultivars of cassava. Findings from the study may help to improve cassava breeding, particularly when combined with future transcriptomic and proteomic research. RESULTS SLCMV-infected and healthy leaves were subjected to metabolite extraction followed by ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-HRMS/MS). The resulting data were analyzed using Compound Discoverer software, the mzCloud, mzVault, and ChemSpider databases, and published literature. Of the 85 differential compounds (SLCMV-infected vs healthy groups), 54 were differential compounds in all three cultivars. These compounds were analyzed using principal component analysis (PCA), hierarchical clustering dendrogram analysis, heatmap analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation. Chlorogenic acid, DL-carnitine, neochlorogenic acid, (E)-aconitic acid, and ascorbyl glucoside were differentially expressed only in TME3 and KU50, with chlorogenic acid, (E)-aconitic acid, and neochlorogenic acid being downregulated in both SLCMV-infected TME3 and KU50, DL-carnitine being upregulated in both SLCMV-infected TME3 and KU50, and ascorbyl glucoside being downregulated in SLCMV-infected TME3 but upregulated in SLCMV-infected KU50. Furthermore, 7-hydroxycoumarine was differentially expressed only in TME3 and R11, while quercitrin, guanine, N-acetylornithine, uridine, vorinostat, sucrose, and lotaustralin were differentially expressed only in KU50 and R11. CONCLUSIONS Metabolic profiling of three cassava landrace cultivars (TME3, KU50, and R11) was performed after SLCMV infection and the profiles were compared with those of healthy samples. Certain differential compounds (SLCMV-infected vs healthy groups) in different cultivars of cassava may be involved in plant-virus interactions and could underlie the tolerance and susceptible responses in this important crop.
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Affiliation(s)
- Somruthai Chaowongdee
- Center for Agricultural Biotechnology, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom, 73140, Thailand
- Center of Excellence on Agricultural Biotechnology (AG-BIO/MHESI), Bangkok, 10900, Thailand
| | - Srihunsa Malichan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand
| | - Pornkanok Pongpamorn
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Atchara Paemanee
- National Omics Center (NOC), National Science and Technology Development Agency (NSTDA), Pathum Thani, 12120, Thailand
| | - Wanwisa Siriwan
- Department of Plant Pathology, Faculty of Agriculture, Kasetsart University, Bangkok, 10900, Thailand.
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Jeger MJ. Tolerance of plant virus disease: Its genetic, physiological, and epidemiological significance. Food Energy Secur 2022. [DOI: 10.1002/fes3.440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Michael John Jeger
- Department of Life Sciences, Silwood Park Imperial College London Ascot UK
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Tarquini G, Martini M, Maestri S, Firrao G, Ermacora P. The Virome of ‘Lamon Bean’: Application of MinION Sequencing to Investigate the Virus Population Associated with Symptomatic Beans in the Lamon Area, Italy. PLANTS 2022; 11:plants11060779. [PMID: 35336661 PMCID: PMC8951528 DOI: 10.3390/plants11060779] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022]
Abstract
‘Lamon bean’ is a protected geographical indication (PGI) for a product of four varieties of bean (Phaseolus vulgaris L.) grown in a specific area of production, which is located in the Belluno district, Veneto region (N.E. of Italy). In the last decade, the ‘Lamon bean’ has been threatened by severe virus epidemics that have compromised its profitability. In this work, the full virome of seven bean samples showing different foliar symptoms was obtained by MinION sequencing. Evidence that emerged from sequencing was validated through RT-PCR and ELISA in a large number of plants, including different ecotypes of Lamon bean and wild herbaceous hosts that may represent a virus reservoir in the field. Results revealed the presence of bean common mosaic virus (BCMV), cucumber mosaic virus (CMV), peanut stunt virus (PSV), and bean yellow mosaic virus (BYMV), which often occurred as mixed infections. Moreover, both CMV and PSV were reported in association with strain-specific satellite RNAs (satRNAs). In conclusion, this work sheds light on the cause of the severe diseases affecting the ‘Lamon bean’ by exploitation of MinION sequencing.
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Affiliation(s)
- Giulia Tarquini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Marta Martini
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Simone Maestri
- Department of Biotechnology, University of Verona, I-37134 Verona, Italy;
| | - Giuseppe Firrao
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
| | - Paolo Ermacora
- Department of Agriculture, Food, Environmental and Animal Sciences, University of Udine, I-33100 Udine, Italy; (G.T.); (M.M.); (G.F.)
- Correspondence:
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Xu W, Guo Y, Li H, Sivasithamparam K, Jones MGK, Chen X, Wylie SJ. Differential Symptom Development and Viral RNA Loads in 10 Nicotiana benthamiana Accessions Infected with the Tobamovirus Yellow Tailflower Mild Mottle Virus. PLANT DISEASE 2022; 106:984-989. [PMID: 34735277 DOI: 10.1094/pdis-08-21-1697-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Yellow tailflower mild mottle virus (YTMMV, genus Tobamovirus) was identified from wild plants of solanaceous species in Australia. Nicotiana benthamiana is a species indigenous to the arid north of Australia. N. benthamiana accession RA-4 (the lab type), which has a mutant, functionally defective, RNA-dependent RNA polymerase 1 (Rdr1) gene (Nb-Rdr1m), has played a significant role in plant virology, but little study has been done regarding responses to virus infection by other accessions of N. benthamiana. All wild-collected N. benthamiana accessions used in this study harbored wild-type Rdr1 genes (Nb-Rdr1). We compared symptoms of YTMMV infection and viral RNA load on RA-4 and nine wild-collected accessions of N. benthamiana from mainland Western Australia, an island, and the Northern Territory. After inoculation with YTMMV, RA-4 plants responded with systemic hypersensitivity and all individuals were dead 35 days postinoculation (dpi). Plants of wild-collected accessions exhibited a range of symptoms, from mild to severe, and some, but not all, died in the same period. Quantitative reverse transcription PCR revealed that the Rdr1 mutation was not a predictor of viral RNA load or symptom severity. For example, wild-collected A019412 plants carried more than twice the viral RNA load of RA-4 plants, but symptom expression was moderate. For plants of most accessions, viral RNA load did not increase after 10 dpi. The exception was plants of accession Barrow-1, in which viral RNA load was low until 15 dpi, after which it increased more than 29-fold. This study revealed differential responses by N. benthamiana accessions to infection by an isolate of YTMMV. The Rdr1 gene, whether mutant or wild-type, did not appear to influence viral RNA load or disease expression. Genetic diversity of the 10 N. benthamiana accessions in some cases reflected geographical location, but in other accessions this was not so.
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Affiliation(s)
- Weinan Xu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yuxia Guo
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou 450002, China
| | - Hua Li
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
| | - Krishnapillai Sivasithamparam
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
| | - Michael G K Jones
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Stephen J Wylie
- Plant Biotechnology Research Group (Virology), Western Australian State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
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7
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Agaoua A, Bendahmane A, Moquet F, Dogimont C. Membrane Trafficking Proteins: A New Target to Identify Resistance to Viruses in Plants. PLANTS 2021; 10:plants10102139. [PMID: 34685948 PMCID: PMC8541145 DOI: 10.3390/plants10102139] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/27/2021] [Accepted: 10/05/2021] [Indexed: 11/16/2022]
Abstract
Replication cycles from most simple-stranded positive RNA viruses infecting plants involve endomembrane deformations. Recent published data revealed several interactions between viral proteins and plant proteins associated with vesicle formation and movement. These plant proteins belong to the COPI/II, SNARE, clathrin and ESCRT endomembrane trafficking mechanisms. In a few cases, variations of these plant proteins leading to virus resistance have been identified. In this review, we summarize all known interactions between these plant cell mechanisms and viruses and highlight strategies allowing fast identification of variant alleles for membrane-associated proteins.
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Affiliation(s)
- Aimeric Agaoua
- INRAE Génétique et Amélioration des Fruits et Légumes (GAFL), 84140 Montfavet, France;
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences-Paris-Saclay (IPS2), Université Paris-Saclay, INRAE, CNRS, Univ Evry, 91405 Orsay, France;
| | | | - Catherine Dogimont
- INRAE Génétique et Amélioration des Fruits et Légumes (GAFL), 84140 Montfavet, France;
- Correspondence:
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Bakayoko Y, Kouakou AM, Kouassi AB, Gomez R, Dibi KEB, Essis BS, N’Zué B, Adebola P, N’Guetta AS, Umber M. Detection and diversity of viruses infecting African yam ( Dioscorea rotundata) in a collection and F 1 progenies in Côte d'Ivoire shed light to plant-to-plant viral transmission. PLANT PATHOLOGY 2021; 70:1486-1495. [PMID: 34413548 PMCID: PMC8360134 DOI: 10.1111/ppa.13393] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 04/02/2021] [Accepted: 04/15/2021] [Indexed: 05/03/2023]
Abstract
Yam (Dioscorea spp.) is a major staple food whose production is hampered by viral diseases. However, the prevalence, diversity, transmission, and impact of yam-infecting viruses remain poorly documented. This study reports on the symptomatology, prevalence, and molecular diversity of eight viruses in 38 D. rotundata accessions from a germplasm collection and 206 F1 hybrid progenies maintained in Côte d'Ivoire. Mean severity scores as assessed from leaf symptoms ranged from 2 to 4 in the germplasm collection and from 1 to 3 in F1 hybrids, respectively. Dioscorea mosaic-associated virus (DMaV), potexviruses, and yam mosaic virus (YMV) were detected by PCR-based diagnosis tools in single and mixed infections in both the D. rotundata collection and F1 progenies, whereas badnaviruses were detected only in the germplasm collection. In contrast, cucumber mosaic virus (CMV), yam macluraviruses, yam asymptomatic virus 1 (YaV1), and yam mild mosaic virus (YMMV) could not be detected. No correlation could be established between severity scores and indexing results. Phylogenetic analysis performed on partial viral sequences amplified from infected samples unveiled the presence of two putative novel viral species belonging to genera Badnavirus and Potexvirus and provided evidence for plant-to-plant transmission of YMV, DMaV, and yam potexviruses.
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Affiliation(s)
- Yacouba Bakayoko
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Amani M. Kouakou
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Abou B. Kouassi
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Rose‐Marie Gomez
- Unité de Recherche Agrosystèmes TropicauxInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’EnvironnementPetit‐BourgGuadeloupeFrance
| | - Konan E. B. Dibi
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Brice S. Essis
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Boni N’Zué
- Station de Recherche sur les Cultures Vivrières (SRCVCentre National de Recherche AgronomiqueBouakéCôte d'Ivoire
| | - Patrick Adebola
- International Institut of Tropical AgricultureIITA‐Abuja StationAbujaNigeria
| | - Assanvon S.‐P. N’Guetta
- Laboratoire de BiotechnologieAgriculture et Valorisation des Ressources BiologiquesUFR BiosciencesUniversité Félix Houphouët BoignyAbidjanCôte d'Ivoire
| | - Marie Umber
- Unité de Recherche Agrosystèmes TropicauxInstitut National de Recherche pour l’Agriculture, l’Alimentation et l’EnvironnementPetit‐BourgGuadeloupeFrance
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9
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Riaz T, Ashfaq M, Khan Z. Evaluation of the Chilli veinal mottle virus CP gene expressing transgenic Nicotiana benthamiana plants for disease resistance against the virus. BRAZ J BIOL 2021; 82:e243692. [PMID: 34161429 DOI: 10.1590/1519-6984.243692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/11/2020] [Indexed: 11/22/2022] Open
Abstract
Vegetables are an important source of income and high-value crops for small farmers. Chilli (Capsicum spp.) is one of the most economically important vegetables of Pakistan and it is grown throughout the country. It is a rich source of nutrition especially vitamins A, B, C and E along with minerals as folic acid, manganese (Mn), potassium (K) and molybdenum (Mo). Chilli possesses seven times more amount of vitamin C than an orange. Vitamin A, C and beta-carotenoids are strong antioxidants to scavenge the free radicals. Chilli production is restricted due to various biotic factors. Among these viruses, Chilli veinal mottle virus (ChiVMV) is one of the most destructive and menacing agents that inflicts heavy and colossal losses that accounted for 50% yield loss both in quality and quantity. Pathogen-Derived Resistance (PDR) approach is considered one of the effective approaches to manage plant viruses. In this study, ChiVMV was characterized on a molecular level, the coat protein (CP) gene of the virus was stably transformed into Nicotiana benthamiana plants using Agrobacterium tumefaciens. The transgenic plants were challenged with the virus to evaluate the level of resistance of plants against the virus. It was observed that the plants expressing CP gene have partial resistance against the virus in terms of symptoms' development and virus accumulation. Translation of this technique into elite chilli varieties will be resulted to mitigate the ChiVMV in the crop as well as an economic benefit to the farmers.
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Affiliation(s)
- T Riaz
- PMAS-Arid Agriculture University, Department of Plant Pathology, Rawalpindi, Pakistan
| | - M Ashfaq
- MNS University of Agriculture, Institute of Plant Protection - IPP, Plant Pathology, Multan, Pakistan
| | - Z Khan
- MNS University of Agriculture, Institute of Plant Breeding and Biotechnology - IPBB, Multan, Pakistan
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10
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Rimbaud L, Papaïx J, Barrett LG, Burdon JJ, Thrall PH. Mosaics, mixtures, rotations or pyramiding: What is the optimal strategy to deploy major gene resistance? Evol Appl 2018; 11:1791-1810. [PMID: 30459830 PMCID: PMC6231482 DOI: 10.1111/eva.12681] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 06/14/2018] [Accepted: 07/06/2018] [Indexed: 01/08/2023] Open
Abstract
Once deployed uniformly in the field, genetically controlled plant resistance is often quickly overcome by pathogens, resulting in dramatic losses. Several strategies have been proposed to constrain the evolutionary potential of pathogens and thus increase resistance durability. These strategies can be classified into four categories, depending on whether resistance sources are varied across time (rotations) or combined in space in the same cultivar (pyramiding), in different cultivars within a field (cultivar mixtures) or among fields (mosaics). Despite their potential to differentially affect both pathogen epidemiology and evolution, to date the four categories of deployment strategies have never been directly compared together within a single theoretical or experimental framework, with regard to efficiency (ability to reduce disease impact) and durability (ability to limit pathogen evolution and delay resistance breakdown). Here, we used a spatially explicit stochastic demogenetic model, implemented in the R package landsepi, to assess the epidemiological and evolutionary outcomes of these deployment strategies when two major resistance genes are present. We varied parameters related to pathogen evolutionary potential (mutation probability and associated fitness costs) and landscape organization (mostly the relative proportion of each cultivar in the landscape and levels of spatial or temporal aggregation). Our results, broadly focused on qualitative resistance to rust fungi of cereal crops, show that evolutionary and epidemiological control are not necessarily correlated and that no deployment strategy is universally optimal. Pyramiding two major genes offered the highest durability, but at high mutation probabilities, mosaics, mixtures and rotations can perform better in delaying the establishment of a universally infective superpathogen. All strategies offered the same short-term epidemiological control, whereas rotations provided the best long-term option, after all sources of resistance had broken down. This study also highlights the significant impact of landscape organization and pathogen evolutionary ability in considering the optimal design of a deployment strategy.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | | | - Luke G. Barrett
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Jeremy J. Burdon
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
| | - Peter H. Thrall
- CSIRO Agriculture and FoodCanberraAustralian Capital TerritoryAustralia
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11
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Role of the Genetic Background in Resistance to Plant Viruses. Int J Mol Sci 2018; 19:ijms19102856. [PMID: 30241370 PMCID: PMC6213453 DOI: 10.3390/ijms19102856] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 01/03/2023] Open
Abstract
In view of major economic problems caused by viruses, the development of genetically resistant crops is critical for breeders but remains limited by the evolution of resistance-breaking virus mutants. During the plant breeding process, the introgression of traits from Crop Wild Relatives results in a dramatic change of the genetic background that can alter the resistance efficiency or durability. Here, we conducted a meta-analysis on 19 Quantitative Trait Locus (QTL) studies of resistance to viruses in plants. Frequent epistatic effects between resistance genes indicate that a large part of the resistance phenotype, conferred by a given QTL, depends on the genetic background. We next reviewed the different resistance mechanisms in plants to survey at which stage the genetic background could impact resistance or durability. We propose that the genetic background may impair effector-triggered dominant resistances at several stages by tinkering the NB-LRR (Nucleotide Binding-Leucine-Rich Repeats) response pathway. In contrast, effects on recessive resistances by loss-of-susceptibility-such as eIF4E-based resistances-are more likely to rely on gene redundancy among the multigene family of host susceptibility factors. Finally, we show how the genetic background is likely to shape the evolution of resistance-breaking isolates and propose how to take this into account in order to breed plants with increased resistance durability to viruses.
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Rimbaud L, Papaïx J, Rey JF, Barrett LG, Thrall PH. Assessing the durability and efficiency of landscape-based strategies to deploy plant resistance to pathogens. PLoS Comput Biol 2018; 14:e1006067. [PMID: 29649208 PMCID: PMC5918245 DOI: 10.1371/journal.pcbi.1006067] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 04/24/2018] [Accepted: 02/27/2018] [Indexed: 11/18/2022] Open
Abstract
Genetically-controlled plant resistance can reduce the damage caused by pathogens. However, pathogens have the ability to evolve and overcome such resistance. This often occurs quickly after resistance is deployed, resulting in significant crop losses and a continuing need to develop new resistant cultivars. To tackle this issue, several strategies have been proposed to constrain the evolution of pathogen populations and thus increase genetic resistance durability. These strategies mainly rely on varying different combinations of resistance sources across time (crop rotations) and space. The spatial scale of deployment can vary from multiple resistance sources occurring in a single cultivar (pyramiding), in different cultivars within the same field (cultivar mixtures) or in different fields (mosaics). However, experimental comparison of the efficiency (i.e. ability to reduce disease impact) and durability (i.e. ability to limit pathogen evolution and delay resistance breakdown) of landscape-scale deployment strategies presents major logistical challenges. Therefore, we developed a spatially explicit stochastic model able to assess the epidemiological and evolutionary outcomes of the four major deployment options described above, including both qualitative resistance (i.e. major genes) and quantitative resistance traits against several components of pathogen aggressiveness: infection rate, latent period duration, propagule production rate, and infectious period duration. This model, implemented in the R package landsepi, provides a new and useful tool to assess the performance of a wide range of deployment options, and helps investigate the effect of landscape, epidemiological and evolutionary parameters. This article describes the model and its parameterisation for rust diseases of cereal crops, caused by fungi of the genus Puccinia. To illustrate the model, we use it to assess the epidemiological and evolutionary potential of the combination of a major gene and different traits of quantitative resistance. The comparison of the four major deployment strategies described above will be the objective of future studies. There are many recent examples which demonstrate the evolutionary potential of plant pathogens to overcome the resistances deployed in agricultural landscapes to protect our crops. Increasingly, it is recognised that how resistance is deployed spatially and temporally can impact on rates of pathogen evolution and resistance breakdown. Such deployment strategies are mainly based on the combination of several sources of resistance at different spatiotemporal scales. However, comparison of these strategies in a predictive sense is not an easy task, owing to the logistical difficulties associated with experiments involving the spread of a pathogen at large spatio-temporal scales. Moreover, both the durability of a strategy and the epidemiological protection it provides to crops must be assessed since these evaluation criteria are not necessarily correlated. Surprisingly, no current simulation model allows a thorough comparison of the different options. Here we describe a spatio-temporal model able to simulate a wide range of deployment strategies and resistance sources. This model, implemented in the R package landsepi, facilitates assessment of both epidemiological and evolutionary outcomes across simulated scenarios. In this work, the model is used to investigate the combination of different sources of resistance against fungal diseases such as rusts of cereal crops.
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Affiliation(s)
- Loup Rimbaud
- CSIRO Agriculture and Food, Canberra, ACT, Australia
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Hébrard E, Pinel-Galzi A, Oludare A, Poulicard N, Aribi J, Fabre S, Issaka S, Mariac C, Dereeper A, Albar L, Silué D, Fargette D. Identification of a Hypervirulent Pathotype of Rice yellow mottle virus: A Threat to Genetic Resistance Deployment in West-Central Africa. PHYTOPATHOLOGY 2018; 108:299-307. [PMID: 28990483 DOI: 10.1094/phyto-05-17-0190-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Rice yellow mottle virus (RYMV) causes high losses to rice production in Africa. Several sources of varietal high resistance are available but the emergence of virulent pathotypes that are able to overcome one or two resistance alleles can sometimes occur. Both resistance spectra and viral adaptability have to be taken into account to develop sustainable rice breeding strategies against RYMV. In this study, we extended previous resistance spectrum analyses by testing the rymv1-4 and rymv1-5 alleles that are carried by the rice accessions Tog5438 and Tog5674, respectively, against isolates that are representative of RYMV genetic and pathogenic diversity. Our study revealed a hypervirulent pathotype, named thereafter pathotype T', that is able to overcome all known sources of high resistance. This pathotype, which is spatially localized in West-Central Africa, appears to be more abundant than previously suspected. To better understand the adaptive processes of pathotype T', molecular determinants of resistance breakdown were identified via Sanger sequencing and validated through directed mutagenesis of an infectious clone. These analyses confirmed the key role of convergent nonsynonymous substitutions in the central part of the viral genome-linked protein to overcome RYMV1-mediated resistance. In addition, deep-sequencing analyses revealed that resistance breakdown does not always coincide with fixed mutations. Actually, virulence mutations that are present in a small proportion of the virus population can be sufficient for resistance breakdown. Considering the spatial distribution of RYMV strains in Africa and their ability to overcome the RYMV resistance genes and alleles, we established a resistance-breaking risk map to optimize strategies for the deployment of sustainable and resistant rice lines in Africa.
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Affiliation(s)
- Eugénie Hébrard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Agnès Pinel-Galzi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Aderonke Oludare
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Nils Poulicard
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Jamel Aribi
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Sandrine Fabre
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Souley Issaka
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Cédric Mariac
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Alexis Dereeper
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Laurence Albar
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Drissa Silué
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
| | - Denis Fargette
- First, second, fourth, fifth, sixth, ninth, eleventh, and twelfth authors: IRD, Cirad, Université Montpellier, IPME, Montpellier, France; third author: AfricaRice Center, 01 BP 2551, Bouaké 01, Côte d'Ivoire; seventh author: FSAE, Université de Tillabéri, BP 175 Tillabéri, Niger; and eighth and tenth authors: IRD, Université Montpellier, DIADE, Montpellier, France
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15
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Moffett P. Transfer and modification of NLR proteins for virus resistance in plants. Curr Opin Virol 2017; 26:43-48. [DOI: 10.1016/j.coviro.2017.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 11/16/2022]
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16
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Pidon H, Ghesquière A, Chéron S, Issaka S, Hébrard E, Sabot F, Kolade O, Silué D, Albar L. Fine mapping of RYMV3: a new resistance gene to Rice yellow mottle virus from Oryza glaberrima. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:807-818. [PMID: 28144699 DOI: 10.1007/s00122-017-2853-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 01/04/2017] [Indexed: 05/24/2023]
Abstract
A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV. The specificity of Tog5307 resistance was analyzed using 18 RYMV isolates. While three of them were able to infect Tog5307 very rapidly, resistance against the others was effective despite infection events attributed to resistance-breakdown or incomplete penetrance of the resistance. Segregation of resistance in an interspecific backcross population derived from a cross between Tog5307 and the susceptible Oryza sativa variety IR64 showed that resistance is dominant and is controlled by a single gene, named RYMV3. RYMV3 was mapped in an approximately 15-kb interval in which two candidate genes, coding for a putative transmembrane protein and a CC-NBS-LRR domain-containing protein, were annotated. Sequencing revealed non-synonymous polymorphisms between Tog5307 and the O. glaberrima susceptible accession CG14 in both candidate genes. An additional resistant O. glaberrima accession, Tog5672, was found to have the Tog5307 genotype for the CC-NBS-LRR gene but not for the putative transmembrane protein gene. Analysis of the cosegregation of Tog5672 resistance with the RYMV3 locus suggests that RYMV3 is also involved in Tog5672 resistance, thereby supporting the CC-NBS-LRR gene as the best candidate for RYMV3.
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Affiliation(s)
- Hélène Pidon
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Alain Ghesquière
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Sophie Chéron
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Souley Issaka
- Africa Rice Center, Cotonou, Benin
- FSAE, Université de Tillabéri, Tillabéri, Niger
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement - Centre de Coopération Internationale en Recherche Agronomique pour le Développement - Université de Montpellier, Montpellier, France
| | - François Sabot
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Olufisayo Kolade
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
- Africa Rice Center, Cotonou, Benin
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | | | - Laurence Albar
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France.
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17
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Wang LJ, Sun R, Vasile T, Chang YC, Li L. High-Throughput Optical Sensing Immunoassays on Smartphone. Anal Chem 2016; 88:8302-8. [DOI: 10.1021/acs.analchem.6b02211] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Li-Ju Wang
- School
of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Rongrong Sun
- School
of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Tina Vasile
- Irrigated
Agriculture Research and Extension Center, Washington State University, Prosser, Washington 99350, United States
| | - Yu-Chung Chang
- School
of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, United States
| | - Lei Li
- School
of Mechanical and Materials Engineering, Washington State University, Pullman, Washington 99164, United States
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18
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Bengyella L, Waikhom SD, Allie F, Rey C. Virus tolerance and recovery from viral induced-symptoms in plants are associated with transcriptome reprograming. PLANT MOLECULAR BIOLOGY 2015; 89:243-52. [PMID: 26358043 DOI: 10.1007/s11103-015-0362-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 08/08/2015] [Indexed: 05/07/2023]
Abstract
Plant recovery from viral infection is characterized by initial severe systemic symptoms which progressively decrease, leading to reduced symptoms or symptomless leaves at the apices. A key feature to plant recovery from invading nucleic acids such as viruses is the degree of the host's initial basal immunity response. We review current links between RNA silencing, recovery and tolerance, and present a model in which, in addition to regulation of resistance (R) and other defence-related genes by RNA silencing, viral infections incite perturbations of the host physiological state that trigger reprogramming of host responses to by-pass severe symptom development, leading to partial or complete recovery. Recovery, in particular in perennial hosts, may trigger tolerance or virus accommodation. We discuss evidence suggesting that plant viruses can avoid total clearance but persistently replicate at low levels, thereby modulating the host transcriptome response which minimizes fitness cost and triggers recovery from viral-symptoms. In some cases a susceptible host may fail to recover from initial viral systemic symptoms, yet, accommodates the persistent virus throughout the life span, a phenomenon herein referred to as non-recovery accommodation, which differs from tolerance in that there is no distinct recovery phase, and differs from susceptibility in that the host is not killed. Recent advances in plant recovery from virus-induced symptoms involving host transcriptome reprogramming are discussed.
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Affiliation(s)
- Louis Bengyella
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts 6, Ave, Johannesburg, Braamfontein, 2000, South Africa
| | - Sayanika D Waikhom
- Centre of Advanced Study in Life Sciences, Manipur University, Imphal, Manipur, 795003, India
- School of Basic and Biomedical Science, University of Health and Allied Sciences, PMB 31, Ho, Volta Region, Ghana
| | - Farhahna Allie
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts 6, Ave, Johannesburg, Braamfontein, 2000, South Africa
| | - Chrissie Rey
- School of Molecular and Cell Biology, University of the Witwatersrand, 1, Jan Smuts 6, Ave, Johannesburg, Braamfontein, 2000, South Africa.
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19
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Poque S, Pagny G, Ouibrahim L, Chague A, Eyquard JP, Caballero M, Candresse T, Caranta C, Mariette S, Decroocq V. Allelic variation at the rpv1 locus controls partial resistance to Plum pox virus infection in Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:159. [PMID: 26109391 PMCID: PMC4479089 DOI: 10.1186/s12870-015-0559-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2015] [Accepted: 06/17/2015] [Indexed: 05/09/2023]
Abstract
BACKGROUND Sharka is caused by Plum pox virus (PPV) in stone fruit trees. In orchards, the virus is transmitted by aphids and by grafting. In Arabidopsis, PPV is transferred by mechanical inoculation, by biolistics and by agroinoculation with infectious cDNA clones. Partial resistance to PPV has been observed in the Cvi-1 and Col-0 Arabidopsis accessions and is characterized by a tendency to escape systemic infection. Indeed, only one third of the plants are infected following inoculation, in comparison with the susceptible Ler accession. RESULTS Genetic analysis showed this partial resistance to be monogenic or digenic depending on the allelic configuration and recessive. It is detected when inoculating mechanically but is overcome when using biolistic or agroinoculation. A genome-wide association analysis was performed using multiparental lines and 147 Arabidopsis accessions. It identified a major genomic region, rpv1. Fine mapping led to the positioning of rpv1 to a 200 kb interval on the long arm of chromosome 1. A candidate gene approach identified the chloroplast phosphoglycerate kinase (cPGK2) as a potential gene underlying the resistance. A virus-induced gene silencing strategy was used to knock-down cPGK2 expression, resulting in drastically reduced PPV accumulation. CONCLUSION These results indicate that rpv1 resistance to PPV carried by the Cvi-1 and Col-0 accessions is linked to allelic variations at the Arabidopsis cPGK2 locus, leading to incomplete, compatible interaction with the virus.
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Affiliation(s)
- S Poque
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Current address: Department of Plant Pathology, National Chung Hsing University, Taichung, 402, Taiwan.
| | - G Pagny
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - L Ouibrahim
- INRA-UR1052, Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, CS 60094, F-84143, Montfavet cedex, France.
| | - A Chague
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - J-P Eyquard
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - M Caballero
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - T Candresse
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
| | - C Caranta
- INRA-UR1052, Genetics and Breeding of Fruits and Vegetables, Dom. St Maurice, CS 60094, F-84143, Montfavet cedex, France.
| | - S Mariette
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Current address: INRA, UMR 1202 Biogeco, F- 33610, Cestas, France.
- Current address: Univ. Bordeaux, UMR1202 Biogeco, F-33400, Talence, France.
| | - V Decroocq
- INRA, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
- Université de Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, cedex, France.
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Faoro F, Gozzo F. Is modulating virus virulence by induced systemic resistance realistic? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2015; 234:1-13. [PMID: 25804804 DOI: 10.1016/j.plantsci.2015.01.011] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 01/17/2015] [Accepted: 01/20/2015] [Indexed: 06/04/2023]
Abstract
Induction of plant resistance, either achieved by chemicals (systemic acquired resistance, SAR) or by rhizobacteria (induced systemic resistance, ISR) is a possible and/or complementary alternative to manage virus infections in crops. SAR mechanisms operating against viruses are diverse, depending on the pathosystem, and may inhibit virus replication as well as cell-to-cell and long-distance movement. Inhibition is often mediated by salicylic acid with the involvement of alternative oxidase and reactive oxygen species. However, salicylate may also stimulate a separate downstream pathway, leading to the induction of an additional mechanism, based on RNA-dependent RNA polymerase 1-mediated RNA silencing. Thus, SAR and RNA silencing would closely cooperate in the defence against virus infection. Despite tremendous recent progress in the knowledge of SAR mechanisms, only a few compounds, including benzothiadiazole and chitosan have been shown to reduce the severity of systemic virus disease in controlled environment and, more modestly, in open field. Finally, ISR induction, has proved to be a promising strategy to control virus disease, particularly by seed bacterization with a mixture of plant growth-promoting rhizobacteria. However, the use of any of these treatments should be integrated with cultivation practices that reduce vector pressure by the use of insecticides, or by Bt crops.
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Affiliation(s)
- Franco Faoro
- Department of Agricultural and Environmental Sciences, University of Milan, Via Celoria 2, 20133 Milano, Italy; CNR, Institute for Sustainable Plant Protection, Strada delle Cacce 73, 10135 Turin, Italy.
| | - Franco Gozzo
- Department of Food, Environmental and Nutritional Sciences, Section of Chemistry and Biomolecular Sciences, University of Milano, Via Celoria 2, 20133 Milano, Italy
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21
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Ammara UE, Mansoor S, Saeed M, Amin I, Briddon RW, Al-Sadi AM. RNA interference-based resistance in transgenic tomato plants against Tomato yellow leaf curl virus-Oman (TYLCV-OM) and its associated betasatellite. Virol J 2015; 12:38. [PMID: 25890080 PMCID: PMC4359554 DOI: 10.1186/s12985-015-0263-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 02/10/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tomato yellow leaf curl virus (TYLCV), a monopartite begomovirus (family Geminiviridae) is responsible for heavy yield losses for tomato production around the globe. In Oman at least five distinct begomoviruses cause disease in tomato, including TYLCV. Unusually, TYLCV infections in Oman are sometimes associated with a betasatellite (Tomato leaf curl betasatellite [ToLCB]; a symptom modulating satellite). RNA interference (RNAi) can be used to develop resistance against begomoviruses at either the transcriptional or post-transcriptional levels. RESULTS A hairpin RNAi (hpRNAi) construct to express double-stranded RNA homologous to sequences of the intergenic region, coat protein gene, V2 gene and replication-associated gene of Tomato yellow leaf curl virus-Oman (TYLCV-OM) was produced. Initially, transient expression of the hpRNAi construct at the site of virus inoculation was shown to reduce the number of plants developing symptoms when inoculated with either TYLCV-OM or TYLCV-OM with ToLCB-OM to Nicotiana benthamiana or tomato. Solanum lycopersicum L. cv. Pusa Ruby was transformed with the hpRNAi construct and nine confirmed transgenic lines were obtained and challenged with TYLCV-OM and ToLCB-OM by Agrobacterium-mediated inoculation. For all but one line, for which all plants remained symptomless, inoculation with TYLCV-OM led to a proportion (≤25%) of tomato plants developing symptoms of infection. For inoculation with TYLCV-OM and ToLCB-OM all lines showed a proportion of plants (≤45%) symptomatic. However, for all infected transgenic plants the symptoms were milder and virus titre in plants was lower than in infected non-transgenic tomato plants. CONCLUSIONS These results show that RNAi can be used to develop resistance against geminiviruses in tomato. The resistance in this case is not immunity but does reduce the severity of infections and virus titer. Also, the betasatellite may compromise resistance, increasing the proportion of plants which ultimately show symptoms.
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Affiliation(s)
- Um e Ammara
- Department of Crop Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, P.O. Box-34, 123, Al-Khod, Oman.
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Muhammad Saeed
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Rob W Briddon
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), P O Box 577, Jhang Road, Faisalabad, Pakistan.
| | - Abdullah Mohammed Al-Sadi
- Department of Crop Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, P.O. Box-34, 123, Al-Khod, Oman.
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Kaweesi T, Kawuki R, Kyaligonza V, Baguma Y, Tusiime G, Ferguson ME. Field evaluation of selected cassava genotypes for cassava brown streak disease based on symptom expression and virus load. Virol J 2014. [PMID: 25526680 DOI: 10.1186/s1j%202985-014-0216-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023] Open
Abstract
BACKGROUND Production of cassava (Manihot esculenta Crantz), a food security crop in sub-Saharan Africa, is threatened by the spread of cassava brown streak disease (CBSD) which manifests in part as a corky necrosis in the storage root. It is caused by either of two virus species, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), resulting in up to 100% yield loss in susceptible varieties. METHODS This study characterized the response of 11 cassava varieties according to CBSD symptom expression and relative CBSV and UCBSV load in a field trial in Uganda. Relative viral load was measured using quantitative RT-PCR using COX as an internal housekeeping gene. RESULTS A complex situation was revealed with indications of different resistance mechanisms that restrict virus accumulation and symptom expression. Four response categories were defined. Symptom expression was not always positively correlated with virus load. Substantially different levels of the virus species were found in many genotypes suggesting either resistance to one virus species or the other, or some form of interaction, antagonism or competition between virus species. CONCLUSIONS A substantial amount of research still needs to be undertaken to fully understand the mechanism and genetic bases of resistance. This information will be useful in informing breeding strategies and restricting virus spread.
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Affiliation(s)
- Tadeo Kaweesi
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Robert Kawuki
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Vincent Kyaligonza
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Yona Baguma
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Geoffrey Tusiime
- Makerere University, College of Agricultural and Environmental Sciences, Kampala, Uganda.
| | - Morag E Ferguson
- International Institute of Tropical Agriculture (IITA), c/o ILRI, P.O Box 30709, Nairobi, 00100, Kenya.
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Kaweesi T, Kawuki R, Kyaligonza V, Baguma Y, Tusiime G, Ferguson ME. Field evaluation of selected cassava genotypes for cassava brown streak disease based on symptom expression and virus load. Virol J 2014; 11:216. [PMID: 25526680 PMCID: PMC4304613 DOI: 10.1186/s12985-014-0216-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 11/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Production of cassava (Manihot esculenta Crantz), a food security crop in sub-Saharan Africa, is threatened by the spread of cassava brown streak disease (CBSD) which manifests in part as a corky necrosis in the storage root. It is caused by either of two virus species, Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), resulting in up to 100% yield loss in susceptible varieties. METHODS This study characterized the response of 11 cassava varieties according to CBSD symptom expression and relative CBSV and UCBSV load in a field trial in Uganda. Relative viral load was measured using quantitative RT-PCR using COX as an internal housekeeping gene. RESULTS A complex situation was revealed with indications of different resistance mechanisms that restrict virus accumulation and symptom expression. Four response categories were defined. Symptom expression was not always positively correlated with virus load. Substantially different levels of the virus species were found in many genotypes suggesting either resistance to one virus species or the other, or some form of interaction, antagonism or competition between virus species. CONCLUSIONS A substantial amount of research still needs to be undertaken to fully understand the mechanism and genetic bases of resistance. This information will be useful in informing breeding strategies and restricting virus spread.
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Affiliation(s)
- Tadeo Kaweesi
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Robert Kawuki
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Vincent Kyaligonza
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Yona Baguma
- National Crops Resources Research Institute, Root Crop Program, Namulonge, Uganda.
| | - Geoffrey Tusiime
- Makerere University, College of Agricultural and Environmental Sciences, Kampala, Uganda.
| | - Morag E Ferguson
- International Institute of Tropical Agriculture (IITA), c/o ILRI, P.O Box 30709, Nairobi, 00100, Kenya.
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Galvez LC, Banerjee J, Pinar H, Mitra A. Engineered plant virus resistance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 228:11-25. [PMID: 25438782 DOI: 10.1016/j.plantsci.2014.07.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 07/16/2014] [Accepted: 07/18/2014] [Indexed: 06/04/2023]
Abstract
Virus diseases are among the key limiting factors that cause significant yield loss and continuously threaten crop production. Resistant cultivars coupled with pesticide application are commonly used to circumvent these threats. One of the limitations of the reliance on resistant cultivars is the inevitable breakdown of resistance due to the multitude of variable virus populations. Similarly, chemical applications to control virus transmitting insect vectors are costly to the farmers, cause adverse health and environmental consequences, and often result in the emergence of resistant vector strains. Thus, exploiting strategies that provide durable and broad-spectrum resistance over diverse environments are of paramount importance. The development of plant gene transfer systems has allowed for the introgression of alien genes into plant genomes for novel disease control strategies, thus providing a mechanism for broadening the genetic resources available to plant breeders. Genetic engineering offers various options for introducing transgenic virus resistance into crop plants to provide a wide range of resistance to viral pathogens. This review examines the current strategies of developing virus resistant transgenic plants.
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Affiliation(s)
- Leny C Galvez
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Joydeep Banerjee
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Hasan Pinar
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA
| | - Amitava Mitra
- Department of Plant Pathology, University of Nebarska, Lincoln, NE 68583-0722, USA.
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Sorel M, Svanella-Dumas L, Candresse T, Acelin G, Pitarch A, Houvenaghel MC, German-Retana S. Key mutations in the cylindrical inclusion involved in lettuce mosaic virus adaptation to eIF4E-mediated resistance in lettuce. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1014-24. [PMID: 25105805 DOI: 10.1094/mpmi-04-14-0111-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We previously showed that allelic genes mol¹ and mo1² used to protect lettuce crops against Lettuce mosaic virus (LMV) correspond to mutant alleles of the gene encoding the eukaryotic translation initiation factor 4E. LMV resistance-breaking determinants map not only to the main potyvirus virulence determinant, a genome-linked viral protein, but also to the C-terminal region of the cylindrical inclusion (CI), with a key role of amino acid at position 621. Here, we show that the propagation of several non-lettuce isolates of LMV in mo1¹ plants is accompanied by a gain of virulence correlated with the presence in the CI C terminus of a serine at position 617 and the accumulation of mutations at positions 602 or 627. Whole-genome sequencing of native and evolved isolates showed that no other mutation could be associated with adaptation to mo1 resistance. Site-directed mutagenesis pinpointed the key role in the virulence of the combination of mutations at positions 602 and 617, in addition to position 621. The impact of these mutations on the fitness of the virus was evaluated, suggesting that the durability of mo1 resistance in the field relies on the fitness cost associated with the resistance-breaking mutations, the nature of the mutations, and their potential antagonistic effects.
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Djian-Caporalino C, Palloix A, Fazari A, Marteu N, Barbary A, Abad P, Sage-Palloix AM, Mateille T, Risso S, Lanza R, Taussig C, Castagnone-Sereno P. Pyramiding, alternating or mixing: comparative performances of deployment strategies of nematode resistance genes to promote plant resistance efficiency and durability. BMC PLANT BIOLOGY 2014; 14:53. [PMID: 24559060 PMCID: PMC3944934 DOI: 10.1186/1471-2229-14-53] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 02/14/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Resistant cultivars are key elements for pathogen control and pesticide reduction, but their repeated use may lead to the emergence of virulent pathogen populations, able to overcome the resistance. Increased research efforts, mainly based on theoretical studies, explore spatio-temporal deployment strategies of resistance genes in order to maximize their durability. We evaluated experimentally three of these strategies to control root-knot nematodes: cultivar mixtures, alternating and pyramiding resistance genes, under controlled and field conditions over a 3-years period, assessing the efficiency and the durability of resistance in a protected crop rotation system with pepper as summer crop and lettuce as winter crop. RESULTS The choice of the resistance gene and the genetic background in which it is introgressed, affected the frequency of resistance breakdown. The pyramiding of two different resistance genes in one genotype suppressed the emergence of virulent isolates. Alternating different resistance genes in rotation was also efficient to decrease virulent populations in fields due to the specificity of the virulence and the trapping effect of resistant plants. Mixing resistant cultivars together appeared as a less efficient strategy to control nematodes. CONCLUSIONS This work provides experimental evidence that, in a cropping system with seasonal sequences of vegetable species, pyramiding or alternating resistance genes benefit yields in the long-term by increasing the durability of resistant cultivars and improving the long-term control of a soil-borne pest. To our knowledge, this result is the first one obtained for a plant-nematode interaction, which helps demonstrate the general applicability of such strategies for breeding and sustainable management of resistant cultivars against pathogens.
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Affiliation(s)
| | - Alain Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS 60094, Montfavet, Cedex F-84143, France
| | - Ariane Fazari
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Nathalie Marteu
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Arnaud Barbary
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Pierre Abad
- INRA, UMR1355 INRA/UNSA/CNRS, Institut Sophia Agrobiotech, BP167, Sophia Antipolis F-06903, France
| | - Anne-Marie Sage-Palloix
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS 60094, Montfavet, Cedex F-84143, France
| | - Thierry Mateille
- IRD, UMR CBGP, Campus de Baillarguet, CS30016, Montferrier-sur-Lez, Cedex F-34988, France
| | - Sabine Risso
- Chambre d’Agriculture des Alpes Maritimes, MIN Fleurs 17 - Box 85, Nice, Cedex 06286, France
| | - Roger Lanza
- Chambre d’Agriculture des Alpes Maritimes, MIN Fleurs 17 - Box 85, Nice, Cedex 06286, France
| | - Catherine Taussig
- APREL, Association Provençale de Recherche et d’Expérimentation Légumière, Route de Mollégès, Saint-Rémy de Provence F-13210, France
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Leroy T, Le Cam B, Lemaire C. When virulence originates from non-agricultural hosts: new insights into plant breeding. INFECTION GENETICS AND EVOLUTION 2014; 27:521-9. [PMID: 24412509 DOI: 10.1016/j.meegid.2013.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 12/11/2013] [Accepted: 12/30/2013] [Indexed: 12/27/2022]
Abstract
Monogenic plant resistance breakdown is a model for testing evolution in action in pathogens. As a rule, plant pathologists argue that virulence - the allele that allows pathogens to overcome resistance - is due to a new mutation at the avirulence locus within the native/endemic population that infects susceptible crops. In this article, we develop an alternative and neglected scenario where a given virulence pre-exists in a non-agricultural host and might be accidentally released or introduced on the matching resistant cultivar in the field. The main difference between the two scenarios is the divergence time expected between the avirulent and the virulent populations. As a consequence, population genetic approaches such as genome scans and Approximate Bayesian Computation methods allow explicit testing of the two scenarios by timing the divergence. This review then explores the fundamental implications of this alternative scenario for plant breeding, including the invasion of virulence or the evolution of more aggressive hybrids, and proposes concrete solutions to achieve a sustainable resistance.
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Affiliation(s)
- Thibault Leroy
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France
| | - Bruno Le Cam
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France
| | - Christophe Lemaire
- Université d'Angers, IRHS, PRES LUNAM, SFR QUASAV, Boulevard Lavoisier, 49045 Angers, France; INRA, IRHS, PRES LUNAM, SFR QUASAV, Rue Georges Morel, 49071 Beaucouzé, France; Agrocampus Ouest, IRHS, PRES LUNAM, SFR QUASAV, Rue Le Nôtre, 49045 Angers, France.
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28
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Abstract
More than 70 well-characterized virus species transmitted by a diversity of vectors may infect cucurbit crops worldwide. Twenty of those cause severe epidemics in major production areas, occasionally leading to complete crop failures. Cucurbit viruses' control is based on three major axes: (i) planting healthy seeds or seedlings in a clean environment, (ii) interfering with vectors activity, and (iii) using resistant cultivars. Seed disinfection and seed or seedling quality controls guarantee growers on the sanitary status of their planting material. Removal of virus or vector sources in the crop environment can significantly delay the onset of viral epidemics. Insecticide or oil application may reduce virus spread in some situations. Diverse cultural practices interfere with or prevent vector reaching the crop. Resistance can be obtained by grafting for soil-borne viruses, by cross-protection, or generally by conventional breeding or genetic engineering. The diversity of the actions that may be taken to limit virus spread in cucurbit crops and their limits will be discussed. The ultimate goal is to provide farmers with technical packages that combine these methods within an integrated disease management program and are adapted to different countries and cropping systems.
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Affiliation(s)
- Hervé Lecoq
- INRA, UR407, Station de Pathologie Végétale, Montfavet Cedex, France.
| | - Nikolaos Katis
- Faculty of Agriculture, Forestry and Natural Environment, School of Agriculture, Plant Pathology Lab, Aristotle University of Thessaloniki, Thessaloniki, Greece
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29
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Bragard C, Caciagli P, Lemaire O, Lopez-Moya JJ, MacFarlane S, Peters D, Susi P, Torrance L. Status and prospects of plant virus control through interference with vector transmission. ANNUAL REVIEW OF PHYTOPATHOLOGY 2013; 51:177-201. [PMID: 23663003 DOI: 10.1146/annurev-phyto-082712-102346] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Most plant viruses rely on vector organisms for their plant-to-plant spread. Although there are many different natural vectors, few plant virus-vector systems have been well studied. This review describes our current understanding of virus transmission by aphids, thrips, whiteflies, leafhoppers, planthoppers, treehoppers, mites, nematodes, and zoosporic endoparasites. Strategies for control of vectors by host resistance, chemicals, and integrated pest management are reviewed. Many gaps in the knowledge of the transmission mechanisms and a lack of available host resistance to vectors are evident. Advances in genome sequencing and molecular technologies will help to address these problems and will allow innovative control methods through interference with vector transmission. Improved knowledge of factors affecting pest and disease spread in different ecosystems for predictive modeling is also needed. Innovative control measures are urgently required because of the increased risks from vector-borne infections that arise from environmental change.
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Affiliation(s)
- C Bragard
- Earth & Life Institute, Université Catholique de Louvain, B-1348 Louvain-la-Neuve, Belgium.
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30
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Fabre F, Rousseau E, Mailleret L, Moury B. Durable strategies to deploy plant resistance in agricultural landscapes. THE NEW PHYTOLOGIST 2012; 193:1064-1075. [PMID: 22260272 DOI: 10.1111/j.1469-8137.2011.04019.x] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The deployment of resistant crops often leads to the emergence of resistance-breaking pathogens that suppress the yield benefit provided by the resistance. Here, we theoretically explored how farmers' main leverages (resistant cultivar choice, resistance deployment strategy, landscape planning and cultural practices) can be best combined to achieve resistance durability while minimizing yield losses as a result of plant viruses. Assuming a gene-for-gene type of interaction, virus epidemics are modelled in a landscape composed of a mosaic of resistant and susceptible fields, subjected to seasonality, and a reservoir hosting viruses year-round. The model links the genetic and the epidemiological processes, shaping at nested scales the demogenetic dynamics of viruses. The choice of the resistance gene (characterized by the equilibrium frequency of the resistance-breaking virus at mutation-selection balance in a susceptible plant) is the most influential leverage of action. Our results showed that optimal strategies of resistance deployment range from 'mixture' (where susceptible and resistant cultivars coexist) to 'pure' strategies (with only resistant cultivar) depending on the resistance characteristics and the epidemiological context (epidemic incidence and landscape connectivity). We demonstrate and discuss gaps concerning virus epidemiology across the agro-ecological interface that must be filled to achieve sustainable disease management.
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Affiliation(s)
- Frédéric Fabre
- INRA, UR 407 Unité De Pathologie Végétale, F-84140 Montfavet, France
| | - Elsa Rousseau
- INRA, UR 407 Unité De Pathologie Végétale, F-84140 Montfavet, France
- INRA, UR 880 URIH, 400 route des Chappes, BP 167, F-06903 Sophia Antipolis, France
| | - Ludovic Mailleret
- INRA, UR 880 URIH, 400 route des Chappes, BP 167, F-06903 Sophia Antipolis, France
- INRIA, Biocore Team, F-06902 Sophia Antipolis, France
| | - Benoit Moury
- INRA, UR 407 Unité De Pathologie Végétale, F-84140 Montfavet, France
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31
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Abstract
Cucurbit crops may be affected by at least 28 different viruses in the Mediterranean basin. Some of these viruses are widely distributed and cause severe yield losses while others are restricted to limited areas or specific crops, and have only a negligible economic impact. A striking feature of cucurbit viruses in the Mediterranean basin is their always increasing diversity. Indeed, new viruses are regularly isolated and over the past 35 years one "new" cucurbit virus has been reported on average every 2 years. Among these "new" viruses some were already reported in other parts of the world, but others such as Zucchini yellow mosaic virus (ZYMV), one of the most severe cucurbit viruses and Cucurbit aphid-borne yellows virus (CABYV), one of the most prevalent cucurbit viruses, were first described in the Mediterranean area. Why this region may be a potential "hot-spot" for cucurbit virus diversity is not fully known. This could be related to the diversity of cropping practices, of cultivar types but also to the important commercial exchanges that always prevailed in this part of the world. This chapter describes the major cucurbit viruses occurring in the Mediterranean basin, discusses factors involved in their emergence and presents options for developing sustainable control strategies.
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Affiliation(s)
- Hervé Lecoq
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, Montfavet, France
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32
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Abstract
Compared to other vegetable crops, the major viral constraints affecting pepper crops in the Mediterranean basin have been remarkably stable for the past 20 years. Among these viruses, the most prevalent ones are the seed-transmitted tobamoviruses; the aphid-transmitted Potato virus Y and Tobacco etch virus of the genus Potyvirus, and Cucumber mosaic virus member of the genus Cucumovirus; and thrips-transmitted tospoviruses. The last major viral emergence concerns the tospovirus Tomato spotted wilt virus (TSWV), which has undergone major outbreaks since the end of the 1980s and the worldwide dispersal of the thrips vector Frankliniella occidentalis from the western part of the USA. TSWV outbreaks in the Mediterranean area might have been the result of both viral introductions from Northern America and local reemergence of indigenous TSWV isolates. In addition to introductions of new viruses, resistance breakdowns constitute the second case of viral emergences. Notably, the pepper resistance gene Tsw toward TSWV has broken down a few years after its deployment in several Mediterranean countries while there has been an expansion of L³-resistance breaking pepper mild mottle tobamovirus isolates. Beyond the agronomical and economical concerns induced by the breakdowns of virus resistance genes in pepper, they also constitute original models to understand plant-virus interactions and (co)evolution.
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Affiliation(s)
- Benoît Moury
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, Montfavet, France
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33
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Fujiwara A, Inukai T, Kim BM, Masuta C. Combinations of a host resistance gene and the CI gene of turnip mosaic virus differentially regulate symptom expression in Brassica rapa cultivars. Arch Virol 2011; 156:1575-81. [PMID: 21625976 DOI: 10.1007/s00705-011-1036-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Accepted: 05/14/2011] [Indexed: 11/28/2022]
Abstract
In the pathosystem of Brassica rapa and turnip mosaic virus (TuMV), the type of symptoms expressed by susceptible plants are determined by the gene combinations between the host cultivar and virus strain. In this study, we found that the resistance reaction and symptoms such as systemic lethal necrosis, leaf malformation and mosaic were differentially determined, depending on the combinations of the genotypes for a host locus or two closely linked host loci and the viral CI gene. Systemic necrosis caused by TuMV-UK1 on some B. rapa subsp. pekinensis cultivars is induced in conjunction with a recessive gene, rnt1-2 (resistance and necrosis to tumv 1-2), which is allelic or closely linked to TuMV resistance gene Rnt1-1 on chromosome R6. rnt1-2 is incompletely recessive to rnt1-3, which does not cause any necrotic responses. The genotype rnt1-2/rnt1-3 caused a mild necrosis along leaf veins of severely malformed leaves. A spontaneous mutant, TuMV-UK1 (UK1m), with the amino acid substitution V1827E in CI, broke Rnt1-1 resistance and altered the systemic necrosis and leaf malformation induced by rnt1-2. This single amino acid in the CI protein of UK1 was also associated with severe mosaic and abnormal leaf development, perhaps interacting with unknown host factors. To clarify the relationship between Rnt1-1 and TuRB01b, which was previously reported as a TuMV-UK1 resistance gene on chromosome R6, the B. rapa cultivar Tropical Delight carrying TuRB01b was inoculated with UK1m or the infectious UK1 clone with the CI V1827E mutation. Because Tropical Delight showed resistance to both mutants, Rnt1-1 might be different from TuRB01b.
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Affiliation(s)
- Ayaka Fujiwara
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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34
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Coutts BA, Kehoe MA, Jones RAC. Minimising losses caused by Zucchini yellow mosaic virus in vegetable cucurbit crops in tropical, sub-tropical and Mediterranean environments through cultural methods and host resistance. Virus Res 2011; 159:141-60. [PMID: 21549770 DOI: 10.1016/j.virusres.2011.04.015] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/14/2011] [Indexed: 11/17/2022]
Abstract
Between 2006 and 2009, 10 field experiments were done at Kununurra, Carnarvon or Medina in Western Australia (WA) which have tropical, sub-tropical and Mediterranean climates, respectively. These experiments investigated the effectiveness of cultural control measures in limiting ZYMV spread in pumpkin, and single-gene resistance in commercial cultivars of pumpkin, zucchini and cucumber. Melon aphids (Aphis gossypii) colonised field experiments at Kununurra; migrant green peach aphids (Myzus persicae) visited but did not colonise at Carnarvon and Medina. Cultural control measures that diminished ZYMV spread in pumpkin included manipulation of planting date to avoid exposing young plants to peak aphid vector populations, deploying tall non-host barriers (millet, Pennisetum glaucum) to protect against incoming aphid vectors and planting upwind of infection sources. Clustering of ZYMV-infected pumpkin plants was greater without a 25m wide non-host barrier between the infection source and the pumpkin plants than when one was present, and downwind compared with upwind of an infection source. Host resistance gene zym was effective against ZYMV isolate Knx-1 from Kununurra in five cultivars of cucumber. In zucchini, host resistance gene Zym delayed spread of infection (partial resistance) in 2 of 14 cultivars but otherwise did not diminish final ZYMV incidence. Zucchini cultivars carrying Zym often developed severe fruit symptoms (8/14), and only the two cultivars in which spread was delayed and one that was tolerant produced sufficiently high marketable yields to be recommended when ZYMV epidemics are anticipated. In three pumpkin cultivars with Zym, this gene was effective against isolate Cvn-1 from Carnarvon under low inoculum pressure, but not against isolate Knx-1 under high inoculum pressure, although symptoms were milder and marketable yields greater in them than in cultivars without Zym. These findings allowed additional cultural control recommendations to be added to the existing Integrated Disease Management strategy for ZYMV in vegetable cucurbits in WA, but necessitated modification of its recommendations over deployment of cultivars with resistance genes.
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Affiliation(s)
- B A Coutts
- Crop Protection Branch, Department of Agriculture and Food Western Australia, Locked Bag No. 4, Bentley Delivery Centre, Perth, WA 6983, Australia.
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35
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Janzac B, Montarry J, Palloix A, Navaud O, Moury B. A point mutation in the polymerase of Potato virus Y confers virulence toward the Pvr4 resistance of pepper and a high competitiveness cost in susceptible cultivar. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2010; 23:823-830. [PMID: 20459321 DOI: 10.1094/mpmi-23-6-0823] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
To understand why the Pvr4 resistance of pepper against Potyvirus spp. remained durable in field conditions while virulent Potato virus Y (PVY) variants could be selected in the laboratory, we studied the molecular mechanisms which generated these variants and the consequences on viral fitness. Using a reverse genetics approach with an infectious cDNA clone of PVY, we found that the region coding for the NIb protein (RNA-dependent RNA polymerase) of PVY was the avirulence factor corresponding to Pvr4 and that a single nonsynonymous nucleotide substitution in that region, an adenosine to guanosine substitution at position 8,424 of the PVY genome (A(8424)G), was sufficient for virulence. This substitution imposed a high competitiveness cost to the virus against an avirulent PVY variant in plants devoid of Pvr4. In addition, during serial passages in susceptible pepper plants, the only observed possibility of the virulent mutant to increase its fitness was through the G(8424)A reversion, strengthening the high durability potential of the Pvr4 resistance. This is in accordance with the fact that the NIb protein is one of the most constrained proteins expressed by the PVY genome and, more generally, by Potyvirus spp., and with a previously developed model predicting the durability of virus resistances as a function of the evolutionary constraint applied on corresponding avirulence factors.
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García-Cano E, Navas-Castillo J, Moriones E, Fernández-Muñoz R. Resistance to Tomato chlorosis virus in wild tomato species that impair virus accumulation and disease symptom expression. PHYTOPATHOLOGY 2010; 100:582-92. [PMID: 20465414 DOI: 10.1094/phyto-100-6-0582] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Tomato chlorosis virus (ToCV) (genus Crinivirus, family Closteroviridae) is an emerging threat to tomato crops worldwide. Although symptoms on fruits are not obvious, yield losses occur through decreased fruit size and number. Control of ToCV epidemics is difficult because the virus is transmitted by several whitefly vector species and its relatively wide host range facilitates establishment in local wild reservoirs. Therefore, breeding for ToCV resistance offers the best control alternative. However, no sources for resistance are available thus far. Here, a screen of tomatoes and wild species relatives was performed in search of ToCV resistance. Two sources of resistance to ToCV were identified in this work, lines '802-11-1' and '821-13-1', each derived by two self-pollinations from ToCV asymptomatic plants of the population 'IAC CN RT' (derived from an interspecific hybrid Solanum lycopersicum x S. peruvianum accession LA0444) and accession LA1028 (S. chmielewskii), respectively. The resistance was expressed by impairing virus accumulation and disease symptom expression, both under natural infection and after challenging with ToCV in controlled inoculations. Genetic control of resistance to ToCV infection in '821-13-1' was conferred by a major locus with mainly additive effects but also partial dominance for higher susceptibility. Also, an additive x dominance epistatic interaction with at least one additional gene was evident.
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Affiliation(s)
- Elena García-Cano
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
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Dedryver CA, Le Ralec A, Fabre F. The conflicting relationships between aphids and men: a review of aphid damage and control strategies. C R Biol 2010; 333:539-53. [PMID: 20541165 DOI: 10.1016/j.crvi.2010.03.009] [Citation(s) in RCA: 183] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this review, after giving some figures on the economic impact of aphids on agricultural production, we describe the different mechanisms leading to yield losses (direct damage due to sieve drain and plant reaction, indirect damage, often the most important, due to virus transmission). Then, after a history of chemical control and of its limits, the main control strategies (chemical control with decision rules, plant resistance, biological control, farming practices) are reviewed in the light of an integrated pest management approach. Several topics tackled in this article are exemplified for cereal aphids, which are among the most important in Europe as direct feeders and virus vectors.
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Affiliation(s)
- Charles-Antoine Dedryver
- Unité mixte de recherche biologie des organismes et des populations appliquée à la protection des plantes (BiO3P), Inra/Agrocampus Ouest/université Rennes 1, domaine de la Motte, BP 35327, 35653 Le Rheu cedex, France.
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Resistance-driven selection of begomoviruses associated with the tomato yellow leaf curl disease. Virus Res 2009; 146:66-72. [DOI: 10.1016/j.virusres.2009.08.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2009] [Revised: 06/25/2009] [Accepted: 08/28/2009] [Indexed: 11/20/2022]
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Rubio M, Nicolaï M, Caranta C, Palloix A. Allele mining in the pepper gene pool provided new complementation effects between pvr2-eIF4E and pvr6-eIF(iso)4E alleles for resistance to pepper veinal mottle virus. J Gen Virol 2009; 90:2808-2814. [DOI: 10.1099/vir.0.013151-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Molecular cloning of recessive resistance genes to potyviruses in a large range of host species identified the eukaryotic translation initiation factor 4E (eIF4E) as an essential determinant in the outcome of potyvirus infection. Resistance results from a few amino acid changes in the eIF4E protein encoded by the recessive resistance allele that disrupt the direct interaction with the potyviral protein VPg. In plants, several loci encode two protein subfamilies, eIF4E and eIF(iso)4E. While most eIF4E-mediated resistance to potyviruses depends on mutations in a single eIF4E protein, simultaneous mutations in eIF4E (corresponding to the pvr2 locus) and eIF(iso)4E (corresponding to the pvr6 locus) are required to prevent pepper veinal mottle virus (PVMV) infection in pepper. We used this model to look for additional alleles at the pvr2-eIF4E locus that result in resistance when combined with the pvr6-eIF(iso)4E resistant allele. Among the 12 pvr2-eIF4E resistance alleles sequenced in the pepper gene pool, three were shown to have a complementary effect with pvr6-eIF(iso)4E for resistance. Two amino acid changes were exclusively shared by these three alleles and were systematically associated with a second amino acid change, suggesting that these substitutions are associated with resistance expression. The availability of new resistant allele combinations increases the possibility for the durable deployment of resistance against this pepper virus which is prevalent in Africa.
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Affiliation(s)
- Manuel Rubio
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
| | - Maryse Nicolaï
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
| | - Carole Caranta
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
| | - Alain Palloix
- INRA, Centre d'Avignon, UR1052, Unité de Génétique et Amélioration des Fruits et Légumes, BP 94, 84143 Montfavet cedex, France
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Janzac B, Fabre F, Palloix A, Moury B. Constraints on evolution of virus avirulence factors predict the durability of corresponding plant resistances. MOLECULAR PLANT PATHOLOGY 2009; 10:599-610. [PMID: 19694951 PMCID: PMC6640373 DOI: 10.1111/j.1364-3703.2009.00554.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
SUMMARY Understanding the factors driving pathogen emergence and re-emergence is a major challenge, particularly in agriculture, where the use of resistant plant cultivars imposes strong selective pressures on plant pathogen populations and leads frequently to 'resistance breakdown'. Presently, durable resistances are only identified after a long period of large-scale cultivation of resistant cultivars. We propose a new predictor of the durability of plant resistance. Because resistance breakdown involves modifications in the avirulence factors of pathogens, we tested for correlations between the evolutionary constraints acting on avirulence factors or their diversity and the durability of the corresponding resistance genes in the case of plant-virus interactions. An analysis performed on 20 virus species-resistance gene combinations revealed that the selective constraints applied on amino acid substitutions in virus avirulence factors correlate with the observed durability of the corresponding resistance genes. On the basis of this result, a model predicting the potential durability of resistance genes as a function of the selective constraints applied on the corresponding avirulence factors is proposed to help breeders to select the most durable resistance genes.
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Affiliation(s)
- Berenger Janzac
- INRA, UR407 Pathologie Végétale, Domaine Saint Maurice, BP94, F-84140 Montfavet, France.
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The fractionated orthology of Bs2 and Rx/Gpa2 supports shared synteny of disease resistance in the Solanaceae. Genetics 2009; 182:1351-64. [PMID: 19474202 DOI: 10.1534/genetics.109.101022] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Comparative genomics provides a powerful tool for the identification of genes that encode traits shared between crop plants and model organisms. Pathogen resistance conferred by plant R genes of the nucleotide-binding-leucine-rich-repeat (NB-LRR) class is one such trait with great agricultural importance that occupies a critical position in understanding fundamental processes of pathogen detection and coevolution. The proposed rapid rearrangement of R genes in genome evolution would make comparative approaches tenuous. Here, we test the hypothesis that orthology is predictive of R-gene genomic location in the Solanaceae using the pepper R gene Bs2. Homologs of Bs2 were compared in terms of sequence and gene and protein architecture. Comparative mapping demonstrated that Bs2 shared macrosynteny with R genes that best fit criteria determined to be its orthologs. Analysis of the genomic sequence encompassing solanaceous R genes revealed the magnitude of transposon insertions and local duplications that resulted in the expansion of the Bs2 intron to 27 kb and the frequently detected duplications of the 5'-end of R genes. However, these duplications did not impact protein expression or function in transient assays. Taken together, our results support a conservation of synteny for NB-LRR genes and further show that their distribution in the genome has been consistent with global rearrangements.
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Atsumi G, Kagaya U, Kitazawa H, Nakahara KS, Uyeda I. Activation of the salicylic acid signaling pathway enhances Clover yellow vein virus virulence in susceptible pea cultivars. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2009; 22:166-75. [PMID: 19132869 DOI: 10.1094/mpmi-22-2-0166] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The wild-type strain (Cl-WT) of Clover yellow vein virus (ClYVV) systemically induces cell death in pea cv. Plant introduction (PI) 118501 but not in PI 226564. A single incompletely dominant gene, Cyn1, controls systemic cell death in PI 118501. Here, we show that activation of the salicylic acid (SA) signaling pathway enhances ClYVV virulence in susceptible pea cultivars. The kinetics of virus accumulation was not significantly different between PI 118501 (Cyn1) and PI 226564 (cyn1); however, the SA-responsive chitinase gene (SA-CHI) and the hypersensitive response (HR)-related gene homologous to tobacco HSR203J were induced only in PI 118501 (Cyn1). Two mutant viruses with mutations in P1/HCPro, which is an RNA-silencing suppressor, reduced the ability to induce cell death and SA-CHI expression. The application of SA and of its analog benzo (1,2,3) thiadiazole-7-carbothioic acid S-methyl ester (BTH) partially complemented the reduced virulence of mutant viruses. These results suggest that high activation of the SA signaling pathway is required for ClYVV virulence. Interestingly, BTH could enhance Cl-WT symptoms in PI 226564 (cyn1). However, it could not enhance symptoms induced by White clover mosaic virus and Bean yellow mosaic virus. Our report suggests that the SA signaling pathway has opposing functions in compatible interactions, depending on the virus-host combination.
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Affiliation(s)
- Go Atsumi
- Pathogen-Plant Interactions Group, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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Fabre F, Bruchou C, Palloix A, Moury B. Key determinants of resistance durability to plant viruses: insights from a model linking within- and between-host dynamics. Virus Res 2009; 141:140-9. [PMID: 19159653 DOI: 10.1016/j.virusres.2008.11.021] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2008] [Indexed: 10/21/2022]
Abstract
The emergence of new genotypes of parasites involves several evolutionary, epidemiological and ecological processes whose individual effects and interactions are difficult to disentangle using experimental approaches. Here, a model is proposed to investigate how these processes lead to the emergence of plant viral genotypes breaking down qualitative resistance genes. At the individual plant scale, selection, drift and mutation processes shape the evolution of viral populations from a set of differential equations. The spatial segregation of virus genotypes in their hosts is also considered. At the host population scale, the epidemiological dynamics is given by an individual-based algorithm. Global sensitivity analyses allowed ranking the ten demo-genetic and epidemiological parameters of the model according to their impact on the mean and variance of the risk of breakdown of a plant resistance. Demo-genetic parameters (number and nature of mutations involved in breakdown, fitness of mutant genotypes) had the largest impact on the mean breakdown risk, whereas epidemiological parameters had more influence on its standard deviation. It is discussed how these results can be used to choose the potentially most durable resistance genes among a pool of candidates. Finally, our analyses point out the parameters which should be estimated more precisely to improve durability predictions.
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Affiliation(s)
- Frédéric Fabre
- INRA, UR 407 Unité Pathologie Végétale, Montfavet, France.
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Gilligan CA, van den Bosch F. Epidemiological models for invasion and persistence of pathogens. ANNUAL REVIEW OF PHYTOPATHOLOGY 2008; 46:385-418. [PMID: 18680429 DOI: 10.1146/annurev.phyto.45.062806.094357] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Motivated by questions such as "Why do some diseases take off, while others die out?" and "How can we optimize the deployment of control methods," we introduce simple epidemiological concepts for the invasion and persistence of plant pathogens. An overarching modeling framework is then presented that can be used to analyze disease invasion and persistence at a range of scales from the microscopic to the regional. Criteria for invasion and persistence are introduced, initially for simple models of epidemics, and then for models with greater biological realism. Some ways in which epidemiological models are used to identify optimal strategies for the control of disease are discussed. Particular attention is given to the spatial structure of host populations and to the role of chance events in determining invasion and persistence of plant pathogens. Finally, three brief case studies are used to illustrate the practical applications of epidemiological theory to understand invasion and persistence of plant pathogens. These comprise long-term predictions for the persistence and control of Dutch elm disease; identification of methods to manage the spread of rhizomania on sugar beet in the U.K. by matching the scale of control with the spatial and temporal scales of the disease; and analysis of evolutionary change in virus control to identify risks of inadvertent selection for damaging virus strains.
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Affiliation(s)
- Christopher A Gilligan
- Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, United Kingdom.
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Cillo F, Pasciuto MM, De Giovanni C, Finetti-Sialer MM, Ricciardi L, Gallitelli D. Response of tomato and its wild relatives in the genus Solanum to cucumber mosaic virus and satellite RNA combinations. J Gen Virol 2007; 88:3166-3176. [PMID: 17947544 DOI: 10.1099/vir.0.83110-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The differential response of 29 genotypes of tomato and wild tomato relatives (Solanum section Lycopersicon species) to cucumber mosaic virus strain Fny (CMV-Fny), alone or in combination with three different satellite RNA (satRNA) variants, allowed the identification of four disease phenotype patterns, each including plants that developed very severe symptoms (leaf malformations, top stunting and lethal necrosis) and plants that remained asymptomatic. No resistance or tolerance to CMV-Fny was observed, whilst individual host genotypes displayed latent infection upon inoculation with one (CMV-Fny/Tfn-satRNA, phenotype patterns 1 and 4), two (CMV-Fny/Tfn-satRNA and CMV-Fny/TTS-satRNA, phenotype pattern 2) or all three (the former two plus CMV-Fny/77-satRNA, phenotype pattern 3) CMV/satRNA combinations. RNA gel-blot analyses showed that latent infection generally correlated with a strong downregulation of CMV RNA accumulation levels. Introgression lines derived from a cross between Solanum habrochaites LA1777, which displayed disease phenotype pattern 2, and Solanum lycopersicum were screened for tolerance to the stunting phenotype induced by CMV-Fny/TTS-satRNA, and only one line, carrying an introgression on chromosome 6, was identified as being partially tolerant. Solanum chilense LA1932xS. lycopersicum back-cross introgression lines were screened for tolerance to lethal necrosis induced by CMV-Fny/77-satRNA (phenotype pattern 3); the tolerant phenotype was observed in 33 % of plants of the BC(1)F(2) progeny and <1 % of plants of the BC(1)F(3) progeny. Thus, potentially useful sources of tolerance to CMV/satRNA-induced diseases were identified, although the tolerant phenotypes appeared to be controlled by complex quantitative trait loci.
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Affiliation(s)
- F Cillo
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi di Bari, and CNR, Istituto di Virologia Vegetale, Via Amendola 165/A, 70126 Bari, Italy
| | - M M Pasciuto
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi di Bari, and CNR, Istituto di Virologia Vegetale, Via Amendola 165/A, 70126 Bari, Italy
| | - C De Giovanni
- Dipartimento di Biologia e Chimica AgroForestale ed Ambientale, Sez. di Genetica e Miglioramento Genetico, Università degli Studi di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - M M Finetti-Sialer
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi di Bari, and CNR, Istituto di Virologia Vegetale, Via Amendola 165/A, 70126 Bari, Italy
| | - L Ricciardi
- Dipartimento di Biologia e Chimica AgroForestale ed Ambientale, Sez. di Genetica e Miglioramento Genetico, Università degli Studi di Bari, Via Amendola 165/A, 70126 Bari, Italy
| | - D Gallitelli
- Dipartimento di Protezione delle Piante e Microbiologia Applicata, Università degli Studi di Bari, and CNR, Istituto di Virologia Vegetale, Via Amendola 165/A, 70126 Bari, Italy
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Estimation of the number of virus particles transmitted by an insect vector. Proc Natl Acad Sci U S A 2007; 104:17891-6. [PMID: 17971440 DOI: 10.1073/pnas.0702739104] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Plant viruses are submitted to narrow population bottlenecks both during infection of their hosts and during horizontal transmission between host individuals. The size of bottlenecks exerted on virus populations during plant invasion has been estimated in a few pathosystems but is not addressed yet for horizontal transmission. Using competition for aphid transmission between two Potato virus Y variants, one of them being noninfectious but equally transmissible, we obtained estimates of the size of bottlenecks exerted on an insect-borne virus during its horizontal transmission. We found that an aphid transmitted on average 0.5-3.2 virus particles, which is extremely low compared with the census viral population into a plant. Such narrow bottlenecks emphasize the strength of stochastic events acting on virus populations, and we illustrate, in modeling virus emergence, why estimating this parameter is important.
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García-Andrés S, Accotto GP, Navas-Castillo J, Moriones E. Founder effect, plant host, and recombination shape the emergent population of begomoviruses that cause the tomato yellow leaf curl disease in the Mediterranean basin. Virology 2007; 359:302-12. [PMID: 17070885 DOI: 10.1016/j.virol.2006.09.030] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2006] [Revised: 08/10/2006] [Accepted: 09/19/2006] [Indexed: 11/28/2022]
Abstract
Tomato yellow leaf curl disease (TYLCD)-associated viruses present a highly structured population in the western Mediterranean basin, depending on host, geographical region and time. About 1,900 tomato and common bean samples were analyzed from which 111 isolates were characterized genetically based on a genome sequence that comprises coding and non-coding regions. Isolates of three distinct begomoviruses previously described were found (Tomato yellow leaf curl virus, TYLCV, Tomato yellow leaf curl Sardinia virus, TYLCSV, and Tomato yellow leaf curl Málaga virus, TYLCMalV), together with a novel recombinant virus. Mixed infections were detected in single plants, rationalizing the occurrence of recombinants. Except for TYLCV-type strain, single, undifferentiated subpopulations were present for each virus type, probably the result of founder effects. Limited genetic variation was observed in genomic regions, with selection against amino acid change in coding regions.
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Affiliation(s)
- Susana García-Andrés
- Estación Experimental "La Mayora", Consejo Superior de Investigaciones Científicas, 29750 Algarrobo-Costa, Málaga, Spain
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Maule AJ, Caranta C, Boulton MI. Sources of natural resistance to plant viruses: status and prospects. MOLECULAR PLANT PATHOLOGY 2007; 8:223-31. [PMID: 20507494 DOI: 10.1111/j.1364-3703.2007.00386.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
SUMMARY Globally, virus diseases are common in agricultural crops and have a major agronomic impact. They are countered through the deployment of genetic resistance against the virus, or through the use of a range of farming practices based upon the propagation of virus-free plant material and the exclusion of the virus vectors from the growing crop. We review here the current status of our knowledge of natural virus resistance genes, and consider the future prospects for the deployment of these genes against virus infection.
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Affiliation(s)
- Andrew J Maule
- John Innes Centre, Norwich Research Park, Colney, Norwich NR4 7UH, UK
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Recombination in the TYLCV Complex: a Mechanism to Increase Genetic Diversity. Implications for Plant Resistance Development. TOMATO YELLOW LEAF CURL VIRUS DISEASE 2007. [PMCID: PMC7121651 DOI: 10.1007/978-1-4020-4769-5_7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Mutation, reassortment, and recombination are the major sources of genetic variation of plant viruses (García-Arenal et al., 2001; Worobey & Holmes, 1999). During mixed infections, viruses can exchange genetic material through recombination or reassortment of segments (when the parental genomes are fragmented) if present in the same cell context of the host plant. Hybrid progeny viruses might then arise, some of them with novel pathogenic characteristics and well adapted in the population that can cause new emerging diseases. Genetic exchange provides organisms with a tool to combine sequences from different origins which might help them to quickly evolve (Crameri et al., 1998). In many DNA and RNA viruses, genetic exchange is achieved through recombination (Froissart et al., 2005; Martin et al., 2005). As increasing numbers of viral sequences become available, recombinant viruses are recognized to be frequent in nature and clear evidence is found for recombination to play a key role in virus evolution (Awadalla, 2003; Chenault & Melcher, 1994; Moonan et al., 2000; Padidam et al., 1999; Revers et al., 1996; García-Arenal et al., 2001; Moreno et al., 2004). Understanding the role of recombination in generating and eliminating variation in viral sequences is thus essential to understand virus evolution and adaptation to changing environments Knowledge about the existence and frequency of recombination in a virus population might help understanding the extent at which genes are exchanged and new virus variants arise. This information is essential, for example, to predict durability of genetic resistance because new recombinant variants might be formed with increased fitness in host-resistant genotypes. Determination of the extent and rate at which genetic rearrangement through recombination does occur in natural populations is also crucial if we use genome and genetic-mapping information to locate genes responsible of important phenotypes such as genes associated with virulence, transmission, or breakdown of resistance. Therefore, better estimates of the rate of recombination will facilitate the development of more robust strategies for virus control (Awadalla, 2003).
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