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Arra Y, Auguy F, Stiebner M, Chéron S, Wudick MM, Miras M, Schepler‐Luu V, Köhler S, Cunnac S, Frommer WB, Albar L. Rice Yellow Mottle Virus resistance by genome editing of the Oryza sativa L. ssp. japonica nucleoporin gene OsCPR5.1 but not OsCPR5.2. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1299-1311. [PMID: 38124291 PMCID: PMC11022797 DOI: 10.1111/pbi.14266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 11/16/2023] [Accepted: 11/27/2023] [Indexed: 12/23/2023]
Abstract
Rice yellow mottle virus (RYMV) causes one of the most devastating rice diseases in Africa. Management of RYMV is challenging. Genetic resistance provides the most effective and environment-friendly control. The recessive resistance locus rymv2 (OsCPR5.1) had been identified in African rice (Oryza glaberrima), however, introgression into Oryza sativa ssp. japonica and indica remains challenging due to crossing barriers. Here, we evaluated whether CRISPR/Cas9 genome editing of the two rice nucleoporin paralogs OsCPR5.1 (RYMV2) and OsCPR5.2 can be used to introduce RYMV resistance into the japonica variety Kitaake. Both paralogs had been shown to complement the defects of the Arabidopsis atcpr5 mutant, indicating partial redundancy. Despite striking sequence and structural similarities between the two paralogs, only oscpr5.1 loss-of-function mutants were fully resistant, while loss-of-function oscpr5.2 mutants remained susceptible, intimating that OsCPR5.1 plays a specific role in RYMV susceptibility. Notably, edited lines with short in-frame deletions or replacements in the N-terminal domain (predicted to be unstructured) of OsCPR5.1 were hypersusceptible to RYMV. In contrast to mutations in the single Arabidopsis AtCPR5 gene, which caused severely dwarfed plants, oscpr5.1 and oscpr5.2 single and double knockout mutants showed neither substantial growth defects nor symptoms indicative lesion mimic phenotypes, possibly reflecting functional differentiation. The specific editing of OsCPR5.1, while maintaining OsCPR5.2 activity, provides a promising strategy for generating RYMV-resistance in elite Oryza sativa lines as well as for effective stacking with other RYMV resistance genes or other traits.
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Affiliation(s)
- Yugander Arra
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Florence Auguy
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Melissa Stiebner
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sophie Chéron
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Michael M. Wudick
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Manuel Miras
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Van Schepler‐Luu
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
| | - Steffen Köhler
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
| | - Sébastien Cunnac
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
| | - Wolf B. Frommer
- Faculty of Mathematics and Natural SciencesInstitute for Molecular Physiology, Heinrich Heine University DüsseldorfDüsseldorfGermany
- Center for Advanced ImagingHeinrich Heine University DüsseldorfDüsseldorfGermany
- Institute of Transformative Bio‐Molecules (ITbM‐WPI)Nagoya UniversityNagoyaJapan
| | - Laurence Albar
- IRD, CIRAD, INRAEPHIM Plant Health Institute of Montpellier, Institut Agro, University MontpellierMontpellierFrance
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2
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Yuan S, Zhou G, Xu G. Translation machinery: the basis of translational control. J Genet Genomics 2024; 51:367-378. [PMID: 37536497 DOI: 10.1016/j.jgg.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 07/23/2023] [Accepted: 07/23/2023] [Indexed: 08/05/2023]
Abstract
Messenger RNA (mRNA) translation consists of initiation, elongation, termination, and ribosome recycling, carried out by the translation machinery, primarily including tRNAs, ribosomes, and translation factors (TrFs). Translational regulators transduce signals of growth and development, as well as biotic and abiotic stresses, to the translation machinery, where global or selective translational control occurs to modulate mRNA translation efficiency (TrE). As the basis of translational control, the translation machinery directly determines the quality and quantity of newly synthesized peptides and, ultimately, the cellular adaption. Thus, regulating the availability of diverse machinery components is reviewed as the central strategy of translational control. We provide classical signaling pathways (e.g., integrated stress responses) and cellular behaviors (e.g., liquid-liquid phase separation) to exemplify this strategy within different physiological contexts, particularly during host-microbe interactions. With new technologies developed, further understanding this strategy will speed up translational medicine and translational agriculture.
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Affiliation(s)
- Shu Yuan
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guilong Zhou
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China
| | - Guoyong Xu
- State Key Laboratory of Hybrid Rice, Institute for Advanced Studies (IAS), Wuhan University, Wuhan, Hubei 430072, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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3
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Simon EV, Hechanova SL, Hernandez JE, Li CP, Tülek A, Ahn EK, Jairin J, Choi IR, Sundaram RM, Jena KK, Kim SR. Available cloned genes and markers for genetic improvement of biotic stress resistance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1247014. [PMID: 37731986 PMCID: PMC10507716 DOI: 10.3389/fpls.2023.1247014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.
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Affiliation(s)
- Eliza Vie Simon
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Sherry Lou Hechanova
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
| | - Jose E. Hernandez
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Charng-Pei Li
- Taiwan Agricultural Research Institute (TARI), Council of Agriculture, Taiwan
| | - Adnan Tülek
- Trakya Agricultural Research Institute, Edirne, Türkiye
| | - Eok-Keun Ahn
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Jirapong Jairin
- Division of Rice Research and Development, Rice Department, Bangkok, Thailand
| | - Il-Ryong Choi
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Raman M. Sundaram
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Kshirod K. Jena
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, Odisha, India
| | - Sung-Ryul Kim
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
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Billard E, Barro M, Sérémé D, Bangratz M, Wonni I, Koala M, Kassankogno AI, Hébrard E, Thébaud G, Brugidou C, Poulicard N, Tollenaere C. Dynamics of the rice yellow mottle disease in western Burkina Faso: Epidemic monitoring, spatio-temporal variation of viral diversity, and pathogenicity in a disease hotspot. Virus Evol 2023; 9:vead049. [PMID: 37649958 PMCID: PMC10465090 DOI: 10.1093/ve/vead049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 07/04/2023] [Accepted: 08/20/2023] [Indexed: 09/01/2023] Open
Abstract
The rice yellow mottle virus (RYMV) is a model in plant virus molecular epidemiology, with the reconstruction of historical introduction routes at the scale of the African continent. However, information on patterns of viral prevalence and viral diversity over multiple years at a local scale remains scarce, in spite of potential implications for crop protection. Here, we describe a 5-year (2015-9) monitoring of RYMV prevalence in six sites from western Burkina Faso (geographic areas of Bama, Banzon, and Karfiguela). It confirmed one irrigated site as a disease hotspot and also found one rainfed lowland (RL) site with occasional high prevalence levels. Within the studied fields, a pattern of disease aggregation was evidenced at a 5-m distance, as expected for a mechanically transmitted virus. Next, we monitored RYMV genetic diversity in the irrigated disease hotspot site, revealing a high viral diversity, with the current coexistence of various distinct genetic groups at the site scale (ca. 520 ha) and also within various specific fields (25 m side). One genetic lineage, named S1bzn, is the most recently emerged group and increased in frequency over the studied period (from 20 per cent or less in 2015-6 to more than 65 per cent in 2019). Its genome results from a recombination between two other lineages (S1wa and S1ca). Finally, experimental work revealed that three rice varieties commonly cultivated in Burkina Faso were not different in terms of resistance level, and we also found no significant effect of RYMV genetic groups on symptom expression and viral load. We found, however, that infection outcome depended on the specific RYMV isolate, with two isolates from the lineage S1bzn accumulating at the highest level at early infections. Overall, this study documents a case of high viral prevalence, high viral diversity, and co-occurrence of divergent genetic lineages at a small geographic scale. A recently emerged lineage, which comprises viral isolates inducing severe symptoms and high accumulation under controlled conditions, could be recently rising through natural selection. Following up the monitoring of RYMV diversity is required to confirm this trend and further understand the factors driving the local maintenance of viral diversity.
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Affiliation(s)
- Estelle Billard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Mariam Barro
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Drissa Sérémé
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Martine Bangratz
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Issa Wonni
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Moustapha Koala
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Virologie et de Biologie Végétale, Kamboinsé, Burkina Faso
| | - Abalo Itolou Kassankogno
- INERA, Institut de l’Environnement et de Recherches Agricoles, Laboratoire de Phytopathologie, Bobo-Dioulasso, Burkina Faso
| | - Eugénie Hébrard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Gaël Thébaud
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Christophe Brugidou
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
| | - Charlotte Tollenaere
- PHIM, Plant Health Institute of Montpellier, Univ. Montpellier, IRD, CIRAD, INRAE, Institute Agro, Montpellier, France
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5
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Vermeulen A, Takken FLW, Sánchez-Camargo VA. Translation Arrest: A Key Player in Plant Antiviral Response. Genes (Basel) 2023; 14:1293. [PMID: 37372472 DOI: 10.3390/genes14061293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/15/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation of nucleotide-binding domain leucine-rich repeat (NLR) receptors. RNAi is associated with viral symptom recovery through translational repression and transcript degradation following recognition of viral double-stranded RNA produced during infection. NLR-mediated immunity is induced upon (in)direct recognition of a viral protein by an NLR receptor, triggering either a hypersensitive response (HR) or an extreme resistance response (ER). During ER, host cell death is not apparent, and it has been proposed that this resistance is mediated by a translational arrest (TA) of viral transcripts. Recent research indicates that translational repression plays a crucial role in plant antiviral resistance. This paper reviews current knowledge on viral translational repression during viral recovery and NLR-mediated immunity. Our findings are summarized in a model detailing the pathways and processes leading to translational arrest of plant viruses. This model can serve as a framework to formulate hypotheses on how TA halts viral replication, inspiring new leads for the development of antiviral resistance in crops.
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Affiliation(s)
- Annemarie Vermeulen
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Frank L W Takken
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Victor A Sánchez-Camargo
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
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6
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Dossou L, Pinel-Galzi A, Aribi J, Poulicard N, Albar L, Fatogoma S, Ndjiondjop MN, Koné D, Hébrard E. Molecular Tools to Infer Resistance-Breaking Abilities of Rice Yellow Mottle Virus Isolates. Viruses 2023; 15:v15040959. [PMID: 37112939 PMCID: PMC10144094 DOI: 10.3390/v15040959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/31/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Rice yellow mottle virus (RYMV) is a major biotic constraint to rice cultivation in Africa. RYMV shows a high genetic diversity. Viral lineages were defined according to the coat protein (CP) phylogeny. Varietal selection is considered as the most efficient way to manage RYMV. Sources of high resistance were identified mostly in accessions of the African rice species, Oryza glaberrima. Emergence of resistance-breaking (RB) genotypes was observed in controlled conditions. The RB ability was highly contrasted, depending on the resistance sources and on the RYMV lineages. A molecular marker linked to the adaptation to susceptible and resistant O. glaberrima was identified in the viral protein genome-linked (VPg). By contrast, as no molecular method was available to identify the hypervirulent lineage able to overcome all known resistance sources, plant inoculation assays were still required. Here, we designed specific RT-PCR primers to infer the RB abilities of RYMV isolates without greenhouse experiments or sequencing steps. These primers were tested and validated on 52 isolates, representative of RYMV genetic diversity. The molecular tools described in this study will contribute to optimizing the deployment strategy of resistant lines, considering the RYMV lineages identified in fields and their potential adaptability.
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Affiliation(s)
- Laurence Dossou
- AfricaRice Center, M'bé Research Station, Bouaké 01 BP 2551, Côte d'Ivoire
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Agnès Pinel-Galzi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Jamel Aribi
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Nils Poulicard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Laurence Albar
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
| | - Sorho Fatogoma
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | | | - Daouda Koné
- WASCAL/CEA-CCBAD, Université Félix Houphouët-Boigny, Abidjan 01 BP V 34, Côte d'Ivoire
| | - Eugénie Hébrard
- PHIM, Plant Health Institute, University Montpellier, IRD, INRAE, CIRAD, SupAgro, 911 Avenue Agropolis, 34394 Montpellier, France
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7
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Zlobin N, Taranov V. Plant eIF4E isoforms as factors of susceptibility and resistance to potyviruses. FRONTIERS IN PLANT SCIENCE 2023; 14:1041868. [PMID: 36844044 PMCID: PMC9950400 DOI: 10.3389/fpls.2023.1041868] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Potyviruses are the largest group of plant-infecting RNA viruses that affect a wide range of crop plants. Plant resistance genes against potyviruses are often recessive and encode translation initiation factors eIF4E. The inability of potyviruses to use plant eIF4E factors leads to the development of resistance through a loss-of-susceptibility mechanism. Plants have a small family of eIF4E genes that encode several isoforms with distinct but overlapping functions in cell metabolism. Potyviruses use distinct eIF4E isoforms as susceptibility factors in different plants. The role of different members of the plant eIF4E family in the interaction with a given potyvirus could differ drastically. An interplay exists between different members of the eIF4E family in the context of plant-potyvirus interactions, allowing different eIF4E isoforms to modulate each other's availability as susceptibility factors for the virus. In this review, possible molecular mechanisms underlying this interaction are discussed, and approaches to identify the eIF4E isoform that plays a major role in the plant-potyvirus interaction are suggested. The final section of the review discusses how knowledge about the interaction between different eIF4E isoforms can be used to develop plants with durable resistance to potyviruses.
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8
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Tatineni S, Hein GL. Plant Viruses of Agricultural Importance: Current and Future Perspectives of Virus Disease Management Strategies. PHYTOPATHOLOGY 2023; 113:117-141. [PMID: 36095333 DOI: 10.1094/phyto-05-22-0167-rvw] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Plant viruses cause significant losses in agricultural crops worldwide, affecting the yield and quality of agricultural products. The emergence of novel viruses or variants through genetic evolution and spillover from reservoir host species, changes in agricultural practices, mixed infections with disease synergism, and impacts from global warming pose continuous challenges for the management of epidemics resulting from emerging plant virus diseases. This review describes some of the most devastating virus diseases plus select virus diseases with regional importance in agriculturally important crops that have caused significant yield losses. The lack of curative measures for plant virus infections prompts the use of risk-reducing measures for managing plant virus diseases. These measures include exclusion, avoidance, and eradication techniques, along with vector management practices. The use of sensitive, high throughput, and user-friendly diagnostic methods is crucial for defining preventive and management strategies against plant viruses. The advent of next-generation sequencing technologies has great potential for detecting unknown viruses in quarantine samples. The deployment of genetic resistance in crop plants is an effective and desirable method of managing virus diseases. Several dominant and recessive resistance genes have been used to manage virus diseases in crops. Recently, RNA-based technologies such as dsRNA- and siRNA-based RNA interference, microRNA, and CRISPR/Cas9 provide transgenic and nontransgenic approaches for developing virus-resistant crop plants. Importantly, the topical application of dsRNA, hairpin RNA, and artificial microRNA and trans-active siRNA molecules on plants has the potential to develop GMO-free virus disease management methods. However, the long-term efficacy and acceptance of these new technologies, especially transgenic methods, remain to be established.
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Affiliation(s)
- Satyanarayana Tatineni
- U.S. Department of Agriculture-Agricultural Research Service and Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68583
| | - Gary L Hein
- Department of Entomology, University of Nebraska-Lincoln, Lincoln, NE 68583
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9
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Bonnamy M, Pinel-Galzi A, Gorgues L, Chalvon V, Hébrard E, Chéron S, Nguyen TH, Poulicard N, Sabot F, Pidon H, Champion A, Césari S, Kroj T, Albar L. Rapid evolution of an RNA virus to escape recognition by a rice nucleotide-binding and leucine-rich repeat domain immune receptor. THE NEW PHYTOLOGIST 2023; 237:900-913. [PMID: 36229931 DOI: 10.1111/nph.18532] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Viral diseases are a major limitation for crop production, and their control is crucial for sustainable food supply. We investigated by a combination of functional genetics and experimental evolution the resistance of rice to the rice yellow mottle virus (RYMV), which is among the most devastating rice pathogens in Africa, and the mechanisms underlying the extremely fast adaptation of the virus to its host. We found that the RYMV3 gene that protects rice against the virus codes for a nucleotide-binding and leucine-rich repeat domain immune receptor (NLRs) from the Mla-like clade of NLRs. RYMV3 detects the virus by forming a recognition complex with the viral coat protein (CP). The virus escapes efficiently from detection by mutations in its CP, some of which interfere with the formation of the recognition complex. This study establishes that NLRs also confer in monocotyledonous plants immunity to viruses, and reveals an unexpected functional diversity for NLRs of the Mla clade that were previously only known as fungal disease resistance proteins. In addition, it provides precise insight into the mechanisms by which viruses adapt to plant immunity and gives important knowledge for the development of sustainable resistance against viral diseases of cereals.
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Affiliation(s)
- Mélia Bonnamy
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Agnès Pinel-Galzi
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Lucille Gorgues
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Véronique Chalvon
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Eugénie Hébrard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Sophie Chéron
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | | | - Nils Poulicard
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - François Sabot
- DIADE, Univ Montpellier, IRD, 34394, Montpellier, France
| | - Hélène Pidon
- DIADE, Univ Montpellier, IRD, 34394, Montpellier, France
- Institute for Resistance Research and Stress Tolerance, Julius Kühn Institute, 06484, Quedlinburg, Germany
| | | | - Stella Césari
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Thomas Kroj
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
| | - Laurence Albar
- PHIM Plant Health Institute, Univ Montpellier, IRD, CIRAD, INRAE, Institut Agro, 34980, Montpellier, France
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10
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Wang P, Liu J, Lyu Y, Huang Z, Zhang X, Sun B, Li P, Jing X, Li H, Zhang C. A Review of Vector-Borne Rice Viruses. Viruses 2022; 14:v14102258. [PMID: 36298813 PMCID: PMC9609659 DOI: 10.3390/v14102258] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/04/2022] [Accepted: 10/09/2022] [Indexed: 11/05/2022] Open
Abstract
Rice (Oryza sativa L.) is one of the major staple foods for global consumption. A major roadblock to global rice production is persistent loss of crops caused by plant diseases, including rice blast, sheath blight, bacterial blight, and particularly various vector-borne rice viral diseases. Since the late 19th century, 19 species of rice viruses have been recorded in rice-producing areas worldwide and cause varying degrees of damage on the rice production. Among them, southern rice black-streaked dwarf virus (SRBSDV) and rice black-streaked dwarf virus (RBSDV) in Asia, rice yellow mottle virus (RYMV) in Africa, and rice stripe necrosis virus (RSNV) in America currently pose serious threats to rice yields. This review systematizes the emergence and damage of rice viral diseases, the symptomatology and transmission biology of rice viruses, the arm races between viruses and rice plants as well as their insect vectors, and the strategies for the prevention and control of rice viral diseases.
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Affiliation(s)
- Pengyue Wang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianjian Liu
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
- Hubei Engineering Research Center for Pest Forewarning and Management, College of Agronomy, Yangtze University, Jingzhou 434025, China
| | - Yajing Lyu
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
- Co-Construction State Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
| | - Ziting Huang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaoli Zhang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Bingjian Sun
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Pengbai Li
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinxin Jing
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Honglian Li
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
| | - Chao Zhang
- Department of Plant Pathology, College of Plant Protection, Henan Agricultural University, Zhengzhou 450002, China
- Correspondence:
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11
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Wu JG, Yang GY, Zhao SS, Zhang S, Qin BX, Zhu YS, Xie HT, Chang Q, Wang L, Hu J, Zhang C, Zhang BG, Zeng DL, Zhang JF, Huang XB, Qian Q, Ding SW, Li Y. Current rice production is highly vulnerable to insect-borne viral diseases. Natl Sci Rev 2022; 9:nwac131. [PMID: 36172397 PMCID: PMC9511884 DOI: 10.1093/nsr/nwac131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/02/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Jian-Guo Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Guo-Yi Yang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Shan-Shan Zhao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Shuai Zhang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Bi-Xia Qin
- Institute of Plant Protection, Guangxi Academy of Agricultural Sciences, China
| | - Yong-Sheng Zhu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, China
| | - Hui-Ting Xie
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Qing Chang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Lu Wang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Jie Hu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Chao Zhang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Bao-Gang Zhang
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Institute of Plant Virology, Fujian Agriculture and Forestry University, China
| | - Da-Li Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, China
| | - Jian-Fu Zhang
- Rice Research Institute, Fujian Academy of Agricultural Sciences, China
| | - Xian-Bo Huang
- Rice Research Institute, Sanming Academy of Agricultural Sciences, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, China
| | - Shou-Wei Ding
- Department of Microbiology and Plant Pathology, Center for Plant Cell Biology, Institute for Integrative Genome Biology, University of California, Riverside, USA
| | - Yi Li
- The State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, China
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12
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Tamisier L, Szadkowski M, Girardot G, Djian‐Caporalino C, Palloix A, Hirsch J, Moury B. Concurrent evolution of resistance and tolerance to potato virus Y in Capsicum annuum revealed by genome-wide association. MOLECULAR PLANT PATHOLOGY 2022; 23:254-264. [PMID: 34729890 PMCID: PMC8743019 DOI: 10.1111/mpp.13157] [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] [Received: 08/04/2021] [Revised: 10/19/2021] [Accepted: 10/20/2021] [Indexed: 05/21/2023]
Abstract
We performed a genome-wide association study of pepper (Capsicum annuum) tolerance to potato virus Y (PVY). For 254 pepper accessions, we estimated the tolerance to PVY as the coefficient of regression of the fresh weight (or height) of PVY-infected and mock-inoculated plants against within-plant virus load. Small (strongly negative) coefficients of regression indicate low tolerance because plant biomass or growth decreases sharply as virus load increases. The tolerance level varied largely, with some pepper accessions showing no symptoms or fairly mild mosaics, whereas about half (48%) of the accessions showed necrotic symptoms. We found two adjacent single-nucleotide polymorphisms (SNPs) at one extremity of chromosome 9 that were significantly associated with tolerance to PVY. Similarly, in three biparental pepper progenies, we showed that the induction of necrosis on PVY systemic infection segregated as a monogenic trait determined by a locus on chromosome 9. Our results also demonstrate the existence of a negative correlation between resistance and tolerance among the cultivated pepper accessions at both the phenotypic and genetic levels. By comparing the distributions of the tolerance-associated SNP alleles and previously identified PVY resistance-associated SNP alleles, we showed that cultivated pepper accessions possess favourable alleles for both resistance and tolerance less frequently than expected under random associations, while the minority of wild pepper accessions frequently combined resistance and tolerance alleles. This divergent evolution of PVY resistance and tolerance could be related to pepper domestication or farmer's selection.
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Affiliation(s)
- Lucie Tamisier
- Pathologie VégétaleINRAEMontfavetFrance
- GAFLINRAEMontfavetFrance
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13
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Hinge VR, Chavhan RL, Kale SP, Suprasanna P, Kadam US. Engineering Resistance Against Viruses in Field Crops Using CRISPR- Cas9. Curr Genomics 2021; 22:214-231. [PMID: 34975291 PMCID: PMC8640848 DOI: 10.2174/1389202922666210412102214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/29/2021] [Accepted: 02/24/2021] [Indexed: 12/26/2022] Open
Abstract
Food security is threatened by various biotic stresses that affect the growth and production of agricultural crops. Viral diseases have become a serious concern for crop plants as they incur huge yield losses. The enhancement of host resistance against plant viruses is a priority for the effective management of plant viral diseases. However, in the present context of the climate change scenario, plant viruses are rapidly evolving, resulting in the loss of the host resistance mechanism. Advances in genome editing techniques, such as CRISPR-Cas9 [clustered regularly interspaced palindromic repeats-CRISPR-associated 9], have been recognized as promising tools for the development of plant virus resistance. CRISPR-Cas9 genome editing tool is widely preferred due to high target specificity, simplicity, efficiency, and reproducibility. CRISPR-Cas9 based virus resistance in plants has been successfully achieved by gene targeting and cleaving the viral genome or altering the plant genome to enhance plant innate immunity. In this article, we have described the CRISPR-Cas9 system, mechanism of plant immunity against viruses and highlighted the use of the CRISPR-Cas9 system to engineer virus resistance in plants. We also discussed prospects and challenges on the use of CRISPR-Cas9-mediated plant virus resistance in crop improvement.
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Affiliation(s)
- Vidya R Hinge
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Rahul L Chavhan
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Sandeep P Kale
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Penna Suprasanna
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
| | - Ulhas S Kadam
- 1Department of Plant Biotechnology, Vilasrao Deshmukh College of Agricultural Biotechnology, Latur; Vasantrao Naik Marathwada Krishi Vidyapeeth (VNMKV), Parbhani 431 402, India; 2USAID-BIRAC International Project, School of Life Sciences, S.R.T.M.U., Nanded, India; 3Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400 085, India; 4Max Planck Institute of Molecular Plant Physiology, Potsdam- Golm, 14476, Germany
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14
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Genome Editing of Rice eIF4G Loci Confers Partial Resistance to Rice Black-Streaked Dwarf Virus. Viruses 2021; 13:v13102100. [PMID: 34696530 PMCID: PMC8539751 DOI: 10.3390/v13102100] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/13/2021] [Indexed: 01/23/2023] Open
Abstract
Rice black-streaked dwarf disease, caused by rice black-streaked dwarf virus (RBSDV), is a serious constraint in Chinese rice production. Breeding disease-resistant varieties through multigene aggregation is considered an effective way to control diseases, but few disease-resistant resources have been characterized thus far. To develop novel resources for resistance to RBSDV through CRISPR/Cas9-mediated genome editing, a guide RNA sequence targeting exon 1 of eIF4G was designed and cloned into a binary vector, pHUE401. This recombinant vector was used to generate mutations in the rice cultivar Nipponbare via Agrobacterium-mediated transformation. This approach produced heritable homozygous mutations in the transgene-free T1 generation. Sequence analysis of the eIF4G target region from T1 transgenic plants identified 3 bp deletion mutants, and analysis of the predicted amino acid sequence identified one amino acid deletion in mutants that possess near full-length eIF4G. Furthermore, our data suggest that eIF4G may plays an important role in rice normal development, as there were no eIF4G knock-out homozygous mutants in T1 generation plants. When homozygous mutant lines were inoculated with RBSDV, they exhibited enhanced tolerance to virus infection, without visibly affecting plant growth and development. However, the eif4g mutant plants showed the same sensitivity to rice stripe virus (RSV) infection as wild-type plants. Notably, the wild-type and mutant N-termini of eIF4G interacted directly with RBSDV P8 in yeast and in planta. Additionally, compared to wild-type plants, the eIF4G transcript level was reduced twofold in the mutant plants. These results indicate that site-specific mutation of rice eIF4G successfully conferred partial resistance specific to RBSDV associated with less transcription of eIF4G in mutants. Therefore, this study demonstrates that the novel eIF4G alleles generated by CRISPR/Cas9 represent valuable disease-resistant resources that can be used to develop RBSDV-resistant varieties.
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Anato VKS, Agnoun Y, Houndjo J, Oludare A, Agbangla C, Akoroda M, Adetimirin VO. Resistance of Oryza sativa and Oryza glaberrima Genotypes to RBe24 Isolate of Rice Yellow Mottle Virus in Benin and Effects of Silicon on Host Response. THE PLANT PATHOLOGY JOURNAL 2021; 37:375-388. [PMID: 34365749 PMCID: PMC8357567 DOI: 10.5423/ppj.oa.09.2020.0180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/15/2021] [Accepted: 07/15/2021] [Indexed: 06/13/2023]
Abstract
Rice yellow mottle virus (RYMV) is the most harmful virus that affects irrigated and lowland rice in Africa. The RBe24 isolate of the virus is the most pathogenic strain in Benin. A total of 79 genotypes including susceptible IR64 (Oryza sativa) and the resistant TOG5681 (O. glaberrima) as checks were screened for their reactions to RBe24 isolate of RYMV and the effects of silicon on the response of host plants to the virus investigated. The experiment was a three-factor factorial consisting of genotypes, inoculation level (inoculated vs. non-inoculated), and silicon dose (0, 5, and 10 g/plant) applied as CaSiO3 with two replications and carried out twice in the screen house. Significant differences were observed among the rice genotypes. Fifteen highly resistant and eight resistant genotypes were identified, and these were mainly O. glaberrima. Silicon application did not affect disease incidence and severity at 21 and 42 days after inoculation (DAI); it, however, significantly increased plant height of inoculated (3.6% for 5 g CaSiO3/plant and 6.3% for 10 g CaSiO3/plant) and non-inoculated (1.9% for 5 g CaSiO3/plant and 4.9% for 10 g CaSiO3/plant) plants at 42 DAI, with a reduction in the number of tillers (12.3% for both 5 and 10 g CaSiO3/plant) and leaves (26.8% for 5 g CaSiO3/plant and 28% for 10 g CaSiO3/plant) under both inoculation treatments. Our results confirm O. glaberrima germplasm as an important source of resistance to RYMV, and critical in developing a comprehensive strategy for the control of RYMV in West Africa.
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Affiliation(s)
- Vital Kouessi Sixte Anato
- Pan African University Institute of Life and Earth Sciences (PAULESI), University of Ibadan, Ibadan 200284, Nigeria
| | - Yves Agnoun
- Université Nationale d’Agriculture (UNA), 01 B.P. 55, Porto-Novo, Benin
| | - Joèl Houndjo
- Pan African University Institute of Life and Earth Sciences (PAULESI), University of Ibadan, Ibadan 200284, Nigeria
| | | | | | - Malachy Akoroda
- Pan African University Institute of Life and Earth Sciences (PAULESI), University of Ibadan, Ibadan 200284, Nigeria
- Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan 200284, Nigeria
| | - Victor O. Adetimirin
- Pan African University Institute of Life and Earth Sciences (PAULESI), University of Ibadan, Ibadan 200284, Nigeria
- Department of Crop and Horticultural Sciences, University of Ibadan, Ibadan 200284, Nigeria
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16
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Odongo PJ, Onaga G, Ricardo O, Natsuaki KT, Alicai T, Geuten K. Insights Into Natural Genetic Resistance to Rice Yellow Mottle Virus and Implications on Breeding for Durable Resistance. FRONTIERS IN PLANT SCIENCE 2021; 12:671355. [PMID: 34267770 PMCID: PMC8276079 DOI: 10.3389/fpls.2021.671355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 05/14/2021] [Indexed: 06/13/2023]
Abstract
Rice is the main food crop for people in low- and lower-middle-income countries in Asia and sub-Saharan Africa (SSA). Since 1982, there has been a significant increase in the demand for rice in SSA, and its growing importance is reflected in the national strategic food security plans of several countries in the region. However, several abiotic and biotic factors undermine efforts to meet this demand. Rice yellow mottle virus (RYMV) caused by Solemoviridae is a major biotic factor affecting rice production and continues to be an important pathogen in SSA. To date, six pathogenic strains have been reported. RYMV infects rice plants through wounds and rice feeding vectors. Once inside the plant cells, viral genome-linked protein is required to bind to the rice translation initiation factor [eIF(iso)4G1] for a compatible interaction. The development of resistant cultivars that can interrupt this interaction is the most effective method to manage this disease. Three resistance genes are recognized to limit RYMV virulence in rice, some of which have nonsynonymous single mutations or short deletions in the core domain of eIF(iso)4G1 that impair viral host interaction. However, deployment of these resistance genes using conventional methods has proved slow and tedious. Molecular approaches are expected to be an alternative to facilitate gene introgression and/or pyramiding and rapid deployment of these resistance genes into elite cultivars. In this review, we summarize the knowledge on molecular genetics of RYMV-rice interaction, with emphasis on host plant resistance. In addition, we provide strategies for sustainable utilization of the novel resistant sources. This knowledge is expected to guide breeding programs in the development and deployment of RYMV resistant rice varieties.
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Affiliation(s)
- Patrick J. Odongo
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Geoffrey Onaga
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
- M’bé Research Station, Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
| | - Oliver Ricardo
- Breeding Innovations Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Keiko T. Natsuaki
- Graduate School of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Titus Alicai
- National Crops Resources Research Institute, National Agriculture Research Organization, Kampala, Uganda
| | - Koen Geuten
- Molecular Biotechnology of Plants and Micro-Organisms, Institute of Botany and Microbiology, KU Leuven, Leuven, Belgium
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17
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Zhao S, Wu Y, Wu J. Arms race between rice and viruses: a review of viral and host factors. Curr Opin Virol 2021; 47:38-44. [PMID: 33530035 DOI: 10.1016/j.coviro.2021.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 12/28/2022]
Abstract
Much is known about the molecular interactions between positive-strand RNA viruses and dicotyledon plants. However, many important viral pathogens of the monocotyledon rice crop contain negative-strand or double-strand RNA genomes. Recent studies have shown that virus-derived small-interfering RNAs (siRNAs), host microRNAs and phytohormones regulate antiviral responses in rice plants and that rice-infecting RNA viruses encode a diverse repertoire of multifunctional proteins with counter-defensive activities. Moreover, the interactions between viral virulence proteins and host susceptibility factors also shape the virus-rice arms race. This review will focus on these recent advances and discuss strategies and challenges in the translation of discoveries made on molecular virus-rice interactions into practical virus control measures.
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Affiliation(s)
- Shanshan Zhao
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yuansheng Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jianguo Wu
- Vector-borne Virus Research Center, Fujian Province Key Laboratory of Plant Virology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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18
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Soler-Garzón A, McClean PE, Miklas PN. Genome-Wide Association Mapping of bc-1 and bc-u Reveals Candidate Genes and New Adjustments to the Host-Pathogen Interaction for Resistance to Bean Common Mosaic Necrosis Virus in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:699569. [PMID: 34267774 PMCID: PMC8277298 DOI: 10.3389/fpls.2021.699569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/21/2021] [Indexed: 05/17/2023]
Abstract
Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for bc-1 and bc-u and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence vs. absence of bc-u; (ii) bc-1 exhibits dominance and incomplete dominance; (iii) bc-1 alone confers resistance to NL-8; (iv) bc-u was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol bc-u d to reflect this change; (v) bc-u d alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and (vi) bc-u d is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean.
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Affiliation(s)
- Alvaro Soler-Garzón
- Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, United States
| | - Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Prosser, WA, United States
- *Correspondence: Phillip N. Miklas, , orcid.org/0000-0002-6636-454X
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Atarashi H, Jayasinghe WH, Kwon J, Kim H, Taninaka Y, Igarashi M, Ito K, Yamada T, Masuta C, Nakahara KS. Artificially Edited Alleles of the Eukaryotic Translation Initiation Factor 4E1 Gene Differentially Reduce Susceptibility to Cucumber Mosaic Virus and Potato Virus Y in Tomato. Front Microbiol 2020; 11:564310. [PMID: 33362728 PMCID: PMC7758215 DOI: 10.3389/fmicb.2020.564310] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/11/2020] [Indexed: 01/27/2023] Open
Abstract
Eukaryotic translation initiation factors, including eIF4E, are susceptibility factors for viral infection in host plants. Mutation and double-stranded RNA-mediated silencing of tomato eIF4E genes can confer resistance to viruses, particularly members of the Potyvirus genus. Here, we artificially mutated the eIF4E1 gene on chromosome 3 of a commercial cultivar of tomato (Solanum lycopersicum L.) by using CRISPR/Cas9. We obtained three alleles, comprising two deletions of three and nine nucleotides (3DEL and 9DEL) and a single nucleotide insertion (1INS), near regions that encode amino acid residues important for binding to the mRNA 5' cap structure and to eIF4G. Plants homozygous for these alleles were termed 3DEL, 9DEL, and 1INS plants, respectively. In accordance with previous studies, inoculation tests with potato virus Y (PVY; type member of the genus Potyvirus) yielded a significant reduction in susceptibility to the N strain (PVYN), but not to the ordinary strain (PVYO), in 1INS plants. 9DEL among three artificial alleles had a deleterious effect on infection by cucumber mosaic virus (CMV, type member of the genus Cucumovirus). When CMV was mechanically inoculated into tomato plants and viral coat accumulation was measured in the non-inoculated upper leaves, the level of viral coat protein was significantly lower in the 9DEL plants than in the parental cultivar. Tissue blotting of microperforated inoculated leaves of the 9DEL plants revealed significantly fewer infection foci compared with those of the parental cultivar, suggesting that 9DEL negatively affects the initial steps of infection with CMV in a mechanically inoculated leaf. In laboratory tests, viral aphid transmission from an infected susceptible plant to 9DEL plants was reduced compared with the parental control. Although many pathogen resistance genes have been discovered in tomato and its wild relatives, no CMV resistance genes have been used in practice. RNA silencing of eIF4E expression has previously been reported to not affect susceptibility to CMV in tomato. Our findings suggest that artificial gene editing can introduce additional resistance to that achieved with mutagenesis breeding, and that edited eIF4E alleles confer an alternative way to manage CMV in tomato fields.
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Affiliation(s)
- Hiroki Atarashi
- Research and Development Division, Kikkoman Corporation, Noda, Chiba, Japan
| | - Wikum Harshana Jayasinghe
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Agricultural Biology, Faculty of Agriculture, University of Peradeniya, Peradeniya, Sri Lanka
| | - Joon Kwon
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Hangil Kim
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Yosuke Taninaka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Kotaro Ito
- Research and Development Division, Kikkoman Corporation, Noda, Chiba, Japan
| | - Tetsuya Yamada
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
| | - Kenji S Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Japan
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Urquidi-Camacho RA, Lokdarshi A, von Arnim AG. Translational gene regulation in plants: A green new deal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1597. [PMID: 32367681 PMCID: PMC9258721 DOI: 10.1002/wrna.1597] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants. This article is categorized under: Translation > Translation Regulation RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Ricardo A. Urquidi-Camacho
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology and UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
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Characterization of Local and Systemic Impact of Whitefly ( Bemisia tabaci) Feeding and Whitefly-Transmitted Tomato Mottle Virus Infection on Tomato Leaves by Comprehensive Proteomics. Int J Mol Sci 2020; 21:ijms21197241. [PMID: 33008056 PMCID: PMC7583044 DOI: 10.3390/ijms21197241] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/21/2020] [Accepted: 09/26/2020] [Indexed: 11/23/2022] Open
Abstract
Tomato mottle virus (ToMoV) is a single-stranded DNA (ssDNA) begomovirus transmitted to solanaceous crops by the whitefly species complex (Bemisia tabaci), causing stunted growth, leaf mottling, and reduced yield. Using a genetic repertoire of seven genes, ToMoV pathogenesis includes the manipulation of multiple plant biological processes to circumvent antiviral defenses. To further understand the effects of whitefly feeding and whitefly-transmitted ToMoV infection on tomato plants (Solanum lycopersicum ‘Florida Lanai’), we generated comprehensive protein profiles of leaves subjected to feeding by either viruliferous whiteflies harboring ToMoV, or non-viruliferous whiteflies, or a no-feeding control. The effects of whitefly feeding and ToMoV infection were measured both locally and systemically by sampling either a mature leaf directly from the site of clip-cage confined whitefly feeding, or from a newly formed leaf 10 days post feeding (dpf). At 3 dpf, tomato’s response to ToMoV included proteins associated with translation initiation and elongation as well as plasmodesmata dynamics. In contrast, systemic impacts of ToMoV on younger leaves 10 dpf were more pronounced and included a virus-specific change in plant proteins associated with mRNA maturation and export, RNA-dependent DNA methylation, and other antiviral plant processes. Our analysis supports previous findings and provides novel insight into tomato’s local and systemic response to whitefly feeding and ToMoV infection.
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Martinez-Seidel F, Beine-Golovchuk O, Hsieh YC, Kopka J. Systematic Review of Plant Ribosome Heterogeneity and Specialization. FRONTIERS IN PLANT SCIENCE 2020; 11:948. [PMID: 32670337 PMCID: PMC7332886 DOI: 10.3389/fpls.2020.00948] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 06/10/2020] [Indexed: 05/25/2023]
Abstract
Plants dedicate a high amount of energy and resources to the production of ribosomes. Historically, these multi-protein ribosome complexes have been considered static protein synthesis machines that are not subject to extensive regulation but only read mRNA and produce polypeptides accordingly. New and increasing evidence across various model organisms demonstrated the heterogeneous nature of ribosomes. This heterogeneity can constitute specialized ribosomes that regulate mRNA translation and control protein synthesis. A prominent example of ribosome heterogeneity is seen in the model plant, Arabidopsis thaliana, which, due to genome duplications, has multiple paralogs of each ribosomal protein (RP) gene. We support the notion of plant evolution directing high RP paralog divergence toward functional heterogeneity, underpinned in part by a vast resource of ribosome mutants that suggest specialization extends beyond the pleiotropic effects of single structural RPs or RP paralogs. Thus, Arabidopsis is a highly suitable model to study this phenomenon. Arabidopsis enables reverse genetics approaches that could provide evidence of ribosome specialization. In this review, we critically assess evidence of plant ribosome specialization and highlight steps along ribosome biogenesis in which heterogeneity may arise, filling the knowledge gaps in plant science by providing advanced insights from the human or yeast fields. We propose a data analysis pipeline that infers the heterogeneity of ribosome complexes and deviations from canonical structural compositions linked to stress events. This analysis pipeline can be extrapolated and enhanced by combination with other high-throughput methodologies, such as proteomics. Technologies, such as kinetic mass spectrometry and ribosome profiling, will be necessary to resolve the temporal and spatial aspects of translational regulation while the functional features of ribosomal subpopulations will become clear with the combination of reverse genetics and systems biology approaches.
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Affiliation(s)
- Federico Martinez-Seidel
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | | | - Yin-Chen Hsieh
- Bioinformatics Subdivision, Wageningen University, Wageningen, Netherlands
| | - Joachim Kopka
- Willmitzer Department, Max Planck-Institute of Molecular Plant Physiology, Potsdam, Germany
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23
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Udagawa H, Koga K, Shinjo A, Kitashiba H, Takakura Y. Reduced susceptibility to a tobacco bushy top virus Malawi isolate by loss of function in host eIF(iso)4E genes. BREEDING SCIENCE 2020; 70:313-320. [PMID: 32714053 PMCID: PMC7372031 DOI: 10.1270/jsbbs.19135] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 12/25/2019] [Indexed: 05/23/2023]
Abstract
Tobacco bushy top disease (TBTD) is a viral disease of tobacco (Nicotiana tabacum L.) caused by mixed infection of Tobacco bushy top virus or Ethiopian tobacco bushy top virus and a helper virus. Despite its damage to tobacco, practical genetic resources for disease resistance have not been found. Here, we report that a mutation of tobacco eIF(iso)4E genes (eIF(iso)4E-S and eIF(iso)4E-T), which encode eukaryotic translation initiation factors, confers resistance (reduced susceptibility) to TBTD caused by a virus from Malawi (designated as tobacco bushy top virus Malawi isolate, TBTV-MW). RNAi lines in which eIF(iso)4E genes were silenced showed reduced susceptibility to TBTV-MW. We also tested chemically-induced single (eIF(iso)4E-S or eIF(iso)4E-T) and double (eIF(iso)4E-S and eIF(iso)4E-T) nonsense mutants for resistance to TBTV-MW. Suppression of eIF(iso)4E-S showed reduced susceptibility, and the resistance of the double mutant tended to be even stronger. eIF(iso)4E mutants also showed reduced susceptibility to TBTV-MW transmitted by aphids. To the best of our knowledge, the eIF(iso)4E-S mutant is the first genetic resource for TBTD resistance breeding in tobacco.
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Affiliation(s)
- Hisashi Udagawa
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900, Idei, Oyama, Tochigi 323-0808, Japan
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Kazuharu Koga
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900, Idei, Oyama, Tochigi 323-0808, Japan
| | - Akira Shinjo
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900, Idei, Oyama, Tochigi 323-0808, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aza-Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Yoshimitsu Takakura
- Leaf Tobacco Research Center, Japan Tobacco, Inc., 1900, Idei, Oyama, Tochigi 323-0808, Japan
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Pidon H, Chéron S, Ghesquière A, Albar L. Allele mining unlocks the identification of RYMV resistance genes and alleles in African cultivated rice. BMC PLANT BIOLOGY 2020; 20:222. [PMID: 32429875 PMCID: PMC7236528 DOI: 10.1186/s12870-020-02433-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 05/07/2020] [Indexed: 05/24/2023]
Abstract
BACKGROUND Rice yellow mottle virus (RYMV) is a major rice pathogen in Africa. Three resistance genes, i.e. RYMV1, RYMV2 and RYMV3, have been previously described. RYMV1 encodes the translation initiation factor eIF(iso)4G1 and the best candidate genes for RYMV2 and RYMV3 encode a homolog of an Arabidopsis nucleoporin (CPR5) and a nucleotide-binding domain and leucine-rich repeat containing domain (NLR) protein, respectively. High resistance is very uncommon in Asian cultivated rice (Oryza sativa), with only two highly resistant accessions identified so far, but it is more frequent in African cultivated rice (Oryza glaberrima). RESULTS Here we report the findings of a resistance survey in a reference collection of 268 O. glaberrima accessions. A total of 40 resistant accessions were found, thus confirming the high frequency of resistance to RYMV in this species. We analysed the variability of resistance genes or candidate genes in this collection based on high-depth Illumina data or Sanger sequencing. Alleles previously shown to be associated with resistance were observed in 31 resistant accessions but not in any susceptible ones. Five original alleles with a frameshift or untimely stop codon in the candidate gene for RYMV2 were also identified in resistant accessions. A genetic analysis revealed that these alleles, as well as T-DNA insertions in the candidate gene, were responsible of RYMV resistance. All 40 resistant accessions were ultimately linked to a validated or candidate resistance allele at one of the three resistance genes to RYMV. CONCLUSION This study demonstrated that the RYMV2 resistance gene is homologous to the Arabidopsis CPR5 gene and revealed five new resistance alleles at this locus. It also confirmed the close association between resistance and an amino-acid substitution in the leucine-rich repeat of the NLR candidate for RYMV3. We also provide an extensive overview of the genetic diversity of resistance to RYMV in the O. glaberrima species, while underlining the contrasted pattern of diversity between O. glaberrima and O. sativa for this trait. The different resistance genes and alleles will be instrumental in breeding varieties with sustainable field resistance to RYMV.
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Affiliation(s)
- Hélène Pidon
- DIADE, Univ. Montpellier, IRD, Montpellier, France
- Present Address: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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Gao L, Luo J, Ding X, Wang T, Hu T, Song P, Zhai R, Zhang H, Zhang K, Li K, Zhi H. Soybean RNA interference lines silenced for eIF4E show broad potyvirus resistance. MOLECULAR PLANT PATHOLOGY 2020; 21:303-317. [PMID: 31860775 PMCID: PMC7036369 DOI: 10.1111/mpp.12897] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/22/2019] [Accepted: 11/26/2019] [Indexed: 05/27/2023]
Abstract
Soybean mosaic virus (SMV), a potyvirus, is the most prevalent and destructive viral pathogen in soybean-planting regions of China. Moreover, other potyviruses, including bean common mosaic virus (BCMV) and watermelon mosaic virus (WMV), also threaten soybean farming. The eukaryotic translation initiation factor 4E (eIF4E) plays a critical role in controlling resistance/susceptibility to potyviruses in plants. In the present study, much higher SMV-induced eIF4E1 expression levels were detected in a susceptible soybean cultivar when compared with a resistant cultivar, suggesting the involvement of eIF4E1 in the response to SMV by the susceptible cultivar. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that soybean eIF4E1 interacted with SMV VPg in the nucleus and with SMV NIa-Pro/NIb in the cytoplasm, revealing the involvement of VPg, NIa-Pro, and NIb in SMV infection and multiplication. Furthermore, transgenic soybeans silenced for eIF4E were produced using an RNA interference approach. Through monitoring for viral symptoms and viral titers, robust and broad-spectrum resistance was confirmed against five SMV strains (SC3/7/15/18 and SMV-R), BCMV, and WMV in the transgenic plants. Our findings represent fresh insights for investigating the mechanism underlying eIF4E-mediated resistance in soybean and also suggest an effective alternative for breeding soybean with broad-spectrum viral resistance.
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Affiliation(s)
- Le Gao
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
- College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinyan Luo
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Xueni Ding
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Tao Wang
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
- Institute of Cereal and Oil CropsHandan Academy of Agricultural SciencesHandanChina
| | - Ting Hu
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Puwen Song
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Rui Zhai
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Hongyun Zhang
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Kai Zhang
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Kai Li
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
| | - Haijian Zhi
- National Center for Soybean ImprovementNanjing Agricultural UniversityNanjingChina
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Liu Q, Deng S, Liu B, Tao Y, Ai H, Liu J, Zhang Y, Zhao Y, Xu M. A helitron-induced RabGDIα variant causes quantitative recessive resistance to maize rough dwarf disease. Nat Commun 2020; 11:495. [PMID: 31980630 PMCID: PMC6981192 DOI: 10.1038/s41467-020-14372-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/01/2020] [Indexed: 12/15/2022] Open
Abstract
Maize rough dwarf disease (MRDD), caused by various species of the genus Fijivirus, threatens maize production worldwide. We previously identified a quantitative locus qMrdd1 conferring recessive resistance to one causal species, rice black-streaked dwarf virus (RBSDV). Here, we show that Rab GDP dissociation inhibitor alpha (RabGDIα) is the host susceptibility factor for RBSDV. The viral P7-1 protein binds tightly to the exon-10 and C-terminal regions of RabGDIα to recruit it for viral infection. Insertion of a helitron transposon into RabGDIα intron 10 creates alternative splicing to replace the wild-type exon 10 with a helitron-derived exon 10. The resultant splicing variant RabGDIα-hel has difficulty being recruited by P7-1, thus leading to quantitative recessive resistance to MRDD. All naturally occurring resistance alleles may have arisen from a recent single helitron insertion event. These resistance alleles are valuable to improve maize resistance to MRDD and potentially to engineer RBSDV resistance in other crops. Maize rough dwarf disease threatens its production. Here, the authors show that a helitron transposon insertion in the Rab GDP dissociation inhibitor alpha leads to recessive viral resistance by affecting its interaction with viral P7-1 protein and that all naturally occurring alleles come from a single mutation event after domestication.
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Affiliation(s)
- Qingcai Liu
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193, P. R. China
| | - Suining Deng
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193, P. R. China
| | - Baoshen Liu
- College of Agronomy/State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, P. R. China
| | - Yongfu Tao
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193, P. R. China
| | - Haiyue Ai
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193, P. R. China
| | - Jianju Liu
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193, P. R. China
| | - Yongzhong Zhang
- College of Agronomy/State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, P. R. China
| | - Yan Zhao
- College of Agronomy/State Key Laboratory of Crop Biology, Shandong Agricultural University, Taian, 271018, P. R. China
| | - Mingliang Xu
- State Key Laboratory of Plant Physiology and Biochemistry/College of Agronomy and Biotechnology/National Maize Improvement Center/Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, 2 West Yuanmingyuan Road, Beijing, 100193, P. R. China.
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27
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Rubio J, Sánchez E, Tricon D, Montes C, Eyquard JP, Chague A, Aguirre C, Prieto H, Decroocq V. Silencing of one copy of the translation initiation factor eIFiso4G in Japanese plum (Prunus salicina) impacts susceptibility to Plum pox virus (PPV) and small RNA production. BMC PLANT BIOLOGY 2019; 19:440. [PMID: 31640557 PMCID: PMC6806492 DOI: 10.1186/s12870-019-2047-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/20/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND In plants, host factors encoded by susceptibility (S) genes are indispensable for viral infection. Resistance is achieved through the impairment or the absence of those susceptibility factors. Many S genes have been cloned from model and crop species and a majority of them are coding for members of the eukaryotic translation initiation complex, mainly eIF4E, eIF4G and their isoforms. The aim of this study was to investigate the role of those translation initiation factors in susceptibility of stone fruit species to sharka, a viral disease due to Plum pox virus (PPV). RESULTS For this purpose, hairpin-inducing silencing constructs based on Prunus persica orthologs were used to generate Prunus salicina (Japanese plum) 4E and 4G silenced plants by Agrobacterium tumefaciens-mediated transformation and challenged with PPV. While down-regulated eIFiso4E transgenic Japanese plums were not regenerated in our conditions, eIFiso4G11-, but not the eIFiso4G10-, silenced plants displayed durable and stable resistance to PPV. We also investigated the alteration of the si- and mi-RNA profiles in transgenic and wild-type Japanese plums upon PPV infection and confirmed that the newly generated small interfering (si) RNAs, which are derived from the engineered inverted repeat construct, are the major contributor of resistance to sharka. CONCLUSIONS Our results indicate that S gene function of the translation initiation complex isoform is conserved in Prunus species. We discuss the possibilities of using RNAi silencing or loss-of-function mutations of the different isoforms of proteins involved in this complex to breed for resistance to sharka in fruit trees.
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Affiliation(s)
- Julia Rubio
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
- Agronomical Sciences Doctoral Program, Campus Sur, University of Chile, Santa Rosa 11315, La Pintana, Santiago Chile
- Present address: Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Providencia, Chile
| | - Evelyn Sánchez
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
- Present address: Integrative Genomics Doctoral Program, Universidad Mayor, Camino La Pirámide 575, Huechuraba, Santiago Chile
| | - David Tricon
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| | - Christian Montes
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
- Present address: Genetics and Genomics Doctoral Program, Iowa State University, 2437 Pammel Drive, Ames, IA 50011–1079 USA
| | - Jean-Philippe Eyquard
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| | - Aurélie Chague
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
| | - Carlos Aguirre
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago Chile
| | - Véronique Decroocq
- INRA, UMR 1332 BFP, Equipe de virologie, 71 Avenue Edouard Bourlaux, 33883 Villenave d’Ornon, France
- Université de Bordeaux, UMR 1332 BFP, CS20032, 33883 Villenave d’Ornon, France
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Macovei A, Sevilla NR, Cantos C, Jonson GB, Slamet‐Loedin I, Čermák T, Voytas DF, Choi I, Chadha‐Mohanty P. Novel alleles of rice eIF4G generated by CRISPR/Cas9-targeted mutagenesis confer resistance to Rice tungro spherical virus. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1918-1927. [PMID: 29604159 PMCID: PMC6181218 DOI: 10.1111/pbi.12927] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 01/27/2018] [Accepted: 03/18/2018] [Indexed: 05/03/2023]
Abstract
Rice tungro disease (RTD) is a serious constraint in rice production across tropical Asia. RTD is caused by the interaction between Rice tungro spherical virus (RTSV) and Rice tungro bacilliform virus. RTSV resistance found in traditional cultivars has contributed to a reduction in the incidence of RTD in the field. Natural RTSV resistance is a recessive trait controlled by the translation initiation factor 4 gamma gene (eIF4G). The Y1059 V1060 V1061 residues of eIF4G are known to be associated with the reactions to RTSV. To develop new sources of resistance to RTD, mutations in eIF4G were generated using the CRISPR/Cas9 system in the RTSV-susceptible variety IR64, widely grown across tropical Asia. The mutation rates ranged from 36.0% to 86.6%, depending on the target site, and the mutations were successfully transmitted to the next generations. Among various mutated eIF4G alleles examined, only those resulting in in-frame mutations in SVLFPNLAGKS residues (mainly NL), adjacent to the YVV residues, conferred resistance. Furthermore, our data suggest that eIF4G is essential for normal development, as alleles resulting in truncated eIF4G could not be maintained in homozygous state. The final products with RTSV resistance and enhanced yield under glasshouse conditions were found to no longer contain the Cas9 sequence. Hence, the RTSV-resistant plants with the novel eIF4G alleles represent a valuable material to develop more diverse RTSV-resistant varieties.
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Affiliation(s)
- Anca Macovei
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
- Present address:
Department of Biology and Biotechnology ‘L. Spallanzani’University of PaviaPaviaItaly
| | - Neah R. Sevilla
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Christian Cantos
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
- Present address:
Huck Institute of the Life SciencesPennsylvania State UniversityUniversity ParkPAUSA
| | - Gilda B. Jonson
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Inez Slamet‐Loedin
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Tomáš Čermák
- Department of GeneticsCell Biology & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Daniel F. Voytas
- Department of GeneticsCell Biology & Development and Center for Genome EngineeringUniversity of MinnesotaMinneapolisMNUSA
| | - Il‐Ryong Choi
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Prabhjit Chadha‐Mohanty
- Genetics and Biotechnology DivisionInternational Rice Research Institute (IRRI)Metro ManilaPhilippines
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Variability in eukaryotic initiation factor iso4E in Brassica rapa influences interactions with the viral protein linked to the genome of Turnip mosaic virus. Sci Rep 2018; 8:13588. [PMID: 30206242 PMCID: PMC6134127 DOI: 10.1038/s41598-018-31739-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 08/21/2018] [Indexed: 12/22/2022] Open
Abstract
Plant potyviruses require eukaryotic translation initiation factors (eIFs) such as eIF4E and eIF(iso)4E to replicate and spread. When Turnip mosaic virus (TuMV) infects a host plant, its viral protein linked to the genome (VPg) needs to interact with eIF4E or eIF(iso)4E to initiate translation. TuMV utilizes BraA.eIF4E.a, BraA.eIF4E.c, BraA.eIF(iso)4E.a, and BraA.eIF(iso)4E.c of Brassica rapa to initiate translation in Arabidopsis thaliana. In this study, the BraA.eIF4E.a, BraA.eIF4E.c, BraA.eIF(iso)4E.a, and BraA.eIF(iso)4E.c genes were cloned and sequenced from eight B. rapa lines, namely, two BraA.eIF4E.a alleles, four BraA.eIF4E.c alleles, four BraA.eIF(iso)4E.a alleles, and two BraA.eIF(iso)4E.c alleles. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) analyses indicated that TuMV VPg could not interact with eIF4E, but only with eIF(iso)4E of B. rapa. In addition, the VPgs of the different TuMV isolates interacted with various eIF(iso)4E copies in B. rapa. In particular, TuMV-UK1/CDN1 VPg only interacted with BraA.eIF(iso)4E.c, not with BraA.eIF(iso)4E.a. Some single nucleotide polymorphisms (SNPs) were identified that may have affected the interaction between eIF(iso)4E and VPg such as the SNP T106C in BraA.eIF(iso)4E.c and the SNP A154C in VPg. Furthermore, a three-dimensional structural model of the BraA.eIF(iso)4E.c-1 protein was constructed to identify the specific conformation of the variable amino acids from BraA.eIF(iso)4E.c. The 36th amino acid in BraA.eIF(iso)4E.c is highly conserved and may play an important role in establishing protein structural stability. The findings of the present study may lay the foundation for future investigations on the co-evolution of TuMV and eIF(iso)4E.
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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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Longue RDS, Traore VSE, Zinga I, Asante MD, Bouda Z, Neya JB, Barro N, Traore O. Pathogenicity of rice yellow mottle virus and screening of rice accessions from the Central African Republic. Virol J 2018; 15:6. [PMID: 29310664 PMCID: PMC5759187 DOI: 10.1186/s12985-017-0912-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/18/2017] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Rice yellow mottle virus (RYMV) of the genus Sobemovirus is the most important viral pathogen of rice causing more damage to rice crop in Sub Saharan Africa. The aim of this study was to conduct pathogenic characterization of RYMV isolates from the Central African Republic (CAR) and to screen commonly cultivated rice accessions in the country for resistance/tolerance to the virus. METHODS The pathogenicity of RYMV isolates was studied by mechanical inoculation with comparison to differential rice lines highly resistant to RYMV available at the Institute of Environment and Agricultural Research (INERA) in Burkina Faso. To screen commonly cultivated rice accessions in CAR, characterized RYMV isolates from the country were used as inoculum sources. Resistant breaking (RB) isolates were used to prepare RB-inoculum, whereas non-resistant breaking isolates (nRB) were used for nRB-inoculum. RESULTS Overall 102 isolates used in this study, 29.4% were able to overcome the high resistance genes in the rice cultivars Gigante and Tog7291. All isolates were distributed within three distinct pathogenic profiles. The first profile constituted of 6.9% of the isolates was able to break down the resistance in rice cultivar Gigante only. The second pathogenic profile made of 19.6% of isolates was able to infect Tog7291 only. The third profile, 2.9% of isolates overcame simultaneously resistance genes in both rice cultivars Gigante and Tog7291. Out of isolates able to break down the resistance gene in cultivar Gigante, a single isolate was found to be non-infectious to the susceptible control IR64. Data from screening showed that all accessions were susceptible to RYMV, although IRAT213 was found to be partially resistant to both nRB-inoculum and RB-inoculum. CONCLUSION The present study can be considered as the first in the Central African Republic, it gives a caution on the high risk of RYMV damage to rice production in the country. Beside, skills of pathogenic profiles of RYMV isolates will contribute to better disease management.
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Affiliation(s)
- Regis Dimitri Sokpe Longue
- Laboratory of Biological and Agronomic Sciences for Development (LaSBAD), Life Science Department, University of Bangui, BP 908 Bangui, Central African Republic
- Institute of Environment and Agricultural Research (INERA), Ouagadougou, 01 BP 476 Burkina Faso
| | | | - Innocent Zinga
- Laboratory of Biological and Agronomic Sciences for Development (LaSBAD), Life Science Department, University of Bangui, BP 908 Bangui, Central African Republic
| | - Maxwell Darko Asante
- Concil for Scientific and Industrial Research –Crop Research Institute, CSIR-CRI, P.O. Box 3785, Kumasi, Ghana
| | - Zakaria Bouda
- Institute of Environment and Agricultural Research (INERA), Ouagadougou, 01 BP 476 Burkina Faso
| | - James Bouma Neya
- Institute of Environment and Agricultural Research (INERA), Ouagadougou, 01 BP 476 Burkina Faso
| | - Nicolas Barro
- Department of Biochemistry and Microbiology, University of Ouagadougou I-Professor Joseph Ki-Zerbo, Ouagadougou, Burkina Faso
| | - Oumar Traore
- Institute of Environment and Agricultural Research (INERA), Ouagadougou, 01 BP 476 Burkina Faso
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Aoun N, Tauleigne L, Lonjon F, Deslandes L, Vailleau F, Roux F, Berthomé R. Quantitative Disease Resistance under Elevated Temperature: Genetic Basis of New Resistance Mechanisms to Ralstonia solanacearum. FRONTIERS IN PLANT SCIENCE 2017; 8:1387. [PMID: 28878784 PMCID: PMC5572249 DOI: 10.3389/fpls.2017.01387] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
In the context of climate warming, plants will be facing an increased risk of epidemics as well as the emergence of new highly aggressive pathogen species. Although a permanent increase of temperature strongly affects plant immunity, the underlying molecular mechanisms involved are still poorly characterized. In this study, we aimed to uncover the genetic bases of resistance mechanisms that are efficient at elevated temperature to the Ralstonia solanacearum species complex (RSSC), one of the most harmful phytobacteria causing bacterial wilt. To start the identification of quantitative trait loci (QTLs) associated with natural variation of response to R. solanacearum, we adopted a genome wide association (GWA) mapping approach using 176 worldwide natural accessions of Arabidopsis thaliana inoculated with the R. solanacearum GMI1000 strain. Following two different procedures of root-inoculation (root apparatus cut vs. uncut), plants were grown either at 27 or 30°C, with the latter temperature mimicking a permanent increase in temperature. At 27°C, the RPS4/RRS1-R locus was the main QTL of resistance detected regardless of the method of inoculation used. This highlights the power of GWA mapping to identify functionally important loci for resistance to the GMI1000 strain. At 30°C, although most of the accessions developed wilting symptoms, we identified several QTLs that were specific to the inoculation method used. We focused on a QTL region associated with response to the GMI1000 strain in the early stages of infection and, by adopting a reverse genetic approach, we functionally validated the involvement of a strictosidine synthase-like 4 (SSL4) protein that shares structural similarities with animal proteins known to play a role in animal immunity.
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Affiliation(s)
| | | | | | | | | | | | - Richard Berthomé
- LIPM, Centre National de la Recherche Scientifique, Institut National de la Recherche Agronomique, INPT, Université de ToulouseCastanet-Tolosan, France
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Genome-wide identification of cucumber green mottle mosaic virus-responsive microRNAs in watermelon. Arch Virol 2017; 162:2591-2602. [DOI: 10.1007/s00705-017-3401-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Accepted: 05/02/2017] [Indexed: 01/01/2023]
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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: 17] [Impact Index Per Article: 2.4] [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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Machado JPB, Calil IP, Santos AA, Fontes EPB. Translational control in plant antiviral immunity. Genet Mol Biol 2017; 40:292-304. [PMID: 28199446 PMCID: PMC5452134 DOI: 10.1590/1678-4685-gmb-2016-0092] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 09/27/2016] [Indexed: 01/11/2023] Open
Abstract
Due to the limited coding capacity of viral genomes, plant viruses depend extensively on the host cell machinery to support the viral life cycle and, thereby, interact with a large number of host proteins during infection. Within this context, as plant viruses do not harbor translation-required components, they have developed several strategies to subvert the host protein synthesis machinery to produce rapidly and efficiently the viral proteins. As a countermeasure against infection, plants have evolved defense mechanisms that impair viral infections. Among them, the host-mediated translational suppression has been characterized as an efficient mean to restrict infection. To specifically suppress translation of viral mRNAs, plants can deploy susceptible recessive resistance genes, which encode translation initiation factors from the eIF4E and eIF4G family and are required for viral mRNA translation and multiplication. Additionally, recent evidence has demonstrated that, alternatively to the cleavage of viral RNA targets, host cells can suppress viral protein translation to silence viral RNA. Finally, a novel strategy of plant antiviral defense based on suppression of host global translation, which is mediated by the transmembrane immune receptor NIK1 (nuclear shuttle protein (NSP)-Interacting Kinase1), is discussed in this review.
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Affiliation(s)
- João Paulo B Machado
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Iara P Calil
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Anésia A Santos
- Department of General Biology, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
| | - Elizabeth P B Fontes
- Department of Biochemistry and Molecular Biology, BIOAGRO, National Institute of Science and Technology in Plant-Pest Interactions, Universidade Federal de Viçosa, 36571.000, Viçosa, MG, Brazil
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Wang J, Haapalainen M, Schott T, Thompson SM, Smith GR, Nissinen AI, Pirhonen M. Genomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes. PLoS One 2017; 12:e0171531. [PMID: 28158295 PMCID: PMC5291501 DOI: 10.1371/journal.pone.0171531] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 01/23/2017] [Indexed: 01/28/2023] Open
Abstract
Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso) are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), were obtained from carrot psyllids (Trioza apicalis) harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.
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Affiliation(s)
- Jinhui Wang
- Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Minna Haapalainen
- Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland
| | | | - Sarah M. Thompson
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
- Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia
| | - Grant R. Smith
- The New Zealand Institute for Plant & Food Research Limited, Lincoln, New Zealand
- Plant Biosecurity Cooperative Research Centre, Canberra, ACT, Australia
- Better Border Biosecurity, Lincoln, New Zealand
| | - Anne I. Nissinen
- Management and Production of Renewable Resources, Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Minna Pirhonen
- Department of Agricultural Sciences, FI-00014 University of Helsinki, Helsinki, Finland
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Pinel-Galzi A, Dubreuil-Tranchant C, Hébrard E, Mariac C, Ghesquière A, Albar L. Mutations in Rice yellow mottle virus Polyprotein P2a Involved in RYMV2 Gene Resistance Breakdown. FRONTIERS IN PLANT SCIENCE 2016; 7:1779. [PMID: 27965688 PMCID: PMC5125353 DOI: 10.3389/fpls.2016.01779] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/11/2016] [Indexed: 05/09/2023]
Abstract
Rice yellow mottle virus (RYMV) is one of the major diseases of rice in Africa. The high resistance of the Oryza glaberrima Tog7291 accession involves a null allele of the RYMV2 gene, whose ortholog in Arabidopsis, CPR5, is a transmembrane nucleoporin involved in effector-triggered immunity. To optimize field deployment of the RYMV2 gene and improve its durability, which is often a weak point in varietal resistance, we analyzed its efficiency toward RYMV isolates representing the genetic diversity of the virus and the molecular basis of resistance breakdown. Tog7291 resistance efficiency was highly variable depending on the isolate used, with infection rates ranging from 0 to 98% of plants. Back-inoculation experiments indicated that infection cases were not due to an incomplete resistance phenotype but to the emergence of resistance-breaking (RB) variants. Interestingly, the capacity of the virus to overcome Tog7291 resistance is associated with a polymorphism at amino-acid 49 of the VPg protein which also affects capacity to overcome the previously studied RYMV1 resistance gene. This polymorphism appeared to be a main determinant of the emergence of RB variants. It acts independently of the resistance gene and rather reflects inter-species adaptation with potential consequences for the durability of resistance. RB mutations were identified by full-length or partial sequencing of the RYMV genome in infected Tog7291 plants and were validated by directed mutagenesis of an infectious viral clone. We found that Tog7291 resistance breakdown involved mutations in the putative membrane anchor domain of the polyprotein P2a. Although the precise effect of these mutations on rice/RYMV interaction is still unknown, our results offer a new perspective for the understanding of RYMV2 mediated resistance mechanisms. Interestingly, in the susceptible IR64 variety, RB variants showed low infectivity and frequent reversion to the wild-type genotype, suggesting that Tog7291 resistance breakdown is associated with a major loss of viral fitness in normally susceptible O. sativa varieties. Despite the high frequency of resistance breakdown in controlled conditions, this loss of fitness is an encouraging element with regards to RYMV2 resistance durability.
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Affiliation(s)
- Agnès Pinel-Galzi
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement – Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Université de MontpellierMontpellier, France
| | - Christine Dubreuil-Tranchant
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Eugénie Hébrard
- Interactions Plantes Microorganismes Environnement, Institut de Recherche pour le Développement – Centre de Coopération Internationale en Recherche Agronomique pour le Développement – Université de MontpellierMontpellier, France
| | - Cédric Mariac
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Alain Ghesquière
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
| | - Laurence Albar
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement – Université de MontpellierMontpellier, France
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Hashimoto M, Neriya Y, Yamaji Y, Namba S. Recessive Resistance to Plant Viruses: Potential Resistance Genes Beyond Translation Initiation Factors. Front Microbiol 2016; 7:1695. [PMID: 27833593 PMCID: PMC5080351 DOI: 10.3389/fmicb.2016.01695] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/11/2016] [Indexed: 12/13/2022] Open
Abstract
The ability of plant viruses to propagate their genomes in host cells depends on many host factors. In the absence of an agrochemical that specifically targets plant viral infection cycles, one of the most effective methods for controlling viral diseases in plants is taking advantage of the host plant’s resistance machinery. Recessive resistance is conferred by a recessive gene mutation that encodes a host factor critical for viral infection. It is a branch of the resistance machinery and, as an inherited characteristic, is very durable. Moreover, recessive resistance may be acquired by a deficiency in a negative regulator of plant defense responses, possibly due to the autoactivation of defense signaling. Eukaryotic translation initiation factor (eIF) 4E and eIF4G and their isoforms are the most widely exploited recessive resistance genes in several crop species, and they are effective against a subset of viral species. However, the establishment of efficient, recessive resistance-type antiviral control strategies against a wider range of plant viral diseases requires genetic resources other than eIF4Es. In this review, we focus on recent advances related to antiviral recessive resistance genes evaluated in model plants and several crop species. We also address the roles of next-generation sequencing and genome editing technologies in improving plant genetic resources for recessive resistance-based antiviral breeding in various crop species.
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Affiliation(s)
- Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo Tokyo, Japan
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Hashimoto M, Neriya Y, Keima T, Iwabuchi N, Koinuma H, Hagiwara-Komoda Y, Ishikawa K, Himeno M, Maejima K, Yamaji Y, Namba S. EXA1, a GYF domain protein, is responsible for loss-of-susceptibility to plantago asiatica mosaic virus in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:120-131. [PMID: 27402258 DOI: 10.1111/tpj.13265] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 06/24/2016] [Accepted: 07/06/2016] [Indexed: 06/06/2023]
Abstract
One of the plant host resistance machineries to viruses is attributed to recessive alleles of genes encoding critical host factors for virus infection. This type of resistance, also referred to as recessive resistance, is useful for revealing plant-virus interactions and for breeding antivirus resistance in crop plants. Therefore, it is important to identify a novel host factor responsible for robust recessive resistance to plant viruses. Here, we identified a mutant from an ethylmethane sulfonate (EMS)-mutagenized Arabidopsis population which confers resistance to plantago asiatica mosaic virus (PlAMV, genus Potexvirus). Based on map-based cloning and single nucleotide polymorphism analysis, we identified a premature termination codon in a functionally unknown gene containing a GYF domain, which binds to proline-rich sequences in eukaryotes. Complementation analyses and robust resistance to PlAMV in a T-DNA mutant demonstrated that this gene, named Essential for poteXvirus Accumulation 1 (EXA1), is indispensable for PlAMV infection. EXA1 contains a GYF domain and a conserved motif for interaction with eukaryotic translation initiation factor 4E (eIF4E), and is highly conserved among monocot and dicot species. Analysis using qRT-PCR and immunoblotting revealed that EXA1 was expressed in all tissues, and was not transcriptionally responsive to PlAMV infection in Arabidopsis plants. Moreover, accumulation of PlAMV and a PlAMV-derived replicon was drastically diminished in the initially infected cells by the EXA1 deficiency. Accumulation of two other potexviruses also decreased in exa1-1 mutant plants. Our results provided a functional annotation to GYF domain-containing proteins by revealing the function of the highly conserved EXA1 gene in plant-virus interactions.
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Affiliation(s)
- Masayoshi Hashimoto
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yutaro Neriya
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Takuya Keima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Nozomu Iwabuchi
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Hiroaki Koinuma
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yuka Hagiwara-Komoda
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kazuya Ishikawa
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Misako Himeno
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Kensaku Maejima
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuyuki Yamaji
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shigetou Namba
- Laboratory of Plant Pathology, Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.
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Pogorelko G, Juvale PS, Rutter WB, Hewezi T, Hussey R, Davis EL, Mitchum MG, Baum TJ. A cyst nematode effector binds to diverse plant proteins, increases nematode susceptibility and affects root morphology. MOLECULAR PLANT PATHOLOGY 2016; 17:832-44. [PMID: 26575318 PMCID: PMC6638508 DOI: 10.1111/mpp.12330] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/08/2015] [Accepted: 10/09/2015] [Indexed: 05/20/2023]
Abstract
Cyst nematodes are plant-parasitic roundworms that are of significance in many cropping systems around the world. Cyst nematode infection is facilitated by effector proteins secreted from the nematode into the plant host. The cDNAs of the 25A01-like effector family are novel sequences that were isolated from the oesophageal gland cells of the soybean cyst nematode (Heterodera glycines). To aid functional characterization, we identified an orthologous member of this protein family (Hs25A01) from the closely related sugar beet cyst nematode H. schachtii, which infects Arabidopsis. Constitutive expression of the Hs25A01 CDS in Arabidopsis plants caused a small increase in root length, accompanied by up to a 22% increase in susceptibility to H. schachtii. A plant-expressed RNA interference (RNAi) construct targeting Hs25A01 transcripts in invading nematodes significantly reduced host susceptibility to H. schachtii. These data document that Hs25A01 has physiological functions in planta and a role in cyst nematode parasitism. In vivo and in vitro binding assays confirmed the specific interactions of Hs25A01 with an Arabidopsis F-box-containing protein, a chalcone synthase and the translation initiation factor eIF-2 β subunit (eIF-2bs), making these proteins probable candidates for involvement in the observed changes in plant growth and parasitism. A role of eIF-2bs in the mediation of Hs25A01 virulence function is further supported by the observation that two independent eIF-2bs Arabidopsis knock-out lines were significantly more susceptible to H. schachtii.
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Affiliation(s)
- Gennady Pogorelko
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - Parijat S Juvale
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
| | - William B Rutter
- Department of Plant Pathology, Kansas State University, Manhattan, KS, 66505, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Richard Hussey
- Department of Plant Pathology, The University of Georgia, Athens, GA, 30602, USA
| | - Eric L Davis
- Department of Plant Pathology, North Carolina State University, Raleigh, NC, 27695, USA
| | - Melissa G Mitchum
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Thomas J Baum
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
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Dossa GS, Oliva R, Maiss E, Vera Cruz C, Wydra K. High Temperature Enhances the Resistance of Cultivated African Rice, Oryza glaberrima, to Bacterial Blight. PLANT DISEASE 2016; 100:380-387. [PMID: 30694136 DOI: 10.1094/pdis-05-15-0536-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Rice bacterial blight (BB) is caused by Xanthomonas oryzae pv. oryzae and is responsible for substantial yield loss worldwide. Host resistance remains the most feasible control measure. However, pathogen variability leads to the failure of certain resistance genes to control the disease, and climate change with high amplitudes of heat predisposes the host plant to pathogen invasion. Due to pressure in natural selection, landrace species often carry a wide range of unique traits conferring tolerance of stress. Therefore, exploring their genetic background for host resistance could enable the identification of broad-spectrum resistance to combined abiotic and biotic stresses. Nineteen Oryza glaberrima accessions and O. sativa rice variety SUPA were evaluated for BB resistance under high temperature (35 and 31°C day and night, respectively) using 14 X. oryzae pv. oryzae strains originated from the Philippines. Under normal temperature, most of the accessions showed resistance to 9 strains (64.3%) and accession TOG6007 showed broad-spectrum resistance to 12 strains (85.7%). Under high temperature, most accessions showed a reduction in BB disease, whereas, accession TOG5620 showed disease reduction from all the X. oryzae pv. oryzae strains under high temperature. Molecular characterization using gene-based and linked markers for BB resistance genes Xa4, xa5, Xa7, xa13, and Xa21 revealed the susceptible alleles of Xa4, xa5, xa13, and Xa21 in O. glaberrima. However, no allele of Xa7 was detected among O. glaberrima accessions. Our results suggest that O. glaberrima accessions contain a BB resistance different from the Xa gene type. Genome-wide association mapping could be used to identify quantitative trait loci that are associated with BB resistance or combined BB resistance and high-temperature tolerance.
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Affiliation(s)
- Gerbert Sylvestre Dossa
- Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute (IRRI), Los Baños, Philippines; and Department of Phytomedicine, Leibniz Universität Hannover, Hannover, Germany
| | | | - Edgar Maiss
- Department of Phytomedicine, Leibniz Universität Hannover
| | | | - Kerstin Wydra
- Department of Phytomedicine, Leibniz Universität Hannover; and Plant Production and Climate Change, Erfurt University of Applied Sciences, Erfurt, Germany
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Leen EN, Sorgeloos F, Correia S, Chaudhry Y, Cannac F, Pastore C, Xu Y, Graham SC, Matthews SJ, Goodfellow IG, Curry S. A Conserved Interaction between a C-Terminal Motif in Norovirus VPg and the HEAT-1 Domain of eIF4G Is Essential for Translation Initiation. PLoS Pathog 2016; 12:e1005379. [PMID: 26734730 PMCID: PMC4703368 DOI: 10.1371/journal.ppat.1005379] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/10/2015] [Indexed: 11/28/2022] Open
Abstract
Translation initiation is a critical early step in the replication cycle of the positive-sense, single-stranded RNA genome of noroviruses, a major cause of gastroenteritis in humans. Norovirus RNA, which has neither a 5´ m7G cap nor an internal ribosome entry site (IRES), adopts an unusual mechanism to initiate protein synthesis that relies on interactions between the VPg protein covalently attached to the 5´-end of the viral RNA and eukaryotic initiation factors (eIFs) in the host cell. For murine norovirus (MNV) we previously showed that VPg binds to the middle fragment of eIF4G (4GM; residues 652–1132). Here we have used pull-down assays, fluorescence anisotropy, and isothermal titration calorimetry (ITC) to demonstrate that a stretch of ~20 amino acids at the C terminus of MNV VPg mediates direct and specific binding to the HEAT-1 domain within the 4GM fragment of eIF4G. Our analysis further reveals that the MNV C terminus binds to eIF4G HEAT-1 via a motif that is conserved in all known noroviruses. Fine mutagenic mapping suggests that the MNV VPg C terminus may interact with eIF4G in a helical conformation. NMR spectroscopy was used to define the VPg binding site on eIF4G HEAT-1, which was confirmed by mutagenesis and binding assays. We have found that this site is non-overlapping with the binding site for eIF4A on eIF4G HEAT-1 by demonstrating that norovirus VPg can form ternary VPg-eIF4G-eIF4A complexes. The functional significance of the VPg-eIF4G interaction was shown by the ability of fusion proteins containing the C-terminal peptide of MNV VPg to inhibit in vitro translation of norovirus RNA but not cap- or IRES-dependent translation. These observations define important structural details of a functional interaction between norovirus VPg and eIF4G and reveal a binding interface that might be exploited as a target for antiviral therapy. Norovirus infections cause acute gastroenteritis and are a growing worldwide problem in human health. A critical early step in infection is translation of the viral RNA genome to produce the proteins needed to assemble new virus particles. In mouse noroviruses (MNV), which provide a useful model for studying human noroviruses, the VPg protein attached to the viral RNA is essential for this process because it interacts with a cellular protein, eIF4G, that is normally involved in initiating protein synthesis from the messenger RNA of host genes. We have used a variety of biochemical and biophysical experiments to measure how well MNV VPg binds to eIF4G and to identify the parts of both proteins that are involved in this interaction. We show that a sequence of about 20 amino acids at one end of MNV VPg–the C terminus– allows it to bind to a well-defined domain within eIF4G (called HEAT-1), and that it may adopt a helical structure when doing so. Our data suggest that this interaction is common to all noroviruses, including types that infect humans. We have also shown that the MNV VPg C-terminal peptide can inhibit norovirus protein synthesis, which raises the possibility that the VPg-eIF4G interaction could be targeted in the design of antiviral drugs.
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Affiliation(s)
- Eoin N Leen
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Frédéric Sorgeloos
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Samantha Correia
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Yasmin Chaudhry
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Fabien Cannac
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Chiara Pastore
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Stephen C Graham
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Ian G Goodfellow
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom
| | - Stephen Curry
- Department of Life Sciences, Imperial College London, London, United Kingdom
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Leung H, Raghavan C, Zhou B, Oliva R, Choi IR, Lacorte V, Jubay ML, Cruz CV, Gregorio G, Singh RK, Ulat VJ, Borja FN, Mauleon R, Alexandrov NN, McNally KL, Sackville Hamilton R. Allele mining and enhanced genetic recombination for rice breeding. RICE (NEW YORK, N.Y.) 2015; 8:34. [PMID: 26606925 PMCID: PMC4659784 DOI: 10.1186/s12284-015-0069-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 11/20/2015] [Indexed: 05/17/2023]
Abstract
Traditional rice varieties harbour a large store of genetic diversity with potential to accelerate rice improvement. For a long time, this diversity maintained in the International Rice Genebank has not been fully used because of a lack of genome information. The publication of the first reference genome of Nipponbare by the International Rice Genome Sequencing Project (IRGSP) marked the beginning of a systematic exploration and use of rice diversity for genetic research and breeding. Since then, the Nipponbare genome has served as the reference for the assembly of many additional genomes. The recently completed 3000 Rice Genomes Project together with the public database (SNP-Seek) provides a new genomic and data resource that enables the identification of useful accessions for breeding. Using disease resistance traits as case studies, we demonstrated the power of allele mining in the 3,000 genomes for extracting accessions from the GeneBank for targeted phenotyping. Although potentially useful landraces can now be identified, their use in breeding is often hindered by unfavourable linkages. Efficient breeding designs are much needed to transfer the useful diversity to breeding. Multi-parent Advanced Generation InterCross (MAGIC) is a breeding design to produce highly recombined populations. The MAGIC approach can be used to generate pre-breeding populations with increased genotypic diversity and reduced linkage drag. Allele mining combined with a multi-parent breeding design can help convert useful diversity into breeding-ready genetic resources.
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Affiliation(s)
- Hei Leung
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines.
| | - Chitra Raghavan
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Bo Zhou
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Ricardo Oliva
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Il Ryong Choi
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Vanica Lacorte
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Mona Liza Jubay
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Casiana Vera Cruz
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Glenn Gregorio
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Rakesh Kumar Singh
- Plant Breeding Genetics and Biotechnology Division and International Rice Research Institute, Los Banos, Philippines
| | - Victor Jun Ulat
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Frances Nikki Borja
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Ramil Mauleon
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Nickolai N Alexandrov
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
| | - Kenneth L McNally
- T.T. Chang Genetic Resource Center, International Rice Research Institute, Los Banos, Philippines
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Hou Y, Qiu J, Tong X, Wei X, Nallamilli BR, Wu W, Huang S, Zhang J. A comprehensive quantitative phosphoproteome analysis of rice in response to bacterial blight. BMC PLANT BIOLOGY 2015; 15:163. [PMID: 26112675 PMCID: PMC4482044 DOI: 10.1186/s12870-015-0541-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 06/05/2015] [Indexed: 05/06/2023]
Abstract
BACKGROUND Rice is a major crop worldwide. Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) has become one of the most devastating diseases for rice. It has been clear that phosphorylation plays essential roles in plant disease resistance. However, the role of phosphorylation is poorly understood in rice-Xoo system. Here, we report the first study on large scale enrichment of phosphopeptides and identification of phosphosites in rice before and 24 h after Xoo infection. RESULTS We have successfully identified 2367 and 2223 phosphosites on 1334 and 1297 representative proteins in 0 h and 24 h after Xoo infection, respectively. A total of 762 differentially phosphorylated proteins, including transcription factors, kinases, epi-genetic controlling factors and many well-known disease resistant proteins, are identified after Xoo infection suggesting that they may be functionally relevant to Xoo resistance. In particular, we found that phosphorylation/dephosphorylation might be a key switch turning on/off many epi-genetic controlling factors, including HDT701, in response to Xoo infection, suggesting that phosphorylation switch overriding the epi-genetic regulation may be a very universal model in the plant disease resistance pathway. CONCLUSIONS The phosphosites identified in this study would be a big complementation to our current knowledge in the phosphorylation status and sites of rice proteins. This research represents a substantial advance in understanding the rice phosphoproteome as well as the mechanism of rice bacterial blight resistance.
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Affiliation(s)
- Yuxuan Hou
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Jiehua Qiu
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiaohong Tong
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Xiangjin Wei
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Babi R Nallamilli
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, 30322, U.S.A..
| | - Weihuai Wu
- Hainan Key Laboratory for Monitoring and Control of Tropical Agricultural Pests, Environment and Plant Protection Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, 571101, China.
| | - Shiwen Huang
- China National Rice Research Institute, Hangzhou, 311400, China.
| | - Jian Zhang
- China National Rice Research Institute, Hangzhou, 311400, China.
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Plant Translation Factors and Virus Resistance. Viruses 2015; 7:3392-419. [PMID: 26114476 PMCID: PMC4517107 DOI: 10.3390/v7072778] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Revised: 06/18/2015] [Accepted: 06/19/2015] [Indexed: 02/06/2023] Open
Abstract
Plant viruses recruit cellular translation factors not only to translate their viral RNAs but also to regulate their replication and potentiate their local and systemic movement. Because of the virus dependence on cellular translation factors, it is perhaps not surprising that many natural plant recessive resistance genes have been mapped to mutations of translation initiation factors eIF4E and eIF4G or their isoforms, eIFiso4E and eIFiso4G. The partial functional redundancy of these isoforms allows specific mutation or knock-down of one isoform to provide virus resistance without hindering the general health of the plant. New possible targets for antiviral strategies have also been identified following the characterization of other plant translation factors (eIF4A-like helicases, eIF3, eEF1A and eEF1B) that specifically interact with viral RNAs and proteins and regulate various aspects of the infection cycle. Emerging evidence that translation repression operates as an alternative antiviral RNA silencing mechanism is also discussed. Understanding the mechanisms that control the development of natural viral resistance and the emergence of virulent isolates in response to these plant defense responses will provide the basis for the selection of new sources of resistance and for the intelligent design of engineered resistance that is broad-spectrum and durable.
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Sõmera M, Sarmiento C, Truve E. Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae. Viruses 2015; 7:3076-115. [PMID: 26083319 PMCID: PMC4488728 DOI: 10.3390/v7062761] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/18/2015] [Accepted: 06/02/2015] [Indexed: 12/26/2022] Open
Abstract
The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.
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Affiliation(s)
- Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Cecilia Sarmiento
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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Abstract
Tomato (Solanum lycopersicum), along with many other economically valuable species, belongs to the Solanaceae family. Understanding how plants in this family defend themselves against pathogens offers the opportunity of improving yield and quality of their edible products. The use of functional genomics has contributed to this purpose through both traditional and recently developed techniques that allow determination of changes in transcript abundance during pathogen attack. Such changes can implicate the affected gene as participating in plant defense. Testing the involvement of these candidate genes in defense has relied largely on posttranscriptional gene silencing, particularly virus-induced gene silencing. We discuss how functional genomics has played a key role in our current understanding of the defense response in tomato and related species and what are the challenges and opportunities for the future.
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Association of VPg and eIF4E in the host tropism at the cellular level of Barley yellow mosaic virus and Wheat yellow mosaic virus in the genus Bymovirus. Virology 2014; 476:159-167. [PMID: 25543966 DOI: 10.1016/j.virol.2014.12.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Revised: 12/02/2014] [Accepted: 12/07/2014] [Indexed: 11/22/2022]
Abstract
Barley yellow mosaic virus (BaYMV) and Wheat yellow mosaic virus (WYMV) are separate species in the genus Bymovirus with bipartite plus-sense RNA genomes. In fields, BaYMV infects only barley and WYMV infects only wheat. Here, we studied the replicative capability of the two viruses in barley and wheat mesophyll protoplasts. BaYMV replicated in both barley and wheat protoplasts, but WYMV replicated only in wheat protoplasts. The expression of wheat translation initiation factor 4E (eIF4E), a common host factor for potyviruses, from the WYMV genome enabled WYMV replication in barley protoplasts. Replacing the BaYMV VPg gene with that of WYMV abolished BaYMV replication in barley protoplasts, whereas the additional expression of wheat eIF4E from BaYMV genome restored the replication of the BaYMV mutant in barley protoplasts. These results indicate that both VPg and the host eIF4E are involved in the host tropism of BaYMV and WYMV at the replication level.
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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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Mandadi KK, Pyle JD, Scholthof KBG. Comparative analysis of antiviral responses in Brachypodium distachyon and Setaria viridis reveals conserved and unique outcomes among C3 and C4 plant defenses. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:1277-1290. [PMID: 25296115 DOI: 10.1094/mpmi-05-14-0152-r] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Viral diseases cause significant losses in global agricultural production, yet little is known about grass antiviral defense mechanisms. We previously reported on host immune responses triggered by Panicum mosaic virus (PMV) and its satellite virus (SPMV) in the model C3 grass Brachypodium distachyon. To aid comparative analyses of C3 and C4 grass antiviral defenses, here, we establish B. distachyon and Setaria viridis (a C4 grass) as compatible hosts for seven grass-infecting viruses, including PMV and SPMV, Brome mosaic virus, Barley stripe mosaic virus, Maize mild mottle virus, Sorghum yellow banding virus, Wheat streak mosaic virus (WSMV), and Foxtail mosaic virus (FoMV). Etiological and molecular characterization of the fourteen grass-virus pathosystems showed evidence for conserved crosstalk among salicylic acid (SA), jasmonic acid, and ethylene pathways in B. distachyon and S. viridis. Strikingly, expression of PHYTOALEXIN DEFICIENT4, an upstream modulator of SA signaling, was consistently suppressed during most virus infections in B. distachyon and S. viridis. Hierarchical clustering analyses further identified unique antiviral responses triggered by two morphologically similar viruses, FoMV and WSMV, and uncovered other host-dependent effects. Together, the results of this study establish B. distachyon and S. viridis as models for the analysis of plant-virus interactions and provide the first framework for conserved and unique features of C3 and C4 grass antiviral defenses.
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