1
|
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.
Collapse
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
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
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: 10] [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: 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.
Collapse
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:
| |
Collapse
|
6
|
Wang H, Umer MJ, Liu F, Cai X, Zheng J, Xu Y, Hou Y, Zhou Z. Genome-Wide Identification and Characterization of CPR5 Genes in Gossypium Reveals Their Potential Role in Trichome Development. Front Genet 2022; 13:921096. [PMID: 35754813 PMCID: PMC9213653 DOI: 10.3389/fgene.2022.921096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/10/2022] [Indexed: 01/18/2023] Open
Abstract
Trichomes protect plants against insects, microbes, herbivores, and abiotic damages and assist seed dispersal. The function of CPR5 genes have been found to be involved in the trichome development but the research on the underlying genetic and molecular mechanisms are extremely limited. Herein, genome wide identification and characterization of CPR5 genes was performed. In total, 26 CPR5 family members were identified in Gossypium species. Phylogenetic analysis, structural characteristics, and synteny analysis of CPR5s showed the conserved evolution relationships of CPR5. The promoter analysis of CPR5 genes revealed hormone, stress, and development-related cis-elements. Gene ontology (GO) enrichment analysis showed that the CPR5 genes were largely related to biological regulation, developmental process, multicellular organismal process. Protein-protein interaction analysis predicted several trichome development related proteins (SIM, LGO, and GRL) directly interacting with CPR5 genes. Further, nine putative Gossypium-miRNAs were also identified, targeting Gossypium CPR5 genes. RNA-Seq data of G. arboreum (with trichomes) and G. herbaceum (with no trichomes) was used to perform the co-expression network analysis. GheCPR5.1 was identified as a hub gene in a co-expression network analysis. RT-qPCR of GheCPR5.1 gene in different tissues suggests that this gene has higher expressions in the petiole and might be a key candidate involved in the trichome development. Virus induced gene silencing of GheCPR5.1 (Ghe02G17590) confirms its role in trichome development and elongation. Current results provide proofs of the possible role of CPR5 genes and provide preliminary information for further studies of GheCPR5.1 functions in trichome development.
Collapse
Affiliation(s)
- Heng Wang
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Jawad Umer
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China
| | - Xiaoyan Cai
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Jie Zheng
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,National Nanfan Research Institute (Sanya), Chinese Academy of Agriculture Sciences, Sanya, China.,Hainan Yazhou Bay Seed Laboratory, Sanya, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Yuqing Hou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Zhongli Zhou
- State Key Laboratory of Cotton Biology /Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Akhter MS, Nakahara KS, Masuta C. Resistance induction based on the understanding of molecular interactions between plant viruses and host plants. Virol J 2021; 18:176. [PMID: 34454519 PMCID: PMC8400904 DOI: 10.1186/s12985-021-01647-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/23/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Viral diseases cause significant damage to crop yield and quality. While fungi- and bacteria-induced diseases can be controlled by pesticides, no effective approaches are available to control viruses with chemicals as they use the cellular functions of their host for their infection cycle. The conventional method of viral disease control is to use the inherent resistance of plants through breeding. However, the genetic sources of viral resistance are often limited. Recently, genome editing technology enabled the publication of multiple attempts to artificially induce new resistance types by manipulating host factors necessary for viral infection. MAIN BODY In this review, we first outline the two major (R gene-mediated and RNA silencing) viral resistance mechanisms in plants. We also explain the phenomenon of mutations of host factors to function as recessive resistance genes, taking the eIF4E genes as examples. We then focus on a new type of virus resistance that has been repeatedly reported recently due to the widespread use of genome editing technology in plants, facilitating the specific knockdown of host factors. Here, we show that (1) an in-frame mutation of host factors necessary to confer viral resistance, sometimes resulting in resistance to different viruses and that (2) certain host factors exhibit antiviral resistance and viral-supporting (proviral) properties. CONCLUSION A detailed understanding of the host factor functions would enable the development of strategies for the induction of a new type of viral resistance, taking into account the provision of a broad resistance spectrum and the suppression of the appearance of resistance-breaking strains.
Collapse
Affiliation(s)
- Md Shamim Akhter
- Plant Pathology Division, Bangladesh Agricultural Research Institute (BARI), Joydebpur, Gazipur, 1701, Bangladesh
| | - Kenji S Nakahara
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan
| | - Chikara Masuta
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido, 060-8589, Japan.
| |
Collapse
|
9
|
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.
Collapse
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
| |
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Verchot J, Pajerowska-Mukhtar KM. UPR signaling at the nexus of plant viral, bacterial, and fungal defenses. Curr Opin Virol 2020; 47:9-17. [PMID: 33360330 DOI: 10.1016/j.coviro.2020.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 11/13/2020] [Accepted: 11/15/2020] [Indexed: 12/24/2022]
Abstract
In recent years there have been significant advances in our understanding of the ER stress responses in plants that are associated with virus infection, as well as bacterial and fungal diseases. In plants, ER stress induced by virus infection includes several signaling pathways that include the unfolded protein response (UPR) to promote the expression of chaperone proteins for proper protein folding. Understanding how facets of ER stress signaling broadly engage in pathogen responses, as well as those that are specific to virus infection is important to distinguishing features essential for broad cellular defenses and processes that may be specifically linked to viral infectivity and disease.
Collapse
Affiliation(s)
- Jeanmarie Verchot
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, TX 77845, USA..
| | | |
Collapse
|
12
|
Assessment of Korean rice lines for their reaction to rice yellow mottle virus in Ghana. Heliyon 2020; 6:e05551. [PMID: 33294693 PMCID: PMC7691548 DOI: 10.1016/j.heliyon.2020.e05551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/22/2020] [Accepted: 11/16/2020] [Indexed: 11/21/2022] Open
Abstract
Rice yellow mottle virus (RYMV) is the most damaging viral disease of rice in Africa and can cause yield losses of up to 100%. The objective of this study was to characterize newly introduced rice lines from Korea into Ghana for their reaction to RYMV infection. One hundred and seventy-two rice lines from Korea were screened for their level of resistance RYMV in a screen house at Fumesua, Ghana. Four checks consisting of two highly resistant lines (Tog7291 and Gigante with rymv1-2 (resistant gene1-allele2) and rymv2 (resistant gene2) respectively), a moderately resistant line (CRI-Amankwatia) and a susceptible cultivar Jasmine 85 were used. The experiment was carried out in a 4 x 44 lattice design with four replicates. Screening for RYMV resistance was conducted by visual symptom scoring and virus-assessment through serology using enzyme linked immunosorbent assay (ELISA) test. Disease incidence and severity were assessed from 2 to 42 dpi. Data for disease severity and incidence were transformed (Log x+1) for ANOVA. Five lines (8261112, 8261119, 8261133, 8261588, and 8261634) were identified to be highly resistant to the disease just like Tog7291 and Gigante. The study also revealed 24 lines that were resistant but not grouping with Tog7291 and Gigante, whereas 100 moderately resistant lines clustered with the moderately resistance check CRI-Amankwatia in a distinct group. Forty-three (43) susceptible lines were identified with the susceptible check Jasmine 85 falling in this group. No highly susceptible line was identified. The newly idenfied resistant genotypes can be used by breeders to develop RYMV resistant varieties.
Collapse
|
13
|
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.
Collapse
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
| | | | | | | |
Collapse
|
14
|
Advances in Molecular Genetics and Genomics of African Rice ( Oryza glaberrima Steud). PLANTS 2019; 8:plants8100376. [PMID: 31561516 PMCID: PMC6843444 DOI: 10.3390/plants8100376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023]
Abstract
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
Collapse
|
15
|
Schmitt-Keichinger C. Manipulating Cellular Factors to Combat Viruses: A Case Study From the Plant Eukaryotic Translation Initiation Factors eIF4. Front Microbiol 2019; 10:17. [PMID: 30804892 PMCID: PMC6370628 DOI: 10.3389/fmicb.2019.00017] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 01/09/2019] [Indexed: 12/20/2022] Open
Abstract
Genes conferring resistance to plant viruses fall in two categories; the dominant genes that mostly code for proteins with a nucleotide binding site and leucine rich repeats (NBS-LRR), and that directly or indirectly, recognize viral avirulence factors (Avr), and the recessive genes. The latter provide a so-called recessive resistance. They represent roughly half of the known resistance genes and are alleles of genes that play an important role in the virus life cycle. Conversely, all cellular genes critical for the viral infection virtually represent recessive resistance genes. Based on the well-documented case of recessive resistance mediated by eukaryotic translation initiation factors of the 4E/4G family, this review is intended to summarize the possible approaches to control viruses via their host interactors. Classically, resistant crops have been developed through introgression of natural variants of the susceptibility factor from compatible relatives or by random mutagenesis and screening. Transgenic methods have also been applied to engineer improved crops by overexpressing the translation factor either in its natural form or after directed mutagenesis. More recently, innovative approaches like silencing or genome editing have proven their great potential in model and crop plants. The advantages and limits of these different strategies are discussed. This example illustrates the need to identify and characterize more host factors involved in virus multiplication and to assess their application potential in the control of viral diseases.
Collapse
|
16
|
Carr JP, Murphy AM, Tungadi T, Yoon JY. Plant defense signals: Players and pawns in plant-virus-vector interactions. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:87-95. [PMID: 30709497 DOI: 10.1016/j.plantsci.2018.04.011] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/07/2018] [Accepted: 04/13/2018] [Indexed: 06/09/2023]
Abstract
Plant viruses face an array of host defenses. Well-studied responses that protect against viruses include effector-triggered immunity, induced resistance (such as systemic acquired resistance mediated by salicylic acid), and RNA silencing. Recent work shows that viruses are also affected by non-host resistance mechanisms; previously thought to affect only bacteria, oomycetes and fungi. However, an enduring puzzle is how viruses are inhibited by several inducible host resistance mechanisms. Many viruses have been shown to encode factors that inhibit antiviral silencing. A number of these, including the cucumoviral 2b protein, the poytviral P1/HC-Pro and, respectively, geminivirus or satellite DNA-encoded proteins such as the C2 or βC1, also inhibit defensive signaling mediated by salicylic acid and jasmonic acid. This helps to explain how viruses can, in some cases, overcome host resistance. Additionally, interference with defensive signaling provides a means for viruses to manipulate plant-insect interactions. This is important because insects, particularly aphids and whiteflies, transmit many viruses. Indeed, there is now substantial evidence that viruses can enhance their own transmission through their effects on hosts. Even more surprisingly, it appears that viruses may be able to manipulate plant interactions with beneficial insects by, for example, 'paying back' their hosts by attracting pollinators.
Collapse
Affiliation(s)
- John P Carr
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom.
| | - Alex M Murphy
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Trisna Tungadi
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom
| | - Ju-Yeon Yoon
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge CB2 3EA, United Kingdom; Virology Unit, Department of Horticultural and Herbal Environment, National Institute of Horticultural and Herbal Science, Rural Development Agency, Wanju, 55365, Republic of Korea
| |
Collapse
|
17
|
Pinel-Galzi A, Hébrard E, Traoré O, Silué D, Albar L. Protocol for RYMV Inoculation and Resistance Evaluation in Rice Seedlings. Bio Protoc 2018; 8:e2863. [PMID: 34285979 DOI: 10.21769/bioprotoc.2863] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Revised: 05/08/2018] [Accepted: 05/13/2018] [Indexed: 11/02/2022] Open
Abstract
Rice yellow mottle virus (RYMV), a mechanically transmitted virus that causes serious damage to cultivated rice plants, is endemic to Africa. Varietal selection for resistance is considered to be the most effective and sustainable management strategy. Standardized resistance evaluation procedures are required for the identification and characterization of resistance sources. This paper describes a protocol for mechanical inoculation of rice seedlings with RYMV and two methods of resistance evaluation - one based on a symptom severity index and the other on virus detection through double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA).
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
Involvement of Arabidopsis thaliana endoplasmic reticulum KDEL-tailed cysteine endopeptidase 1 (AtCEP1) in powdery mildew-induced and AtCPR5-controlled cell death. PLoS One 2017; 12:e0183870. [PMID: 28846731 PMCID: PMC5573131 DOI: 10.1371/journal.pone.0183870] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 08/11/2017] [Indexed: 12/02/2022] Open
Abstract
Programmed cell death (PCD) is a prerequisite for successful development and it limits the spread of biotrophic pathogens in a rapid hypersensitive response at the site of infection. KDEL-tailed cysteine endopeptidases (KDEL CysEP) are a subgroup of papain-type cysteine endopeptidases expressed in tissues undergoing PCD. In Arabidopsis, three KDEL CysEPs (AtCEP1, AtCEP2, and AtCEP3) are expressed. We have previously shown that AtCEP1 is a factor of basal resistance to powdery mildew caused by the biotrophic ascomycete Erysiphe cruciferarum, and is expressed in spatiotemporal association with the late fungal development on Arabidopsis leaves. The endoplasmic reticulum-localized proenzyme of AtCEP1 was further visualized at the haustorial complex encased with callose. The AtCPR5 gene (CONSTITUTIVE EXPRESSION OF PR GENES 5) is a regulator of expression of pathogenesis related genes. Loss of AtCPR5 leads to spontaneous expression of chlorotic lesions which was associated with enhanced expression of AtCEP1. We used the atcpr5-2 mutant plants and the atcep1 atcpr5-2 double mutants harboring a non-functional reporter (PCEP1::pre-pro-3xHA-EGFP-KDEL) for visualization of AtCEP1 promoter activity. We found the specific up-regulation of AtCEP1 in direct neighborhood of spreading leaf lesions thus likely representing cells undergoing PCD. Furthermore, we found a strong resistance of atcpr5 mutant plants against infection with E. cruciferarum. Loss of AtCEP1 had no obvious influence on the strong resistance of atcpr5-2 mutant plants against infection with E. cruciferarum. However, the area of necrotic leaf lesions associated with E. cruciferarum colonies was significantly larger in atcpr5-2 as compared to atcep1 atcpr5-2 double mutant plants. The presence of AtCEP1 thus contributes to AtCPR5-controlled PCD at the sites of powdery mildew infection.
Collapse
|
20
|
Tock AJ, Fourie D, Walley PG, Holub EB, Soler A, Cichy KA, Pastor-Corrales MA, Song Q, Porch TG, Hart JP, Vasconcellos RCC, Vicente JG, Barker GC, Miklas PN. Genome-Wide Linkage and Association Mapping of Halo Blight Resistance in Common Bean to Race 6 of the Globally Important Bacterial Pathogen. FRONTIERS IN PLANT SCIENCE 2017; 8:1170. [PMID: 28736566 PMCID: PMC5500643 DOI: 10.3389/fpls.2017.01170] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 05/11/2023]
Abstract
Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).
Collapse
Affiliation(s)
- Andrew J. Tock
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
- Department of Plant Sciences, Faculty of Biology, University of CambridgeCambridge, United Kingdom
| | - Deidré Fourie
- ARC-Grain Crops InstitutePotchefstroom, South Africa
| | - Peter G. Walley
- Functional and Comparative Genomics, Institute of Integrative Biology, University of LiverpoolLiverpool, United Kingdom
| | - Eric B. Holub
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Alvaro Soler
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
| | - Karen A. Cichy
- Sugarbeet and Bean Research Unit, Agricultural Research Service, US Department of AgricultureEast Lansing, MI, United States
| | - Marcial A. Pastor-Corrales
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Agricultural Research Service, US Department of AgricultureBeltsville, MD, United States
| | - Timothy G. Porch
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | - John P. Hart
- Tropical Agriculture Research Station, Agricultural Research Service, US Department of AgricultureMayagüez, Puerto Rico
| | | | - Joana G. Vicente
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Guy C. Barker
- School of Life Sciences, Faculty of Science, University of WarwickWellesbourne, United Kingdom
| | - Phillip N. Miklas
- Grain Legume Genetics and Physiology Research Unit, Agricultural Research Service, US Department of AgricultureProsser, WA, United States
| |
Collapse
|
21
|
Yue E, Liu Z, Li C, Li Y, Liu Q, Xu JH. Overexpression of miR529a confers enhanced resistance to oxidative stress in rice (Oryza sativa L.). PLANT CELL REPORTS 2017; 36:1171-1182. [PMID: 28451819 DOI: 10.1007/s00299-017-2146-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 04/18/2017] [Indexed: 05/23/2023]
Abstract
Overexpressing miR529a can enhance oxidative stress resistance by targeting OsSPL2 and OsSPL14 genes that can regulate the expression of their downstream SOD and POD related genes. MicroRNAs are involved in the regulation of plant developmental and physiological processes, and their expression can be altered when plants suffered environment stresses, including salt, oxidative, drought and Cadmium. The expression of microRNA529 (miR529) can be induced under oxidative stress. However, its biological function under abiotic stress responses is still unclear. In this study, miR529a was overexpressed to investigate the function of miR529a under oxidative stress in rice. Our results demonstrated that the expression of miR529a can be induced by exogenous H2O2, and overexpressing miR529a can increase plant tolerance to high level of H2O2, resulting in increased seed germination rate, root tip cell viability, reduced leaf rolling rate and chlorophyll retention. The expression of oxidative stress responsive genes and the activities of superoxide dismutase (SOD) and peroxidase (POD) were increased in miR529a overexpression plant, which could help to reduce redundant reactive oxygen species (ROS). Furthermore, only OsSPL2 and OsSPL14 were targeted by miR529a in rice seedlings, repressing their expression in miR529aOE plants could lead to strengthen plant tolerance to oxidation stress. Our study provided the evidence that overexpression of miR529a could strengthen oxidation resistance, and its target genes OsSPL2 and OsSPL14 were responsible for oxidative tolerance, implied the manipulation of miR529a and its target genes regulation on H2O2 related response genes could improve oxidative stress tolerance in rice.
Collapse
Affiliation(s)
- Erkui Yue
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Zhen Liu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Chao Li
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Yu Li
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Qiuxiang Liu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China
| | - Jian-Hong Xu
- Zhejiang Key Laboratory of Crop Germplasm, Institute of Crop Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, Zhejiang, China.
| |
Collapse
|
22
|
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.
Collapse
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.
| |
Collapse
|
23
|
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.
Collapse
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
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
Chauhan RP, Wijayasekara D, Webb MA, Verchot J. A Reliable and Rapid Multiplex RT-PCR Assay for Detection of Two Potyviruses and a Pararetrovirus Infecting Canna Plants. PLANT DISEASE 2015; 99:1695-1703. [PMID: 30699506 DOI: 10.1094/pdis-02-15-0225-re] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Canna plants are subject to serious virus diseases. The three most common viruses identified in canna plants are Bean yellow mosaic virus, Canna yellow mottle virus, and Canna yellow streak virus. Recent studies indicate that canna plants are commonly infected with more than one virus. Thus, the efficient control of these viruses in canna plants requires the availability of a reliable method for detecting mixed virus infection. This report presents a two-step multiplex reverse-transcription polymerase chain reaction (RT-PCR) that was developed to simultaneously detect two potyviruses and one pararetrovirus genome. We optimized the method for nucleic acid isolation for managing a large population of samples, and the primer concentrations to ensure sensitivity and reliability of the assay, and determined the detection limit in simplex and multiplex RT-PCR assays using plasmid controls and nucleic acids isolated from virus-infected plants. Combined with an automated method for total nucleic acid isolation, this multiplex RT-PCR procedure could be routinely used for virus detection in research and diagnostic laboratories.
Collapse
Affiliation(s)
- Ravendra P Chauhan
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater 74078
| | - Dulanjani Wijayasekara
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater 74078
| | - Mark A Webb
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater 74078
| | - Jeanmarie Verchot
- Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater 74078
| |
Collapse
|
26
|
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.
Collapse
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
| | | |
Collapse
|
27
|
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.
Collapse
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.
| |
Collapse
|
28
|
Orjuela J, Sabot F, Chéron S, Vigouroux Y, Adam H, Chrestin H, Sanni K, Lorieux M, Ghesquière A. An extensive analysis of the African rice genetic diversity through a global genotyping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:2211-23. [PMID: 25119871 DOI: 10.1007/s00122-014-2374-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 07/29/2014] [Indexed: 05/04/2023]
Abstract
We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species. Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O. glaberrima, selected both for their impact in current breeding and for their geographical distribution, and 101 O. barthii, chosen based on their geographic origin, using a set of 235 SNPs specifically designed for African rice diversity. Using those data, we were able to structure the individuals from our sample in three populations for O. barthii, related to geography, and two populations in O. glaberrima; these two last populations cannot be linked however to any currently phenotyped trait. Moreover, we were also able to identify misclassification in O. glaberrima as well as in O. barthii and identified new form of O. sativa from the set of African varieties.
Collapse
Affiliation(s)
- Julie Orjuela
- DIADE UMR IRD/UM2, 911 Avenue Agropolis, BP 64501, 34394, Montpellier Cedex 5, France
| | | | | | | | | | | | | | | | | |
Collapse
|
29
|
Ye S, Jiang Y, Duan Y, Karim A, Fan D, Yang L, Zhao X, Yin J, Luo K. Constitutive expression of the poplar WRKY transcription factor PtoWRKY60 enhances resistance to Dothiorella gregaria Sacc. in transgenic plants. TREE PHYSIOLOGY 2014; 34:1118-29. [PMID: 25281841 DOI: 10.1093/treephys/tpu079] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
WRKY proteins are involved in various physiological processes in plants, especially in coping with diverse biotic and abiotic stresses. However, limited information is available on the roles of specific WRKY transcription factors in poplar defense. In this study, we reported the characterization of PtoWRKY60, a Group IIa WRKY member, from Populus tomentosa Carr. The gene expression profile of PtoWRKY60 in various tissues showed that it significantly accumulated in old leaves. Phylogenetic analyses revealed that PtoWRKY60 had a close relationship with AtWRKY18, AtWRKY40 and AtWRKY60. PtoWRKY60 was induced mainly by salicylic acid (SA) and slightly by Dothiorella gregaria Sacc., jasmonic acid, wounding treatment, low temperature and salinity stresses. Overexpression of PtoWRKY60 in poplar resulted in increased resistance to D. gregaria. The defense-associated genes, such as PR5.1, PR5.2, PR5.4, PR5.5 and CPR5, were markedly up-regulated in transgenic plants overexpressing PtoWRKY60. These results indicate that PtoWRKY60 might be partly involved in the signal transduction pathway initiated by SA in Populus.
Collapse
Affiliation(s)
- Shenglong Ye
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Yuanzhong Jiang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Yanjiao Duan
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Abdul Karim
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Di Fan
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Li Yang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Xin Zhao
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China
| | - Jia Yin
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Keming Luo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, No. 2, Tiansheng Road, Beibei, Chongqing 400715, China Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| |
Collapse
|