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Longya A, Chaipanya C, Franceschetti M, Maidment JHR, Banfield MJ, Jantasuriyarat C. Gene Duplication and Mutation in the Emergence of a Novel Aggressive Allele of the AVR-Pik Effector in the Rice Blast Fungus. Mol Plant Microbe Interact 2019; 32:740-749. [PMID: 30601714 DOI: 10.1094/mpmi-09-18-0245-r] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Higher yield potential and greater yield stability are common targets for crop breeding programs, including those in rice. Despite these efforts, biotic and abiotic stresses continue to impact rice production. Rice blast disease, caused by Magnaporthe oryzae, is the most devastating disease affecting rice worldwide. In the field, resistant varieties are unstable and can become susceptible to disease within a few years of release due to the adaptive potential of the blast fungus, specifically in the effector (avirulence [AVR]) gene pool. Here, we analyzed genetic variation of the effector gene AVR-Pik in 58 rice blast isolates from Thailand and examined the interaction between AVR-Pik and the cognate rice resistance gene Pik. Our results reveal that Thai rice blast isolates are very diverse. We observe four AVR-Pik variants in the population, including three previously identified variants, AVR-PikA, AVR-PikD, and AVR-PikE, and one novel variant, which we named AVR-PikF. Interestingly, 28 of the isolates contained two copies of AVR-Pik, always in the combination of AVR-PikD and AVR-PikF. Blast isolates expressing only AVR-PikF show high virulence to rice cultivars encoding allelic Pik resistance genes, and the AVR-PikF protein does not interact with the integrated heavy metal-associated domain of the Pik resistance protein in vitro, suggesting a mechanism for immune evasion.
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Affiliation(s)
- Apinya Longya
- 1 Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- 2 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Chaivarakun Chaipanya
- 1 Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
| | - Marina Franceschetti
- 2 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Josephine H R Maidment
- 2 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Mark J Banfield
- 2 Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, U.K.; and
| | - Chatchawan Jantasuriyarat
- 1 Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, 10900, Thailand
- 3 Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University
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Chaipanya C, Telebanco-Yanoria MJ, Quime B, Longya A, Korinsak S, Korinsak S, Toojinda T, Vanavichit A, Jantasuriyarat C, Zhou B. Dissection of broad-spectrum resistance of the Thai rice variety Jao Hom Nin conferred by two resistance genes against rice blast. Rice (N Y) 2017; 10:18. [PMID: 28493203 PMCID: PMC5425360 DOI: 10.1186/s12284-017-0159-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Accepted: 05/04/2017] [Indexed: 05/19/2023]
Abstract
BACKGROUND Rice (Oryza sativa) is one of the most important food crops in the world. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is one of the most destructive rice diseases worldwide. To effectively cope with this problem, the use of rice blast resistance varieties through innovative breeding programs is the best strategy to date. The Thai rice variety Jao Hom Nin (JHN) showed broad-spectrum resistance against Thai rice blast isolates. Two QTLs for blast resistance in JHN were reported on chromosome 1 (QTL1) and 11 (QTL11). RESULTS Monogenic lines of QTL1 (QTL1-C) and QTL11 (QTL11-C) in the CO39 genetic background were generated. Cluster analysis based on the disease reaction pattern of QTL1-C and QTL11-C, together with IRBLs, showed that those two monogenic lines were clustered with IRBLsh-S (Pish) and IRBL7-M (Pi7), respectively. Moreover, sequence analysis revealed that Pish and Pi7 were embedded within the QTL1 and QTL11 delimited genomic intervals, respectively. This study thus concluded that QTL1 and QTL11 could encode alleles of Pish and Pi7, designated as Pish-J and Pi7-J, respectively. To validate this hypothesis, the genomic regions of Pish-J and Pi7-J were cloned and sequenced. Protein sequence comparison revealed that Pish-J and Pi7-J were identical to Pish and Pi7, respectively. The holistic disease spectrum of JHN was found to be exactly attributed to the additive ones of both QTL1-C and QTL11-C. CONCLUSION JHN showed broad spectrum resistance against Thai and Philippine rice blast isolates. As this study demonstrated, the combination of two resistance genes, Pish-J and Pi7-J, in JHN, with each controlling broad-spectrum resistance to rice blast disease, explains the high level of resistance. Thus, the combination of Pish and Pi7 can provide a practical scheme for breeding durable resistance in rice against rice blast disease.
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Affiliation(s)
- Chaivarakun Chaipanya
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | | | - Berlaine Quime
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines
| | - Apinya Longya
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Siripar Korinsak
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Siriporn Korinsak
- Rice Gene Discovery Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Theerayut Toojinda
- Plant Biotechnology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathum Thani, 12120, Thailand
| | - Apichart Vanavichit
- Rice Science Center, Kasetsart University, Kamphaeng Saen, Nakhon Pathom, 73140, Thailand
- Agronomy Department Faculty of Agriculture at Kamphaeng Saen, Kasetsart University, Nakhon Pathom, 73140, Thailand
| | - Chatchawan Jantasuriyarat
- Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASNAR, NRU-KU), Chatuchak, Bangkok, 10900, Thailand.
| | - Bo Zhou
- Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, 4031, Philippines.
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Selisana SM, Yanoria MJ, Quime B, Chaipanya C, Lu G, Opulencia R, Wang GL, Mitchell T, Correll J, Talbot NJ, Leung H, Zhou B. Avirulence (AVR) Gene-Based Diagnosis Complements Existing Pathogen Surveillance Tools for Effective Deployment of Resistance (R) Genes Against Rice Blast Disease. Phytopathology 2017; 107:711-720. [PMID: 28168930 DOI: 10.1094/phyto-12-16-0451-r] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Avirulence (AVR) genes in Magnaporthe oryzae, the fungal pathogen that causes the devastating rice blast disease, have been documented to be major targets subject to mutations to avoid recognition by resistance (R) genes. In this study, an AVR-gene-based diagnosis tool for determining the virulence spectrum of a rice blast pathogen population was developed and validated. A set of 77 single-spore field isolates was subjected to pathotype analysis using differential lines, each containing a single R gene, and classified into 20 virulent pathotypes, except for 4 isolates that lost pathogenicity. In all, 10 differential lines showed low frequency (<24%) of resistance whereas 8 lines showed a high frequency (>95%), inferring the effectiveness of R genes present in the respective differential lines. In addition, the haplotypes of seven AVR genes were determined by polymerase chain reaction amplification and sequencing, if applicable. The calculated frequency of different AVR genes displayed significant variations in the population. AVRPiz-t and AVR-Pii were detected in 100 and 84.9% of the isolates, respectively. Five AVR genes such as AVR-Pik-D (20.5%) and AVR-Pik-E (1.4%), AVRPiz-t (2.7%), AVR-Pita (0%), AVR-Pia (0%), and AVR1-CO39 (0%) displayed low or even zero frequency. The frequency of AVR genes correlated almost perfectly with the resistance frequency of the cognate R genes in differential lines, except for International Rice Research Institute-bred blast-resistant lines IRBLzt-T, IRBLta-K1, and IRBLkp-K60. Both genetic analysis and molecular marker validation revealed an additional R gene, most likely Pi19 or its allele, in these three differential lines. This can explain the spuriously higher resistance frequency of each target R gene based on conventional pathotyping. This study demonstrates that AVR-gene-based diagnosis provides a precise, R-gene-specific, and differential line-free assessment method that can be used for determining the virulence spectrum of a rice blast pathogen population and for predicting the effectiveness of target R genes in rice varieties.
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Affiliation(s)
- S M Selisana
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - M J Yanoria
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - B Quime
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - C Chaipanya
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - G Lu
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - R Opulencia
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - G-L Wang
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - T Mitchell
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - J Correll
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - N J Talbot
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - H Leung
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
| | - B Zhou
- First and sixth authors: Institute of Biological Sciences, College of Arts and Sciences, University of the Philippines Los Baños, Laguna, Philippines; second, third, fourth, eleventh, and twelfth authors: Genetics and Biotechnology Division, International Rice Research Institute, Los Baños, Laguna, Philippines; fourth author: Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand; fifth author: The Key Laboratory of Biopesticide and Chemistry Biology, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, China; seventh and eighth authors: Department of Plant Pathology, The Ohio State University, Columbus; ninth author: Department of Plant Pathology, University of Arkansas, Fayetteville; and tenth author: Biosciences Department, Exeter University, UK
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