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Ji H, Cheon KS, Shin Y, Lee C, Son S, Oh H, Yoon DK, Lee S, Cho M, Jun S, Lee GS, Baek J, Kim SL, Ahn IP, Oh JH, Yoon HJ, Cha YS, Kim KH. Map-Based Cloning and Characterization of a Major QTL Gene, FfR1, Which Confers Resistance to Rice Bakanae Disease. Int J Mol Sci 2024; 25:6214. [PMID: 38892403 PMCID: PMC11172731 DOI: 10.3390/ijms25116214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, is a serious threat to rice production worldwide. Breeding elite rice varieties resistant to BD requires the identification of resistance genes. Previously, we discovered a resistant quantitative trait locus (QTL), qFfR1, in a Korean japonica rice variety, Nampyeong. In this study, we fine-mapped qFfR1 with a Junam*4/Nampyeong BC3F3 population and delimited its location to a 37.1 kb region on chromosome 1. Complementation experiments with seven candidate genes in this region revealed that OsI_02728 is the gene for qFfR1. This gene encodes a protein with a typical leucine-rich repeat (LRR) receptor-like protein structure. RNA-sequencing-based transcriptomic analysis revealed that FfR1 induces the transcription of defense genes, including lignin and terpenoid biosynthesis genes, pathogenesis-related genes, and thionin genes. These results may facilitate investigations into the molecular mechanisms underlying BD resistance, including molecular patterns of Fusarium fujikuroi interacting with FfR1 and players working in signal transduction pathways downstream of FfR1, and the breeding of new BD-resistant varieties by providing a BD resistance gene with its precise selection marker. This will contribute to efficient control of BD, which is becoming more prevalent according to temperature rises due to climate change.
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Affiliation(s)
- Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Kyeong-Seong Cheon
- Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Republic of Korea
| | - Yunji Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Chaewon Lee
- Department of Central Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Suwon 16429, Republic of Korea
| | - Seungmin Son
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Dong-Kyung Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration (RDA), Miryang 50424, Republic of Korea
| | - Seoyeon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Mihyun Cho
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Soojin Jun
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
- Coastal Agriculture Research Institute, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Song Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Il-Pyung Ahn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Jae-Hyeon Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Hye-Jin Yoon
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Young-Soon Cha
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Republic of Korea
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Queiroz CA, Caniato FF, Siqueira VKS, de Moraes Catarino A, Hanada RE, O'Donnell K, Laraba I, Rehner SA, Sousa NR, Silva GF. Population Genetic Analysis of Fusarium decemcellulare, a Guaraná Pathogen, Reveals High Genetic Diversity in the Amazonas State, Brazil. PLANT DISEASE 2023:PDIS01220083RE. [PMID: 36350732 DOI: 10.1094/pdis-01-22-0083-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Guaraná is indigenous to the Brazilian Amazon where it has cultural and agroeconomic significance. However, its cultivation is constrained by a disease termed oversprouting of guaraná caused by Fusarium decemcellulare, with yield losses reaching as high as 100%. The disease can affect different parts of the plant, causing floral hypertrophy and hyperplasia, stem galls, and oversprouting of vegetative buds. To date, no study has been conducted characterizing the genetic diversity and population structure of this pathogen. Here, we report genetic diversity and genetic structure among 224 isolates from eight guaraná production areas of Amazonas State, Brazil, that were genotyped using a set of 10 inter-simple-sequence repeat (ISSR) markers. Despite moderate gene diversity (Hexp = 0.21 to 0.32), genotypic diversity was at or near maximum (223 multilocus genotypes among 224 isolates). Population genetic analysis of the 10 ISSR marker fragments with STRUCTURE software identified two populations designated C1 and C2 within the F. decemcellulare collection from the eight sites. Likewise, UPGMA hierarchical clustering and discriminant analysis of principal components of the strains from guaraná resolved these same two groups. Analysis of molecular variance demonstrated that 71% of genetic diversity occurred within the C1 and C2 populations. A pairwise comparison of sampling sites for both genetic populations revealed that 59 of 66 were differentiated from one another (P < 0.05), and high and significant gene flow was detected only between sampling sites assigned to the same genetic population. The presence of MAT1-1 and MAT1-2 strains, in conjunction with the high genotypic diversity and no significant linkage disequilibrium, suggests that each population of F. decemcellulare might be undergoing sexual reproduction. Isolation by distance was not observed (R2 = 0.02885, P > 0.05), which suggests that human-mediated movement of seedlings may have played a role in shaping the F. decemcellulare genetic structure in Amazonas State, Brazil.
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Affiliation(s)
- Claudia A Queiroz
- Departamento de Biologia, Universidade Federal do Amazonas, Manaus, Brazil
| | - Fernanda F Caniato
- Departamento de Ciências Fundamentais e Desenvolvimento Agrícola, Universidade Federal do Amazonas, Manaus, Brazil
| | | | | | | | - Kerry O'Donnell
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, USDA, Peoria, IL 61604, U.S.A
| | - Imane Laraba
- Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service, USDA, Peoria, IL 61604, U.S.A
| | - Stephen A Rehner
- Mycology and Nematology Genetic Diversity and Biology Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705, U.S.A
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