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Simon EV, Hechanova SL, Hernandez JE, Li CP, Tülek A, Ahn EK, Jairin J, Choi IR, Sundaram RM, Jena KK, Kim SR. Available cloned genes and markers for genetic improvement of biotic stress resistance in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1247014. [PMID: 37731986 PMCID: PMC10507716 DOI: 10.3389/fpls.2023.1247014] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/14/2023] [Indexed: 09/22/2023]
Abstract
Biotic stress is one of the major threats to stable rice production. Climate change affects the shifting of pest outbreaks in time and space. Genetic improvement of biotic stress resistance in rice is a cost-effective and environment-friendly way to control diseases and pests compared to other methods such as chemical spraying. Fast deployment of the available and suitable genes/alleles in local elite varieties through marker-assisted selection (MAS) is crucial for stable high-yield rice production. In this review, we focused on consolidating all the available cloned genes/alleles conferring resistance against rice pathogens (virus, bacteria, and fungus) and insect pests, the corresponding donor materials, and the DNA markers linked to the identified genes. To date, 48 genes (independent loci) have been cloned for only major biotic stresses: seven genes for brown planthopper (BPH), 23 for blast, 13 for bacterial blight, and five for viruses. Physical locations of the 48 genes were graphically mapped on the 12 rice chromosomes so that breeders can easily find the locations of the target genes and distances among all the biotic stress resistance genes and any other target trait genes. For efficient use of the cloned genes, we collected all the publically available DNA markers (~500 markers) linked to the identified genes. In case of no available cloned genes yet for the other biotic stresses, we provided brief information such as donor germplasm, quantitative trait loci (QTLs), and the related papers. All the information described in this review can contribute to the fast genetic improvement of biotic stress resistance in rice for stable high-yield rice production.
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Affiliation(s)
- Eliza Vie Simon
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Sherry Lou Hechanova
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
| | - Jose E. Hernandez
- Institute of Crop Science (ICropS), University of the Philippines Los Baños, Laguna, Philippines
| | - Charng-Pei Li
- Taiwan Agricultural Research Institute (TARI), Council of Agriculture, Taiwan
| | - Adnan Tülek
- Trakya Agricultural Research Institute, Edirne, Türkiye
| | - Eok-Keun Ahn
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Jirapong Jairin
- Division of Rice Research and Development, Rice Department, Bangkok, Thailand
| | - Il-Ryong Choi
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
- National Institute of Crop Science, Rural Development Administration (RDA), Republic of Korea
| | - Raman M. Sundaram
- ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Kshirod K. Jena
- School of Biotechnology, KIIT Deemed University, Bhubaneswar, Odisha, India
| | - Sung-Ryul Kim
- Rice Breeding Innovation Department, International Rice Research Institute (IRRI), Laguna, Philippines
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Sinha DK, Gupta A, Padmakumari AP, Bentur JS, Nair S. Infestation of Rice by Gall Midge Influences Density and Diversity of Pseudomonas and Wolbachia in the Host Plant Microbiome. Curr Genomics 2022; 23:126-136. [PMID: 36778977 PMCID: PMC9878839 DOI: 10.2174/1389202923666220401101604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/16/2022] [Accepted: 02/28/2022] [Indexed: 11/22/2022] Open
Abstract
Background: The virulence of phytophagous insects is predominantly determined by their ability to evade or suppress host defense for their survival. The rice gall midge (GM, Orseolia oryzae), a monophagous pest of rice, elicits a host defense similar to the one elicited upon pathogen attack. This could be due to the GM feeding behaviour, wherein the GM endosymbionts are transferred to the host plant via oral secretions, and as a result, the host mounts an appropriate defense response(s) (i.e., up-regulation of the salicylic acid pathway) against these endosymbionts. Methods: The current study aimed to analyze the microbiome present at the feeding site of GM maggots to determine the exchange of bacterial species between GM and its host and to elucidate their role in rice-GM interaction using a next-generation sequencing approach. Results: Our results revealed differential representation of the phylum Proteobacteria in the GM-infested and -uninfested rice tissues. Furthermore, analysis of the species diversity of Pseudomonas and Wolbachia supergroups at the feeding sites indicated the exchange of bacterial species between GM and its host upon infestation. Conclusion: As rice-GM microbial associations remain relatively unstudied, these findings not only add to our current understanding of microbe-assisted insect-plant interactions but also provide valuable insights into how these bacteria drive insect-plant coevolution. Moreover, to the best of our knowledge, this is the first report analyzing the microbiome of a host plant (rice) at the feeding site of its insect pest (GM).
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Affiliation(s)
| | - Ayushi Gupta
- These authors contributed equally in this manuscript.
| | | | | | - Suresh Nair
- Address correspondence to this author at the Plant-Insect Interaction Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110 067, India; Tel: 91-11-26741242; Fax: 91-11-26742316; E-mail:
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Zhou H, Wang X, Mo Y, Li Y, Yan L, Li Z, Shu W, Cheng L, Huang F, Qiu Y. Genetic analysis and fine mapping of the gall midge resistance gene Gm5 in rice (Oryza sativa L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2021-2033. [PMID: 32166371 DOI: 10.1007/s00122-020-03575-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/28/2020] [Indexed: 06/10/2023]
Abstract
The rice gall midge resistance gene, Gm5, confers remarkable antibiosis and is located in the same region on chromosome 12 in three different rice varieties. Fine mapping narrowed this region to a 49-kb segment and identified two candidate genes showing remarkable response to GM infestation. The Asian rice gall midge (GM; Orseolia oryzae; Diptera: Cecidomyiidae) invades rice shoots and forms galls, adversely affecting plant growth and yield production. Thus, the development of resistant varieties through the identification, mapping, and application of GM resistance genes is considered the most efficient strategy for managing this insect. Here, a GM resistance survey of F2 populations derived from intercrosses between resistant rice varieties 'ARC5984,' '570011,' and 'ARC5833' indicated that the resistance gene Gm5 was located on the same chromosomal region in the three varieties. For the initial mapping, three independent F2 mapping populations were developed for the three resistant varieties, and the Gm5 gene was consistently mapped to the same chromosomal region near marker 12M22.6. Fine mapping, which was conducted using the BC1F2 and BC2F2 populations derived from the 9311/ARC5984 cross, narrowed the Gm5 gene region to a 49-kb segment flanked by the markers Z57 and Z64. In the final mapped region, we detected 10 candidate genes, of which six were analyzed for their relative expression. Consequently, two of these genes, Os12g36830 and Os12g36880, showed significantly higher expression in GM-resistant plants than in GM-susceptible plants at 24 and 72 h after GM infestation. Finally, the PCR amplification of markers 12M22.5 and 12M22.6 yielded clear single bands, and these markers were effectively applied for the marker-assisted selection (MAS) of the Gm5 gene. With the developed MAS markers, the fine mapping of this resistance gene will facilitate its map-based cloning and incorporation into insect-resistant rice varieties through breeding.
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Affiliation(s)
- Hailian Zhou
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Xinyi Wang
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Yi Mo
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Yang Li
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Liuhui Yan
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Zhihua Li
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
| | - Wan Shu
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Ling Cheng
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Fengkuan Huang
- Guangxi Key Laboratory of Biology for Crop Diseases and Insect Pests, Guangxi Academy of Agricultural Science, Nanning, 530007, China
| | - Yongfu Qiu
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China.
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Leelagud P, Kongsila S, Vejchasarn P, Darwell K, Phansenee Y, Suthanthangjai A, Uparang C, Kawichai R, Yajai P, Boonsa-Nga K, Chamarerk V, Jairin J. Genetic diversity of Asian rice gall midge based on mtCOI gene sequences and identification of a novel resistance locus gm12 in rice cultivar MN62M. Mol Biol Rep 2020; 47:4273-4283. [PMID: 32468258 DOI: 10.1007/s11033-020-05546-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/23/2020] [Indexed: 11/30/2022]
Abstract
The rice gall midge (RGM), Orseolia oryzae (Wood-Mason), is one of the most destructive insect pests of rice, and it causes significant yield losses annually in Asian countries. The development of resistant rice varieties is considered as the most effective and economical approach for maintaining yield stability by controlling RGM. Identification of resistance genes will help in marker-assisted selection (MAS) to pyramid the resistance genes and develop a durable resistance variety against RGM in areas with frequent outbreaks. In this study, a mitochondrial cytochrome oxidase subunit I (mtCOI) was used to analyze the genetic diversity among Thai RGM populations. The phylogenetic tree indicated that the Thai RGM populations were homogeneously distributed throughout the country. The reactions of the resistant rice varieties carrying different resistance genes revealed different RGM biotypes in Thailand. The Thai rice landrace MN62M showed resistance to all RGM populations used in this study. We identified a novel genetic locus for resistance to RGM, designated as gm12, on the short arm of rice chromosome 2. The locus was identified using linkage analysis in 144 F2 plants derived from a cross between susceptible cultivar KDML105 and RGM-resistant cultivar MN62M with single nucleotide polymorphism (SNP) markers and F2:3 phenotype. The locus was mapped between two flanking markers, S2_76222 and S2_419160. In conclusion, we identified a new RGM resistance gene, gm12, on rice chromosome 2 in the Thai rice landrace MN62M. This finding yielded DNA markers that can be used in MAS to develop cultivars with broad-spectrum resistance to RGM. Moreover, the new resistance gene provides essential information for the identification of RGM biotypes in Thailand and Southeast Asia.
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Affiliation(s)
- P Leelagud
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - S Kongsila
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - P Vejchasarn
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - K Darwell
- Phrae Rice Research Center, Mueang, Phrae, Thailand
| | - Y Phansenee
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - A Suthanthangjai
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - C Uparang
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - R Kawichai
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand
| | - P Yajai
- Phrae Rice Research Center, Mueang, Phrae, Thailand
| | - K Boonsa-Nga
- Chiang Rai Rice Research Center, Phan, Chiang Rai, Thailand
| | - V Chamarerk
- Division of Rice Research and Development, Rice Department, Chatuchak, Bangkok, Thailand
| | - J Jairin
- Ubon Ratchathani Rice Research Center, Mueang, Ubon Ratchathani, Thailand.
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Bai J, Wang X, Wu H, Ling F, Zhao Y, Lin Y, Wang R. Comprehensive construction strategy of bidirectional green tissue-specific synthetic promoters. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:668-678. [PMID: 31393049 PMCID: PMC7004895 DOI: 10.1111/pbi.13231] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 05/03/2023]
Abstract
Bidirectional green tissue-specific promoters have important application prospects in genetic engineering and crop genetic improvement. However, there is no report on the application of them, mainly due to undiscovered natural bidirectional green tissue-specific promoters and the lack of a comprehensive approach for the synthesis of these promoters. In order to compensate for this vacancy, the present study reports a novel strategy for the expression regulatory sequence selection and the bidirectional green tissue-specific synthetic promoter construction. Based on this strategy, seven promoters were synthesized and introduced into rice by agrobacterium-mediated transformation. The functional identification of these synthetic promoters was performed by the expression pattern of GFP and GUS reporter genes in two reverse directions in transgenic rice. The results indicated that all the synthetic promoters possessed bidirectional expression activities in transgenic rice, and four synthetic promoters (BiGSSP2, BiGSSP3, BiGSSP6, BiGSSP7) showed highly bidirectional expression efficiencies specifically in green tissues (leaf, sheath, panicle, stem), which could be widely applied to agricultural biotechnology. Our study provided a feasible strategy for the construction of synthetic promoters, and we successfully created four bidirectional green tissue-specific synthetic promoters. It is the first report on bidirectional green tissue-specific promoters that could be efficiently applied in genetic engineering.
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Affiliation(s)
- Jiuyuan Bai
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Xin Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Hao Wu
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Fei Ling
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Yun Zhao
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Rui Wang
- Key Laboratory of Bio‐Resource and Eco‐Environment of Ministry of EducationCollege of life sciencesSichuan UniversityChengduChina
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Li Y, Mo Y, Li Z, Yang M, Tang L, Cheng L, Qiu Y. Characterization and application of a gall midge resistance gene (Gm6) from Oryza sativa 'Kangwenqingzhan'. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:579-591. [PMID: 31745579 DOI: 10.1007/s00122-019-03488-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 11/13/2019] [Indexed: 06/10/2023]
Abstract
The resistance gene Gm6 was mapped and characterized using near-isogenic and pyramided lines, followed by marker-assisted selection to develop lines with resistance to both gall midge and brown planthopper. The Asian rice gall midge (GM; Orseolia oryzae; Diptera: Cecidomyiidae) is a major destructive pest affecting rice cultivation regions. The characterization of GM-resistance genes and the breeding of resistant varieties are together considered the most efficient strategy for managing this insect. Here, the Gm6 resistance gene derived from the Kangwenqingzhan (KW) variety was found to be located on the long arm of chromosome 4 using the F2 population of 9311/KW. The region was narrowed to a 90-kb segment flanked by the markers YW91 and YW3-4 using backcrossing populations. Based on no-choice feeding and host choice tests, GM development and growth in near-isogenic lines (NILs) were severely restricted compared to that in the 9311 control. On day 8, the average GM body length was 0.69 mm and 0.56 mm on NILs and 9311, respectively, and the differences were more significant at later time points. However, GM insects exhibited no host preference between NILs and 9311, and there was normal egg hatching on the resistant plants. We developed pyramided lines carrying BPH27, BPH36, and Gm6 by crossing and backcrossing with marker-assisted selection. These lines were similar to the KW parent in terms of agronomic traits while also exhibiting high resistance to brown planthopper (BPH) and GM. The present mapping and characterization of Gm6 will facilitate map-based cloning of this important resistance gene and its application in the breeding of insect-resistant rice varieties.
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Affiliation(s)
- Yang Li
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Yi Mo
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Zhihua Li
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Meng Yang
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Lihua Tang
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China
| | - Ling Cheng
- College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Yongfu Qiu
- Agricultural College, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning, 530005, China.
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