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Mishra R, Joshi RK, Zhao K. Genome Editing in Rice: Recent Advances, Challenges, and Future Implications. FRONTIERS IN PLANT SCIENCE 2018; 9:1361. [PMID: 30283477 PMCID: PMC6156261 DOI: 10.3389/fpls.2018.01361] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/28/2018] [Indexed: 05/03/2023]
Abstract
Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.
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Affiliation(s)
- Rukmini Mishra
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Bhubaneswar, India
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Kaijun Zhao,
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Mishra R, Joshi RK, Zhao K. Genome Editing in Rice: Recent Advances, Challenges, and Future Implications. FRONTIERS IN PLANT SCIENCE 2018; 9:1361. [PMID: 30283477 DOI: 10.33389/fpls.2018.01361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/28/2018] [Indexed: 05/18/2023]
Abstract
Rice (Oryza sativa L.) is the major food source for more than three billion people of the world. In the last few decades, the classical, mutational, and molecular breeding approaches have brought about tremendous increase in rice productivity with the development of novel rice varieties. However, stagnation in rice yield has been reported in recent decade owing to several factors including the emergence of pests and phyto pathogens, climate change, and other environmental issues posing great threat to global food security. There is an urgent need to produce more rice and associated cereals to satisfy the mammoth task of feeding a still growing population expected to reach 9.7 billion by 2050. Advances in genomics and emergence of multiple genome-editing technologies through use of engineered site-specific nucleases (SSNs) have revolutionized the field of plant science and agriculture. Among them, the CRISPR/Cas9 system is the most advanced and widely accepted because of its simplicity, robustness, and high efficiency. The availability of huge genomic resources together with a small genome size makes rice more suitable and feasible for genetic manipulation. As such, rice has been increasingly used to test the efficiency of different types of genome editing technologies to study the functions of various genes and demonstrate their potential in genetic improvement. Recently developed approaches including CRISPR/Cpf1 system and base editors have evolved as more efficient and accurate genome editing tools which might accelerate the pace of crop improvement. In the present review, we focus on the genome editing strategies for rice improvement, thereby highlighting the applications and advancements of CRISPR/Cas9 system. This review also sheds light on the role of CRISPR/Cpf1 and base editors in the field of genome editing highlighting major challenges and future implications of these tools in rice improvement.
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Affiliation(s)
- Rukmini Mishra
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women's University, Bhubaneswar, India
| | - Kaijun Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Xiao G, Borja FN, Mauleon R, Padilla J, Telebanco-Yanoria MJ, Yang J, Lu G, Dionisio-Sese M, Zhou B. Identification of resistant germplasm containing novel resistance genes at or tightly linked to the Pi2/9 locus conferring broad-spectrum resistance against rice blast. RICE (NEW YORK, N.Y.) 2017; 10:37. [PMID: 28779340 PMCID: PMC5544663 DOI: 10.1186/s12284-017-0176-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 07/31/2017] [Indexed: 05/04/2023]
Abstract
BACKGROUND The rice Pi2/9 locus harbors multiple resistance (R) genes each controlling broad-spectrum resistance against diverse isolates of Magnaporthe oryzae, a fungal pathogen causing devastating blast disease to rice. Identification of more resistance germplasm containing novel R genes at or tightly linked to the Pi2/9 locus would promote breeding of resistance rice cultivars. RESULTS In this study, we aim to identify resistant germplasm containing novel R genes at or tightly linked to the Pi2/9 locus using a molecular marker, designated as Pi2/9-RH (Pi2/9 resistant haplotype), developed from the 5' portion of the Pi2 sequence which was conserved only in the rice lines containing functional Pi2/9 alleles. DNA analysis using Pi2/9-RH identified 24 positive lines in 55 shortlisted landraces which showed resistance to 4 rice blast isolates. Analysis of partial sequences of the full-length cDNAs of Pi2/9 homologues resulted in the clustering of these 24 lines into 5 haplotypes each containing different Pi2/9 homologues which were designated as Pi2/9-A5, -A15, -A42, -A53, and -A54. Interestingly, Pi2/9-A5 and Pi2/9-A54 are identical to Piz-t and Pi2, respectively. To validate the association of other three novel Pi2/9 homologues with the blast resistance, monogenic lines at BC3F3 generation were generated by marker assisted backcrossing (MABC). Resistance assessment of the derived monogenic lines in both the greenhouse and the field hotspot indicated that they all controlled broad-spectrum resistance against rice blast. Moreover, genetic analysis revealed that the blast resistance of these three monogenic lines was co-segregated with Pi2/9-RH, suggesting that the Pi2/9 locus or tightly linked loci could be responsible for the resistance. CONCLUSION The newly developed marker Pi2/9-RH could be used as a potentially diagnostic marker for the quick identification of resistant donors containing functional Pi2/9 alleles or unknown linked R genes. The three new monogenic lines containing the Pi2/9 introgression segment could be used as valuable materials for disease assessment and resistance donors in breeding program.
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Affiliation(s)
- Gui Xiao
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Institute of Biological Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Frances Nikki Borja
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ramil Mauleon
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jonas Padilla
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Mary Jeanie Telebanco-Yanoria
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Jianxia Yang
- Fujian Agriculture and Forest University, Fuzhou, 350002 China
| | - Guodong Lu
- Fujian Agriculture and Forest University, Fuzhou, 350002 China
| | - Maribel Dionisio-Sese
- Institute of Biological Sciences, University of the Philippines Los Baños, 4031 Laguna, Philippines
| | - Bo Zhou
- Genetics and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Garrett KA, Andersen KF, Asche F, Bowden RL, Forbes GA, Kulakow PA, Zhou B. Resistance Genes in Global Crop Breeding Networks. PHYTOPATHOLOGY 2017; 107:1268-1278. [PMID: 28742460 DOI: 10.1094/phyto-03-17-0082-fi] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Resistance genes are a major tool for managing crop diseases. The networks of crop breeders who exchange resistance genes and deploy them in varieties help to determine the global landscape of resistance and epidemics, an important system for maintaining food security. These networks function as a complex adaptive system, with associated strengths and vulnerabilities, and implications for policies to support resistance gene deployment strategies. Extensions of epidemic network analysis can be used to evaluate the multilayer agricultural networks that support and influence crop breeding networks. Here, we evaluate the general structure of crop breeding networks for cassava, potato, rice, and wheat. All four are clustered due to phytosanitary and intellectual property regulations, and linked through CGIAR hubs. Cassava networks primarily include public breeding groups, whereas others are more mixed. These systems must adapt to global change in climate and land use, the emergence of new diseases, and disruptive breeding technologies. Research priorities to support policy include how best to maintain both diversity and redundancy in the roles played by individual crop breeding groups (public versus private and global versus local), and how best to manage connectivity to optimize resistance gene deployment while avoiding risks to the useful life of resistance genes. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
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Affiliation(s)
- K A Garrett
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - K F Andersen
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - F Asche
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - R L Bowden
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - G A Forbes
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - P A Kulakow
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
| | - B Zhou
- First and second authors: Plant Pathology Department, Emerging Pathogens Institute, and Institute for Sustainable Food Systems, University of Florida, Gainesville 32611; third author: School of Forest Resources and Conservation and Institute for Sustainable Food Systems, University of Florida, Gainesville; fourth author: United States Department of Agriculture-Agricultural Research Service Hard Winter Wheat Genetics Research Unit, 4008 Throckmorton Hall, Kansas State University, Manhattan 66506; fifth author: International Potato Center, Lima, Peru; sixth author: International Institute of Tropical Agriculture, Ibadan, Nigeria; and seventh author: International Rice Research Institute, Manila, Philippines
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Lv Q, Huang Z, Xu X, Tang L, Liu H, Wang C, Zhou Z, Xin Y, Xing J, Peng Z, Li X, Zheng T, Zhu L. Allelic variation of the rice blast resistance gene Pid3 in cultivated rice worldwide. Sci Rep 2017; 7:10362. [PMID: 28871108 PMCID: PMC5583387 DOI: 10.1038/s41598-017-10617-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 08/11/2017] [Indexed: 11/12/2022] Open
Abstract
In this study, the re-sequencing data from 3,000 rice genomes project (3 K RGP) was used to analyze the allelic variation at the rice blast resistance (R) Pid3 locus. A total of 40 haplotypes were identified based on 71 nucleotide polymorphic sites among 2621 Pid3 homozygous alleles in the 3k genomes. Pid3 alleles in most japonica rice accessions were pseudogenes due to premature stop mutations, while those in most indica rice accessions were identical to the functional haplotype Hap_6, which had a similar resistance spectrum as the previously reported Pid3 gene. By sequencing and CAPS marker analyzing the Pid3 alleles in widespread cultivars in China, we verified that Hap_6 had been widely deployed in indica rice breeding of China. Thus, we suggest that the priority for utilization of the Pid3 locus in rice breeding should be on introducing the functional Pid3 alleles into japonica rice cultivars and the functional alleles of non-Hap_6 haplotypes into indica rice cultivars for increasing genetic diversity.
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Affiliation(s)
- Qiming Lv
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China.,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zhiyuan Huang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Xiao Xu
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Hai Liu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Chunchao Wang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhuangzhi Zhou
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yeyun Xin
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Junjie Xing
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Zhirong Peng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Xiaobing Li
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Tianqing Zheng
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Lihuang Zhu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China. .,State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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De Novo Assembly, Annotation, and Characterization of Root Transcriptomes of Three Caladium Cultivars with a Focus on Necrotrophic Pathogen Resistance/Defense-Related Genes. Int J Mol Sci 2017; 18:ijms18040712. [PMID: 28346370 PMCID: PMC5412298 DOI: 10.3390/ijms18040712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 03/21/2017] [Accepted: 03/24/2017] [Indexed: 01/11/2023] Open
Abstract
Roots are vital to plant survival and crop yield, yet few efforts have been made to characterize the expressed genes in the roots of non-model plants (root transcriptomes). This study was conducted to sequence, assemble, annotate, and characterize the root transcriptomes of three caladium cultivars (Caladium × hortulanum) using RNA-Seq. The caladium cultivars used in this study have different levels of resistance to Pythiummyriotylum, the most damaging necrotrophic pathogen to caladium roots. Forty-six to 61 million clean reads were obtained for each caladium root transcriptome. De novo assembly of the reads resulted in approximately 130,000 unigenes. Based on bioinformatic analysis, 71,825 (52.3%) caladium unigenes were annotated for putative functions, 48,417 (67.4%) and 31,417 (72.7%) were assigned to Gene Ontology (GO) and Clusters of Orthologous Groups (COG), respectively, and 46,406 (64.6%) unigenes were assigned to 128 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. A total of 4518 distinct unigenes were observed only in Pythium-resistant "Candidum" roots, of which 98 seemed to be involved in disease resistance and defense responses. In addition, 28,837 simple sequence repeat sites and 44,628 single nucleotide polymorphism sites were identified among the three caladium cultivars. These root transcriptome data will be valuable for further genetic improvement of caladium and related aroids.
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Liu H, Guo Z, Gu F, Ke S, Sun D, Dong S, Liu W, Huang M, Xiao W, Yang G, Liu Y, Guo T, Wang H, Wang J, Chen Z. 4-Coumarate-CoA Ligase-Like Gene OsAAE3 Negatively Mediates the Rice Blast Resistance, Floret Development and Lignin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2017; 7:2041. [PMID: 28119718 PMCID: PMC5222848 DOI: 10.3389/fpls.2016.02041] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 12/20/2016] [Indexed: 05/23/2023]
Abstract
Although adenosine monophosphate (AMP) binding domain is widely distributed in multiple plant species, detailed molecular functions of AMP binding proteins (AMPBPs) in plant development and plant-pathogen interaction remain unclear. In the present study, we identified an AMPBP OsAAE3 from a previous analysis of early responsive genes in rice during Magnaporthe oryzae infection. OsAAE3 is a homolog of Arabidopsis AAE3 in rice, which encodes a 4-coumarate-Co-A ligase (4CL) like protein. A phylogenetic analysis showed that OsAAE3 was most likely 4CL-like 10 in an independent group. OsAAE3 was localized to cytoplasm, and it could be expressed in various tissues. Histochemical staining of transgenic plants carrying OsAAE3 promoter-driven GUS (β-glucuronidase) reporter gene suggested that OsAAE3 was expressed in all tissues of rice. Furthermore, OsAAE3-OX plants showed increased susceptibility to M. Oryzae, and this finding was attributable to decreased expression of pathogen-related 1a (PR1) and low level of peroxidase (POD) activity. Moreover, OsAAE3 over-expression resulted in increased content of H2O2, leading to programmed cell-death induced by reactive oxygen species (ROS). In addition, OsAAE3 over-expression repressed the floret development, exhibiting dramatically twisted glume and decreased fertility rate of anther. Meanwhile, the expressions of lignin biosynthesis genes were significantly decreased in OsAAE3-OX plants, thereby leading to reduced lignin content. Taken together, OsAAE3 functioned as a negative regulator in rice blast resistance, floret development, and lignin biosynthesis. Our findings further expanded the knowledge in functions of AMBPs in plant floret development and the regulation of rice-fungus interaction.
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Affiliation(s)
- Hao Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Zhenhua Guo
- Department of Rice Breeding, Jiamusi Rice Research Institute of Heilongjiang Academy of Agricultural SciencesJiamusi, China
| | - Fengwei Gu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Shanwen Ke
- Department of Plant Breeding, College of Agricultural, South China Agricultural UniversityGuangzhou, China
| | - Dayuan Sun
- Plant Protection Research Institute Guangdong Academy of Agricultural Sciences/Guangdong Provincial key Laboratory of High Technology for Plant ProtectionGuangzhou, China
| | - Shuangyu Dong
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Wei Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Ming Huang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Wuming Xiao
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Guili Yang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Yongzhu Liu
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Tao Guo
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Hui Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Jiafeng Wang
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
| | - Zhiqiang Chen
- National Engineering Research Center of Plant Space Breeding, South China Agricultural UniversityGuangzhou, China
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Raboin LM, Ballini E, Tharreau D, Ramanantsoanirina A, Frouin J, Courtois B, Ahmadi N. Association mapping of resistance to rice blast in upland field conditions. RICE (NEW YORK, N.Y.) 2016; 9:59. [PMID: 27830537 PMCID: PMC5102990 DOI: 10.1186/s12284-016-0131-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 10/26/2016] [Indexed: 05/22/2023]
Abstract
BACKGROUND Rice blast is one of the most damaging disease of rice. The use of resistant cultivars is the only practical way to control the disease in developing countries where most farmers cannot afford fungicides. However resistance often breaks down. Genome wide association studies (GWAS) allow high resolution exploration of rice genetic diversity for quantitative and qualitative resistance alleles that can be combined in breeding programs to achieve durability. We undertook a GWAS of resistance to rice blast using a tropical japonica panel of 150 accessions genotyped with 10,937 markers and an indica panel of 190 accessions genotyped with 14,187 markers. RESULTS The contrasted distribution of blast disease scores between the indica and tropical japonica groups observed in the field suggest a higher level of quantitative resistance in the japonica panel than in the indica panel. In the japonica panel, two different loci significantly associated with blast resistance were identified in two experimental sites. The first, detected by seven SNP markers located on chromosome 1, colocalized with a cluster of four NBS-LRR including the two cloned resistance genes Pi37 and Pish/Pi35. The second is located on chromosome 12 and is associated with partial resistance to blast. In the indica panel, we identified only one locus associated with blast resistance. The three markers significantly detected at this locus were located on chromosome 8 in the 240 kb region carrying Pi33, which encompasses a cluster of three nucleotide binding site-leucine-rich repeat (NBS-LRRs) and six LRR-kinases in the Nipponbare sequence. Within this region, there is an insertion in the IR64 sequence compared to the Nipponbare sequence which also contains resistance gene analogs. Pi33 may belong to this insertion. The analysis of haplotype diversity in the target region revealed two distinct haplotypes, both associated with Pi33 resistance. CONCLUSIONS It was possible to identify three chromosomal regions associated with resistance in the field through GWAS in this study. Future research should concentrate on specific indica markers targeting the identified insertion in the Pi33 zone. Specific experimental designs should also be implemented to dissect quantitative resistance among tropical japonica varieties.
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Affiliation(s)
- Louis-Marie Raboin
- CIRAD, UPR AIDA, TA B-115/02, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Elsa Ballini
- Montpellier SupAgro, UMR BGPI, TA A-54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 5, France
| | - Didier Tharreau
- CIRAD, UMR BGPI, TA A-54/K, Campus international de Baillarguet, 34398 Montpellier Cedex 5, France
| | | | - Julien Frouin
- CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Brigitte Courtois
- CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
| | - Nourollah Ahmadi
- CIRAD, UMR AGAP, TA A-108/03, Avenue Agropolis, 34398 Montpellier Cedex 5, France
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Azizi P, Rafii MY, Abdullah SNA, Hanafi MM, Maziah M, Sahebi M, Ashkani S, Taheri S, Jahromi MF. Over-Expression of the Pikh Gene with a CaMV 35S Promoter Leads to Improved Blast Disease (Magnaporthe oryzae) Tolerance in Rice. FRONTIERS IN PLANT SCIENCE 2016; 7:773. [PMID: 27379107 PMCID: PMC4911359 DOI: 10.3389/fpls.2016.00773] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/17/2016] [Indexed: 05/04/2023]
Abstract
Magnaporthe oryzae is a rice blast fungus and plant pathogen that causes a serious rice disease and, therefore, poses a threat to the world's second most important food security crop. Plant transformation technology has become an adaptable system for cultivar improvement and to functionally analyze genes in plants. The objective of this study was to determine the effects (through over-expressing and using the CaMV 35S promoter) of Pikh on MR219 resistance because it is a rice variety that is susceptible to the blast fungus pathotype P7.2. Thus, a full DNA and coding DNA sequence (CDS) of the Pikh gene, 3172 bp, and 1206 bp in length, were obtained through amplifying the gDNA and cDNA template from a PH9-resistant rice variety using a specific primer. Agrobacterium-mediated transformation technology was also used to introduce the Pikh gene into the MR219 callus. Subsequently, transgenic plants were evaluated from the DNA to protein stages using polymerase chain reaction (PCR), semi-quantitative RT-PCR, real-time quantitative PCR and high performance liquid chromatography (HPLC). Transgenic plants were also compared with a control using a real-time quantification technique (to quantify the pathogen population), and transgenic and control plants were challenged with the local most virulent M. oryzae pathotype, P7.2. Based on the results, the Pikh gene encodes a hydrophilic protein with 18 sheets, 4 helixes, and 21 coils. This protein contains 401 amino acids, among which the amino acid sequence from 1 to 376 is a non-cytoplasmic region, that from 377 to 397 is a transmembrane region, and that from 398 to 401 is a cytoplasmic region with no identified disordered regions. The Pikh gene was up-regulated in the transgenic plants compared with the control plants. The quantity of the amino acid leucine in the transgenic rice plants increased significantly from 17.131 in the wild-type to 47.865 mg g(-1) in transgenic plants. The M. oryzae population was constant at 31, 48, and 72 h after inoculation in transgenic plants, while it was increased in the inoculated control plants. This study successfully clarified that over-expression of the Pikh gene in transgenic plants can improve their blast resistance against the M. oryzae pathotype P7.2.
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Affiliation(s)
- Parisa Azizi
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohd Y. Rafii
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Siti N. A. Abdullah
- Laboratory of Plantation Crop, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohamed M. Hanafi
- Laboratory of Plantation Crop, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - M. Maziah
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Science, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mahbod Sahebi
- Laboratory of Plantation Crop, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Sadegh Ashkani
- Laboratory of Food Crops, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
- Department of Agronomy and Plant Breeding, Shahr-e-Rey Branch, Islamic Azad UniversityTehran, Iran
| | - Sima Taheri
- Depatment of Crop Science, Faculty of Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
| | - Mohammad F. Jahromi
- Laboratory of animal production, Institute of Tropical Agriculture, Universiti Putra MalaysiaSerdang, Malaysia
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