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Li X, Bu F, Wang L, Kim C, Xue W, Zhang M, Kawabata S, Zhang Q, Li Y, Zhang Y. Optimization of CRISPR-Cas9 system in Eustoma grandiflorum. iScience 2024; 27:109053. [PMID: 38361623 PMCID: PMC10864798 DOI: 10.1016/j.isci.2024.109053] [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: 09/13/2023] [Revised: 12/10/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The optimization of the CRISPR-Cas9 system for enhancing editing efficiency holds significant value in scientific research. In this study, we optimized single guide RNA and Cas9 promoters of the CRISPR-Cas9 vector and established an efficient protoplast isolation and transient transformation system in Eustoma grandiflorum, and we successfully applied the modified CRISPR-Cas9 system to detect editing efficiency of the EgPDS gene. The activity of the EgU6-2 promoter in E. grandiflorum protoplasts was approximately three times higher than that of the GmU6 promoter. This promoter, along with the EgUBQ10 promoter, was applied in the CRISPR-Cas9 cassette, the modified CRISPR-Cas9 vectors that pEgU6-2::sgRNA-2/pEgUBQ10::Cas9-2 editing efficiency was 37.7%, which was 30.3% higher than that of the control, and the types of mutation are base substitutions, small fragment deletions and insertions. Finally we obtained an efficient gene editing vector for E. grandiflorum. This project provides an important technical platform for the study of gene function in E. grandiflorum.
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Affiliation(s)
- Xueqi Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fanqi Bu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Cholmin Kim
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Branch of Biotechnology, State Academy of Sciences, Pyongyang, the Democratic People’s Republic of Korea
| | - Wanjie Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Man Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Saneyuki Kawabata
- Institute for Sustainable Agroecosystem Services, Graduate School of Agriculture and Life Science, The University of Tokyo, Tokyo, Japan
| | - Qingzhu Zhang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yuhua Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yang Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Zhou J, Liu G, Zhao Y, Zhang R, Tang X, Li L, Jia X, Guo Y, Wu Y, Han Y, Bao Y, He Y, Han Q, Yang H, Zheng X, Qi Y, Zhang T, Zhang Y. An efficient CRISPR-Cas12a promoter editing system for crop improvement. NATURE PLANTS 2023; 9:588-604. [PMID: 37024659 DOI: 10.1038/s41477-023-01384-2] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Promoter editing represents an innovative approach to introduce quantitative trait variation (QTV) in crops. However, an efficient promoter editing system for QTV needs to be established. Here we develop a CRISPR-Cas12a promoter editing (CAPE) system that combines a promoter key-region estimating model and an efficient CRISPR-Cas12a-based multiplexed or singular editing system. CAPE is benchmarked in rice to produce QTV continuums for grain starch content and size by targeting OsGBSS1 and OsGS3, respectively. We then apply CAPE for promoter editing of OsD18, a gene encoding GA3ox in the gibberellin biosynthesis pathway. The resulting lines carry a QTV continuum of semidwarfism without significantly compromising grain measures. Field trials demonstrated that the OsD18 promoter editing lines have the same yield performance and antilodging phenotype as the Green Revolution OsSD1 mutants in different genetic backgrounds. Hence, promoter editing of OsD18 generates a quantitative Green Revolution trait. Together, we demonstrate a CAPE-based promoter editing and tuning pipeline for efficient production of useful QTV continuum in crops.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yuxin Zhao
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Rui Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Ling Li
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xinyu Jia
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yachong Guo
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qinqin Han
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Han Yang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Rockville, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China.
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China.
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China.
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and Physiology, Agricultural College, Yangzhou University, Yangzhou, China.
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Kuzmin AA, Tomilin AN. Building Blocks of Artificial CRISPR-Based Systems beyond Nucleases. Int J Mol Sci 2022; 24:ijms24010397. [PMID: 36613839 PMCID: PMC9820447 DOI: 10.3390/ijms24010397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/19/2022] [Accepted: 12/19/2022] [Indexed: 12/28/2022] Open
Abstract
Tools developed in the fields of genome engineering, precise gene regulation, and synthetic gene networks have an increasing number of applications. When shared with the scientific community, these tools can be used to further unlock the potential of precision medicine and tissue engineering. A large number of different genetic elements, as well as modifications, have been used to create many different systems and to validate some technical concepts. New studies have tended to optimize or improve existing elements or approaches to create complex synthetic systems, especially those based on the relatively new CRISPR technology. In order to maximize the output of newly developed approaches and to move from proof-of-principle experiments to applications in regenerative medicine, it is important to navigate efficiently through the vast number of genetic elements to choose those most suitable for specific needs. In this review, we have collected information regarding the main genetic elements and their modifications, which can be useful in different synthetic systems with an emphasis of those based on CRISPR technology. We have indicated the most suitable elements and approaches to choose or combine in planning experiments, while providing their deeper understanding, and have also stated some pitfalls that should be avoided.
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Gouthu S, Mandelli C, Eubanks BA, Deluc LG. Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations. FRONTIERS IN PLANT SCIENCE 2022; 13:979742. [PMID: 36325537 PMCID: PMC9621297 DOI: 10.3389/fpls.2022.979742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.
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Affiliation(s)
- Satyanarayana Gouthu
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Christian Mandelli
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
| | - Britt A. Eubanks
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Laurent G. Deluc
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
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Pan W, Liu X, Li D, Zhang H. Establishment of an Efficient Genome Editing System in Lettuce Without Sacrificing Specificity. FRONTIERS IN PLANT SCIENCE 2022; 13:930592. [PMID: 35812897 PMCID: PMC9257259 DOI: 10.3389/fpls.2022.930592] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The efficiency of the CRISPR/Cas9 genome editing system remains limited in many crops. Utilizing strong promoters to boost the expression level of Cas9 are commonly used to improve the editing efficiency. However, these strategies also increase the risk of off-target mutation. Here, we developed a new strategy to utilize intron-mediated enhancement (IME)-assisted 35S promoter to drive Cas9 and sgRNA in a single transcript, which escalates the editing efficiency by moderately enhancing the expression of both Cas9 and sgRNA. In addition, we developed another strategy to enrich cells highly expressing Cas9/sgRNA by co-expressing the developmental regulator gene GRF5, which has been proved to ameliorate the transformation efficiency, and the transgenic plants from these cells also exhibited enhanced editing efficiency. This system elevated the genome editing efficiency from 14-28% to 54-81% on three targets tested in lettuce (Lactuca sativa) without increasing the off-target editing efficiency. Thus, we established a new genome editing system with highly improved on-target editing efficiency and without obvious increasement in off-target effects, which can be used to characterize genes of interest in lettuce and other crops.
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Affiliation(s)
- Wenbo Pan
- Peking University Institute of Advanced Agricultural Science, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xue Liu
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Dayong Li
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing, China
- Beijing Key Laboratory of Vegetable Germplasm Improvement, Beijing, China
| | - Huawei Zhang
- Peking University Institute of Advanced Agricultural Science, Weifang, China
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6
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Niazian M, Belzile F, Torkamaneh D. CRISPR/Cas9 in Planta Hairy Root Transformation: A Powerful Platform for Functional Analysis of Root Traits in Soybean. PLANTS (BASEL, SWITZERLAND) 2022; 11:1044. [PMID: 35448772 PMCID: PMC9027312 DOI: 10.3390/plants11081044] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/07/2022] [Accepted: 04/08/2022] [Indexed: 12/22/2022]
Abstract
Sequence and expression data obtained by next-generation sequencing (NGS)-based forward genetics methods often allow the identification of candidate causal genes. To provide true experimental evidence of a gene's function, reverse genetics techniques are highly valuable. Site-directed mutagenesis through transfer DNA (T-DNA) delivery is an efficient reverse screen method in plant functional analysis. Precise modification of targeted crop genome sequences is possible through the stable and/or transient delivery of clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (CRISPR/Cas) reagents. Currently, CRISPR/Cas9 is the most powerful reverse genetics approach for fast and precise functional analysis of candidate genes/mutations of interest. Rapid and large-scale analyses of CRISPR/Cas-induced mutagenesis is achievable through Agrobacterium rhizogenes-mediated hairy root transformation. The combination of A. rhizogenes hairy root-CRISPR/Cas provides an extraordinary platform for rapid, precise, easy, and cost-effective "in root" functional analysis of genes of interest in legume plants, including soybean. Both hairy root transformation and CRISPR/Cas9 techniques have their own complexities and considerations. Here, we discuss recent advancements in soybean hairy root transformation and CRISPR/Cas9 techniques. We highlight the critical factors required to enhance mutation induction and hairy root transformation, including the new generation of reporter genes, methods of Agrobacterium infection, accurate gRNA design strategies, Cas9 variants, gene regulatory elements of gRNAs and Cas9 nuclease cassettes and their configuration in the final binary vector to study genes involved in root-related traits in soybean.
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Affiliation(s)
- Mohsen Niazian
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
- Field and Horticultural Crops Research Department, Kurdistan Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj 6616936311, Iran
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada; (M.N.); (F.B.)
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
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Zhong Z, Zhang Y. Protoplast Isolation and Transfection in Rice. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2464:83-90. [PMID: 35258826 DOI: 10.1007/978-1-0716-2164-6_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Rice (Oryza sativa) is an important cereal crop and a model monocot plant for biology research. The reliable system of foreign DNA transformation and expression is a valuable strategy for basic research and molecular breeding application in rice. The Agrobacterium tumefaciens-mediated foreign DNA transformation system was a powerful tool for genetic research. However, it needs a long period to obtain the stable transformants for further analysis and the transformation rate limits in some organism. Protoplasts are plant cells without a cell wall, and it is much easier for foreign DNA transformation and expression. It has been widely applied in transient expression. Here, we describe a simple method for efficient protoplast isolation and transfection in rice.
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Affiliation(s)
- Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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Wu Y, He Y, Sretenovic S, Liu S, Cheng Y, Han Y, Liu G, Bao Y, Fang Q, Zheng X, Zhou J, Qi Y, Zhang Y, Zhang T. CRISPR-BETS: a base-editing design tool for generating stop codons. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:499-510. [PMID: 34669232 PMCID: PMC8882796 DOI: 10.1111/pbi.13732] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/17/2021] [Indexed: 06/12/2023]
Abstract
Cytosine base editors (CBEs) can install a predefined stop codon at the target site, representing a more predictable and neater method for creating genetic knockouts without altering the genome size. Due to the enhanced predictability of the editing outcomes, it is also more efficient to obtain homozygous mutants in the first generation. With the recent advancement of CBEs on improved editing activity, purify and specificity in plants and animals, base editing has become a more appealing technology for generating knockouts. However, there is a lack of design tools that can aid the adoption of CBEs for achieving such a purpose, especially in plants. Here, we developed a user-friendly design tool named CRISPR-BETS (base editing to stop), which helps with guide RNA (gRNA) design for introducing stop codons in the protein-coding genes of interest. We demonstrated in rice and tomato that CRISPR-BETS is easy-to-use, and its generated gRNAs are highly specific and efficient for generating stop codons and obtaining homozygous knockout lines. While we tailored the tool for the plant research community, CRISPR-BETS can also serve non-plant species.
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Affiliation(s)
- Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yao He
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Shishi Liu
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yanhao Cheng
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Qing Fang
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xuelian Zheng
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Jianping Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Yong Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of Education/Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
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Zhou J, Zhang R, Jia X, Tang X, Guo Y, Yang H, Zheng X, Qian Q, Qi Y, Zhang Y. CRISPR-Cas9 mediated OsMIR168a knockout reveals its pleiotropy in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:310-322. [PMID: 34555252 PMCID: PMC8753357 DOI: 10.1111/pbi.13713] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/31/2021] [Accepted: 09/15/2021] [Indexed: 05/21/2023]
Abstract
MicroRNA168 (MIR168) is a key miRNA that targets the main RNA-induced silencing complex component Argonaute 1 (AGO1) to regulate plant growth and environmental stress responses. However, the regulatory functions of MIR168 need to be further elucidated in rice. In this paper, we generated clean OsMIR168a deletion mutants by CRISPR-Cas9 strategy. We then phenotypically and molecularly characterized these mutants. The rice OsMIR168a mutants grew rapidly at the seedling stage, produced more tillers and matured early. Compared to the wild-type plants, the mutants were shorter at maturity and produced smaller spikelets and seeds. Analysis of gene expression showed that the transcription levels of OsMIR168a's target genes such as OsAGO1a, OsAGO1b and OsAGO1d were elevated significantly in the OsMIR168a mutants. Intriguingly, OsAGO18, a member of a new AGO clade that is conserved in monocots, was confirmed to be a target of OsMIR168a not only by informatic prediction but also by expression analysis and a cell-based cleavage assay in the OsMIR168a mutants. Many protein-coding genes and miRNAs showed differential expression in the OsMIR168a mutants, suggesting OsMIR168a exerts a major transcriptional regulatory role, likely through its potential target genes such as OsAGO1s and OsAGO18. KEGG enrichment analysis of these differentially expressed genes pointed to OsMIR168a's involvement in important processes such as plant hormone signalling transduction and plant-pathogen interaction. These data collectively support that the complex regulation module of OsMIR168a-OsAGO1/OsAGO18-miRNAs-target genes contributes to agronomically important traits, which sheds light on miRNA-mediated crop breeding.
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Affiliation(s)
- Jianping Zhou
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Rui Zhang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xinyu Jia
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xu Tang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yachong Guo
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Han Yang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xuelian Zheng
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Yong Zhang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
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Hassan MM, Zhang Y, Yuan G, De K, Chen JG, Muchero W, Tuskan GA, Qi Y, Yang X. Construct design for CRISPR/Cas-based genome editing in plants. TRENDS IN PLANT SCIENCE 2021; 26:1133-1152. [PMID: 34340931 DOI: 10.1016/j.tplants.2021.06.015] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 06/21/2021] [Accepted: 06/24/2021] [Indexed: 05/06/2023]
Abstract
CRISPR construct design is a key step in the practice of genome editing, which includes identification of appropriate Cas proteins, design and selection of guide RNAs (gRNAs), and selection of regulatory elements to express gRNAs and Cas proteins. Here, we review the choices of CRISPR-based genome editors suited for different needs in plant genome editing applications. We consider the technical aspects of gRNA design and the associated computational tools. We also discuss strategies for the design of multiplex CRISPR constructs for high-throughput manipulation of complex biological processes or polygenic traits. We provide recommendations for different elements of CRISPR constructs and discuss the remaining challenges of CRISPR construct optimization in plant genome editing.
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Affiliation(s)
- Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali-8602, Bangladesh
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kuntal De
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA.
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
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11
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Ren Q, Sretenovic S, Liu G, Zhong Z, Wang J, Huang L, Tang X, Guo Y, Liu L, Wu Y, Zhou J, Zhao Y, Yang H, He Y, Liu S, Yin D, Mayorga R, Zheng X, Zhang T, Qi Y, Zhang Y. Improved plant cytosine base editors with high editing activity, purity, and specificity. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2052-2068. [PMID: 34042262 PMCID: PMC8486236 DOI: 10.1111/pbi.13635] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/30/2021] [Accepted: 05/17/2021] [Indexed: 05/09/2023]
Abstract
Cytosine base editors (CBEs) are great additions to the expanding genome editing toolbox. To improve C-to-T base editing in plants, we first compared seven cytidine deaminases in the BE3-like configuration in rice. We found A3A/Y130F-CBE_V01 resulted in the highest C-to-T base editing efficiency in both rice and Arabidopsis. Furthermore, we demonstrated this A3A/Y130F cytidine deaminase could be used to improve iSpyMacCas9-mediated C-to-T base editing at A-rich PAMs. To showcase its applications, we first applied A3A/Y130F-CBE_V01 for multiplexed editing to generate microRNA-resistant mRNA transcripts as well as pre-mature stop codons in multiple seed trait genes. In addition, we harnessed A3A/Y130F-CBE_V01 for efficient artificial evolution of novel ALS and EPSPS alleles which conferred herbicide resistance in rice. To further improve C-to-T base editing, multiple CBE_V02, CBE_V03 and CBE_V04 systems were developed and tested in rice protoplasts. The CBE_V04 systems were found to have improved editing activity and purity with focal recruitment of more uracil DNA glycosylase inhibitors (UGIs) by the engineered single guide RNA 2.0 scaffold. Finally, we used whole-genome sequencing (WGS) to compare six CBE_V01 systems and four CBE_V04 systems for genome-wide off-target effects in rice. Different levels of cytidine deaminase-dependent and sgRNA-independent off-target effects were indeed revealed by WGS among edited lines by these CBE systems. We also investigated genome-wide sgRNA-dependent off-target effects by different CBEs in rice. This comprehensive study compared 21 different CBE systems, and benchmarked PmCDA1-CBE_V04 and A3A/Y130F-CBE_V04 as next-generation plant CBEs with high editing efficiency, purity, and specificity.
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Affiliation(s)
- Qiurong Ren
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Zhaohui Zhong
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Jiaheng Wang
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Lan Huang
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xu Tang
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yachong Guo
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Li Liu
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Jie Zhou
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yuxin Zhao
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Han Yang
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yao He
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shishi Liu
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Desuo Yin
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Food Crop InstituteHubei Academy of Agricultural SciencesWuhanHubeiChina
| | - Rocio Mayorga
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Xuelian Zheng
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/ Key Laboratory of Plant Functional Genomics of the Ministry of Education/ Jiangsu Key Laboratory of Crop Genomics and Molecular BreedingAgricultural College of Yangzhou UniversityYangzhouChina
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
- Joint International Research Laboratory of Agriculture and Agri‐Product SafetyThe Ministry of Education of ChinaYangzhou UniversityYangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMarylandUSA
| | - Yong Zhang
- Department of BiotechnologySchool of Life Science and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
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12
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Sretenovic S, Liu S, Li G, Cheng Y, Fan T, Xu Y, Zhou J, Zheng X, Coleman G, Zhang Y, Qi Y. Exploring C-To-G Base Editing in Rice, Tomato, and Poplar. Front Genome Ed 2021; 3:756766. [PMID: 34713268 PMCID: PMC8525388 DOI: 10.3389/fgeed.2021.756766] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 09/06/2021] [Indexed: 12/26/2022] Open
Abstract
As a precise genome editing technology, base editing is broadly used in both basic and applied plant research. Cytosine base editors (CBEs) and adenine base editors (ABEs) represent the two commonly used base editor types that mediate C-to-T and A-to-G base transition changes at the target sites, respectively. To date, no transversion base editors have been described in plants. Here, we assessed three C-to-G base editors (CGBEs) for targeting sequences with SpCas9's canonical NGG protospacer adjacent motifs (PAMs) as well as three PAM-less SpRY-based CGBEs for targeting sequences with relaxed PAM requirements. The analyses in rice and tomato protoplasts showed that these CGBEs could make C-to-G conversions at the target sites, and they preferentially edited the C6 position in the 20-nucleotide target sequence. C-to-T edits, insertions and deletions (indels) were major byproducts induced by these CGBEs in the protoplast systems. Further assessment of these CGBEs in stably transformed rice and poplar plants revealed the preference for editing of non-GC sites, and C-to-T edits are major byproducts. Successful C-to-G editing in stably transgenic rice plants was achieved by rXRCC1-based CGBEs with monoallelic editing efficiencies up to 38% in T0 lines. The UNG-rAPOBEC1 (R33A)-based CGBE resulted in successful C-to-G editing in polar, with monoallelic editing efficiencies up to 6.25% in T0 lines. Overall, this study revealed that different CGBEs have different preference on preferred editing sequence context, which could be influenced by cell cycles, DNA repair pathways, and plant species.
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Affiliation(s)
- Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Shishi Liu
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Center for Informational Biology, Chengdu, China
| | - Gen Li
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
| | - Tingting Fan
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Center for Informational Biology, Chengdu, China
| | - Yang Xu
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Center for Informational Biology, Chengdu, China
| | - Jianping Zhou
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Center for Informational Biology, Chengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Center for Informational Biology, Chengdu, China
| | - Gary Coleman
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, University of Electronic Science and Technology of China, Center for Informational Biology, Chengdu, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, United States
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, United States
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13
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Mishra R, Mohanty JN, Mahanty B, Joshi RK. A single transcript CRISPR/Cas9 mediated mutagenesis of CaERF28 confers anthracnose resistance in chilli pepper (Capsicum annuum L.). PLANTA 2021; 254:5. [PMID: 34132917 DOI: 10.1007/s00425-021-03660-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/10/2021] [Indexed: 05/09/2023]
Abstract
T-DNA-free homozygous mutant lines developed through a single transcript CRISPR/Cas9 system harboring the desired modification in the CaERF28 locus exhibited significantly enhanced resistance to the anthracnose pathogen Colletotrichum truncatum coupled with the improved expression of defense responsive genes. Anthracnose, caused by Colletotrichum species, is a major disease of chilli (Capsicum annuum) accounting for significant pre- and post-harvest yield losses across the tropical and subtropical regions of the world. Management of chilli anthracnose using traditional methods have not met with noticeable success. In the present study, we have demonstrated an enhanced anthracnose resistance through a single transcript unit CRISPR/Cas9 mediated alteration of the susceptibility gene CaERF28 in C. annuum. A construct with a single Pol II promoter-driven expression of Cas9, sgRNA and a hammerhead ribozyme (RZ) was designed to modify the CaERF28 gene in the susceptible chilli genotype Arka Lohit. Fourty-five C-ERF28-induced mutant lines (72.5%) were identified from 62 T0 transgenic plants. Further, simultaneously targeted multiple sites within CaERF28 showed increased mutation (85.7%) efficiency. DNA sequence analysis showed that these plants harboured multiple InDels at the target site. The allelic mutants of C-ERF28 were transferred to the following generations by simple Mendelian inheritance. Segregation in the T1 and T2 generations resulted in the identification of T-DNA free and marker-free C-ERF28 mutant lines. Five homozygous mutants demonstrated enhanced resistance to anthracnose compared to wild type as demonstrated by reduced spore count and fungal growth as well as induced expression of defense-related genes. Our results demonstrated that the STU-CRISPR/Cas9 mediated editing of the CaERF28 gene is a rapid, safe and versatile approach for enhancing anthracnose resistance in chilli pepper and pave way for its utilization in the improvement of other solanaceous crops.
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Affiliation(s)
- Rukmini Mishra
- School of Applied Science, Centurion University of Technology and Management, Bhubaneswar, 752050, India
| | - Jatindra Nath Mohanty
- Centre for Biomedical Informatics, Siksha O Anusandhan University, Bhubaneswar, 751003, India
| | - Bijayalaxmi Mahanty
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, 751022, India
| | - Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women's University, Vidya Vihar, Bhubaneswar, 751022, India.
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14
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Zhou J, Yuan M, Zhao Y, Quan Q, Yu D, Yang H, Tang X, Xin X, Cai G, Qian Q, Qi Y, Zhang Y. Efficient deletion of multiple circle RNA loci by CRISPR-Cas9 reveals Os06circ02797 as a putative sponge for OsMIR408 in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:1240-1252. [PMID: 33440058 PMCID: PMC8196656 DOI: 10.1111/pbi.13544] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/29/2020] [Accepted: 12/22/2020] [Indexed: 05/05/2023]
Abstract
CRISPR-Cas9 is an emerging genome editing tool for reverse genetics in plants. However, its application for functional study of non-coding RNAs in plants is still at its infancy. Despite being a major class of non-coding RNAs, the biological roles of circle RNAs (circRNAs) remain largely unknown in plants. Previous plant circRNA studies have focused on identification and annotation of putative circRNAs, with their functions largely uninvestigated by genetic approaches. Here, we applied a multiplexed CRISPR-Cas9 strategy to efficiently acquire individual null mutants for four circRNAs in rice. We showed each of these rice circRNA loci (Os02circ25329, Os06circ02797, Os03circ00204 and Os05circ02465) can be deleted at 10% or higher efficiency in both protoplasts and stable transgenic T0 lines. Such high efficiency deletion enabled the generation of circRNA null allele plants without the CRISPR-Cas9 transgene in the T1 generation. Characterization of the mutants reveals these circRNAs' participation in salt stress response during seed germination and in particular the Os05circ02465 null mutant showed high salt tolerance. Notably, the seedlings of the Os06circ02797 mutant showed rapid growth phenotype after seed germination with the seedlings containing higher chlorophyll A/B content. Further molecular and computational analyses suggested a circRNA-miRNA-mRNA regulatory network where Os06circ02797 functions to bind and sequester OsMIR408, an important and conserved microRNA in plants. This study not only presents genetic evidence for the first time in plants that certain circRNAs may serve as sponges to negatively regulate miRNAs, a phenomenon previously demonstrated in mammalian cells, but also provides important insights for improving agronomic traits through gene editing of circRNA loci in crops.
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Affiliation(s)
- Jianping Zhou
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Mingzhu Yuan
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yuxin Zhao
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Quan Quan
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Dong Yu
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
- Sichuan Grass Industry Technology Research and Promotion CenterChengduChina
| | - Han Yang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xu Tang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Xuhui Xin
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Guangze Cai
- School of Agricultural scienceXichang UniversityXichangChina
| | - Qian Qian
- State Key Laboratory of Rice BiologyChina National Rice Research InstituteHangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Yong Zhang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
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15
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Zhang Y, Ren Q, Tang X, Liu S, Malzahn AA, Zhou J, Wang J, Yin D, Pan C, Yuan M, Huang L, Yang H, Zhao Y, Fang Q, Zheng X, Tian L, Cheng Y, Le Y, McCoy B, Franklin L, Selengut JD, Mount SM, Que Q, Zhang Y, Qi Y. Expanding the scope of plant genome engineering with Cas12a orthologs and highly multiplexable editing systems. Nat Commun 2021; 12:1944. [PMID: 33782402 PMCID: PMC8007695 DOI: 10.1038/s41467-021-22330-w] [Citation(s) in RCA: 69] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas12a is a promising genome editing system for targeting AT-rich genomic regions. Comprehensive genome engineering requires simultaneous targeting of multiple genes at defined locations. Here, to expand the targeting scope of Cas12a, we screen nine Cas12a orthologs that have not been demonstrated in plants, and identify six, ErCas12a, Lb5Cas12a, BsCas12a, Mb2Cas12a, TsCas12a and MbCas12a, that possess high editing activity in rice. Among them, Mb2Cas12a stands out with high editing efficiency and tolerance to low temperature. An engineered Mb2Cas12a-RVRR variant enables editing with more relaxed PAM requirements in rice, yielding two times higher genome coverage than the wild type SpCas9. To enable large-scale genome engineering, we compare 12 multiplexed Cas12a systems and identify a potent system that exhibits nearly 100% biallelic editing efficiency with the ability to target as many as 16 sites in rice. This is the highest level of multiplex edits in plants to date using Cas12a. Two compact single transcript unit CRISPR-Cas12a interference systems are also developed for multi-gene repression in rice and Arabidopsis. This study greatly expands the targeting scope of Cas12a for crop genome engineering.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Qiurong Ren
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xu Tang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Aimee A Malzahn
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Jianping Zhou
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Jiaheng Wang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Desuo Yin
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- Food Crop Institute, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Mingzhu Yuan
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lan Huang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Han Yang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yuxin Zhao
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing Fang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Tian
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
- College of Agriculture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Ysa Le
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Bailey McCoy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Lidiya Franklin
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Jeremy D Selengut
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA
| | - Stephen M Mount
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA
| | | | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
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16
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Ren C, Liu Y, Guo Y, Duan W, Fan P, Li S, Liang Z. Optimizing the CRISPR/Cas9 system for genome editing in grape by using grape promoters. HORTICULTURE RESEARCH 2021; 8:52. [PMID: 33642575 PMCID: PMC7917103 DOI: 10.1038/s41438-021-00489-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 05/05/2023]
Abstract
The efficacy of the CRISPR/Cas9 system in grapevine (Vitis vinifera L.) has been documented, but the optimization of this system, as well as CRISPR/Cas9-mediated multiplex genome editing, has not been explored in this species. Herein, we identified four VvU3 and VvU6 promoters and two ubiquitin (UBQ) promoters in grapevine and demonstrated that the use of the identified VvU3/U6 and UBQ2 promoters could significantly increase the editing efficiency in grape by improving the expression of sgRNA and Cas9, respectively. Furthermore, we conducted multiplex genome editing using the optimized CRISPR/Cas9 vector that contained the conventional multiple sgRNA expression cassettes or the polycistronic tRNA-sgRNA cassette (PTG) by targeting the sugar-related tonoplastic monosaccharide transporter (TMT) family members TMT1 and TMT2, and the overall editing efficiencies were higher than 10%. The simultaneous editing of TMT1 and TMT2 resulted in reduced sugar levels, which indicated the role of these two genes in sugar accumulation in grapes. Moreover, the activities of the VvU3, VvU6, and UBQ2 promoters in tobacco genome editing were demonstrated by editing the phytoene desaturase (PDS) gene in Nicotiana benthamiana leaves. Our study provides materials for the optimization of the CRISPR/Cas9 system. To our knowledge, our simultaneous editing of the grape TMT family genes TMT1 and TMT2 constitutes the first example of multiplex genome editing in grape. The multiplex editing systems described in this manuscript expand the toolbox of grape genome editing, which would facilitate basic research and molecular breeding in grapevine.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China
| | - Yanfei Liu
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Yuchen Guo
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China
- University of Chinese Academy of Sciences, 100049, Beijing, People's Republic of China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, The Innovative Academy of Seed Design, The Chinese Academy of Sciences, 100093, Beijing, People's Republic of China.
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17
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Ren Q, Sretenovic S, Liu S, Tang X, Huang L, He Y, Liu L, Guo Y, Zhong Z, Liu G, Cheng Y, Zheng X, Pan C, Yin D, Zhang Y, Li W, Qi L, Li C, Qi Y, Zhang Y. PAM-less plant genome editing using a CRISPR-SpRY toolbox. NATURE PLANTS 2021; 7:25-33. [PMID: 33398158 DOI: 10.1038/s41477-020-00827-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 12/03/2020] [Indexed: 05/20/2023]
Abstract
The rapid development of the CRISPR-Cas9, -Cas12a and -Cas12b genome editing systems has greatly fuelled basic and translational plant research1-6. DNA targeting by these Cas nucleases is restricted by their preferred protospacer adjacent motifs (PAMs). The PAM requirement for the most popular Streptococcus pyogenes Cas9 (SpCas9) is NGG (N = A, T, C, G)7, limiting its targeting scope to GC-rich regions. Here, we demonstrate genome editing at relaxed PAM sites in rice (a monocot) and the Dahurian larch (a coniferous tree), using an engineered SpRY Cas9 variant8. Highly efficient targeted mutagenesis can be readily achieved by SpRY at relaxed PAM sites in the Dahurian larch protoplasts and in rice transgenic lines through non-homologous end joining (NHEJ). Furthermore, an SpRY-based cytosine base editor was developed and demonstrated by directed evolution of new herbicide resistant OsALS alleles in rice. Similarly, a highly active SpRY adenine base editor was developed based on ABE8e (ref. 9) and SpRY-ABE8e was able to target relaxed PAM sites in rice plants, achieving up to 79% editing efficiency with high product purity. Thus, the SpRY toolbox breaks a PAM restriction barrier in plant genome engineering by enabling DNA editing in a PAM-less fashion. Evidence was also provided for secondary off-target effects by de novo generated single guide RNAs (sgRNAs) due to SpRY-mediated transfer DNA self-editing, which calls for more sophisticated programmes for designing highly specific sgRNAs when implementing the SpRY genome editing toolbox.
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Affiliation(s)
- Qiurong Ren
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Shishi Liu
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Xu Tang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Lan Huang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yao He
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Li Liu
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yachong Guo
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Changtian Pan
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Desuo Yin
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Wanfeng Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Liwang Qi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, Harbin, China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, USA.
| | - Yong Zhang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China.
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18
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CRISPR-Cas9 System for Plant Genome Editing: Current Approaches and Emerging Developments. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10071033] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Targeted genome editing using CRISPR-Cas9 has been widely adopted as a genetic engineering tool in various biological systems. This editing technology has been in the limelight due to its simplicity and versatility compared to other previously known genome editing platforms. Several modifications of this editing system have been established for adoption in a variety of plants, as well as for its improved efficiency and portability, bringing new opportunities for the development of transgene-free improved varieties of economically important crops. This review presents an overview of CRISPR-Cas9 and its application in plant genome editing. A catalog of the current and emerging approaches for the implementation of the system in plants is also presented with details on the existing gaps and limitations. Strategies for the establishment of the CRISPR-Cas9 molecular construct such as the selection of sgRNAs, PAM compatibility, choice of promoters, vector architecture, and multiplexing approaches are emphasized. Progress in the delivery and transgene detection methods, together with optimization approaches for improved on-target efficiency are also detailed in this review. The information laid out here will provide options useful for the effective and efficient exploitation of the system for plant genome editing and will serve as a baseline for further developments of the system. Future combinations and fine-tuning of the known parameters or factors that contribute to the editing efficiency, fidelity, and portability of CRISPR-Cas9 will indeed open avenues for new technological advancements of the system for targeted gene editing in plants.
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