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Zhong Z, Sretenovic S, Ren Q, Yang L, Bao Y, Qi C, Yuan M, He Y, Liu S, Liu X, Wang J, Huang L, Wang Y, Baby D, Wang D, Zhang T, Qi Y, Zhang Y. Improving Plant Genome Editing with High-Fidelity xCas9 and Non-canonical PAM-Targeting Cas9-NG. MOLECULAR PLANT 2019; 12:1027-1036. [PMID: 30928637 DOI: 10.1016/j.molp.2019.03.011] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 03/21/2019] [Accepted: 03/23/2019] [Indexed: 05/22/2023]
Abstract
Two recently engineered SpCas9 variants, namely xCas9 and Cas9-NG, show promising potential in improving targeting specificity and broadening the targeting range. In this study, we evaluated these Cas9 variants in the model and crop plant, rice. We first tested xCas9-3.7, the most effective xCas9 variant in mammalian cells, for targeted mutagenesis at 16 possible NGN PAM (protospacer adjacent motif) combinations in duplicates. xCas9 exhibited nearly equivalent editing efficiency to wild-type Cas9 (Cas9-WT) at most canonical NGG PAM sites tested, whereas it showed limited activity at non-canonical NGH (H = A, C, T) PAM sites. High editing efficiency of xCas9 at NGG PAMs was further demonstrated with C to T base editing by both rAPOBEC1 and PmCDA1 cytidine deaminases. With mismatched sgRNAs, we found that xCas9 had improved targeting specificity over the Cas9-WT. Furthermore, we tested two Cas9-NG variants, Cas9-NGv1 and Cas9-NG, for targeting NGN PAMs. Both Cas9-NG variants showed higher editing efficiency at most non-canonical NG PAM sites tested, and enabled much more efficient editing than xCas9 at AT-rich PAM sites such as GAT, GAA, and CAA. Nevertheless, we found that Cas9-NG variants showed significant reduced activity at the canonical NGG PAM sites. In stable transgenic rice lines, we demonstrated that Cas9-NG had much higher editing efficiency than Cas9-NGv1 and xCas9 at NG PAM sites. To expand the base-editing scope, we developed an efficient C to T base-editing system by making fusion of Cas9-NG nickase (D10A version), PmCDA1, and UGI. Taken together, our work benchmarked xCas9 as a high-fidelity nuclease for targeting canonical NGG PAMs and Cas9-NG as a preferred variant for targeting relaxed PAMs for plant genome editing.
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Affiliation(s)
- Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Lijia Yang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Caiyan Qi
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Mingzhu Yuan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Yao He
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Xiaopei Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Jiaheng Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Lan Huang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Yan Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China
| | - Dibin Baby
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Indian Institute of Science Education and Research, Tirupati, Andhra Pradesh 517507, India
| | - David Wang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA; Seven Lakes High School, Katy, TX 77494, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - 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.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu 610054, China.
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Tang X, Ren Q, Yang L, Bao Y, Zhong Z, He Y, Liu S, Qi C, Liu B, Wang Y, Sretenovic S, Zhang Y, Zheng X, Zhang T, Qi Y, Zhang Y. Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1431-1445. [PMID: 30582653 PMCID: PMC6576101 DOI: 10.1111/pbi.13068] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 05/03/2023]
Abstract
CRISPR-Cas9 and Cas12a are two powerful genome editing systems. Expression of CRISPR in plants is typically achieved with a mixed dual promoter system, in which Cas protein is expressed by a Pol II promoter and a guide RNA is expressed by a species-specific Pol III promoter such as U6 or U3. To achieve coordinated expression and compact vector packaging, it is desirable to express both CRISPR components under a single Pol II promoter. Previously, we demonstrated a first-generation single transcript unit (STU)-Cas9 system, STU-Cas9-RZ, which is based on hammerhead ribozyme for processing single guide RNAs (sgRNAs). In this study, we developed two new STU-Cas9 systems and one STU-Cas12a system for applications in plants, collectively called the STU CRISPR 2.0 systems. We demonstrated these systems for genome editing in rice with both transient expression and stable transgenesis. The two STU-Cas9 2.0 systems process the sgRNAs with Csy4 ribonuclease and endogenous tRNA processing system respectively. Both STU-Cas9-Csy4 and STU-Cas9-tRNA systems showed more robust genome editing efficiencies than our first-generation STU-Cas9-RZ system and the conventional mixed dual promoter system. We further applied the STU-Cas9-tRNA system to compare two C to T base editing systems based on rAPOBEC1 and PmCDA1 cytidine deaminases. The results suggest STU-based PmCDA1 base editor system is highly efficient in rice. The STU-Cas12a system, based on Cas12a' self-processing of a CRISPR RNA (crRNA) array, was also developed and demonstrated for expression of a single crRNA and four crRNAs. Altogether, our STU CRISPR 2.0 systems further expanded the CRISPR toolbox for plant genome editing and other applications.
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Affiliation(s)
- Xu Tang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Qiurong Ren
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Lijia Yang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyJiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Zhaohui Zhong
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yao He
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shishi Liu
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Caiyan Qi
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Binglin Liu
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yan Wang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Xuelian Zheng
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyJiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Yong Zhang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
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Li J, Manghwar H, Sun L, Wang P, Wang G, Sheng H, Zhang J, Liu H, Qin L, Rui H, Li B, Lindsey K, Daniell H, Jin S, Zhang X. Whole genome sequencing reveals rare off-target mutations and considerable inherent genetic or/and somaclonal variations in CRISPR/Cas9-edited cotton plants. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:858-868. [PMID: 30291759 PMCID: PMC6587709 DOI: 10.1111/pbi.13020] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 05/19/2023]
Abstract
The CRISPR/Cas9 system has been extensively applied for crop improvement. However, our understanding of Cas9 specificity is very limited in Cas9-edited plants. To identify on- and off-target mutation in an edited crop, we described whole genome sequencing (WGS) of 14 Cas9-edited cotton plants targeted to three genes, and three negative (Ne) control and three wild-type (WT) plants. In total, 4188-6404 unique single-nucleotide polymorphisms (SNPs) and 312-745 insertions/deletions (indels) were detected in 14 Cas9-edited plants compared to WT, negative and cotton reference genome sequences. Since the majority of these variations lack a protospacer-adjacent motif (PAM), we demonstrated that the most variations following Cas9-edited are due either to somaclonal variation or/and pre-existing/inherent variation from maternal plants, but not off-target effects. Of a total of 4413 potential off-target sites (allowing ≤5 mismatches within the 20-bp sgRNA and 3-bp PAM sequences), the WGS data revealed that only four are bona fide off-target indel mutations, validated by Sanger sequencing. Moreover, inherent genetic variation of WT can generate novel off-target sites and destroy PAMs, which suggested great care should be taken to design sgRNA for the minimizing of off-target effect. These findings suggested that CRISPR/Cas9 system is highly specific for cotton plants.
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Affiliation(s)
- Jianying Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hakim Manghwar
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lin Sun
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Pengcheng Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hanyan Sheng
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Jie Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hao Liu
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
- Agricultural Bioinformatics Key Laboratory of Hubei ProvinceCollege of InformaticsHuazhong Agricultural UniversityWuhanHubeiChina
| | - Lei Qin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Hangping Rui
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Bo Li
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | | | - Henry Daniell
- Department of BiochemistrySchool of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
| | - Xianlong Zhang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanHubeiChina
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154
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Nandy S, Pathak B, Zhao S, Srivastava V. Heat-shock-inducible CRISPR/Cas9 system generates heritable mutations in rice. PLANT DIRECT 2019; 3:e00145. [PMID: 31404128 PMCID: PMC6603394 DOI: 10.1002/pld3.145] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/08/2019] [Accepted: 05/13/2019] [Indexed: 05/22/2023]
Abstract
Transient expression of CRISPR/Cas9 is an effective approach for limiting its activities and improving its precision in genome editing. Here, we describe the heat-shock-inducible CRISPR/Cas9 for controlled genome editing, and demonstrate its efficiency in the model crop, rice. Using the soybean heat-shock protein gene promoter and the rice U3 promoter to express Cas9 and sgRNA, respectively, we developed the heat-shock (HS)-inducible CRISPR/Cas9 system, and tested its efficacy in targeted mutagenesis. Two loci were targeted in rice, and the presence of targeted mutations was determined before and after the HS treatment. Only a low rate of targeted mutagenesis was detected before HS (~16%), but an increased rate of mutagenesis was observed after the HS treatment among the transgenic lines (50-63%). Analysis of regenerated plants harboring HS-CRISPR/Cas9 revealed that targeted mutagenesis was suppressed in the plants but induced by HS, which was detectable by Sanger sequencing after a few weeks of HS treatments. Most importantly, the HS-induced mutations were transmitted to the progeny at a high rate, generating monoallelic and biallelic mutations that independently segregated from the Cas9 gene. Additionally, off-target mutations were either undetectable or found at a lower rate in HS-CRISPR/Cas9 lines as compared to the constitutive-overexpression CRISPR/Cas9 lines. Taken together, this work shows that HS-CRISPR/Cas9 is a controlled and reasonably efficient platform for genome editing, and therefore, a promising tool for limiting genome-wide off-target effects and improving the precision of genome editing.
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Affiliation(s)
- Soumen Nandy
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
| | - Bhuvan Pathak
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas
| | - Shan Zhao
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
| | - Vibha Srivastava
- Department of Crop, Soil & Environmental Sciences University of Arkansas Fayetteville Arkansas
- Cell and Molecular Biology Program University of Arkansas Fayetteville Arkansas
- Department of Horticulture University of Arkansas Fayetteville Arkansas
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155
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Vanegas KG, Jarczynska ZD, Strucko T, Mortensen UH. Cpf1 enables fast and efficient genome editing in Aspergilli. Fungal Biol Biotechnol 2019; 6:6. [PMID: 31061713 PMCID: PMC6492335 DOI: 10.1186/s40694-019-0069-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 04/19/2019] [Indexed: 12/21/2022] Open
Abstract
Background CRISPR technology has revolutionized fungal genetic engineering by increasing the speed and complexity of the experiments that can be performed. Moreover, the efficiency of the system often allows genetic engineering to be introduced in non-model species. The efficiency of CRISPR gene editing is due to the formation of specific DNA double-strand breaks made by RNA guided nucleases. In filamentous fungi, only Cas9 has so far been used as the CRISPR nuclease. Since, gene editing with Cas9 is limited by its 5′-NGG-3′ protospacer adjacent motif (PAM) sequence, it is important to introduce RNA guided nucleases that depend on other PAM sequences in order to be able to target a larger repertoire of genomic sites. Cpf1 from Lachnospiraceae bacterium employs a PAM sequence composed of 5′-TTTN-3′ and therefore serves as an attractive option towards this goal. Results In this study we showed that Lb_cpf1 codon optimized for Aspergillus nidulans can be used for CRISPR based gene editing in filamentous fungi. We have developed a vector-based setup for Cpf1-mediated CRISPR experiments and showed that it works efficiently at different loci in A. nidulans and in A. niger. Specifically, we used our setup to demonstrate that Cpf1 is able to catalyze oligonucleotide-mediated genomic site-directed mutagenesis and marker-free gene targeting. Conclusions In this paper we introduce Cpf1 as a new tool in the fungal CRISPR toolbox. Our experiments demonstrate that Cpf1 can be efficiently used in Aspergilli for gene editing thereby expanding the range of genomic DNA sequences that can be targeted by CRISPR technologies. Electronic supplementary material The online version of this article (10.1186/s40694-019-0069-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherina Garcia Vanegas
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby, Denmark
| | - Zofia Dorota Jarczynska
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby, Denmark
| | - Tomas Strucko
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby, Denmark
| | - Uffe Hasbro Mortensen
- Eukaryotic Molecular Cell Biology, Section for Synthetic Biology, Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby, Denmark
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156
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Mao Y, Botella JR, Liu Y, Zhu JK. Gene editing in plants: progress and challenges. Natl Sci Rev 2019; 6:421-437. [PMID: 34691892 PMCID: PMC8291443 DOI: 10.1093/nsr/nwz005] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 12/11/2018] [Accepted: 01/15/2019] [Indexed: 12/26/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 (Cas9) genome editing system is a powerful tool for targeted gene modifications in a wide range of species, including plants. Over the last few years, this system has revolutionized the way scientists perform genetic studies and crop breeding, due to its simplicity, flexibility, consistency and high efficiency. Considerable progress has been made in optimizing CRISPR/Cas9 systems in plants, particularly for targeted gene mutagenesis. However, there are still a number of important challenges ahead, including methods for the efficient delivery of CRISPR and other editing tools to most plants, and more effective strategies for sequence knock-ins and replacements. We provide our viewpoint on the goals, potential concerns and future challenges for the development and application of plant genome editing tools.
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Affiliation(s)
- Yanfei Mao
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
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157
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Young J, Zastrow-Hayes G, Deschamps S, Svitashev S, Zaremba M, Acharya A, Paulraj S, Peterson-Burch B, Schwartz C, Djukanovic V, Lenderts B, Feigenbutz L, Wang L, Alarcon C, Siksnys V, May G, Chilcoat ND, Kumar S. CRISPR-Cas9 Editing in Maize: Systematic Evaluation of Off-target Activity and Its Relevance in Crop Improvement. Sci Rep 2019; 9:6729. [PMID: 31040331 PMCID: PMC6491584 DOI: 10.1038/s41598-019-43141-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/15/2019] [Indexed: 12/18/2022] Open
Abstract
CRISPR-Cas9 enabled genome engineering has great potential for improving agriculture productivity, but the possibility of unintended off-target edits has evoked some concerns. Here we employ a three-step strategy to investigate Cas9 nuclease specificity in a complex plant genome. Our approach pairs computational prediction with genome-wide biochemical off-target detection followed by validation in maize plants. Our results reveal high frequency (up to 90%) on-target editing with no evidence of off-target cleavage activity when guide RNAs were bioinformatically predicted to be specific. Predictable off-target edits were observed but only with a promiscuous guide RNA intentionally designed to validate our approach. Off-target editing can be minimized by designing guide RNAs that are different from other genomic locations by at least three mismatches in combination with at least one mismatch occurring in the PAM proximal region. With well-designed guides, genetic variation from Cas9 off-target cleavage in plants is negligible, and much less than inherent variation.
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Affiliation(s)
- Joshua Young
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Gina Zastrow-Hayes
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Stéphane Deschamps
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Sergei Svitashev
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University, Vilnius, LT, 10257, Lithuania
| | - Ananta Acharya
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Sushmitha Paulraj
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | | | - Chris Schwartz
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Vesna Djukanovic
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Brian Lenderts
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Lanie Feigenbutz
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Lijuan Wang
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Clara Alarcon
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Vilnius, LT, 10257, Lithuania
| | - Gregory May
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - N Doane Chilcoat
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA
| | - Sandeep Kumar
- Corteva Agriscience™, Agriculture Division of DowDuPont™, Johnston, IA, 50131, USA.
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158
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 631] [Impact Index Per Article: 126.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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Satheesh V, Zhang H, Wang X, Lei M. Precise editing of plant genomes - Prospects and challenges. Semin Cell Dev Biol 2019; 96:115-123. [PMID: 31002868 DOI: 10.1016/j.semcdb.2019.04.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 04/15/2019] [Accepted: 04/15/2019] [Indexed: 12/26/2022]
Abstract
The past decade has witnessed unprecedented development in genome engineering, a process that enables targeted modification of genomes. The identification of sequence-specific nucleases such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the CRISPR/Cas system, in particular, has led to precise and efficient introduction of genetic variations into genomes of various organisms. Since the CRISPR/Cas system is highly versatile, cost-effective and much superior to ZFNs and TALENs, its widespread adoption by the research community has been inevitable. In plants, a number of studies have shown that CRISPR/Cas could be a potential tool in basic research where insertion, deletion and/or substitution in the genetic sequence could help answer fundamental questions about plant processes, and in applied research these technologies could help build or reverse-engineer plant systems to make them more useful. In this review article, we summarize technologies for precise editing of genomes with a special focus on the CRISPR/Cas system, highlight the latest developments in the CRISPR/Cas system and discuss the challenges and prospects in using the system for plant biology research.
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Affiliation(s)
- Viswanathan Satheesh
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hui Zhang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xianting Wang
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Mingguang Lei
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
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160
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Zhou J, Xin X, He Y, Chen H, Li Q, Tang X, Zhong Z, Deng K, Zheng X, Akher SA, Cai G, Qi Y, Zhang Y. Multiplex QTL editing of grain-related genes improves yield in elite rice varieties. PLANT CELL REPORTS 2019; 38:475-485. [PMID: 30159598 DOI: 10.1007/s00299-00018-02340-00293] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/24/2018] [Indexed: 05/19/2023]
Abstract
Significant yield increase has been achieved by simultaneous introduction of three trait-related QTLs in three rice varieties with multiplex editing by CRISPR-Cas9. Using traditional breeding approaches to develop new elite rice varieties with high yield and superior quality is challenging. It usually requires introduction of multiple trait-related quantitative trait loci (QTLs) into an elite background through multiple rounds of crossing and selection. CRISPR-Cas9-based multiplex editing of QTLs represents a new breeding strategy that is straightforward and cost effective. To test this approach, we simultaneously targeted three yield-related QTLs for editing in three elite rice varieties, namely J809, L237 and CNXJ. The chosen yield-related QTL genes are OsGS3, OsGW2 and OsGn1a, which have been identified to negatively regulate the grain size, width and weight, and number, respectively. Our approach rapidly generated all seven combinations of single, double and triple mutants for the target genes in elite backgrounds. Detailed analysis of these mutants revealed differential contributions of QTL mutations to yield performance such as grain length, width, number and 1000-grain weight. Overall, the contributions are additive, resulting in 68 and 30% yield per panicle increase in triple mutants of J809 and L237, respectively. Our data hence demonstrates a promising genome editing approach for rapid breeding of QTLs in elite crop varieties.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuhui Xin
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Yao He
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Hongqiao Chen
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qian Li
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xu Tang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Kejun Deng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Sayed Abdul Akher
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Guangze Cai
- Xichang University, Xichang, 615013, Sichuan, China
| | - 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.
| | - Yong Zhang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
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161
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Hahn F, Nekrasov V. CRISPR/Cas precision: do we need to worry about off-targeting in plants? PLANT CELL REPORTS 2019; 38:437-441. [PMID: 30426198 PMCID: PMC6469637 DOI: 10.1007/s00299-018-2355-9] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/07/2018] [Indexed: 05/14/2023]
Abstract
The CRISPR/Cas technology has recently become the tool of choice for targeted genome modification in plants and beyond. Although CRSIPR/Cas offers a rapid and facile way of introducing changes at genomic loci of interest, its application is associated with off-targeting, i.e. introduction of unintended mutations at off-target sites within the genome, which has been reported frequently in the mammalian field. Here we summarise the current knowledge on the precision of CRISPR/Cas in plant systems and provide a summary of state-of the-art strategies for avoiding off-target mutations, as well as unintended on-target changes, in plants. These include using natural (e.g. Cas12a) or engineered (e.g. SpCas9-HF) CRISPR/Cas nucleases characterised by higher precision, as compared to the commonly used wild type SpCas9. In addition, we discuss the usage of CRISPR/Cas nucleases in the form of ribonucleoproteins (RNPs) as an option for reducing off-targeting in plants. Finally, we conclude that the most important factor for reducing CRISPR/Cas off-targeting remains careful selection of target sequences, for which we provide an overview of available online software tools and experimental guidance.
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Affiliation(s)
- Florian Hahn
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | - Vladimir Nekrasov
- Plant Sciences Department, Rothamsted Research, Harpenden, AL5 2JQ, UK.
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162
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Affiliation(s)
- Jintao Tang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Letian Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, China
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, China.
- Key Laboratory of Plant Functional Genomics and Biotechnology of Guangdong Provincial Higher Education Institutions, South China Agricultural University, Guangzhou, China.
- College of Life Sciences, South China Agricultural University, Guangzhou, China.
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163
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Zhou J, Xin X, He Y, Chen H, Li Q, Tang X, Zhong Z, Deng K, Zheng X, Akher SA, Cai G, Qi Y, Zhang Y. Multiplex QTL editing of grain-related genes improves yield in elite rice varieties. PLANT CELL REPORTS 2019; 38:475-485. [PMID: 30159598 DOI: 10.1007/s00299-018-2340-3] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 08/24/2018] [Indexed: 05/21/2023]
Abstract
Significant yield increase has been achieved by simultaneous introduction of three trait-related QTLs in three rice varieties with multiplex editing by CRISPR-Cas9. Using traditional breeding approaches to develop new elite rice varieties with high yield and superior quality is challenging. It usually requires introduction of multiple trait-related quantitative trait loci (QTLs) into an elite background through multiple rounds of crossing and selection. CRISPR-Cas9-based multiplex editing of QTLs represents a new breeding strategy that is straightforward and cost effective. To test this approach, we simultaneously targeted three yield-related QTLs for editing in three elite rice varieties, namely J809, L237 and CNXJ. The chosen yield-related QTL genes are OsGS3, OsGW2 and OsGn1a, which have been identified to negatively regulate the grain size, width and weight, and number, respectively. Our approach rapidly generated all seven combinations of single, double and triple mutants for the target genes in elite backgrounds. Detailed analysis of these mutants revealed differential contributions of QTL mutations to yield performance such as grain length, width, number and 1000-grain weight. Overall, the contributions are additive, resulting in 68 and 30% yield per panicle increase in triple mutants of J809 and L237, respectively. Our data hence demonstrates a promising genome editing approach for rapid breeding of QTLs in elite crop varieties.
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Affiliation(s)
- Jianping Zhou
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuhui Xin
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Yao He
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Hongqiao Chen
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qian Li
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xu Tang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Zhaohui Zhong
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Kejun Deng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Sayed Abdul Akher
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Guangze Cai
- Xichang University, Xichang, 615013, Sichuan, China
| | - 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.
| | - Yong Zhang
- Department of Biotechnology, Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
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164
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Zhang H, Wang X, Pan Q, Li P, Liu Y, Lu X, Zhong W, Li M, Han L, Li J, Wang P, Li D, Liu Y, Li Q, Yang F, Zhang YM, Wang G, Li L. QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples. MOLECULAR PLANT 2019; 12:426-437. [PMID: 30597214 DOI: 10.1016/j.molp.2018.12.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/20/2018] [Accepted: 12/24/2018] [Indexed: 05/08/2023]
Abstract
Deciphering the genetic mechanisms underlying agronomic traits is of great importance for crop improvement. Most of these traits are controlled by multiple quantitative trait loci (QTLs), and identifying the underlying genes by conventional QTL fine-mapping is time-consuming and labor-intensive. Here, we devised a new method, named quantitative trait gene sequencing (QTG-seq), to accelerate QTL fine-mapping. QTG-seq combines QTL partitioning to convert a quantitative trait into a near-qualitative trait, sequencing of bulked segregant pools from a large segregating population, and the use of a robust new algorithm for identifying candidate genes. Using QTG-seq, we fine-mapped a plant-height QTL in maize (Zea mays L.), qPH7, to a 300-kb genomic interval and verified that a gene encoding an NF-YC transcription factor was the functional gene. Functional analysis suggested that qPH7-encoding protein might influence plant height by interacting with a CO-like protein and an AP2 domain-containing protein. Selection footprint analysis indicated that qPH7 was subject to strong selection during maize improvement. In summary, QTG-seq provides an efficient method for QTL fine-mapping in the era of "big data".
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Affiliation(s)
- Hongwei Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Xi Wang
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Qingchun Pan
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Pei Li
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunjun Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoduo Lu
- Institute of Molecular Breeding for Maize, Qilu Normal University, Jinan 250200, China
| | - Wanshun Zhong
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Minqi Li
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Linqian Han
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Juan Li
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingxi Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dongdong Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Liu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qing Li
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Fang Yang
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuan-Ming Zhang
- Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Guoying Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Lin Li
- National Key Laboratory of Crop Genetic Improvement, Crop Information Center, Huazhong Agricultural University, Wuhan 430070, China.
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165
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Malzahn AA, Tang X, Lee K, Ren Q, Sretenovic S, Zhang Y, Chen H, Kang M, Bao Y, Zheng X, Deng K, Zhang T, Salcedo V, Wang K, Zhang Y, Qi Y. Application of CRISPR-Cas12a temperature sensitivity for improved genome editing in rice, maize, and Arabidopsis. BMC Biol 2019; 17:9. [PMID: 30704461 PMCID: PMC6357469 DOI: 10.1186/s12915-019-0629-5] [Citation(s) in RCA: 126] [Impact Index Per Article: 25.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/14/2019] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND CRISPR-Cas12a (formerly Cpf1) is an RNA-guided endonuclease with distinct features that have expanded genome editing capabilities. Cas12a-mediated genome editing is temperature sensitive in plants, but a lack of a comprehensive understanding on Cas12a temperature sensitivity in plant cells has hampered effective application of Cas12a nucleases in plant genome editing. RESULTS We compared AsCas12a, FnCas12a, and LbCas12a for their editing efficiencies and non-homologous end joining (NHEJ) repair profiles at four different temperatures in rice. We found that AsCas12a is more sensitive to temperature and that it requires a temperature of over 28 °C for high activity. Each Cas12a nuclease exhibited distinct indel mutation profiles which were not affected by temperatures. For the first time, we successfully applied AsCas12a for generating rice mutants with high frequencies up to 93% among T0 lines. We next pursued editing in the dicot model plant Arabidopsis, for which Cas12a-based genome editing has not been previously demonstrated. While LbCas12a barely showed any editing activity at 22 °C, its editing activity was rescued by growing the transgenic plants at 29 °C. With an early high-temperature treatment regime, we successfully achieved germline editing at the two target genes, GL2 and TT4, in Arabidopsis transgenic lines. We then used high-temperature treatment to improve Cas12a-mediated genome editing in maize. By growing LbCas12a T0 maize lines at 28 °C, we obtained Cas12a-edited mutants at frequencies up to 100% in the T1 generation. Finally, we demonstrated DNA binding of Cas12a was not abolished at lower temperatures by using a dCas12a-SRDX-based transcriptional repression system in Arabidopsis. CONCLUSION Our study demonstrates the use of high-temperature regimes to achieve high editing efficiencies with Cas12a systems in rice, Arabidopsis, and maize and sheds light on the mechanism of temperature sensitivity for Cas12a in plants.
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Affiliation(s)
- Aimee A Malzahn
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Xu Tang
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Keunsub Lee
- Crop Bioengineering Center, Iowa State University, Ames, Iowa, 50011, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, 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, 610054, China
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Hongqiao Chen
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Minjeong Kang
- Crop Bioengineering Center, Iowa State University, Ames, Iowa, 50011, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, USA
- Interdepartmental Plant Biology Major, Iowa State University, Ames, Iowa, 50011, USA
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, 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, 610054, China
| | - Kejun Deng
- Department of Biotechnology, School of Life Science and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou, 225009, China
| | - Valeria Salcedo
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Kan Wang
- Crop Bioengineering Center, Iowa State University, Ames, Iowa, 50011, USA
- Department of Agronomy, Iowa State University, Ames, Iowa, 50011, 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, 610054, China.
| | - 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.
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166
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Parry G, Harrison CJ. GARNet gene editing workshop. THE NEW PHYTOLOGIST 2019; 221:640-643. [PMID: 30569609 DOI: 10.1111/nph.15573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Geraint Parry
- GARNet, School of Biosciences, Cardiff University, Cardiff, CF10 3AX, UK
| | - C Jill Harrison
- School of Biological Sciences, University of Bristol, 24 Tyndall Avenue, Bristol, BS8 1TQ, UK
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167
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Ren Q, Zhong Z, Wang Y, You Q, Li Q, Yuan M, He Y, Qi C, Tang X, Zheng X, Zhang T, Qi Y, Zhang Y. Bidirectional Promoter-Based CRISPR-Cas9 Systems for Plant Genome Editing. FRONTIERS IN PLANT SCIENCE 2019; 10:1173. [PMID: 31616455 PMCID: PMC6764340 DOI: 10.3389/fpls.2019.01173] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 08/27/2019] [Indexed: 05/21/2023]
Abstract
CRISPR-Cas systems can be expressed in multiple ways, with different capabilities regarding tissue-specific expression, efficiency, and expression levels. Thus far, three expression strategies have been demonstrated in plants: mixed dual promoter systems, dual Pol II promoter systems, and single transcript unit (STU) systems. We explored a fourth strategy to express CRISPR-Cas9 in the model and crop plant, rice, where a bidirectional promoter (BiP) is used to express Cas9 and single guide RNA (sgRNA) in opposite directions. We first tested an engineered BiP system based on double-mini 35S promoter and an Arabidopsis enhancer, which resulted in 20.7% and 52.9% genome editing efficiencies at two target sites in T0 stable transgenic rice plants. We further improved the BiP system drastically by using a rice endogenous BiP, OsBiP1. The endogenous BiP expression system had higher expression strength and led to 75.9-93.3% genome editing efficiencies in rice T0 generation, when the sgRNAs were processed by either tRNA or Csy4. We provided a proof-of-concept study of applying BiP systems for expressing two-component CRISPR-Cas9 genome editing reagents in rice. Our work could promote future research and adoption of BiP systems for CRISPR-Cas-based genome engineering in plants.
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Affiliation(s)
- Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Yan Wang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qi You
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of 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 of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Qian Li
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
| | - Mingzhu Yuan
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, 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
| | - Caiyan Qi
- 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
| | - 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
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of 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 of the Ministry of Education, Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang, ; Yiping Qi, ; Yong Zhang,
| | - 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
- *Correspondence: Tao Zhang, ; Yiping Qi, ; Yong Zhang,
| | - 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
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College of Yangzhou University, Yangzhou, China
- *Correspondence: Tao Zhang, ; Yiping Qi, ; Yong Zhang,
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168
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Abstract
CRISPR systems have greatly promoted research in genome editing and transcriptional regulation. CRISPR-based transcriptional repression and activation systems will be valuable for applications in engineering plant immunity, boosting metabolic production, and enhancing our knowledge of gene regulatory networks. Multiplexing of CRISPR allows multiple genes to be targeted without significant additional effort. Here, we describe our CRISPR-Act2.0 system which is an improved multiplexing transcriptional activation system in plants.
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169
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Holme IB, Gregersen PL, Brinch-Pedersen H. Induced Genetic Variation in Crop Plants by Random or Targeted Mutagenesis: Convergence and Differences. FRONTIERS IN PLANT SCIENCE 2019; 10:1468. [PMID: 31803209 PMCID: PMC6868598 DOI: 10.3389/fpls.2019.01468] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/22/2019] [Indexed: 05/18/2023]
Abstract
New Breeding Techniques (NBTs) include several new technologies for introduction of new variation into crop plants for plant breeding, in particular the methods that aim to make targeted mutagenesis at specific sites in the plant genome (NBT mutagenesis). However, following that the French highest legislative body for administrative justice, the Conseil d'État, has sought advice from The Court of Justice of the European Union (CJEU) in interpreting the scope of the genetically modified organisms (GMO) Directive, CJEU in a decision from 2018, stated that organisms modified by these new techniques are not exempted from the current EU GMO legislation. The decision was based in a context of conventional plant breeding using mutagenesis of crop plants by physical or chemical treatments. These plants are explicitly exempted from the EU GMO legislation, based on the long-termed use of mutagenesis. Following its decision, the EU Court considers that the NBTs operate "at a rate out of all proportion to those resulting from the application of conventional methods of mutagenesis." In this paper, we argue that in fact this is not the case anymore; instead, a convergence has taken place between conventional mutagenesis and NBTs, in particular due to the possibilities of TILLING methods that allow the fast detection of mutations in any gene of a genome. Thus, by both strategies mutations in any gene across the genome can be obtained at a rather high speed. However, the differences between the strategies are 1) the precision of the exact site of mutation in a target gene, and 2) the number of off-target mutations affecting other genes than the target gene. Both aspects favour the NBT methods, which provide more precision and fewer off-target mutations. This is in stark contrast to the different status of the two technologies with respect to EU GMO legislation. In the future, this situation is not sustainable for the European plant breeding industry, since it is expected that restrictions on the use of NBTs will be weaker outside Europe. This calls for reconsiderations of the EU legislation of plants generated via NBT mutagenesis.
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170
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Agapito-Tenfen SZ, Okoli AS, Bernstein MJ, Wikmark OG, Myhr AI. Revisiting Risk Governance of GM Plants: The Need to Consider New and Emerging Gene-Editing Techniques. FRONTIERS IN PLANT SCIENCE 2018; 9:1874. [PMID: 30622546 PMCID: PMC6308909 DOI: 10.3389/fpls.2018.01874] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 12/04/2018] [Indexed: 05/14/2023]
Abstract
New and emerging gene-editing techniques make it possible to target specific genes in species with greater speed and specificity than previously possible. Of major relevance for plant breeding, regulators and scientists are discussing how to regulate products developed using these gene-editing techniques. Such discussions include whether to adopt or adapt the current framework for GMO risk governance in evaluating the impacts of gene-edited plants, and derived products, on the environment, human and animal health and society. Product classification or definition is one of several aspects of the current framework being criticized. Further, knowledge gaps related to risk assessments of gene-edited organisms-for example of target and off-target effects of intervention in plant genomes-are also of concern. Resolving these and related aspects of the current framework will involve addressing many subjective, value-laden positions, for example how to specify protection goals through ecosystem service approaches. A process informed by responsible research and innovation practices, involving a broader community of people, organizations, experts, and interest groups, could help scientists, regulators, and other stakeholders address these complex, value-laden concerns related to gene-editing of plants with and for society.
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Affiliation(s)
| | - Arinze S. Okoli
- GenØk - Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
| | | | - Odd-Gunnar Wikmark
- GenØk - Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
- Unit for Environmental Science and Management, North West University, Potchefstroom, South Africa
| | - Anne I. Myhr
- GenØk - Centre for Biosafety, SIVA Innovation Centre, Tromsø, Norway
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171
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Kumlehn J, Pietralla J, Hensel G, Pacher M, Puchta H. The CRISPR/Cas revolution continues: From efficient gene editing for crop breeding to plant synthetic biology. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1127-1153. [PMID: 30387552 DOI: 10.1111/jipb.12734] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/30/2018] [Indexed: 05/18/2023]
Abstract
Since the discovery that nucleases of the bacterial CRISPR (clustered regularly interspaced palindromic repeat)-associated (Cas) system can be used as easily programmable tools for genome engineering, their application massively transformed different areas of plant biology. In this review, we assess the current state of their use for crop breeding to incorporate attractive new agronomical traits into specific cultivars of various crop plants. This can be achieved by the use of Cas9/12 nucleases for double-strand break induction, resulting in mutations by non-homologous recombination. Strategies for performing such experiments - from the design of guide RNA to the use of different transformation technologies - are evaluated. Furthermore, we sum up recent developments regarding the use of nuclease-deficient Cas9/12 proteins, as DNA-binding moieties for targeting different kinds of enzyme activities to specific sites within the genome. Progress in base deamination, transcriptional induction and transcriptional repression, as well as in imaging in plants, is also discussed. As different Cas9/12 enzymes are at hand, the simultaneous application of various enzyme activities, to multiple genomic sites, is now in reach to redirect plant metabolism in a multifunctional manner and pave the way for a new level of plant synthetic biology.
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Affiliation(s)
- Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland OT Gatersleben, Germany
| | - Janine Pietralla
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Goetz Hensel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Seeland OT Gatersleben, Germany
| | - Michael Pacher
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
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