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Sretenovic S, Green Y, Wu Y, Cheng Y, Zhang T, Van Eck J, Qi Y. Genome- and transcriptome-wide off-target analyses of a high-efficiency adenine base editor in tomato. PLANT PHYSIOLOGY 2023; 193:291-303. [PMID: 37315207 DOI: 10.1093/plphys/kiad347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 05/22/2023] [Accepted: 05/26/2023] [Indexed: 06/16/2023]
Abstract
Adenine base editors (ABEs) are valuable, precise genome editing tools in plants. In recent years, the highly promising ADENINE BASE EDITOR8e (ABE8e) was reported for efficient A-to-G editing. However, compared to monocots, comprehensive off-target analyses for ABE8e are lacking in dicots. To determine the occurrence of off-target effects in tomato (Solanum lycopersicum), we assessed ABE8e and a high-fidelity version, ABE8e-HF, at 2 independent target sites in protoplasts, as well as stable T0 lines. Since ABE8e demonstrated higher on-target efficiency than ABE8e-HF in tomato protoplasts, we focused on ABE8e for off-target analyses in T0 lines. We conducted whole-genome sequencing (WGS) of wild-type (WT) tomato plants, green fluorescent protein (GFP)-expressing T0 lines, ABE8e-no-gRNA control T0 lines, and edited T0 lines. No guide RNA (gRNA)-dependent off-target edits were detected. Our data showed an average of approximately 1,200 to 1,500 single-nucleotide variations (SNVs) in either GFP control plants or base-edited plants. Also, no specific enrichment of A-to-G mutations were found in base-edited plants. We also conducted RNA sequencing (RNA-seq) of the same 6 base-edited and 3 GFP control T0 plants. On average, approximately 150 RNA-level SNVs were discovered per plant for either base-edited or GFP controls. Furthermore, we did not find enrichment of a TA motif on mutated adenine in the genomes and transcriptomes in base-edited tomato plants, as opposed to the recent discovery in rice (Oryza sativa). Hence, we could not find evidence for genome- and transcriptome-wide off-target effects by ABE8e in tomato.
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Affiliation(s)
- Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Yumi Green
- The Boyce Thompson Institute, Ithaca, NY 14853, USA
| | - Yuechao Wu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yanhao Cheng
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Joyce Van Eck
- The Boyce Thompson Institute, Ithaca, NY 14853, USA
- Plant Breeding and Genetics Section, Cornell University, Ithaca, NY 14853, 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
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Virus-Induced Gene Editing and Its Applications in Plants. Int J Mol Sci 2022; 23:ijms231810202. [PMID: 36142116 PMCID: PMC9499690 DOI: 10.3390/ijms231810202] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/28/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
CRISPR/Cas-based genome editing technologies, which allow the precise manipulation of plant genomes, have revolutionized plant science and enabled the creation of germplasms with beneficial traits. In order to apply these technologies, CRISPR/Cas reagents must be delivered into plant cells; however, this is limited by tissue culture challenges. Recently, viral vectors have been used to deliver CRISPR/Cas reagents into plant cells. Virus-induced genome editing (VIGE) has emerged as a powerful method with several advantages, including high editing efficiency and a simplified process for generating gene-edited DNA-free plants. Here, we briefly describe CRISPR/Cas-based genome editing. We then focus on VIGE systems and the types of viruses used currently for CRISPR/Cas9 cassette delivery and genome editing. We also highlight recent applications of and advances in VIGE in plants. Finally, we discuss the challenges and potential for VIGE in plants.
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Wu Y, Ren Q, Zhong Z, Liu G, Han Y, Bao Y, Liu L, Xiang S, Liu S, Tang X, Zhou J, Zheng X, Sretenovic S, Zhang T, Qi Y, Zhang Y. Genome-wide analyses of PAM-relaxed Cas9 genome editors reveal substantial off-target effects by ABE8e in rice. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1670-1682. [PMID: 35524459 PMCID: PMC9398351 DOI: 10.1111/pbi.13838] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 04/28/2022] [Indexed: 05/04/2023]
Abstract
PAM-relaxed Cas9 nucleases, cytosine base editors and adenine base editors are promising tools for precise genome editing in plants. However, their genome-wide off-target effects are largely unexplored. Here, we conduct whole-genome sequencing (WGS) analyses of transgenic plants edited by xCas9, Cas9-NGv1, Cas9-NG, SpRY, nCas9-NG-PmCDA1, nSpRY-PmCDA1 and nSpRY-ABE8e in rice. Our results reveal that Cas9 nuclease and base editors, when coupled with the same guide RNA (gRNA), prefer distinct gRNA-dependent off-target sites. De novo generated gRNAs by SpRY editors lead to additional, but insubstantial, off-target mutations. Strikingly, ABE8e results in ~500 genome-wide A-to-G off-target mutations at TA motif sites per transgenic plant. ABE8e's preference for the TA motif is also observed at the target sites. Finally, we investigate the timeline and mechanism of somaclonal variation due to tissue culture, which chiefly contributes to the background mutations. This study provides a comprehensive understanding on the scale and mechanisms of off-target and background mutations occurring during PAM-relaxed genome editing in plants.
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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
- 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
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Qiurong Ren
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Zhaohui Zhong
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou 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
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Yangshuo Han
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou 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
- 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
- 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
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Li Liu
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shuyue Xiang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shuo Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou 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
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - Xu Tang
- Department of BiotechnologySchool of Life Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Jianping Zhou
- 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
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMarylandUSA
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Jiangsu Key Laboratory of Crop Genetics and PhysiologyAgricultural College of Yangzhou 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
- Jiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsYangzhou UniversityYangzhouChina
| | - 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 Sciences and TechnologyCenter for Informational BiologyUniversity of Electronic Science and Technology of ChinaChengduChina
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Dhakate P, Sehgal D, Vaishnavi S, Chandra A, Singh A, Raina SN, Rajpal VR. Comprehending the evolution of gene editing platforms for crop trait improvement. Front Genet 2022; 13:876987. [PMID: 36082000 PMCID: PMC9445674 DOI: 10.3389/fgene.2022.876987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system was initially discovered as an underlying mechanism for conferring adaptive immunity to bacteria and archaea against viruses. Over the past decade, this has been repurposed as a genome-editing tool. Numerous gene editing-based crop improvement technologies involving CRISPR/Cas platforms individually or in combination with next-generation sequencing methods have been developed that have revolutionized plant genome-editing methodologies. Initially, CRISPR/Cas nucleases replaced the earlier used sequence-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs), to address the problem of associated off-targets. The adaptation of this platform led to the development of concepts such as epigenome editing, base editing, and prime editing. Epigenome editing employed epi-effectors to manipulate chromatin structure, while base editing uses base editors to engineer precise changes for trait improvement. Newer technologies such as prime editing have now been developed as a “search-and-replace” tool to engineer all possible single-base changes. Owing to the availability of these, the field of genome editing has evolved rapidly to develop crop plants with improved traits. In this review, we present the evolution of the CRISPR/Cas system into new-age methods of genome engineering across various plant species and the impact they have had on tweaking plant genomes and associated outcomes on crop improvement initiatives.
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Affiliation(s)
- Priyanka Dhakate
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), México-Veracruz, Mexico
| | | | - Atika Chandra
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity Institute of Biotechnology, Amity University, Noida, India
- *Correspondence: Vijay Rani Rajpal, ; Soom Nath Raina,
| | - Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
- *Correspondence: Vijay Rani Rajpal, ; Soom Nath Raina,
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Zeng D, Zheng Z, Liu Y, Liu T, Li T, Liu J, Luo Q, Xue Y, Li S, Chai N, Yu S, Xie X, Liu YG, Zhu Q. Exploring C-to-G and A-to-Y Base Editing in Rice by Using New Vector Tools. Int J Mol Sci 2022; 23:ijms23147990. [PMID: 35887335 PMCID: PMC9318980 DOI: 10.3390/ijms23147990] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 11/18/2022] Open
Abstract
CRISPR/Cas9-based cytosine base editors (CBEs) and adenine base editors (ABEs) can efficiently mediate C-to-T/G-to-A and A-to-G/T-to-C substitutions, respectively; however, achieving base transversions (C-to-G/C-to-A and A-to-T/A-to-C) is challenging and has been rarely studied in plants. Here, we constructed new plant C-to-G base editors (CGBEs) and new A-to-Y (T/C) base editors and explored their base editing characteristics in rice. First, we fused the highly active cytidine deaminase evoFENRY and the PAM-relaxed Cas9-nickase variant Cas9n-NG with rice and human uracil DNA N-glycosylase (rUNG and hUNG), respectively, to construct CGBE-rUNG and CGBE-hUNG vector tools. The analysis of five NG-PAM target sites showed that these CGBEs achieved C-to-G conversions with monoallelic editing efficiencies of up to 27.3% in T0 rice, with major byproducts being insertion/deletion mutations. Moreover, for the A-to-Y (C or T) editing test, we fused the highly active adenosine deaminase TadA8e and the Cas9-nickase variant SpGn (with NG-PAM) with Escherichia coli endonuclease V (EndoV) and human alkyladenine DNA glycosylase (hAAG), respectively, to generate ABE8e-EndoV and ABE8e-hAAG vectors. An assessment of five NG-PAM target sites showed that these two vectors could efficiently produce A-to-G substitutions in a narrow editing window; however, no A-to-Y editing was detected. Interestingly, the ABE8e-EndoV also generated precise small fragment deletions in the editing window from the 5′-deaminated A base to the SpGn cleavage site, suggesting its potential value in producing predictable small-fragment deletion mutations. Overall, we objectively evaluated the editing performance of CGBEs in rice, explored the possibility of A-to-Y editing, and developed a new ABE8e-EndoV tool, thus providing a valuable reference for improving and enriching base editing tools in plants.
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Affiliation(s)
- Dongchang Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Zhiye Zheng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Yuxin Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Taoli Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Tie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Jianhong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Qiyu Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Yang Xue
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Shengting Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Suize Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
| | - Xianrong Xie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China; (D.Z.); (Z.Z.); (Y.L.); (T.L.); (T.L.); (J.L.); (Q.L.); (Y.X.); (S.L.); (N.C.); (S.Y.); (X.X.); (Y.-G.L.)
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
- Correspondence:
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Hua K, Han P, Zhu JK. Improvement of base editors and prime editors advances precision genome engineering in plants. PLANT PHYSIOLOGY 2022; 188:1795-1810. [PMID: 34962995 PMCID: PMC8968349 DOI: 10.1093/plphys/kiab591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 11/22/2021] [Indexed: 05/11/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein (Cas)-mediated gene disruption has revolutionized biomedical research as well as plant and animal breeding. However, most disease-causing mutations and agronomically important genetic variations are single base polymorphisms (single-nucleotide polymorphisms) that require precision genome editing tools for correction of the sequences. Although homology-directed repair of double-stranded breaks (DSBs) can introduce precise changes, such repairs are inefficient in differentiated animal and plant cells. Base editing and prime editing are two recently developed genome engineering approaches that can efficiently introduce precise edits into target sites without requirement of DSB formation or donor DNA templates. They have been applied in several plant species with promising results. Here, we review the extensive literature on improving the efficiency, target scope, and specificity of base editors and prime editors in plants. We also highlight recent progress on base editing in plant organellar genomes and discuss how these precision genome editing tools are advancing basic plant research and crop breeding.
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Huang X, Wang Y, Wang N. Base Editors for Citrus Gene Editing. Front Genome Ed 2022; 4:852867. [PMID: 35296063 PMCID: PMC8919994 DOI: 10.3389/fgeed.2022.852867] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022] Open
Abstract
Base editors, such as adenine base editors (ABE) and cytosine base editors (CBE), provide alternatives for precise genome editing without generating double-strand breaks (DSBs), thus avoiding the risk of genome instability and unpredictable outcomes caused by DNA repair. Precise gene editing mediated by base editors in citrus has not been reported. Here, we have successfully adapted the ABE to edit the TATA box in the promoter region of the canker susceptibility gene LOB1 from TATA to CACA in grapefruit (Citrus paradise) and sweet orange (Citrus sinensis). TATA-edited plants are resistant to the canker pathogen Xanthomonas citri subsp. citri (Xcc). In addition, CBE was successfully used to edit the acetolactate synthase (ALS) gene in citrus. ALS-edited plants were resistant to the herbicide chlorsulfuron. Two ALS-edited plants did not show green fluorescence although the starting construct for transformation contains a GFP expression cassette. The Cas9 gene was undetectable in the herbicide-resistant citrus plants. This indicates that the ALS edited plants are transgene-free, representing the first transgene-free gene-edited citrus using the CRISPR technology. In summary, we have successfully adapted the base editors for precise citrus gene editing. The CBE base editor has been used to generate transgene-free citrus via transient expression.
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Abdallah NA, Hamwieh A, Radwan K, Fouad N, Prakash C. Genome editing techniques in plants: a comprehensive review and future prospects toward zero hunger. GM CROPS & FOOD 2021; 12:601-615. [PMID: 35135438 PMCID: PMC9208631 DOI: 10.1080/21645698.2021.2021724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Promoting sustainable agriculture and improving nutrition are the main united nation sustainable development goals by 2030. New technologies are required to achieve zero hunger, and genome editing technology is the most promising one. In the last decade, genome editing (GE) using the CRISPR/Cas system has attracted researchers as a safer and easy tool for genome editing in several living organisms. GE has revolutionized the field of agriculture by improving biotic and abiotic stresses and yield improvement. GE technologies were developed fast lately to avoid the obstacles that face GM crops. GE technology, depending on site directed nuclease (SDN), is divided into three categories according to the modification methods. Developing transgenic-free edited plants without introducing foreign DNA meet the acceptance and regulatory ratification of several countries. There are several ongoing efforts from different countries that are rapidly expanding to adopt the current technological innovations. This review summarizes the different GE technologies and their application as a way to help in ending hunger.
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Affiliation(s)
- Naglaa A. Abdallah
- Department of Genetics Faculty of Agriculture, Cairo University, Cairo, Egypt
- National Biotechnology Network of Expertise, ASRT, Egypt
| | - Aladdin Hamwieh
- Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled Radwan
- National Biotechnology Network of Expertise, ASRT, Egypt
- Department of Biotechnology, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Nourhan Fouad
- Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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9
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Molla KA, Sretenovic S, Bansal KC, Qi Y. Precise plant genome editing using base editors and prime editors. NATURE PLANTS 2021; 7:1166-1187. [PMID: 34518669 DOI: 10.1038/s41477-021-00991-1] [Citation(s) in RCA: 119] [Impact Index Per Article: 39.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Accepted: 07/26/2021] [Indexed: 05/06/2023]
Abstract
The development of CRISPR-Cas systems has sparked a genome editing revolution in plant genetics and breeding. These sequence-specific RNA-guided nucleases can induce DNA double-stranded breaks, resulting in mutations by imprecise non-homologous end joining (NHEJ) repair or precise DNA sequence replacement by homology-directed repair (HDR). However, HDR is highly inefficient in many plant species, which has greatly limited precise genome editing in plants. To fill the vital gap in precision editing, base editing and prime editing technologies have recently been developed and demonstrated in numerous plant species. These technologies, which are mainly based on Cas9 nickases, can introduce precise changes into the target genome at a single-base resolution. This Review provides a timely overview of the current status of base editors and prime editors in plants, covering both technological developments and biological applications.
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Affiliation(s)
- Kutubuddin A Molla
- Crop Improvement Division, ICAR-National Rice Research Institute, Cuttack, India.
| | - Simon Sretenovic
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, USA
| | - Kailash C Bansal
- The Alliance of Bioversity International and the International Centre for Tropical Agriculture, Asia-India, New Delhi, India
| | - 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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