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Li X, Bu F, Wang L, Kim C, Xue W, Zhang M, Kawabata S, Zhang Q, Li Y, Zhang Y. Optimization of CRISPR-Cas9 system in Eustoma grandiflorum. iScience 2024; 27:109053. [PMID: 38361623 PMCID: PMC10864798 DOI: 10.1016/j.isci.2024.109053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/10/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The optimization of the CRISPR-Cas9 system for enhancing editing efficiency holds significant value in scientific research. In this study, we optimized single guide RNA and Cas9 promoters of the CRISPR-Cas9 vector and established an efficient protoplast isolation and transient transformation system in Eustoma grandiflorum, and we successfully applied the modified CRISPR-Cas9 system to detect editing efficiency of the EgPDS gene. The activity of the EgU6-2 promoter in E. grandiflorum protoplasts was approximately three times higher than that of the GmU6 promoter. This promoter, along with the EgUBQ10 promoter, was applied in the CRISPR-Cas9 cassette, the modified CRISPR-Cas9 vectors that pEgU6-2::sgRNA-2/pEgUBQ10::Cas9-2 editing efficiency was 37.7%, which was 30.3% higher than that of the control, and the types of mutation are base substitutions, small fragment deletions and insertions. Finally we obtained an efficient gene editing vector for E. grandiflorum. This project provides an important technical platform for the study of gene function in E. grandiflorum.
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Affiliation(s)
- Xueqi Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fanqi Bu
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Lishan Wang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Cholmin Kim
- College of Life Science, Northeast Forestry University, Harbin 150040, China
- Branch of Biotechnology, State Academy of Sciences, Pyongyang, the Democratic People’s Republic of Korea
| | - Wanjie Xue
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Man Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Saneyuki Kawabata
- Institute for Sustainable Agroecosystem Services, Graduate School of Agriculture and Life Science, The University of Tokyo, Tokyo, Japan
| | - Qingzhu Zhang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yuhua Li
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yang Zhang
- Key Laboratory of Saline-alkali Vegetation Ecology Restoration (Northeast Forestry University), Ministry of Education, Harbin 150040, China
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Pavese V, Moglia A, Milani AM, Marino LA, Martinez MT, Torello Marinoni D, Botta R, Corredoira E. Advances in Quercus ilex L. breeding: the CRISPR/Cas9 technology via ribonucleoproteins. Front Plant Sci 2024; 15:1323390. [PMID: 38439988 PMCID: PMC10910054 DOI: 10.3389/fpls.2024.1323390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
The CRISPR/Cas9 ribonucleoprotein (RNP)-mediated technology represents a fascinating tool for modifying gene expression or mutagenesis as this system allows for obtaining transgene-free plants, avoiding exogenous DNA integration. Holm oak (Quercus ilex) has an important social, economic, and ecological role in the Mediterranean climate zones of Western Europe and North Africa and is severely affected by oak decline syndrome. Here we report the first example of the application of the CRISPR/Cas9-RNP technology in holm oak. Firstly, we evaluated the protoplast isolation from both in vitro leaves and proembryogenic masses. Proembryogenic masses represented the best material to get high protoplast yield (11 x 106 protoplasts/ml) and viability. Secondly, the protoplast transfection ability was evaluated through a vector expressing green fluorescence protein as marker gene of transfection, reaching a transfection percentage of 62% after 24 hours. CRISPR/Cas9 RNPs were successfully delivered into protoplasts resulting in 5.6% ± 0.5% editing efficiency at phytoene desaturase (pds) target genomic region. Protoplasts were then cultured in semisolid media and, after 45 days in culture, developed embryogenic calli were observed in a Murashige and Skoog media with half concentration of NH4NO3 and KNO3 supplemented with 0.1 mg/L benzylaminopurine and 0.1 mg/L 2,4-dichlorophenoxyacetic acid.
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Affiliation(s)
- Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Anna Maria Milani
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Lorenzo Antonio Marino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Maria Teresa Martinez
- Mision Biologica de Galicia, Sede de Santiago, Consejo Superior de Investigaciones Cientificas, Santiago de Compostela, Spain
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Elena Corredoira
- Mision Biologica de Galicia, Sede de Santiago, Consejo Superior de Investigaciones Cientificas, Santiago de Compostela, Spain
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Subburaj S, Agapito-Tenfen SZ. Establishment of targeted mutagenesis in soybean protoplasts using CRISPR/Cas9 RNP delivery via electro-transfection. Front Plant Sci 2023; 14:1255819. [PMID: 37841627 PMCID: PMC10570537 DOI: 10.3389/fpls.2023.1255819] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/08/2023] [Indexed: 10/17/2023]
Abstract
The soybean (Glycine max L.) is an important crop with high agronomic value. The improvement of agronomic traits through gene editing techniques has broad application prospects in soybean. The polyethylene glycol (PEG)-mediated cell transfection has been successfully used to deliver the CRISPR/Cas9-based ribonucleoprotein (RNP) into soybean protoplasts. However, several downstream analyses or further cell regeneration protocols might be hampered by PEG contamination within the samples. Here in this study, we attempted to transfect CRISPR/Cas9 RNPs into trifoliate leaf-derived soybean protoplasts using Neon electroporation to overcome the need for PEG transfection for the first time. We investigated different electroporation parameters including pulsing voltage (V), strength and duration of pulses regarding protoplast morphology, viability, and delivery of CRISPR/Cas9. Electroporation at various pulsing voltages with 3 pulses and 10 ms per pulse was found optimal for protoplast electro-transfection. Following electro-transfection at various pulsing voltages (500 V, 700 V, 1,000 V, and 1,300 V), intact protoplasts were observed at all treatments. However, the relative frequency of cell viability and initial cell divisions decreased with increasing voltages. Confocal laser scanning microscopy (CLSM) confirmed that the green fluorescent protein (GFP)-tagged Cas9 was successfully internalized into the protoplasts. Targeted deep sequencing results revealed that on-target insertion/deletion (InDel) frequencies were increased with increasing voltages in protoplasts electro-transfected with CRISPR/Cas9 RNPs targeting constitutive pathogen response 5 (CPR5). InDel patterns ranged from +1 bp to -6 bp at three different target sites in CPR5 locus with frequencies ranging from 3.8% to 8.1% following electro-transfection at 1,300 V and 2.1% to 3.8% for 700 V and 1,000 V, respectively. Taken together, our results demonstrate that the CRISPR/Cas9 RNP system can be delivered into soybean protoplasts by the Neon electroporation system for efficient and effective gene editing. The electro-transfection system developed in this study would also further facilitate and serve as an alternative delivery method for DNA-free genome editing of soybean and other related species for genetic screens and potential trait improvement.
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Affiliation(s)
| | - Sarah Zanon Agapito-Tenfen
- NORCE Norwegian Research Centre AS, Climate & Environment Department, Siva Innovasjonssenter, Tromsø, Norway
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Nawade B, Bosamia TC, Lee JH, Jang JH, Lee OR. Genome-wide characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response. Front Plant Sci 2023; 14:1216082. [PMID: 37745995 PMCID: PMC10514519 DOI: 10.3389/fpls.2023.1216082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 08/22/2023] [Indexed: 09/26/2023]
Abstract
The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified 14 genes from the DMP family in soybean (Glycine max) and characterized their physiochemical properties, subcellular location, gene structure, and promoter regions using bioinformatics tools. Additionally, their tissue-specific and stress-responsive expressions were analyzed using publicly available transcriptome data. Phylogenetic analysis of 198 DMPs from monocots and dicots revealed six clades, with clade-I encoding senescence-related AtDMP1/2 orthologues and clade-II including pollen-specific AtDMP8/9 orthologues. The largest clade, clade-III, predominantly included monocot DMPs, while monocot- and dicot-specific DMPs were assembled in clade-IV and clade-VI, respectively. Evolutionary analysis suggests that soybean GmDMPs underwent purifying selection during evolution. Using 68 transcriptome datasets, expression profiling revealed expression in diverse tissues and distinct responses to abiotic and biotic stresses. The genes Glyma.09G237500 and Glyma.18G098300 showed pistil-abundant expression by qPCR, suggesting they could be potential targets for female organ-mediated haploid induction. Furthermore, cis-acting regulatory elements primarily related to stress-, hormone-, and light-induced pathways regulate GmDMPs, which is consistent with their divergent expression and suggests involvement in growth and stress responses. Overall, our study provides a comprehensive report on the soybean GmDMP family and a framework for further biological functional analysis of DMP genes in soybean or other crops.
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Affiliation(s)
- Bhagwat Nawade
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Tejas C. Bosamia
- Plant Omics Division, Council of Scientific and Industrial Research-Central Salt and Marine Chemical Research Institute (CSIR-CSMCRI), Bhavnagar, Gujarat, India
| | - Jae Hyun Lee
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Jin Hoon Jang
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
| | - Ok Ran Lee
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju, Republic of Korea
- Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju, Republic of Korea
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Thevendran R, Maheswaran S. Recognizing CRISPR as the new age disease-modifying drug: Strategies to bioengineer CRISPR/Cas for direct in vivo delivery. Biotechnol J 2023; 18:e2300077. [PMID: 37179485 DOI: 10.1002/biot.202300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 05/07/2023] [Accepted: 05/10/2023] [Indexed: 05/15/2023]
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) have established itself as a frontier technology in genetic engineering. Researchers have successfully used the CRISPR/Cas system as precise gene editing tools and have further expanded their scope beyond both imaging and diagnostic applications. The most prominent utility of CRISPR is its capacity for gene therapy, serving as the contemporary, disease-modifying drug at the genetic level of human medical disorders. Correcting these diseases using CRISPR-based gene editing has developed to the extent of preclinical trials and possible patient treatments. A major impediment in actualizing this is the complications associated with in vivo delivery of the CRISPR/Cas complex. Currently, only the viral vectors (e.g., lentivirus) and non-viral encapsulation (e.g., lipid particles, polymer-based, and gold nanoparticles) techniques have been extensively reviewed, neglecting the efficiency of direct delivery. However, the direct delivery of CRISPR/Cas for in vivo gene editing therapies is an intricate process with numerous drawbacks. Hence, this paper discusses in detail both the need and the strategies that can potentially improve the direct delivery aspects of CRISPR/Cas biomolecules for gene therapy of human diseases. Here, we focus on enhancing the molecular and functional features of the CRISPR/Cas system for targeted in vivo delivery such as on-site localization, internalization, reduced immunogenicity, and better in vivo stability. We additionally emphasize the CRISPR/Cas complex as a multifaceted, biomolecular vehicle for co-delivery with therapeutic agents in targeted disease treatments. The delivery formats of efficient CRISPR/Cas systems for human gene editing are also briefly elaborated.
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Affiliation(s)
- Ramesh Thevendran
- Department of Biotechnology, Faculty of Applied Science, AIMST University, Bedong, Kedah, Malaysia
| | - Solayappan Maheswaran
- Department of Biotechnology, Faculty of Applied Science, AIMST University, Bedong, Kedah, Malaysia
- Centre of Excellence for Nanotechnology and Nanomedicine (CoExNano), AIMST University, Bedong, Kedah, Malaysia
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Su H, Wang Y, Xu J, Omar AA, Grosser JW, Calovic M, Zhang L, Feng Y, Vakulskas CA, Wang N. Generation of the transgene-free canker-resistant Citrus sinensis using Cas12a/crRNA ribonucleoprotein in the T0 generation. Nat Commun 2023; 14:3957. [PMID: 37402755 DOI: 10.1038/s41467-023-39714-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/26/2023] [Indexed: 07/06/2023] Open
Abstract
Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is a destructive citrus disease worldwide. Generating disease-resistant cultivars is the most effective, environmentally friendly and economic approach for disease control. However, citrus traditional breeding is lengthy and laborious. Here, we develop transgene-free canker-resistant Citrus sinensis lines in the T0 generation within 10 months through transformation of embryogenic protoplasts with Cas12a/crRNA ribonucleoprotein to edit the canker susceptibility gene CsLOB1. Among the 39 regenerated lines, 38 are biallelic/homozygous mutants, demonstrating a 97.4% biallelic/homozygous mutation rate. No off-target mutations are detected in the edited lines. Canker resistance of the cslob1-edited lines results from both abolishing canker symptoms and inhibiting Xcc growth. The transgene-free canker-resistant C. sinensis lines have received regulatory approval by USDA APHIS and are exempted from EPA regulation. This study provides a sustainable and efficient citrus canker control solution and presents an efficient transgene-free genome-editing strategy for citrus and other crops.
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Affiliation(s)
- Hang Su
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Yuanchun Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Jin Xu
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Ahmad A Omar
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
- Biochemistry Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Jude W Grosser
- Citrus Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Milica Calovic
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | - Liyang Zhang
- Integrated DNA Technologies, Inc, Coralville, IA, USA
| | - Yu Feng
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA
| | | | - Nian Wang
- Citrus Research and Education Center, Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Lake Alfred, FL, USA.
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Zhao Y, Yang D, Liu Y, Han F, Li Z. A highly efficient genetic transformation system for broccoli and subcellular localization. Front Plant Sci 2023; 14:1091588. [PMID: 36937998 PMCID: PMC10018207 DOI: 10.3389/fpls.2023.1091588] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Agrobacterium-mediated genetic transformation has been widely used for the identification of functional genes and regulatory and developmental mechanisms in plants. However, there are still some problems of low genetic transformation efficiency and high genotype dependence in cruciferous crops. METHODS In this study, broccoli, a worldwide Brassica crop, was used to investigate the effects of genotype, explant type, concentration of hygromycin B used during seedling selection, overexpression vector type, RNAi and CRISPR/cas9 on the genetic transformation efficiency. At the same time, two vectors, PHG-031350 and PHG-CRa, were used for subcellular localization of the glucoraphanin synthesis-related gene FMOGS-OX5 and clubroot resistance gene by a PEG-Ca2+-mediated transient transformation system for broccoli protoplasts. Finally, the Agrobacterium-mediated genetic transformation system of broccoli was optimized and improved. RESULTS AND DISCUSSION This study showed that hypocotyl explants are more suitable for Agrobacterium-mediated transgene and CRISPR/Cas9 gene editing of broccoli. In contrast to previous studies, we found that 5 mg/L hygromycin B was more advantageous for the selection of resistant broccoli sprouts, and genotype 19B42 reached the highest transformation rate of 26.96%, which is higher than that in Brassica oleracea crops. In addition, the inbred line 19B42 successfully achieved high genetic transformation of overexpression, RNAi and CRISPR/Cas9 vectors; thus, it is powerful recipient material for the genetic transformation of broccoli. Subcellular localization proved that the glucoraphanin metabolism-related gene Bol031350 and clubroot resistance gene CRa were both expressed in the cytoplasm and nucleus, which provided a scientific basis for studying the regulation of glucosinolate metabolism and clubroot resistance in cruciferous crops. Therefore, these findings will provide new insight into the improvement of the genetic transformation and molecular breeding of Brassica oleracea crops.
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Poddar S, Tanaka J, Running KLD, Kariyawasam GK, Faris JD, Friesen TL, Cho MJ, Cate JHD, Staskawicz B. Optimization of highly efficient exogenous-DNA-free Cas9-ribonucleoprotein mediated gene editing in disease susceptibility loci in wheat ( Triticum aestivum L.). Front Plant Sci 2023; 13:1084700. [PMID: 36704157 PMCID: PMC9872142 DOI: 10.3389/fpls.2022.1084700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
The advancement of precision engineering for crop trait improvement is important in the face of rapid population growth, climate change, and disease. To this end, targeted double-stranded break technology using RNA-guided Cas9 has been adopted widely for genome editing in plants. Agrobacterium or particle bombardment-based delivery of plasmids encoding Cas9 and guide RNA (gRNA) is common, but requires optimization of expression and often results in random integration of plasmid DNA into the plant genome. Recent advances have described gene editing by the delivery of Cas9 and gRNA as pre-assembled ribonucleoproteins (RNPs) into various plant tissues, but with moderate efficiency in resulting regenerated plants. In this report we describe significant improvements to Cas9-RNP mediated gene editing in wheat. We demonstrate that Cas9-RNP assays in protoplasts are a fast and effective tool for rational selection of optimal gRNAs for gene editing in regenerable immature embryos (IEs), and that high temperature treatment enhances gene editing rates in both tissue types. We also show that Cas9-mediated editing persists for at least 14 days in gold particle bombarded wheat IEs. The regenerated edited wheat plants in this work are recovered at high rates in the absence of exogenous DNA and selection. With this method, we produce knockouts of a set of three homoeologous genes and two pathogenic effector susceptibility genes, engineering insensitivity to corresponding necrotrophic effectors produced by Parastagonospora nodorum. The establishment of highly efficient, exogenous DNA-free gene editing technology holds promise for accelerated trait diversity production in an expansive array of crops.
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Affiliation(s)
- Snigdha Poddar
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Jaclyn Tanaka
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | | | - Gayan K. Kariyawasam
- Department of Plant Pathology, North Dakota State University, Fargo, ND, United States
| | - Justin D. Faris
- United States Department of Agriculture (USDA)-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Timothy L. Friesen
- United States Department of Agriculture (USDA)-Agricultural Research Service, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, United States
| | - Myeong-Je Cho
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jamie H. D. Cate
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, United States
| | - Brian Staskawicz
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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Rigoulot SB, Barco B, Zhang Y, Zhang C, Meier KA, Moore M, Fabish J, Whinna R, Park J, Seaberry EM, Gopalan A, Dong S, Chen Z, Que Q. Automated, High-Throughput Protoplast Transfection for Gene Editing and Transgene Expression Studies. Methods Mol Biol 2023; 2653:129-149. [PMID: 36995624 DOI: 10.1007/978-1-0716-3131-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
In an era of cost-efficient gene synthesis and high-throughput construct assembly, the onus of scientific experimentation is on the rate of in vivo testing for the identification of top performing candidates or designs. Assay platforms that are relevant to the species of interest and in the tissue of choice are highly desirable. A protoplast isolation and transfection method that is compatible with a large repertoire of species and tissues would be the platform of choice. A necessary aspect of this high-throughput screening approach is the need to handle many delicate protoplast samples at the same time, which is a bottleneck for manual operation. Such bottlenecks can be mitigated with the use of automated liquid handlers for the execution of protoplast transfection steps. The method described within this chapter utilizes a 96-well head for simultaneous, high-throughput initiation of transfection. While initially developed and optimized for use with etiolated maize leaf protoplasts, the automated protocol has also been demonstrated to be compatible with other established protoplast systems, such as soybean immature embryo derived protoplast, similarly described within. This chapter also includes instructions for a sample randomization design to reduce the impact of edge effects, which might be present when microplates are used for fluorescence readout following transfection. We also describe a streamlined, expedient, and cost-effective protocol for determining gene editing efficiencies using the T7E1 endonuclease cleavage assay with a publicly available image analysis tool.
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Affiliation(s)
| | - Brenden Barco
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Yingxiao Zhang
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Chengjin Zhang
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Kerry A Meier
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Matthew Moore
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Jonathan Fabish
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Rachel Whinna
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Jeongmoo Park
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Erin M Seaberry
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Aditya Gopalan
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Shujie Dong
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Zhongying Chen
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Qiudeng Que
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA.
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Nuzzo F, Gambino G, Perrone I. Unlocking grapevine in vitro regeneration: Issues and perspectives for genetic improvement and functional genomic studies. Plant Physiol Biochem 2022; 193:99-109. [PMID: 36343465 DOI: 10.1016/j.plaphy.2022.10.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 10/24/2022] [Accepted: 10/27/2022] [Indexed: 06/16/2023]
Abstract
In vitro plant regeneration is a pivotal process in genetic engineering to obtain large numbers of transgenic, cisgenic and gene edited plants in the frame of functional gene or genetic improvement studies. However, several issues emerge as regeneration is not universally possible across the plant kingdom and many variables must be considered. In grapevine (Vitis spp.), as in other woody and fruit tree species, the regeneration process is impaired by a recalcitrance that depends on numerous factors such as genotype and explant-dependent responses. This is one of the major obstacles in developing gene editing approaches and functional genome studies in grapevine and it is therefore crucial to understand how to achieve efficient regeneration across different genotypes. Further issues that emerge in regeneration need to be addressed, such as somaclonal mutations which do not allow the regeneration of individuals identical to the original mother plant, an essential factor for commercial use of the improved grapevines obtained through the New Breeding Techniques. Over the years, the evolution of protocols to achieve plant regeneration has relied mainly on optimizing protocols for genotypes of interest whilst nowadays with new genomic data available there is an emerging opportunity to have a clearer picture of its molecular regulation. The goal of this review is to discuss the latest information available about different aspects of grapevine in vitro regeneration, to address the main factors that can impair the efficiency of the plant regeneration process and cause post-regeneration problems and to propose strategies for investigating and solving them.
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Affiliation(s)
- Floriana Nuzzo
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
| | - Giorgio Gambino
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy.
| | - Irene Perrone
- Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Strada Delle Cacce 73, 10135, Torino, Italy
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Fierlej Y, Jacquier NMA, Guille L, Just J, Montes E, Richard C, Loue-Manifel J, Depège-Fargeix N, Gaillard A, Widiez T, Rogowsky PM. Evaluation of genome and base editing tools in maize protoplasts. Front Plant Sci 2022; 13:1010030. [PMID: 36518521 PMCID: PMC9744195 DOI: 10.3389/fpls.2022.1010030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 11/03/2022] [Indexed: 06/17/2023]
Abstract
INTRODUCTION Despite its rapid worldwide adoption as an efficient mutagenesis tool, plant genome editing remains a labor-intensive process requiring often several months of in vitro culture to obtain mutant plantlets. To avoid a waste in time and money and to test, in only a few days, the efficiency of molecular constructs or novel Cas9 variants (clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9) prior to stable transformation, rapid analysis tools are helpful. METHODS To this end, a streamlined maize protoplast system for transient expression of CRISPR/Cas9 tools coupled to NGS (next generation sequencing) analysis and a novel bioinformatics pipeline was established. RESULTS AND DISCUSSION Mutation types found with high frequency in maize leaf protoplasts had a trend to be the ones observed after stable transformation of immature maize embryos. The protoplast system also allowed to conclude that modifications of the sgRNA (single guide RNA) scaffold leave little room for improvement, that relaxed PAM (protospacer adjacent motif) sites increase the choice of target sites for genome editing, albeit with decreased frequency, and that efficient base editing in maize could be achieved for certain but not all target sites. Phenotypic analysis of base edited mutant maize plants demonstrated that the introduction of a stop codon but not the mutation of a serine predicted to be phosphorylated in the bHLH (basic helix loop helix) transcription factor ZmICEa (INDUCER OF CBF EXPRESSIONa) caused abnormal stomata, pale leaves and eventual plant death two months after sowing.
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Affiliation(s)
- Yannick Fierlej
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
- Department Research and Development, MAS Seeds, Haut-Mauco, France
| | - Nathanaël M. A. Jacquier
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Loïc Guille
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Jérémy Just
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Emilie Montes
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Christelle Richard
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Jeanne Loue-Manifel
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Nathalie Depège-Fargeix
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Antoine Gaillard
- Department Research and Development, MAS Seeds, Haut-Mauco, France
| | - Thomas Widiez
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
| | - Peter M. Rogowsky
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, Ecole Normale Supérieure (ENS) de Lyon, Université Claude Bernard (UCB) Lyon 1, Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l'Agriculture, l'alimentation et l'Environnement (INRAE), Lyon, France
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12
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Chu P, Agapito-Tenfen SZ. Unintended Genomic Outcomes in Current and Next Generation GM Techniques: A Systematic Review. Plants (Basel) 2022; 11:plants11212997. [PMID: 36365450 PMCID: PMC9655061 DOI: 10.3390/plants11212997] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 05/27/2023]
Abstract
Classical genetic engineering and new genome editing techniques, especially the CRISPR/Cas technology, increase the possibilities for modifying the genetic material in organisms. These technologies have the potential to provide novel agricultural traits, including modified microorganisms and environmental applications. However, legitimate safety concerns arise from the unintended genetic modifications (GM) that have been reported as side-effects of such techniques. Here, we systematically review the scientific literature for studies that have investigated unintended genomic alterations in plants modified by the following GM techniques: Agrobacterium tumefaciens-mediated gene transfer, biolistic bombardment, and CRISPR-Cas9 delivered via Agrobacterium-mediated gene transfer (DNA-based), biolistic bombardment (DNA-based) and as ribonucleoprotein complexes (RNPs). The results of our literature review show that the impact of such techniques in host genomes varies from small nucleotide polymorphisms to large genomic variation, such as segmental duplication, chromosome truncation, trisomy, chromothripsis, breakage fusion bridge, including large rearrangements of DNA vector-backbone sequences. We have also reviewed the type of analytical method applied to investigate the genomic alterations and found that only five articles used whole genome sequencing in their analysis methods. In addition, larger structural variations detected in some studies would not be possible without long-read sequencing strategies, which shows a potential underestimation of such effects in the literature. As new technologies are constantly evolving, a more thorough examination of prospective analytical methods should be conducted in the future. This will provide regulators working in the field of genetically modified and gene-edited organisms with valuable information on the ability to detect and identify genomic interventions.
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13
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Gouthu S, Mandelli C, Eubanks BA, Deluc LG. Transgene-free genome editing and RNAi ectopic application in fruit trees: Potential and limitations. Front Plant Sci 2022; 13:979742. [PMID: 36325537 PMCID: PMC9621297 DOI: 10.3389/fpls.2022.979742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 09/20/2022] [Indexed: 06/16/2023]
Abstract
For the past fifteen years, significant research advances in sequencing technology have led to a substantial increase in fruit tree genomic resources and databases with a massive number of OMICS datasets (transcriptomic, proteomics, metabolomics), helping to find associations between gene(s) and performance traits. Meanwhile, new technology tools have emerged for gain- and loss-of-function studies, specifically in gene silencing and developing tractable plant models for genetic transformation. Additionally, innovative and adapted transformation protocols have optimized genetic engineering in most fruit trees. The recent explosion of new gene-editing tools allows for broadening opportunities for functional studies in fruit trees. Yet, the fruit tree research community has not fully embraced these new technologies to provide large-scale genome characterizations as in cereals and other staple food crops. Instead, recent research efforts in the fruit trees appear to focus on two primary translational tools: transgene-free gene editing via Ribonucleoprotein (RNP) delivery and the ectopic application of RNA-based products in the field for crop protection. The inherent nature of the propagation system and the long juvenile phase of most fruit trees are significant justifications for the first technology. The second approach might have the public favor regarding sustainability and an eco-friendlier environment for a crop production system that could potentially replace the use of chemicals. Regardless of their potential, both technologies still depend on the foundational knowledge of gene-to-trait relationships generated from basic genetic studies. Therefore, we will discuss the status of gene silencing and DNA-based gene editing techniques for functional studies in fruit trees followed by the potential and limitations of their translational tools (RNP delivery and RNA-based products) in the context of crop production.
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Affiliation(s)
- Satyanarayana Gouthu
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Christian Mandelli
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
| | - Britt A. Eubanks
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
| | - Laurent G. Deluc
- Department of Horticulture, Oregon State University, Corvallis, OR, United States
- Oregon Wine Research Institute, Oregon State University, Corvallis, OR, United States
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14
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Rustgi S, Naveed S, Windham J, Zhang H, Demirer GS. Plant biomacromolecule delivery methods in the 21st century. Front Genome Ed 2022; 4:1011934. [PMID: 36311974 PMCID: PMC9614364 DOI: 10.3389/fgeed.2022.1011934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 10/03/2022] [Indexed: 11/06/2022] Open
Abstract
The 21st century witnessed a boom in plant genomics and gene characterization studies through RNA interference and site-directed mutagenesis. Specifically, the last 15 years marked a rapid increase in discovering and implementing different genome editing techniques. Methods to deliver gene editing reagents have also attempted to keep pace with the discovery and implementation of gene editing tools in plants. As a result, various transient/stable, quick/lengthy, expensive (requiring specialized equipment)/inexpensive, and versatile/specific (species, developmental stage, or tissue) methods were developed. A brief account of these methods with emphasis on recent developments is provided in this review article. Additionally, the strengths and limitations of each method are listed to allow the reader to select the most appropriate method for their specific studies. Finally, a perspective for future developments and needs in this research area is presented.
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Affiliation(s)
- Sachin Rustgi
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States,*Correspondence: Sachin Rustgi, ; Gözde S. Demirer,
| | - Salman Naveed
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
| | - Jonathan Windham
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC, United States
| | - Huan Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Gözde S. Demirer
- Department of Chemical Engineering, California Institute of Technology, Pasadena, CA, United States,*Correspondence: Sachin Rustgi, ; Gözde S. Demirer,
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15
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Aksoy E, Yildirim K, Kavas M, Kayihan C, Yerlikaya BA, Çalik I, Sevgen İ, Demirel U. General guidelines for CRISPR/Cas-based genome editing in plants. Mol Biol Rep 2022; 49:12151-12164. [DOI: 10.1007/s11033-022-07773-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
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16
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Biswas S, Bridgeland A, Irum S, Thomson MJ, Septiningsih EM. Optimization of Prime Editing in Rice, Peanut, Chickpea, and Cowpea Protoplasts by Restoration of GFP Activity. Int J Mol Sci 2022; 23:9809. [PMID: 36077206 PMCID: PMC9456013 DOI: 10.3390/ijms23179809] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/19/2022] [Accepted: 08/26/2022] [Indexed: 01/23/2023] Open
Abstract
Precise editing of the plant genome has long been desired for functional genomic research and crop breeding. Prime editing is a newly developed precise editing technology based on CRISPR-Cas9, which uses an engineered reverse transcriptase (RT), a catalytically impaired Cas9 endonuclease (nCas9), and a prime editing guide RNA (pegRNA). In addition, prime editing has a wider range of editing types than base editing and can produce nearly all types of edits. Although prime editing was first established in human cells, it has recently been applied to plants. As a relatively new technique, optimization will be needed to increase the editing efficiency in different crops. In this study, we successfully edited a mutant GFP in rice, peanut, chickpea, and cowpea protoplasts. In rice, up to 16 times higher editing efficiency was achieved with a dual pegRNA than the single pegRNA containing vectors. Edited-mutant GFP protoplasts have also been obtained in peanut, chickpea, and cowpea after transformation with the dual pegRNA vectors, albeit with much lower editing efficiency than in rice, ranging from 0.2% to 0.5%. These initial results promise to expedite the application of prime editing in legume breeding programs to accelerate crop improvement.
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Affiliation(s)
- Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Aya Bridgeland
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Samra Irum
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA
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17
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Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. Front Plant Sci 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
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Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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18
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Subburaj S, Zanatta CB, Nunn JAL, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. A DNA-Free Editing Platform for Genetic Screens in Soybean via CRISPR/Cas9 Ribonucleoprotein Delivery. Front Plant Sci 2022; 13:939997. [PMID: 35903231 PMCID: PMC9315425 DOI: 10.3389/fpls.2022.939997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/06/2023]
Abstract
CRISPR/Cas9-based ribonucleoprotein (RNP)-mediated system has the property of minimizing the effects related to the unwanted introduction of vector DNA and random integration of recombinant DNA. Here, we describe a platform based on the direct delivery of Cas9 RNPs to soybean protoplasts for genetic screens in knockout gene-edited soybean lines without the transfection of DNA vectors. The platform is based on the isolation of soybean protoplasts and delivery of Cas RNP complex. To empirically test our platform, we have chosen a model gene from the soybean genetic toolbox. We have used five different guide RNA (gRNA) sequences that targeted the constitutive pathogen response 5 (CPR5) gene associated with the growth of trichomes in soybean. In addition, efficient protoplast transformation, concentration, and ratio of Cas9 and gRNAs were optimized for soybean for the first time. Targeted mutagenesis insertion and deletion frequency and sequences were analyzed using both Sanger and targeted deep sequencing strategies. We were able to identify different mutation patterns within insertions and deletions (InDels) between + 5 nt and -30 bp and mutation frequency ranging from 4.2 to 18.1% in the GmCPR5 locus. Our results showed that DNA-free delivery of Cas9 complexes to protoplasts is a useful approach to perform early-stage genetic screens and anticipated analysis of Cas9 activity in soybeans.
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Affiliation(s)
- Saminathan Subburaj
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
| | - Caroline Bedin Zanatta
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Jennifer A. L. Nunn
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Sarah Zanon Agapito-Tenfen
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
- *Correspondence: Sarah Zanon Agapito-Tenfen,
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Augustine SM, Cherian AV, Seiling K, Di Fiore S, Raven N, Commandeur U, Schillberg S. Targeted mutagenesis in Nicotiana tabacum ADF gene using shockwave-mediated ribonucleoprotein delivery increases osmotic stress tolerance. Physiol Plant 2021; 173:993-1007. [PMID: 34265107 DOI: 10.1111/ppl.13499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
DNA-free genome editing involves the direct introduction of ribonucleoprotein (RNP) complexes into cells, but this strategy has rarely been successful in plants. In the present study, we describe a new technique for the introduction of RNPs into plant cells involving the generation of cavitation bubbles using a pulsed laser. The resulting shockwave achieves the efficient transfection of walled cells in tissue explants by creating transient membrane pores. RNP-containing cells were rapidly identified by fluorescence microscopy, followed by regeneration and the screening of mutant plants by high-resolution melt analysis. We used this technique in Nicotiana tabacum to target the endogenous phytoene desaturase (PDS) and actin depolymerizing factor (ADF) genes. Genome-edited plants were produced with an efficiency of 35.2% for PDS and 16.5% for ADF. Further we evaluated the physiological, cellular and molecular effects of ADF mutations in T2 mutant plants under drought and salinity stress. The results suggest that ADF acts as a key regulator of osmotic stress tolerance in plants.
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Affiliation(s)
- Sruthy Maria Augustine
- Institute of Molecular Biotechnology, RWTH Aachen University, Worringer Weg 1, Aachen, Germany
- Department of Plant breeding, IFZ Research Center for Biosystems, Land Use and Nutrition, Justus Liebig University, Heinrich-Buff-Ring 26, Giessen, Germany
| | - Anoop Vadakan Cherian
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, Aachen, Germany
- Center for Infection and Genomics of the Lung (CIGL), Justus-Liebig-Universität Gießen - Institut für Klinische Immunologie und Transfusionsmedizin, Aulweg 132, Giessen, Germany
| | - Kerstin Seiling
- Institute of Molecular Biotechnology, RWTH Aachen University, Worringer Weg 1, Aachen, Germany
- Institute for Anatomy and Molecular neurobiology, Universitätsklinikum Münster, Vesaliusweg 2-4, Münster, Germany
| | - Stefano Di Fiore
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, Aachen, Germany
| | - Nicole Raven
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, Aachen, Germany
| | - Ulrich Commandeur
- Institute of Molecular Biotechnology, RWTH Aachen University, Worringer Weg 1, Aachen, Germany
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstraße 6, Aachen, Germany
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20
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Dong S, Qin YL, Vakulskas CA, Collingwood MA, Marand M, Rigoulot S, Zhu L, Jiang Y, Gu W, Fan C, Mangum A, Chen Z, Yarnall M, Zhong H, Elumalai S, Shi L, Que Q. Efficient Targeted Mutagenesis Mediated by CRISPR-Cas12a Ribonucleoprotein Complexes in Maize. Front Genome Ed 2021; 3:670529. [PMID: 34713259 PMCID: PMC8525364 DOI: 10.3389/fgeed.2021.670529] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/14/2021] [Indexed: 12/26/2022] Open
Abstract
Recent advances in the development of CRISPR-Cas genome editing technologies have made it possible to perform targeted mutagenesis and precise gene replacement in crop plants. CRISPR-Cas9 and CRISPR-Cas12a are two main types of widely used genome editing systems. However, when CRISPR-Cas12a editing machinery is expressed from a transgene, some chromosomal targets encountered low editing frequency in important crops like maize and soybean. Here, we report efficient methods to directly generate genome edited lines by delivering Cas12a-gRNA ribonucleoprotein complex (RNP) to immature maize embryos through particle bombardment in an elite maize variety. Genome edited lines were obtained at ~7% frequency without any selection during regeneration via biolistic delivery of Cas12a RNP into immature embryos. Strikingly, the gene editing rate was increased to 60% on average and up to 100% in some experiments when the Cas12a RNP was co-delivered with a PMI selectable marker gene cassette and the induced callus cultures were selected with mannose. We also show that use of higher activity Cas12a mutants resulted in improved editing efficiency in more recalcitrant target sequence. The advances described here provide useful tools for genetic improvement of maize.
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Affiliation(s)
- Shujie Dong
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Yinping Lucy Qin
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | | | | | - Mariam Marand
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Stephen Rigoulot
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Ling Zhu
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Yaping Jiang
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Weining Gu
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Chunyang Fan
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Anna Mangum
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Zhongying Chen
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Michele Yarnall
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Heng Zhong
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Sivamani Elumalai
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Liang Shi
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
| | - Qiudeng Que
- Syngenta Crop Protection, Research Triangle Park, Durham, NC, United States
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21
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Tussipkan D, Manabayeva SA. Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops. Front Plant Sci 2021; 12:747476. [PMID: 34764969 PMCID: PMC8576567 DOI: 10.3389/fpls.2021.747476] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/04/2021] [Indexed: 05/07/2023]
Abstract
New breeding technologies have not only revolutionized biological science, but have also been employed to generate transgene-free products. Genome editing is a powerful technology that has been used to modify genomes of several important crops. This review describes the basic mechanisms, advantages and disadvantages of genome editing systems, such as ZFNs, TALENs, and CRISPR/Cas. Secondly, we summarize in detail all studies of the CRISPR/Cas system applied to potato and other tuber crops, such as sweet potato, cassava, yam, and carrot. Genes associated with self-incompatibility, abiotic-biotic resistance, nutrient-antinutrient content, and post-harvest factors targeted utilizing the CRISPR/Cas system are analyzed in this review. We hope that this review provides fundamental information that will be useful for future breeding of tuber crops to develop novel cultivars.
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Affiliation(s)
| | - Shuga A. Manabayeva
- Plant Genetic Engineering Laboratory, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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Fiaz S, Ahmar S, Saeed S, Riaz A, Mora-Poblete F, Jung KH. Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security. Int J Mol Sci 2021; 22:5585. [PMID: 34070430 PMCID: PMC8197453 DOI: 10.3390/ijms22115585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Sajjad Saeed
- Department of Forestry and Wildlife Management, University of Haripur, Haripur 22620, Pakistan
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
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Amritha PP, Shah JM. Can genetic engineering-based methods for gene function identification be eclipsed by genome editing in plants? A comparison of methodologies. Mol Genet Genomics 2021; 296:485-500. [PMID: 33751237 DOI: 10.1007/s00438-021-01769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Finding and explaining the functions of genes in plants have promising applications in crop improvement and bioprospecting and hence, it is important to compare various techniques available for gene function identification in plants. Today, the most popular technology among researchers to identify the functions of genes is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-based genome editing method. But by no means can we say that CRISPR/Cas9 is the go-to method for all purposes. It comes with its own baggage. Researchers will agree and have lived through at least seven more technologies deployed to find the functions of genes, which come under three umbrellas: 1. genetic engineering, 2. transient expression, and 3. chemical/physical mutagenesis. Each of the methods evolved when the previous one ran into an insurmountable problem. In this review, we compare the eight technologies against one another on 14 parameters. This review lays bare the pros and cons, and similarities and dissimilarities of various methods. Every method comes with its advantages and disadvantages. For example, the CRISPR/Cas9-based genome editing is an excellent method for modifying gene sequences, creating allelic versions of genes, thereby aiding the understanding of gene function. But it comes with the baggage of unwanted or off-target mutations. Then, we have methods based on random or targeted knockout of the gene, knockdown, and overexpression of the gene. Targeted disruption of genes is required for complete knockout of gene function, which may not be accomplished by editing. We have also discussed the strategies to overcome the shortcomings of the targeted gene-knockout and the CRISPR/Cas9-based methods. This review serves as a comprehensive guide towards the understanding and comparison of various technologies available for gene function identification in plants and hence, it will find application for crop improvement and bioprospecting related research.
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Affiliation(s)
- P P Amritha
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India.
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Zhang Y, Iaffaldano B, Qi Y. CRISPR ribonucleoprotein-mediated genetic engineering in plants. Plant Commun 2021; 2:100168. [PMID: 33898980 PMCID: PMC8060726 DOI: 10.1016/j.xplc.2021.100168] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 05/15/2023]
Abstract
CRISPR-derived biotechnologies have revolutionized the genetic engineering field and have been widely applied in basic plant research and crop improvement. Commonly used Agrobacterium- or particle bombardment-mediated transformation approaches for the delivery of plasmid-encoded CRISPR reagents can result in the integration of exogenous recombinant DNA and potential off-target mutagenesis. Editing efficiency is also highly dependent on the design of the expression cassette and its genomic insertion site. Genetic engineering using CRISPR ribonucleoproteins (RNPs) has become an attractive approach with many advantages: DNA/transgene-free editing, minimal off-target effects, and reduced toxicity due to the rapid degradation of RNPs and the ability to titrate their dosage while maintaining high editing efficiency. Although RNP-mediated genetic engineering has been demonstrated in many plant species, its editing efficiency remains modest, and its application in many species is limited by difficulties in plant regeneration and selection. In this review, we summarize current developments and challenges in RNP-mediated genetic engineering of plants and provide future research directions to broaden the use of this technology.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Brian Iaffaldano
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, 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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Jeong YY, Lee HY, Kim SW, Noh YS, Seo PJ. Optimization of protoplast regeneration in the model plant Arabidopsis thaliana. Plant Methods 2021; 17:21. [PMID: 33622383 PMCID: PMC7901198 DOI: 10.1186/s13007-021-00720-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/08/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Plants have a remarkable reprogramming potential, which facilitates plant regeneration, especially from a single cell. Protoplasts have the ability to form a cell wall and undergo cell division, allowing whole plant regeneration. With the growing need for protoplast regeneration in genetic engineering and genome editing, fundamental studies that enhance our understanding of cell cycle re-entry, pluripotency acquisition, and de novo tissue regeneration are essential. To conduct these studies, a reproducible and efficient protoplast regeneration method using model plants is necessary. RESULTS Here, we optimized cell and tissue culture methods for improving protoplast regeneration efficiency in Arabidopsis thaliana. Protoplasts were isolated from whole seedlings of four different Arabidopsis ecotypes including Columbia (Col-0), Wassilewskija (Ws-2), Nossen (No-0), and HR (HR-10). Among these ecotypes, Ws-2 showed the highest potential for protoplast regeneration. A modified thin alginate layer was applied to the protoplast culture at an optimal density of 1 × 106 protoplasts/mL. Following callus formation and de novo shoot regeneration, the regenerated inflorescence stems were used for de novo root organogenesis. The entire protoplast regeneration process was completed within 15 weeks. The in vitro regenerated plants were fertile and produced morphologically normal progenies. CONCLUSION The cell and tissue culture system optimized in this study for protoplast regeneration is efficient and reproducible. This method of Arabidopsis protoplast regeneration can be used for fundamental studies on pluripotency establishment and de novo tissue regeneration.
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Affiliation(s)
- Yeong Yeop Jeong
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea
- Research Institute of Basic Sciences, Seoul National University, Seoul, 08826, Korea
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Hun-Young Lee
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
| | - Suk Weon Kim
- Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56212, Korea
| | - Yoo-Sun Noh
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul, 08826, Korea.
- Research Institute of Basic Sciences, Seoul National University, Seoul, 08826, Korea.
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, 08826, Korea.
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Affiliation(s)
- Tsveta Tsanova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Lidia Stefanova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Lora Topalova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | | | - Ivelin Pantchev
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
- Joint Genomic Center Ltd, Sofia, Bulgaria
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