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Khmeleva SA, Ptitsyn KG, Kurbatov LK, Timoshenko OS, Suprun EV, Radko SP, Lisitsa AV. Biosensing platforms for DNA diagnostics based on CRISPR/Cas nucleases: towards the detection of nucleic acids at the level of single molecules in non-laboratory settings. BIOMEDITSINSKAIA KHIMIIA 2024; 70:287-303. [PMID: 39324194 DOI: 10.18097/pbmc20247005287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2024]
Abstract
The use of CRISPR/Cas nucleases for the development of DNA diagnostic systems in out-of-laboratory conditions (point-of-need testing, PONT) has demonstrated rapid growth in the last few years, starting with the appearance in 2017-2018 of the first diagnostic platforms known as DETECTR and SHERLOCK. The platforms are based on a combination of methods of nucleic acid isothermal amplification with selective CRISPR/Cas detection of target amplicons. This significantly improves the sensitivity and specificity of PONT, making them comparable with or even superior to the sensitivity and specificity of polymerase chain reaction, considered as the "gold standard" of DNA diagnostics. The review considers modern approaches to the coupling of CRISPR/Cas detection using Cas9, Cas12a, Cas12b, Cas13a, Cas14, and Cas3 nucleases to various methods of nucleic acid isothermal amplification, with an emphasis on works in which sensitivity at the level of single molecules (attomolar and subattomolar concentrations of the target) is achieved. The properties of CRISPR/Cas nucleases used for targeted DNA diagnostics and the features of methods of nucleic acid isothermal amplification are briefly considered in the context of the development of diagnostic biosensing platforms. Special attention is paid to the most promising directions for the development of DNA diagnostics using CRISPR/Cas nuclease.
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Affiliation(s)
- S A Khmeleva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - K G Ptitsyn
- Institute of Biomedical Chemistry, Moscow, Russia
| | - L K Kurbatov
- Institute of Biomedical Chemistry, Moscow, Russia
| | | | - E V Suprun
- Chemistry Faculty of M.V. Lomonosov Moscow State University, Moscow, Russia
| | - S P Radko
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A V Lisitsa
- Institute of Biomedical Chemistry, Moscow, Russia
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Singh PK, Devanna BN, Dubey H, Singh P, Joshi G, Kumar R. The potential of genome editing to create novel alleles of resistance genes in rice. Front Genome Ed 2024; 6:1415244. [PMID: 38933684 PMCID: PMC11201548 DOI: 10.3389/fgeed.2024.1415244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 05/21/2024] [Indexed: 06/28/2024] Open
Abstract
Rice, a staple food for a significant portion of the global population, faces persistent threats from various pathogens and pests, necessitating the development of resilient crop varieties. Deployment of resistance genes in rice is the best practice to manage diseases and reduce environmental damage by reducing the application of agro-chemicals. Genome editing technologies, such as CRISPR-Cas, have revolutionized the field of molecular biology, offering precise and efficient tools for targeted modifications within the rice genome. This study delves into the application of these tools to engineer novel alleles of resistance genes in rice, aiming to enhance the plant's innate ability to combat evolving threats. By harnessing the power of genome editing, researchers can introduce tailored genetic modifications that bolster the plant's defense mechanisms without compromising its essential characteristics. In this study, we synthesize recent advancements in genome editing methodologies applicable to rice and discuss the ethical considerations and regulatory frameworks surrounding the creation of genetically modified crops. Additionally, it explores potential challenges and future prospects for deploying edited rice varieties in agricultural landscapes. In summary, this study highlights the promise of genome editing in reshaping the genetic landscape of rice to confront emerging challenges, contributing to global food security and sustainable agriculture practices.
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Affiliation(s)
- Pankaj Kumar Singh
- Department of Biotechnology, University Centre for Research & Development, Chandigarh University, Mohali, Punjab, India
| | | | - Himanshu Dubey
- Seri-Biotech Research Laboratory, Central Silk Board, Bangalore, India
| | - Prabhakar Singh
- Botany Department, Banaras Hindu University, Varanasi, India
| | - Gaurav Joshi
- Department of Pharmaceutical Sciences, Hemvati Nandan Bahuguna Garhwal (A Central University), Tehri Garhwal, Uttarakhand, India
| | - Roshan Kumar
- Department of Microbiology, Central University of Punjab, Bathinda, Punjab, India
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Motoche-Monar C, Ordoñez JE, Chang O, Gonzales-Zubiate FA. gRNA Design: How Its Evolution Impacted on CRISPR/Cas9 Systems Refinement. Biomolecules 2023; 13:1698. [PMID: 38136570 PMCID: PMC10741458 DOI: 10.3390/biom13121698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 12/24/2023] Open
Abstract
Over the past decade, genetic engineering has witnessed a revolution with the emergence of a relatively new genetic editing tool based on RNA-guided nucleases: the CRISPR/Cas9 system. Since the first report in 1987 and characterization in 2007 as a bacterial defense mechanism, this system has garnered immense interest and research attention. CRISPR systems provide immunity to bacteria against invading genetic material; however, with specific modifications in sequence and structure, it becomes a precise editing system capable of modifying the genomes of a wide range of organisms. The refinement of these modifications encompasses diverse approaches, including the development of more accurate nucleases, understanding of the cellular context and epigenetic conditions, and the re-designing guide RNAs (gRNAs). Considering the critical importance of the correct performance of CRISPR/Cas9 systems, our scope will emphasize the latter approach. Hence, we present an overview of the past and the most recent guide RNA web-based design tools, highlighting the evolution of their computational architecture and gRNA characteristics over the years. Our study explains computational approaches that use machine learning techniques, neural networks, and gRNA/target interactions data to enable predictions and classifications. This review could open the door to a dynamic community that uses up-to-date algorithms to optimize and create promising gRNAs, suitable for modern CRISPR/Cas9 engineering.
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Affiliation(s)
- Cristofer Motoche-Monar
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Julián E. Ordoñez
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
| | - Oscar Chang
- Departamento de Electrónica, Universidad Simon Bolivar, Caracas 1080, Venezuela
- MIND Research Group, Model Intelligent Networks Development, Urcuquí 100119, Ecuador
| | - Fernando A. Gonzales-Zubiate
- School of Biological Sciences and Engineering, Yachay Tech University, Urcuquí 100119, Ecuador
- MIND Research Group, Model Intelligent Networks Development, Urcuquí 100119, Ecuador
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Maghsoud Y, Jayasinghe-Arachchige VM, Kumari P, Cisneros GA, Liu J. Leveraging QM/MM and Molecular Dynamics Simulations to Decipher the Reaction Mechanism of the Cas9 HNH Domain to Investigate Off-Target Effects. J Chem Inf Model 2023; 63:6834-6850. [PMID: 37877218 DOI: 10.1021/acs.jcim.3c01284] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) technology is an RNA-guided targeted genome-editing tool using Cas family proteins. Two magnesium-dependent nuclease domains of the Cas9 enzyme, termed HNH and RuvC, are responsible for cleaving the target DNA (t-DNA) and nontarget DNA strands, respectively. The HNH domain is believed to determine the DNA cleavage activity of both endonuclease domains and is sensitive to complementary RNA-DNA base pairing. However, the underlying molecular mechanisms of CRISPR-Cas9, by which it rebukes or accepts mismatches, are poorly understood. Thus, investigation of the structure and dynamics of the catalytic state of Cas9 with either matched or mismatched t-DNA can provide insights into improving its specificity by reducing off-target cleavages. Here, we focus on a recently discovered catalytic-active form of the Streptococcus pyogenes Cas9 (SpCas9) and employ classical molecular dynamics and coupled quantum mechanics/molecular mechanics simulations to study two possible mechanisms of t-DNA cleavage reaction catalyzed by the HNH domain. Moreover, by designing a mismatched t-DNA structure called MM5 (C to G at the fifth position from the protospacer adjacent motif region), the impact of single-guide RNA (sgRNA) and t-DNA complementarity on the catalysis process was investigated. Based on these simulations, our calculated binding affinities, minimum energy paths, and analysis of catalytically important residues provide atomic-level details of the differences between matched and mismatched cleavage reactions. In addition, several residues exhibit significant differences in their catalytic roles for the two studied systems, including K253, K263, R820, K896, and K913.
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Affiliation(s)
- Yazdan Maghsoud
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Vindi M Jayasinghe-Arachchige
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - Pratibha Kumari
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Jin Liu
- Department of Pharmaceutical Sciences, University of North Texas System College of Pharmacy, University of North Texas Health Science Center, Fort Worth, Texas 76107, United States
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Tyumentseva M, Tyumentsev A, Akimkin V. CRISPR/Cas9 Landscape: Current State and Future Perspectives. Int J Mol Sci 2023; 24:16077. [PMID: 38003266 PMCID: PMC10671331 DOI: 10.3390/ijms242216077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 11/06/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 is a unique genome editing tool that can be easily used in a wide range of applications, including functional genomics, transcriptomics, epigenetics, biotechnology, plant engineering, livestock breeding, gene therapy, diagnostics, and so on. This review is focused on the current CRISPR/Cas9 landscape, e.g., on Cas9 variants with improved properties, on Cas9-derived and fusion proteins, on Cas9 delivery methods, on pre-existing immunity against CRISPR/Cas9 proteins, anti-CRISPR proteins, and their possible roles in CRISPR/Cas9 function improvement. Moreover, this review presents a detailed outline of CRISPR/Cas9-based diagnostics and therapeutic approaches. Finally, the review addresses the future expansion of genome editors' toolbox with Cas9 orthologs and other CRISPR/Cas proteins.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (A.T.); (V.A.)
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Yigider E, Taspinar MS, Agar G. Advances in bread wheat production through CRISPR/Cas9 technology: a comprehensive review of quality and other aspects. PLANTA 2023; 258:55. [PMID: 37522927 DOI: 10.1007/s00425-023-04199-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 06/30/2023] [Indexed: 08/01/2023]
Abstract
MAIN CONCLUSION This review provides a comprehensive overview of the CRISPR/Cas9 technique and the research areas of this gene editing tool in improving wheat quality. Wheat (Triticum aestivum L.), the basic nutrition for most of the human population, contributes 20% of the daily energy needed because of its, carbohydrate, essential amino acids, minerals, protein, and vitamin content. Wheat varieties that produce high yields and have enhanced nutritional quality will be required to fulfill future demands. Hexaploid wheat has A, B, and D genomes and includes three like but not identical copies of genes that influence important yield and quality. CRISPR/Cas9, which allows multiplex genome editing provides major opportunities in genome editing studies of plants, especially complicated genomes such as wheat. In this overview, we discuss the CRISPR/Cas9 technique, which is credited with bringing about a paradigm shift in genome editing studies. We also provide a summary of recent research utilizing CRISPR/Cas9 to investigate yield, quality, resistance to biotic/abiotic stress, and hybrid seed production. In addition, we provide a synopsis of the laboratory experience-based solution alternatives as well as the potential obstacles for wheat CRISPR studies. Although wheat's extensive genome and complicated polyploid structure previously slowed wheat genetic engineering and breeding progress, effective CRISPR/Cas9 systems are now successfully used to boost wheat development.
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Affiliation(s)
- Esma Yigider
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey
| | - Mahmut Sinan Taspinar
- Faculty of Agriculture, Department of Agricultural Biotechnology, Atatürk University, 25240, Erzurum, Turkey.
| | - Guleray Agar
- Faculty of Science, Department of Biology, Atatürk University, 25240, Erzurum, Turkey
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Zhou J, Luan X, Liu Y, Wang L, Wang J, Yang S, Liu S, Zhang J, Liu H, Yao D. Strategies and Methods for Improving the Efficiency of CRISPR/Cas9 Gene Editing in Plant Molecular Breeding. PLANTS (BASEL, SWITZERLAND) 2023; 12:1478. [PMID: 37050104 PMCID: PMC10097296 DOI: 10.3390/plants12071478] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/21/2023] [Accepted: 03/22/2023] [Indexed: 06/19/2023]
Abstract
Following recent developments and refinement, CRISPR-Cas9 gene-editing technology has become increasingly mature and is being widely used for crop improvement. The application of CRISPR/Cas9 enables the generation of transgene-free genome-edited plants in a short period and has the advantages of simplicity, high efficiency, high specificity, and low production costs, which greatly facilitate the study of gene functions. In plant molecular breeding, the gene-editing efficiency of the CRISPR-Cas9 system has proven to be a key step in influencing the effectiveness of molecular breeding, with improvements in gene-editing efficiency recently becoming a focus of reported scientific research. This review details strategies and methods for improving the efficiency of CRISPR/Cas9 gene editing in plant molecular breeding, including Cas9 variant enzyme engineering, the effect of multiple promoter driven Cas9, and gRNA efficient optimization and expression strategies. It also briefly introduces the optimization strategies of the CRISPR/Cas12a system and the application of BE and PE precision editing. These strategies are beneficial for the further development and optimization of gene editing systems in the field of plant molecular breeding.
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Affiliation(s)
- Junming Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Xinchao Luan
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Yixuan Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Lixue Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jiaxin Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Songnan Yang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Shuying Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Jun Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China; (S.Y.); (J.Z.)
| | - Huijing Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
| | - Dan Yao
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (J.Z.); (X.L.); (Y.L.); (L.W.); (J.W.); (S.L.)
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Yang T, Curtis S, Bai A, Young A, Derosier D, Ripley S, Bai S. CRISPR/Cas9 targeting liposomes knocked down multidrug resistance proteins in brain endothelial cells as a model to predict potential pharmacoresistance. Colloids Surf B Biointerfaces 2023; 222:113103. [PMID: 36571980 PMCID: PMC9899320 DOI: 10.1016/j.colsurfb.2022.113103] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 11/01/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
This investigation aimed to use CRISPR-Cas9 gene-editing to knock down P-glycoprotein (P-gp) expression and then establish a feasible cell line to evaluate the potential pharmacoresistance of therapeutic agents mediated by efflux. A cationic liposome was prepared as a "smart bomb" by conjugating with a peptide-based targeting ligand (THRPPMWSPVWP), specifically binding to transferrin receptors at the blood-brain barrier (BBB), and then formed a nanocomplex with P-gp knockdown CRISPR/Cas9 plasmid. Higher uptakes of targeted and stable liposomes in bEND.3 cells were observed compared to non-peptide conjugated ones (p < 0.05). The P-gp transporters were successfully knocked down by the cell-nontoxic CRISPR/Cas9 targeted liposomes and P-gp associated ATP activities were higher in the transfected cells (p < 0.05). Functional studies of knocked down cells were evaluated by using prototypical P-gp substrates rhodamine 123 and doxorubicin. More accumulation of rhodamine 123 and higher cytotoxic sensitivity of doxorubicin was observed in the transfected cells as compared with those in the wild-type cells.
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Affiliation(s)
- Tianzhi Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Skye Curtis
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Albert Bai
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Abby Young
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Derek Derosier
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Shannon Ripley
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA
| | - Shuhua Bai
- Department of Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME 04401, USA.
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Sharma M, Bhushan S, Sharma D, Kaul S, Dhar MK. A Brief Review of Plant Cell Transfection, Gene Transcript Expression, and Genotypic Integration for Enhancing Compound Production. Methods Mol Biol 2023; 2575:153-179. [PMID: 36301475 DOI: 10.1007/978-1-0716-2716-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Plants possess a plethora of important secondary metabolites, which are unique sources of natural pigments, pharmaceutical compounds, food additives, natural pesticides, and other industrial components. The commercial significance of such metabolites/compounds has directed the research toward their production and exploration of methods for enhancement of production. Biotechnological tools are critical in selecting, integrating, multiplying, improving, and analyzing medicinal plants for secondary metabolite production. Out of many techniques that are being explored to enhance secondary metabolite production, "plant cell transfection" is the latest tool to achieve maximum output from the plant source. It is based upon the introduction of foreign DNA into the plant cell relying on physical treatment such as electroporation, cell squeezing, sonoporation, optical transfection nanoparticles, magnetofection, and chemical treatment or biological treatment that depends upon carrier. One of the promising tools that have been exploited is CRISPR-Cas9. Overall, the abovementioned tools focus on the stable transfection of desired gene transcripts. Since the integration and continuous expression of transfected gene of particular trait represents stable transfection of host cell genome, resulting from transfer of required trait to daughter cells ultimately leading to enhanced production of secondary metabolites of interest. This chapter will review a set of biotechnological tools that are candidates for achieving the enhanced bioactive compound production indicated here to be used for drug discovery.
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Affiliation(s)
- Munish Sharma
- Department of Plant Sciences, Central University of Himachal Pradesh, Shahpur, Kangra, Himachal Pradesh, India.
| | - Sakshi Bhushan
- Department of Botany, Central University of Jammu, Jammu, Jammu and Kashmir, India
| | - Deepak Sharma
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Sanjana Kaul
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
| | - Manoj K Dhar
- Genome Research Laboratory, School of Biotechnology, University of Jammu, Jammu, Jammu and Kashmir, India
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CRISPR/Cas9-engineered mesenchymal stromal/stem cells and their extracellular vesicles: A new approach to overcoming cell therapy limitations. Biomed Pharmacother 2022; 156:113943. [DOI: 10.1016/j.biopha.2022.113943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022] Open
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de Lange J, Nalley LL, Yang W, Shew A, de Steur H. The future of CRISPR gene editing according to plant scientists. iScience 2022; 25:105012. [PMID: 36093047 PMCID: PMC9460836 DOI: 10.1016/j.isci.2022.105012] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
This study surveyed 669 plant scientists globally to elicit how (which outcomes of gene editing), where (which continent) and what (which crops) are most likely to benefit from CRISPR research and if there is a consensus about specific barriers to commercial adoption in agriculture. Further, we disaggregated public and private plant scientists to see if there was heterogeneity in their views of the future of CRISPR research. Our findings suggest that maize and soybeans are anticipated to benefit the most from CRISPR technology with fungus and virus resistance the most common vehicle for its implementation. Across the board, plant scientists viewed consumer perception/knowledge gap to be the most impeding barrier of CRISPR adoption. Although CRISPR has been hailed as a technology that can help alleviate food insecurity and improve agricultural sustainability, our study has shown that plant scientists believe there are some large concerns about the consumer perceptions of CRISPR.
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Affiliation(s)
- Job de Lange
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lawton Lanier Nalley
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Wei Yang
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Aaron Shew
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hans de Steur
- Department of Agricultural Economics, University of Gent, Gent, Belgium
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Mohr T, Horstman J, Gu YQ, Elarabi NI, Abdallah NA, Thilmony R. CRISPR-Cas9 Gene Editing of the Sal1 Gene Family in Wheat. PLANTS 2022; 11:plants11172259. [PMID: 36079639 PMCID: PMC9460255 DOI: 10.3390/plants11172259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/24/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
The highly conserved Sal1 encodes a bifunctional enzyme with inositol polyphosphate-1-phosphatase and 3′ (2′), 5′-bisphosphate nucleotidase activity and has been shown to alter abiotic stress tolerance in plants when disrupted. Precise gene editing techniques were used to generate Sal1 mutants in hexaploid bread wheat. The CRISPR (Clustered Regulatory Interspaced Short Palindromic Repeats) Cas9 system with three guide RNAs (gRNAs) was used to inactivate six Sal1 homologous genes within the Bobwhite wheat genome. The resulting mutant wheat plants with all their Sal1 genes disabled had slimmer stems, had a modest reduction in biomass and senesced more slowly in water limiting conditions, but did not exhibit improved yield under drought conditions. Our results show that multiplexed gRNAs enabled effective targeted gene editing of the Sal1 gene family in hexaploid wheat. These Sal1 mutant wheat plants will be a resource for further research studying the function of this gene family in wheat.
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Affiliation(s)
- Toni Mohr
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - James Horstman
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Yong Q. Gu
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
| | - Nagwa I. Elarabi
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Naglaa A. Abdallah
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Roger Thilmony
- USDA-ARS, Crop Improvement and Genetics Unit, Albany, CA 94710, USA
- Correspondence: ; Tel.: +1-(510)-559-5761
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Jedličková V, Mácová K, Štefková M, Butula J, Staveníková J, Sedláček M, Robert HS. Hairy root transformation system as a tool for CRISPR/Cas9-directed genome editing in oilseed rape ( Brassica napus). FRONTIERS IN PLANT SCIENCE 2022; 13:919290. [PMID: 35991410 PMCID: PMC9386449 DOI: 10.3389/fpls.2022.919290] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
Our study examined the mutation efficiency of the CRISPR/Cas9 method for tryptophan aminotransferase BnaTAA1 genes involved in the auxin biosynthesis pathway. We made nine CRISPR/Cas9 constructs with various promoters driving the expression of a Cas9 from Staphylococcus aureus (SaCas9) or a plant-codon-optimized Streptococcus pyogenes Cas9 (pcoCas9). We developed a fast and efficient system for evaluating the variety and frequency of mutations caused by each construct using Brassica napus hairy roots. We showed that pcoCas9 is more efficient in mutating the targeted loci than SaCas9 and the presence of the NLS signal enhanced the chance of mutagenesis by 25%. The mutations were studied further in regenerated lines, and we determined the BnaTAA1 gene expression and heritability of the gene modifications in transgenic plants. Hairy root transformation combined with CRISPR/Cas9-mediated gene editing represents a fast and straightforward system for studying target gene function in the important oilseed crop B. napus.
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Affiliation(s)
- Veronika Jedličková
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Kateřina Mácová
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czechia
| | - Marie Štefková
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Jan Butula
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Jana Staveníková
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Marek Sedláček
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
| | - Hélène S. Robert
- CEITEC MU – Central European Institute of Technology, Masaryk University, Brno, Czechia
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14
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Fernandez-Pozo N, Haas FB, Gould SB, Rensing SA. An overview of bioinformatics, genomics, and transcriptomics resources for bryophytes. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4291-4305. [PMID: 35148385 DOI: 10.1093/jxb/erac052] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Bryophytes are useful models for the study of plant evolution, development, plant-fungal symbiosis, stress responses, and gametogenesis. Additionally, their dominant haploid gametophytic phase makes them great models for functional genomics research, allowing straightforward genome editing and gene knockout via CRISPR or homologous recombination. Until 2016, however, the only bryophyte genome sequence published was that of Physcomitrium patens. Throughout recent years, several other bryophyte genomes and transcriptome datasets became available, enabling better comparative genomics in evolutionary studies. The increase in the number of bryophyte genome and transcriptome resources available has yielded a plethora of annotations, databases, and bioinformatics tools to access the new data, which covers the large diversity of this clade and whose biology comprises features such as association with arbuscular mycorrhiza fungi, sex chromosomes, low gene redundancy, or loss of RNA editing genes for organellar transcripts. Here we provide a guide to resources available for bryophytes with regards to genome and transcriptome databases and bioinformatics tools.
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Affiliation(s)
- Noe Fernandez-Pozo
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- Department of Subtropical and Mediterranean Fruit Crops, Institute for Mediterranean and Subtropical Horticulture "La Mayora" (IHSM-CSIC-UMA), Málaga, Spain
| | - Fabian B Haas
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
| | - Sven B Gould
- Evolutionary Cell Biology, Institute for Molecular Evolution, Heinrich-Heine-University Düsseldorf, D-40225 Düsseldorf, Germany
| | - Stefan A Rensing
- Plant Cell Biology, Department of Biology, University of Marburg, Marburg, Germany
- BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany
- LOEWE Center for Synthetic Microbiology (SYNMIKRO), Philipps University of Marburg, Marburg, Germany
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15
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Hafeez M, Ullah F, Khan MM, Li X, Zhang Z, Shah S, Imran M, Assiri MA, Fernández-Grandon GM, Desneux N, Rehman M, Fahad S, Lu Y. Metabolic-based insecticide resistance mechanism and ecofriendly approaches for controlling of beet armyworm Spodoptera exigua: a review. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:1746-1762. [PMID: 34709552 DOI: 10.1007/s11356-021-16974-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
The beet army worm, Spodoptera exigua, is a widely distributed polyphagous pest of economically important crops worldwide. The management of this pest insect continues to face many challenges. Despite synthetic chemicals posing a serious threat to the environment, these remain the conventional approach for controlling S. exigua in the field. An over-reliance on chemical control has not only led to selection for resistance to insecticides and to a reduction of natural enemies, but has also polluted various components of ecosystem. Given these increasing pressures on the ecosystem, there is a need to implement integrated pest management (IPM) approaches exploiting a wider range of tools (biotechnological approaches, microbial control, biological control, cultural control, and use of host plant resistance) for an alternative to chemical control. The IPM approach can not only reduce the hazard of chemical residues in the environment and associated health problems, but may also provide best strategies to control insect pests. This review synthesizes published information on insecticide resistance of S. exigua and explores alternative IPM approaches to control S. exigua.
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Affiliation(s)
- Muhammad Hafeez
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Farman Ullah
- Department of Entomology, College of Plant Protection, China Agricultural University, Beijing, 100193, China
| | - Muhammad Musa Khan
- Key Laboratory of Bio-Pesticide Innovation and Application, Guangdong Province, South China Agricultural University, Guangzhou, 510642, China
| | - Xiaowei Li
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Zhijun Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Sakhawat Shah
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Hubei, People's Republic of China
| | - Muhammad Imran
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | - Mohammed A Assiri
- Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha, 61413, Saudi Arabia
| | | | - Nicolas Desneux
- UMR ISA, Université Côte d'Azur, INRAE, CNRS, 06000, Nice, France
| | - Muzammal Rehman
- School of Agriculture, Yunnan University, Kunming, 650504, Yunnan, China
| | - Shah Fahad
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228, Hainan, China.
- Department of Agronomy, University of Haripur, Khyber Pakhtunkhwa, 22620, Pakistan.
| | - Yaobin Lu
- State Key Laboratory for Managing Biotic and Chemical Threats To the Quality and Safety of Agro-Products, Institute of Plant Protection and Microbiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China.
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16
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Verma AK, Mandal S, Tiwari A, Monachesi C, Catassi GN, Srivastava A, Gatti S, Lionetti E, Catassi C. Current Status and Perspectives on the Application of CRISPR/Cas9 Gene-Editing System to Develop a Low-Gluten, Non-Transgenic Wheat Variety. Foods 2021; 10:foods10102351. [PMID: 34681400 PMCID: PMC8534962 DOI: 10.3390/foods10102351] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 09/10/2021] [Accepted: 09/28/2021] [Indexed: 12/23/2022] Open
Abstract
Wheat gluten contains epitopes that trigger celiac disease (CD). A life-long strict gluten-free diet is the only treatment accepted for CD. However, very low-gluten wheat may provide an alternative treatment to CD. Conventional plant breeding methods have not been sufficient to produce celiac-safe wheat. RNA interference technology, to some extent, has succeeded in the development of safer wheat varieties. However, these varieties have multiple challenges in terms of their implementation. Clustered Regularly Interspaced Short Palindromic Repeats-associated nuclease 9 (CRISPR/Cas9) is a versatile gene-editing tool that has the ability to edit immunogenic gluten genes. So far, only a few studies have applied CRISPR/Cas9 to modify the wheat genome. In this article, we reviewed the published literature that applied CRISPR/Cas9 in wheat genome editing to investigate the current status of the CRISPR/Cas9 system to produce a low-immunogenic wheat variety. We found that in recent years, the CRISPR/Cas9 system has been continuously improved to edit the complex hexaploid wheat genome. Although some reduced immunogenic wheat varieties have been reported, CRISPR/Cas9 has still not been fully explored in terms of editing the wheat genome. We conclude that further studies are required to apply the CRISPR/Cas9 gene-editing system efficiently for the development of a celiac-safe wheat variety and to establish it as a "tool to celiac safe wheat".
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Affiliation(s)
- Anil K. Verma
- Celiac Disease Research Laboratory, Polytechnic University of Marche, 60123 Ancona, Italy;
- Correspondence: or ; Tel.: +39-0715962834
| | - Sayanti Mandal
- Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune 411007, Maharashtra, India;
| | - Aadhya Tiwari
- Department of System Biology, MD Anderson Cancer Center, Houston, TX 77030, USA;
- Laboratory of Cell Biology, Department of Orthopaedic Surgery, University Hospital of Tübingen, Waldhörnlestraße 22, D-72072 Tübingen, Germany
| | - Chiara Monachesi
- Celiac Disease Research Laboratory, Polytechnic University of Marche, 60123 Ancona, Italy;
| | - Giulia N. Catassi
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Akash Srivastava
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02906, USA;
| | - Simona Gatti
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Elena Lionetti
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
| | - Carlo Catassi
- Division of Pediatrics, DISCO Department, Polytechnic University of Marche, 60123 Ancona, Italy; (G.N.C.); (S.G.); (E.L.); (C.C.)
- Mucosal Immunology and Biology Research Center, Division of Pediatric Gastroenterology and Nutrition, Massachusetts General Hospital, Boston, MA 02114, USA
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17
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Liu S, Fang SY, An YF. [Gene editing for the treatment of primary immunodeficiency disease]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2021; 23:743-748. [PMID: 34266535 PMCID: PMC8292649 DOI: 10.7499/j.issn.1008-8830.2103150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/17/2021] [Indexed: 06/13/2023]
Abstract
Gene editing is an advanced technique based on artificial nucleases and can precisely modify genome sequences. It has shown great application prospects in the field of medicine and has provided a new precision therapy for diseases. Primary immunodeficiency disease is a group of diseases caused by single gene mutation and characterized by recurrent and refractory infections, with an extremely high mortality rate. The application of gene editing has brought hope for curing these diseases. This article reviews the development of gene editing technology and briefly introduces the research and application of gene editing technology in primary immunodeficiency disease.
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Affiliation(s)
- Shan Liu
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - Shu-Yu Fang
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
| | - Yun-Fei An
- Department of Rheumatology and Immunology, Children's Hospital of Chongqing Medical University/National Clinical Research Center for Child Health and Disorders/Ministry of Education Key Laboratory of Child Development and Disorders/Chongqing Key Laboratory of Child Infection and Immunity, Chongqing 400014, China
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18
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Bhattacharya A, Parkhi V, Char B. Genome editing for crop improvement: A perspective from India. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2021; 57:565-573. [PMID: 34075289 PMCID: PMC8152710 DOI: 10.1007/s11627-021-10184-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/12/2021] [Indexed: 05/11/2023]
Abstract
Human population is expected to reach to about 10 billion by 2050. Climate change affects crop production, thus posing food security challenges. Conventional breeding alone will not bridge the gap between current level of crop production and expected levels in the decades to come in the food production systems. Rate of genetic gain with time has remained narrow considerably. Biotechnology-enabled crops developed through genome editing will have a part to play in improving crop productivity, meeting food, nutrition security besides catering to regional preferences and fetching valuable foreign exchange. Political, social, economical proposition, scientific will, retailer and consumer acceptance are a must for genome editing (GE) to succeed and add value in the food value chain. This will also help to make agriculture a lucrative profession and attract youth. Therefore, the present review looks into existing regulations governing crops developed using biotechnology in India, institutes involved in genome editing, prospects of new tools developed in this sphere such as DNA-free editing systems, nanotechnology, their applicability in crop improvement efforts, social and future prospects taking cue from recent global developments. This will make GE more appealing to stakeholders and defray any safety concerns.
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Affiliation(s)
- Anjanabha Bhattacharya
- Mahyco Research Centre, Mahyco Private Limited, Jalna-Aurangabad Road, Dawalwadi, Jalna, Maharashtra 431203 India
| | - Vilas Parkhi
- Mahyco Research Centre, Mahyco Private Limited, Jalna-Aurangabad Road, Dawalwadi, Jalna, Maharashtra 431203 India
| | - Bharat Char
- Mahyco Research Centre, Mahyco Private Limited, Jalna-Aurangabad Road, Dawalwadi, Jalna, Maharashtra 431203 India
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19
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CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering. Cells 2020; 9:cells9112518. [PMID: 33233344 PMCID: PMC7700487 DOI: 10.3390/cells9112518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
The identification of the robust clustered regularly interspersed short palindromic repeats (CRISPR) associated endonuclease (Cas9) system gene-editing tool has opened up a wide range of potential therapeutic applications that were restricted by more complex tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Nevertheless, the high frequency of CRISPR system off-target activity still limits its applications, and, thus, advanced strategies for highly specific CRISPR/Cas9-mediated genome editing are continuously under development including CRISPR–FokI dead Cas9 (fdCas9). fdCas9 system is derived from linking a FokI endonuclease catalytic domain to an inactive Cas9 protein and requires a pair of guide sgRNAs that bind to the sense and antisense strands of the DNA in a protospacer adjacent motif (PAM)-out orientation, with a defined spacer sequence range around the target site. The dimerization of FokI domains generates DNA double-strand breaks, which activates the DNA repair machinery and results in genomic edit. So far, all the engineered fdCas9 variants have shown promising gene-editing activities in human cells when compared to other platforms. Herein, we review the advantages of all published variants of fdCas9 and their current applications in genome engineering.
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20
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Wang H, Lu H, Lei YS, Gong CY, Chen Z, Luan YQ, Li Q, Jian YZ, Wang HZ, Wu FL, Tao CL, Shen H, Bo HB, Shao HW, Zhang WF. Development of a Self-Restricting CRISPR-Cas9 System to Reduce Off-Target Effects. Mol Ther Methods Clin Dev 2020; 18:390-401. [PMID: 32695841 PMCID: PMC7358219 DOI: 10.1016/j.omtm.2020.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/05/2020] [Indexed: 12/26/2022]
Abstract
Development of the CRISPR-Cas9 gene-editing system has given rise to a new era of gene editing with wide applications in biology, medicine, agriculture, and other fields. However, the overexpression of Cas9 nuclease causes off-target effects and may trigger an immune response in vivo. Therefore, we constructed a self-restricting CRISPR-Cas9 system, where the target gene sequence corresponding to the guide RNA (gRNA) is inserted on either end of the Cas9 promoter. When double-strand breaks (DSBs) are induced in the target gene sequence, the Cas9 promoter is cut off and transcription ceases. With this system, expression of Cas9 protein at 60 h after transfection is only 10% that of the wild-type system, with about 70% promoter deletion efficiency. The target site editing efficiency and homologous recombination efficiency of the self-restricting system remain at about 50% and 30%, respectively, while the frequency of off-target indel formation decreased by 76.7%. Further, the number of indel types was also reduced from 13 to 2. Because this system does not include additional gRNA sequences, the possibility of introducing new off-target mutations is decreased. Importantly, this system is composed of a single plasmid, which could potentially be easily introduced in vivo using a viral vector or nanoparticles.
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Affiliation(s)
- Hui Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hua Lu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Ying-Shou Lei
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Chen-Yu Gong
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Zhao Chen
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Ying-Qiao Luan
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Qiang Li
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Ying-Zhen Jian
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hao-Zheng Wang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Feng-Lin Wu
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Chang-Li Tao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Han Shen
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hua-Ben Bo
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Hong-Wei Shao
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
| | - Wen-Feng Zhang
- Guangdong Province Key Laboratory of Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China.,School of Biosciences and Biopharmaceutics, Guangdong Pharmaceutical University, Guangzhou, People's Republic of China
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21
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Filho DM, de Carvalho Ribeiro P, Oliveira LF, Dos Santos ALRT, Parreira RC, Pinto MCX, Resende RR. Enhancing the Therapeutic Potential of Mesenchymal Stem Cells with the CRISPR-Cas System. Stem Cell Rev Rep 2020; 15:463-473. [PMID: 31147819 DOI: 10.1007/s12015-019-09897-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Mesenchymal stem cells (MSCs), also known as multipotent mesenchymal stromal stem cells, are found in the perivascular space of several tissues. These cells have been subject of intense research in the last decade due to their low teratogenicity, as well as their ability to differentiate into mature cells and to secrete immunomodulatory and trophic factors. However, they usually promote only a modest benefit when transplanted in experimental disease models, one of the limitations for their clinical application. The CRISPR-Cas system, in turn, is highlighted as a simple and effective tool for genetic engineering. This system was tested in clinical trials over a relatively short period of time after establishing its applicability to the edition of the mammalian cell genome. Similar to the research evolution in MSCs, the CRISPR-Cas system demonstrated inconsistencies that limited its clinical application. In this review, we outline the evolution of MSC research and its applicability, and the progress of the CRISPR-Cas system from its discovery to the most recent clinical trials. We also propose perspectives on how the CRISPR-Cas system may improve the therapeutic potential of MSCs, making it more beneficial and long lasting.
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Affiliation(s)
- Daniel Mendes Filho
- Department of Physiology, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Sao Paulo, Brazil
| | - Patrícia de Carvalho Ribeiro
- Laboratory of Immunology and Experimental Transplantation, São José do Rio Preto Medical School, São José do Rio Preto, São Paulo, Brazil.,Division of Thoracic Surgery, Department of Surgery, Massachusetts General Hospital, Boston, MA, USA
| | - Lucas Felipe Oliveira
- Department of Physiology, Biological and Natural Sciences Institute, Triangulo Mineiro Federal University, Uberaba, Minas Gerais, Brazil.,National Institute of Science and Technology for Regenerative Medicine (INCT-REGENERA-CNPq), Rio de Janeiro, RJ, Brazil.,Minas Gerais Network for Tissue Engineering and Cell Therapy (REMETTECFAPEMIG), Belo Horizonte, MG, Brazil
| | | | - Ricardo Cambraia Parreira
- Department of Pharmacology, Biological Sciences Institute, Goias Federal University, Goiania, Goias, Brazil.
| | - Mauro Cunha Xavier Pinto
- Department of Pharmacology, Biological Sciences Institute, Goias Federal University, Goiania, Goias, Brazil
| | - Rodrigo Ribeiro Resende
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
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22
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Xu L, Pan R, Zhang W. Membrane lipids are involved in plant response to oxygen deprivation. PLANT SIGNALING & BEHAVIOR 2020; 15:1771938. [PMID: 32463337 PMCID: PMC8570748 DOI: 10.1080/15592324.2020.1771938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Membrane lipids change drastically in plants when they suffered from hypoxia (oxygen deficiency) stress. Overall, hypoxia stress lowers the contents of total lipids, inhabits lipid biosynthesis, and stimulates lipid degradation, leading to the accumulation of free fatty acids. Lipid alterations include changes in the contents of lipid classes, the extent of saturation, and the length of acyl chains. But the detail and systematic studies about lipid changes, as well as the function mechanism in hypoxia stress are poorly understood. Here, the major unanswered questions and suggestions on the study of the function of lipid in hypoxia stress were provided.
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Affiliation(s)
- Le Xu
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Rui Pan
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
| | - Wenying Zhang
- Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou, China
- CONTACT Wenying Zhang Hubei Collaborative Innovation Centre for Grain Industry/Engineering Research Centre of Ecology and Agricultural Use of Wetland, Ministry of Education, Yangtze University, Jingzhou434025, China
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23
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Song L, Xie K. Engineering CRISPR/Cas9 to mitigate abundant host contamination for 16S rRNA gene-based amplicon sequencing. MICROBIOME 2020; 8:80. [PMID: 32493511 PMCID: PMC7268715 DOI: 10.1186/s40168-020-00859-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 05/08/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND High-throughput sequencing of bacterial 16S rRNA gene (16S-seq) is a useful and common method for studying bacterial community structures. However, contamination of the 16S rRNA genes from the mitochondrion and plastid hinders the sensitive bacterial 16S-seq in plant microbiota profiling, especially for some plant species such as rice. To date, efficiently mitigating such host contamination without a bias is challenging in 16S rRNA gene-based amplicon sequencing. RESULTS We developed Cas-16S-seq method to reduce abundant host contamination for plant microbiota profiling. This method utilizes the Cas9 nuclease and specific guide RNA (gRNA) to cut 16S rRNA targets during library construction, thereby removing host contamination in 16S-seq. We used rice as an example to validate the feasibility and effectiveness of Cas-16S-seq. We established a bioinformatics pipeline to design gRNAs that specifically target rice 16S rRNA genes without bacterial 16S rRNA off-targets. We compared the effectiveness of Cas-16S-seq with that of the commonly used 16S-seq method for artificially mixed 16S rRNA gene communities, paddy soil, rice root, and phyllosphere samples. The results showed that Cas-16S-seq substantially reduces the fraction of rice 16S rRNA gene sequences from 63.2 to 2.9% in root samples and from 99.4 to 11.6% in phyllosphere samples on average. Consequently, Cas-16S-seq detected more bacterial species than the 16S-seq in plant samples. Importantly, when analyzing soil samples, Cas-16S-seq and 16S-seq showed almost identical bacterial communities, suggesting that Cas-16S-seq with host-specific gRNAs that we designed has no off-target in rice microbiota profiling. CONCLUSION Our Cas-16S-seq can efficiently remove abundant host contamination without a bias for 16S rRNA gene-based amplicon sequencing, thereby enabling deeper bacterial community profiling with a low cost and high flexibility. Thus, we anticipate that this method would be a useful tool for plant microbiomics. Video Abstract.
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Affiliation(s)
- Luyang Song
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District, Wuhan, 430070 China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, No.1 Shizishan Street, Hongshan District, Wuhan, 430070 China
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24
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Golicz AA, Bayer PE, Bhalla PL, Batley J, Edwards D. Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications. Trends Genet 2019; 36:132-145. [PMID: 31882191 DOI: 10.1016/j.tig.2019.11.006] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/09/2019] [Accepted: 11/12/2019] [Indexed: 02/01/2023]
Abstract
The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.
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Affiliation(s)
- Agnieszka A Golicz
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia.
| | - Philipp E Bayer
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - Prem L Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, VIC, Australia
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Crawley, WA, Australia.
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Biswal AK, Mangrauthia SK, Reddy MR, Yugandhar P. CRISPR mediated genome engineering to develop climate smart rice: Challenges and opportunities. Semin Cell Dev Biol 2019; 96:100-106. [DOI: 10.1016/j.semcdb.2019.04.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/06/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022]
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[Establishment of a congenital chloride diarrhea-associated SLC26A3 c.392C>G (p.P131R) polymorphism-expressing cell model and a preliminary analysis of its mechanism of action]. ZHONGGUO DANG DAI ER KE ZA ZHI = CHINESE JOURNAL OF CONTEMPORARY PEDIATRICS 2019; 21. [PMID: 31753097 PMCID: PMC7389292 DOI: 10.7499/j.issn.1008-8830.2019.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
OBJECTIVE To establish a congenital chloride diarrhea (CCD)-associated SLC26A3 c.392C>G (p.P131R) polymorphism-expressing cell model, and to investigate its biological function. METHODS The sequence of the SLC26A3 gene in GenBank was used to design the upstream and downstream single-guide RNA (sgRNA) that could specifically recognize the 392 locus of the SLC26A3 gene, and the sgRNA was mixed with the pSpCas9-puro vector after enzyme digestion to construct an eukaryotic recombinant expression plasmid (pSpCas9-SLC26A3). Caco-2 cells were transfected with the recombinant plasmid and synthesized single-stranded DNA oligonucleotides (ssODNs), and Taqman genotyping assay and Sanger sequencing were used to identify the expression of SLC26A3 c.392C>G (p.P131R) in Caco-2 cells. Wild-type Caco-2 cells were selected as normal control group and the Caco-2 cells with successful expression of SLC26A3 c.392C>G (p.P131R) was selected as P131R group. Both groups were treated with 100 ng/mL tumor necrosis factor-α (TNF-α), and then the normal control group was named as TNF-α group, and the P131R group was named as TNF-α+P131R group. Electric cell-substrate impedance sensing (ECIS) assay was used to evaluate the change in the monolayer barrier function of intestinal epithelial cells in the above four groups, and Western blot was used to measure the change in the expression of SLC26A3 protein in the normal control group and the P131R group. RESULTS The eukaryotic recombinant expression plasmid (pSpCas9-SLC26A3) was successfully constructed. Both Taqman genotyping assay and Sanger sequencing confirmed the successful establishment of the Caco-2 cell model of SLC26A3 c.392C>G (p.P131R) expression. ECIS assay showed that compared with the normal control group, the P131R group had a significant increase in the monolayer permeability of intestinal epithelial cells (P<0.05), and at the same time, the P131R group had a significantly greater increase in cell membrane permeability after the induction with 100 ng/mL TNF-α (P<0.05). Western blot showed that compared with the normal control group, the P131R group had a significant reduction in the expression of SLC26A3 protein (P=0.001). CONCLUSIONS SLC26A3 c.392C>G (p.P131R) can reduce the expression of SLC26A3 protein, increase the monolayer permeability of intestinal epithelial cells, and thus lead to diarrhea.
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Cram D, Kulkarni M, Buchwaldt M, Rajagopalan N, Bhowmik P, Rozwadowski K, Parkin IAP, Sharpe AG, Kagale S. WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BMC PLANT BIOLOGY 2019; 19:474. [PMID: 31694550 PMCID: PMC6836449 DOI: 10.1186/s12870-019-2097-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 10/23/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND CRISPR/Cas9 gene editing has become a revolutionary technique for crop improvement as it can facilitate fast and efficient genetic changes without the retention of transgene components in the final plant line. Lack of robust bioinformatics tools to facilitate the design of highly specific functional guide RNAs (gRNAs) and prediction of off-target sites in wheat is currently an obstacle to effective application of CRISPR technology to wheat improvement. DESCRIPTION We have developed a web-based bioinformatics tool to design specific gRNAs for genome editing and transcriptional regulation of gene expression in wheat. A collaborative study between the Broad Institute and Microsoft Research used large-scale empirical evidence to devise algorithms (Doech et al., 2016, Nature Biotechnology 34, 184-191) for predicting the on-target activity and off-target potential of CRISPR/SpCas9 (Streptococcus pyogenes Cas9). We applied these prediction models to determine on-target specificity and potential off-target activity for individual gRNAs targeting specific loci in the wheat genome. The genome-wide gRNA mappings and the corresponding Doench scores predictive of the on-target and off-target activities were used to create a gRNA database which was used as a data source for the web application termed WheatCRISPR. CONCLUSION The WheatCRISPR tool allows researchers to browse all possible gRNAs targeting a gene or sequence of interest and select effective gRNAs based on their predicted high on-target and low off-target activity scores, as well as other characteristics such as position within the targeted gene. It is publicly available at https://crispr.bioinfo.nrc.ca/WheatCrispr/ .
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Affiliation(s)
- Dustin Cram
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Manoj Kulkarni
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Miles Buchwaldt
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | | | - Pankaj Bhowmik
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Kevin Rozwadowski
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Isobel A. P. Parkin
- Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2 Canada
| | - Andrew G. Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
- Global Institute for Food Security, University of Saskatchewan, 110 Gymnasium Place, Saskatoon, SK S7N 4J8 Canada
| | - Sateesh Kagale
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
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Gladman N, Jiao Y, Lee YK, Zhang L, Chopra R, Regulski M, Burow G, Hayes C, Christensen SA, Dampanaboina L, Chen J, Burke J, Ware D, Xin Z. Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module. Int J Mol Sci 2019; 20:ijms20194951. [PMID: 31597271 PMCID: PMC6801740 DOI: 10.3390/ijms20194951] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 01/07/2023] Open
Abstract
As in other cereal crops, the panicles of sorghum (Sorghum bicolor (L.) Moench) comprise two types of floral spikelets (grass flowers). Only sessile spikelets (SSs) are capable of producing viable grains, whereas pedicellate spikelets (PSs) cease development after initiation and eventually abort. Consequently, grain number per panicle (GNP) is lower than the total number of flowers produced per panicle. The mechanism underlying this differential fertility is not well understood. To investigate this issue, we isolated a series of ethyl methane sulfonate (EMS)-induced multiseeded (msd) mutants that result in full spikelet fertility, effectively doubling GNP. Previously, we showed that MSD1 is a TCP (Teosinte branched/Cycloidea/PCF) transcription factor that regulates jasmonic acid (JA) biosynthesis, and ultimately floral sex organ development. Here, we show that MSD2 encodes a lipoxygenase (LOX) that catalyzes the first committed step of JA biosynthesis. Further, we demonstrate that MSD1 binds to the promoters of MSD2 and other JA pathway genes. Together, these results show that a JA-induced module regulates sorghum panicle development and spikelet fertility. The findings advance our understanding of inflorescence development and could lead to new strategies for increasing GNP and grain yield in sorghum and other cereal crops.
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Affiliation(s)
- Nicholas Gladman
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Yinping Jiao
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Young Koung Lee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- Plasma Technology Research Center, National Fusion Research Institute, 37, Dongjangsan-ro, Gunsan-si, Jeollabuk-do 54004, Korea.
| | - Lifang Zhang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Ratan Chopra
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
- Current address: Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA.
| | - Michael Regulski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| | - Gloria Burow
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Chad Hayes
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Shawn A Christensen
- Chemistry Research Unit, USDA-ARS, 1700 S.W. 23RD DRIVE, Gainesville, FL 32608, USA.
| | - Lavanya Dampanaboina
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Junping Chen
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - John Burke
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
- U.S. Department of Agriculture-Agricultural Research Service, NEA Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA.
| | - Zhanguo Xin
- Plant Stress and Germplasm Development Unit, Cropping Systems Research Laboratory, U.S. Department of Agriculture-Agricultural Research Service, Lubbock, TX 79415, USA.
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Zheng X, Zheng P, Zhang K, Cairns TC, Meyer V, Sun J, Ma Y. 5S rRNA Promoter for Guide RNA Expression Enabled Highly Efficient CRISPR/Cas9 Genome Editing in Aspergillus niger. ACS Synth Biol 2019; 8:1568-1574. [PMID: 29687998 DOI: 10.1021/acssynbio.7b00456] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The CRISPR/Cas9 system is a revolutionary genome editing tool. However, in eukaryotes, search and optimization of a suitable promoter for guide RNA expression is a significant technical challenge. Here we used the industrially important fungus, Aspergillus niger, to demonstrate that the 5S rRNA gene, which is both highly conserved and efficiently expressed in eukaryotes, can be used as a guide RNA promoter. The gene editing system was established with 100% rates of precision gene modifications among dozens of transformants using short (40-bp) homologous donor DNA. This system was also applicable for generation of designer chromosomes, as evidenced by deletion of a 48 kb gene cluster required for biosynthesis of the mycotoxin fumonisin B1. Moreover, this system also facilitated simultaneous mutagenesis of multiple genes in A. niger. We anticipate that the use of the 5S rRNA gene as guide RNA promoter can broadly be applied for engineering highly efficient eukaryotic CRISPR/Cas9 toolkits. Additionally, the system reported here will enable development of designer chromosomes in model and industrially important fungi.
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Affiliation(s)
- Xiaomei Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , 300308 , China
- Key Laboratory of Systems Microbial Biotechnology , Chinese Academy of Sciences , Tianjin , 300308 , China
| | - Ping Zheng
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , 300308 , China
- Key Laboratory of Systems Microbial Biotechnology , Chinese Academy of Sciences , Tianjin , 300308 , China
| | - Kun Zhang
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , 300308 , China
- Key Laboratory of Systems Microbial Biotechnology , Chinese Academy of Sciences , Tianjin , 300308 , China
- University of Chinese Academy of Sciences , Beijing , 100049 , China
| | - Timothy C Cairns
- Department Applied and Molecular Microbiology , Institute of Biotechnology, Technische Universität Berlin , Berlin , 13355 , Germany
| | - Vera Meyer
- Department Applied and Molecular Microbiology , Institute of Biotechnology, Technische Universität Berlin , Berlin , 13355 , Germany
| | - Jibin Sun
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , 300308 , China
- Key Laboratory of Systems Microbial Biotechnology , Chinese Academy of Sciences , Tianjin , 300308 , China
| | - Yanhe Ma
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences , Tianjin , 300308 , China
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Petersen BL, Möller SR, Mravec J, Jørgensen B, Christensen M, Liu Y, Wandall HH, Bennett EP, Yang Z. Improved CRISPR/Cas9 gene editing by fluorescence activated cell sorting of green fluorescence protein tagged protoplasts. BMC Biotechnol 2019; 19:36. [PMID: 31208390 PMCID: PMC6580576 DOI: 10.1186/s12896-019-0530-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 05/29/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND CRISPR/Cas9 is widely used for precise genetic editing in various organisms. CRISPR/Cas9 editing may in many plants be hampered by the presence of complex and high ploidy genomes and inefficient or poorly controlled delivery of the CRISPR/Cas9 components to gamete cells or cells with regenerative potential. Optimized strategies and methods to overcome these challenges are therefore in demand. RESULTS In this study we investigated the feasibility of improving CRISPR/Cas9 editing efficiency by Fluorescence Activated Cell Sorting (FACS) of protoplasts. We used Agrobacterium infiltration in leaves of Nicotiana benthamiana for delivery of viral replicons for high level expression of gRNAs designed to target two loci in the genome, NbPDS and NbRRA, together with the Cas9 nuclease in fusion with the 2A self-splicing sequence and GFP (Cas9-2A-GFP). Protoplasts isolated from the infiltrated leaves were then subjected to FACS for selection of GFP enriched protoplast populations. This procedure resulted in a 3-5 fold (from 20 to 30% in unsorted to more than 80% in sorted) increase in mutation frequencies as evidenced by restriction enzyme analysis and the Indel Detection by Amplicon Analysis, which allows for high throughput profiling and quantification of the generated mutations. CONCLUSIONS FACS of protoplasts expressing GFP tagged CRISPR/Cas9, delivered through A. tumefaciens leaf infiltration, facilitated clear CRISPR/Cas9 mediated mutation enrichment in selected protoplast populations.
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Affiliation(s)
- Bent Larsen Petersen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Svenning Rune Möller
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Present Address: Centre for Novel Agricultural Products, University of York, Woodsmill Quay, Skeldergate, York, YO1 6DX UK
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Mikkel Christensen
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Present Address: UIT - Department of Chemistry, The Arctic University of Norway, Forskningsparken. 3, 9019 Tromsø, Norway
| | - Ying Liu
- Department of Plant and Environmental Sciences, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Hans H. Wandall
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Eric Paul Bennett
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Molecular and Cellular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, DK-2200 Copenhagen N, Denmark
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Eriksson D, Kershen D, Nepomuceno A, Pogson BJ, Prieto H, Purnhagen K, Smyth S, Wesseler J, Whelan A. A comparison of the EU regulatory approach to directed mutagenesis with that of other jurisdictions, consequences for international trade and potential steps forward. THE NEW PHYTOLOGIST 2019; 222:1673-1684. [PMID: 30548610 DOI: 10.1111/nph.15627] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/02/2018] [Indexed: 05/11/2023]
Abstract
A special regulatory regime applies to products of recombinant nucleic acid modifications. A ruling from the European Court of Justice has interpreted this regulatory regime in a way that it also applies to emerging mutagenesis techniques. Elsewhere regulatory progress is also ongoing. In 2015, Argentina launched a regulatory framework, followed by Chile in 2017 and recently Brazil and Colombia. In March 2018, the USDA announced that it will not regulate genome-edited plants differently if they could have also been developed through traditional breeding. Canada has an altogether different approach with their Plants with Novel Traits regulations. Australia is currently reviewing its Gene Technology Act. This article illustrates the deviation of the European Union's (EU's) approach from the one of most of the other countries studied here. Whereas the EU does not implement a case-by-case approach, this approach is taken by several other jurisdictions. Also, the EU court ruling adheres to a process-based approach while most other countries have a stronger emphasis on the regulation of the resulting product. It is concluded that, unless a functioning identity preservation system for products of directed mutagenesis can be established, the deviation results in a risk of asynchronous approvals and disruptions in international trade.
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Affiliation(s)
- Dennis Eriksson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden
| | - Drew Kershen
- College of Law, University of Oklahoma, 300 Timberdell Road, Norman, OK, 73019-5081, USA
| | - Alexandre Nepomuceno
- Brazilian Agricultural Research Cooperation - Embrapa, Brazilian Biosafety Technical Commission - CTNBio, PO Box 231, ZIP 86001-970, Londrina, PR, Brazil
| | - Barry J Pogson
- Global Plant Council and ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, 2601, ACT, Australia
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago de Chile, Chile
| | - Kai Purnhagen
- Law and Governance Group, Department of Social Sciences, Wageningen University, Hollandseweg 1, 6706 KN, Wageningen, the Netherlands
- Rotterdam Institute of Law and Economics, Law School, Erasmus University of Rotterdam, Burg. Oudlaan 50, 3062 PA, Rotterdam, the Netherlands
| | - Stuart Smyth
- Department of Agricultural and Resource Economics, University of Saskatchewan, 51 Campus Drive, Saskatoon, Sask., S7N 5A8, Canada
| | - Justus Wesseler
- Agricultural Economics and Rural Policy Group, Department of Social Sciences, Wageningen University, Hollandseweg 1, 6706 KN, Wageningen, the Netherlands
| | - Agustina Whelan
- Biotechnology Directorate, Ministry of AgroIndustry, Buenos Aires, Argentina
- National University of Quilmes, Bernal, Argentina
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Haroth S, Feussner K, Kelly AA, Zienkiewicz K, Shaikhqasem A, Herrfurth C, Feussner I. The glycosyltransferase UGT76E1 significantly contributes to 12- O-glucopyranosyl-jasmonic acid formation in wounded Arabidopsis thaliana leaves. J Biol Chem 2019; 294:9858-9872. [PMID: 31072871 DOI: 10.1074/jbc.ra119.007600] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/07/2019] [Indexed: 11/06/2022] Open
Abstract
Jasmonoyl-isoleucine (JA-Ile) is a phytohormone that orchestrates plant defenses in response to wounding, feeding insects, or necrotrophic pathogens. JA-Ile metabolism has been studied intensively, but its catabolism as a potentially important mechanism for the regulation of JA-Ile-mediated signaling is not well-understood. Especially the enzyme(s) responsible for specifically glycosylating 12-hydroxy-jasmonic acid (12-OH-JA) and thereby producing 12-O-glucopyranosyl-jasmonic acid (12-O-Glc-JA) is still elusive. Here, we used co-expression analyses of available Arabidopsis thaliana transcriptomic data, identifying four UDP-dependent glycosyltransferase (UGT) genes as wound-induced and 12-OH-JA-related, namely, UGT76E1, UGT76E2, UGT76E11, and UGT76E12 We heterologously expressed and purified the corresponding proteins to determine their individual substrate specificities and kinetic parameters. We then used an ex vivo metabolite-fingerprinting approach to investigate these proteins in conditions as close as possible to their natural environment, with an emphasis on greatly extending the range of potential substrates. As expected, we found that UGT76E1 and UGT76E2 are 12-OH-JA-UGTs, with UGT76E1 contributing a major in vivo UGT activity, as deduced from Arabidopsis mutants with abolished or increased UGT gene expression. In contrast, recombinant UGT76E11 acted on an unidentified compound and also glycosylated two other oxylipins, 11-hydroxy-7,9,13-hexadecatrienoic acid (11-HHT) and 13-hydroxy-9,11,15-octadecatrienoic acid (13-HOT), which were also accepted by recombinant UGT76E1, UGT76E2, and UGT76E12 enzymes. UGT76E12 glycosylated 12-OH-JA only to a low extent, but also accepted an artificial hydroxylated fatty acid and low amounts of kaempferol. In conclusion, our findings have elucidated the missing step in the wound-induced synthesis of 12-O-glucopyranosyl-jasmonic acid in A. thaliana.
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Affiliation(s)
- Sven Haroth
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and
| | - Kirstin Feussner
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and.,the Service Unit for Metabolomics and Lipidomics and
| | - Amélie A Kelly
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and
| | - Krzysztof Zienkiewicz
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and
| | - Alaa Shaikhqasem
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and
| | - Cornelia Herrfurth
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and.,the Service Unit for Metabolomics and Lipidomics and
| | - Ivo Feussner
- From the Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, Goettingen D-37077 and .,the Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, D-37077 Germany
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Prado GS, Bamogo PKA, de Abreu JAC, Gillet FX, dos Santos VO, Silva MCM, Brizard JP, Bemquerer MP, Bangratz M, Brugidou C, Sérémé D, Grossi-de-Sa MF, Lacombe S. Nicotiana benthamiana is a suitable transient system for high-level expression of an active inhibitor of cotton boll weevil α-amylase. BMC Biotechnol 2019; 19:15. [PMID: 30849970 PMCID: PMC6408794 DOI: 10.1186/s12896-019-0507-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 03/04/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Insect resistance in crops represents a main challenge for agriculture. Transgenic approaches based on proteins displaying insect resistance properties are widely used as efficient breeding strategies. To extend the spectrum of targeted pathogens and overtake the development of resistance, molecular evolution strategies have been used on genes encoding these proteins to generate thousands of variants with new or improved functions. The cotton boll weevil (Anthonomus grandis) is one of the major pests of cotton in the Americas. An α-amylase inhibitor (α-AIC3) variant previously developed via molecular evolution strategy showed inhibitory activity against A. grandis α-amylase (AGA). RESULTS We produced in a few days considerable amounts of α-AIC3 using an optimised transient heterologous expression system in Nicotiana benthamiana. This high α-AIC3 accumulation allowed its structural and functional characterizations. We demonstrated via MALDI-TOF MS/MS technique that the protein was processed as expected. It could inhibit up to 100% of AGA biological activity whereas it did not act on α-amylase of two non-pathogenic insects. These data confirmed that N. benthamiana is a suitable and simple system for high-level production of biologically active α-AIC3. Based on other benefits such as economic, health and environmental that need to be considerate, our data suggested that α-AIC3 could be a very promising candidate for the production of transgenic crops resistant to cotton boll weevil without lethal effect on at least two non-pathogenic insects. CONCLUSIONS We propose this expression system can be complementary to molecular evolution strategies to identify the most promising variants before starting long-lasting stable transgenic programs.
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Affiliation(s)
- Guilherme Souza Prado
- Embrapa Genetic Resources and Biotechnology, Brasília, DF Brazil
- Catholic University of Brasília, Brasília, DF Brazil
| | - Pingdwende Kader Aziz Bamogo
- IRD, CIRAD, Université Montpellier, Interactions Plantes Microorganismes et Environnement (IPME), Montpellier, France
- INERA/LMI Patho-Bios, Institut de L’Environnement et de Recherches Agricoles (INERA), Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | | | | | | | | | - Jean-Paul Brizard
- IRD, CIRAD, Université Montpellier, Interactions Plantes Microorganismes et Environnement (IPME), Montpellier, France
| | | | - Martine Bangratz
- IRD, CIRAD, Université Montpellier, Interactions Plantes Microorganismes et Environnement (IPME), Montpellier, France
- INERA/LMI Patho-Bios, Institut de L’Environnement et de Recherches Agricoles (INERA), Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - Christophe Brugidou
- IRD, CIRAD, Université Montpellier, Interactions Plantes Microorganismes et Environnement (IPME), Montpellier, France
- INERA/LMI Patho-Bios, Institut de L’Environnement et de Recherches Agricoles (INERA), Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - Drissa Sérémé
- INERA/LMI Patho-Bios, Institut de L’Environnement et de Recherches Agricoles (INERA), Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
| | - Maria Fatima Grossi-de-Sa
- Embrapa Genetic Resources and Biotechnology, Brasília, DF Brazil
- Catholic University of Brasília, Brasília, DF Brazil
| | - Séverine Lacombe
- IRD, CIRAD, Université Montpellier, Interactions Plantes Microorganismes et Environnement (IPME), Montpellier, France
- INERA/LMI Patho-Bios, Institut de L’Environnement et de Recherches Agricoles (INERA), Laboratoire de Virologie et de Biotechnologies Végétales, Ouagadougou, Burkina Faso
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Nadeem M, Li J, Yahya M, Wang M, Ali A, Cheng A, Wang X, Ma C. Grain Legumes and Fear of Salt Stress: Focus on Mechanisms and Management Strategies. Int J Mol Sci 2019; 20:E799. [PMID: 30781763 PMCID: PMC6412900 DOI: 10.3390/ijms20040799] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 12/27/2022] Open
Abstract
Salinity is an ever-present major constraint and a major threat to legume crops, particularly in areas with irrigated agriculture. Legumes demonstrate high sensitivity, especially during vegetative and reproductive phases. This review gives an overview of legumes sensitivity to salt stress (SS) and mechanisms to cope with salinity stress under unfavorable conditions. It also focuses on the promising management approaches, i.e., agronomic practices, breeding approaches, and genome editing techniques to improve performance of legumes under SS. Now, the onus is on researchers to comprehend the plants physiological and molecular mechanisms, in addition to various responses as part of their stress tolerance strategy. Due to their ability to fix biological nitrogen, high protein contents, dietary fiber, and essential mineral contents, legumes have become a fascinating group of plants. There is an immense need to develop SS tolerant legume varieties to meet growing demand of protein worldwide. This review covering crucial areas ranging from effects, mechanisms, and management strategies, may elucidate further the ways to develop SS-tolerant varieties and to produce legume crops in unfavorable environments.
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Affiliation(s)
- Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Jiajia Li
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Muhammad Yahya
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Minghua Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Asif Ali
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China.
| | - Andong Cheng
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Xiaobo Wang
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
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Abstract
Precise genome engineering can be efficiently made using the revolutionary tool named CRISPR/Cas (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein) systems. Adapted from the bacterial immune system, CRISPR/Cas systems can generate highly specific double-strand breaks (DSBs) at the target site, and desired sequence modifications can be introduced during the DSB repair process, such as nonhomologous end-joining (NHEJ) or homology-directed repair (HDR) pathways. CRISPR/Cas9 is the most widely used genome editing tool for targeted mutagenesis, precise sequence modification, transcriptional reprogramming, epigenome editing, disease treatment, and many more. The ease of use and high specificity make CRISPR/Cas9 a great tool not only for basic researches but also for crop trait improvements, such as higher grain yield, better tolerance to abiotic stresses, enhanced disease resistance, and better nutritional contents. In this protocol, we present a step-by-step guide to the CRISPR/Cas9-mediated targeted mutagenesis in maize Hi II genotype. Detailed procedures will guide through the essential steps including gRNA design, CRISPR/Cas9 vector construction, Agrobacterium-mediated maize immature embryo transformation, and molecular analysis of the transgenic plants to identify desired mutant lines.
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Gasparis S, Kała M, Przyborowski M, Łyżnik LA, Orczyk W, Nadolska-Orczyk A. A simple and efficient CRISPR/Cas9 platform for induction of single and multiple, heritable mutations in barley ( Hordeum vulgare L.). PLANT METHODS 2018; 14:111. [PMID: 30568723 PMCID: PMC6297969 DOI: 10.1186/s13007-018-0382-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 12/10/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Genome editing of monocot plants can be accomplished by using the components of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR associated Cas9) technology specifically optimized for these types of plants. Here, we present the development of RNA-guided Cas9 system for simplex and multiplex genome editing in barley. RESULTS We developed a set of customizable RNA-guided Cas9 binary vectors and sgRNA modules for simplex and multiplex editing in barley. To facilitate the design of RNA-guided Cas9 constructs, the pBract derived binary vectors were adapted to Gateway cloning and only one restriction enzyme was required for construction of the sgRNA. We designed a synthetic, codon optimized Cas9 gene containing the N terminal SV40 nuclear localization signal and the UBQ10 Arabidopsis 1st intron. Two different sgRNAs were constructed for simplex editing and one polycistronic tRNA-gRNA construct (PTG) for multiplex editing using an endogenous tRNA processing system. The RNA-guided Cas9 constructs were validated in transgenic barley plants produced by Agrobacterium-mediated transformation. The highest mutation rate was observed in simplex editing of the cytokinin oxidase/dehydrogenase HvCKX1 gene, where mutations at the hvckx1 locus were detected in 88% of the screened T0 plants. We also proved the efficacy of the PTG construct in the multiplex editing of two CKX genes by obtaining 9 plants (21% of all edited plants) with mutations induced in both HvCKX1 and HvCKX3. Analysis of the T1 lines revealed that mutations in the HvCKX1 gene were transmitted to the next generation of plants. Among 220 screened T1 plants we identified 85 heterozygous and 28 homozygous mutants, most of them bearing frameshift mutations in the HvCKX1 gene. We also observed independent segregation of mutations and the Cas9-sgRNA T-DNA insert in several T1 plants. Moreover, the knockout mutations of the Nud gene generated phenotype mutants with naked grains, and the phenotypic changes were identifiable in T0 plants. CONCLUSIONS We demonstrated the effectiveness of an optimized RNA-guided Cas9 system that can be used for generating homozygous knockout mutants in the progeny of transgenic barely plants. This is also the first report of successful multiplex editing in barley using a tRNA processing system.
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Affiliation(s)
- Sebastian Gasparis
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute – National Research Institute, 05-870 Radzików, Błonie, Poland
| | - Maciej Kała
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute – National Research Institute, 05-870 Radzików, Błonie, Poland
| | - Mateusz Przyborowski
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute – National Research Institute, 05-870 Radzików, Błonie, Poland
| | - Leszek A. Łyżnik
- Department of Plant Genetics, Breeding and Biotechnology, Warsaw University of Life Sciences (SGGW), 02-776 Warsaw, Poland
| | - Wacław Orczyk
- Department of Genetic Engineering, Plant Breeding and Acclimatization Institute – National Research Institute, 05-870 Radzików, Błonie, Poland
| | - Anna Nadolska-Orczyk
- Department of Functional Genomics, Plant Breeding and Acclimatization Institute – National Research Institute, 05-870 Radzików, Błonie, Poland
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Eriksson D. The Swedish policy approach to directed mutagenesis in a European context. PHYSIOLOGIA PLANTARUM 2018; 164:385-395. [PMID: 29602252 DOI: 10.1111/ppl.12740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/22/2018] [Accepted: 03/25/2018] [Indexed: 05/29/2023]
Abstract
This review describes the Swedish approach to directed mutagenesis in plants and puts it in a comparative European perspective. Directed mutagenesis is accomplished by a number of genome editing techniques; however, the legal status of these techniques and their resulting products is uncertain in the European Union (EU) as there is no political consensus on whether or not these should be regulated as genetically modified organisms (GMOs). A number of cases have developed over the past few years, putting the GMO regulatory framework to the test. These include oilseed rape developed by oligonucleotide-directed mutagenesis, Arabidopsis developed by clustered regularly interspaced short palindromic repeat-Cas9, and the case on mutagenesis for which the French Court requested a preliminary ruling from the Court of Justice of the EU. In this review, the involvement of the Swedish Government and governmental authorities in these cases is described and compared with that of other EU member states and/or EU entity statements and reports. Various approaches to the definition of recombinant nucleic acids are also discussed, as this is crucial for the EU GMO definition thus affecting the legal status of products developed by directed mutagenesis.
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Affiliation(s)
- Dennis Eriksson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, Alnarp, Sweden
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Qian X, Xiang Q, Yang T, Ma H, Ding XS, Tao X. Molecular Co-Chaperone SGT1 Is Critical for Cell-to-Cell Movement and Systemic Infection of Tomato Spotted Wild Virus in Nicotiana benthamiana. Viruses 2018; 10:E647. [PMID: 30453630 PMCID: PMC6267219 DOI: 10.3390/v10110647] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 11/06/2018] [Accepted: 11/15/2018] [Indexed: 12/20/2022] Open
Abstract
Tospovirus is a tripartite negative stranded RNA virus and is considered as one of the most devastating plant viruses. Successful virus infection in plant requires many host factors. To date, very few host factors have been identified as important in Tospovirus infection in plants. We reported earlier that NSm protein encoded by Tomato spotted wilt virus (TSWV), a type species of the genus Orthotospovirus, plays critical roles in viral cell-to-cell and long-distance movement. In this study, we determined that molecular co-chaperone NbSGT1 interacted with TSWV NSm in Nicotianabenthamiana. TSWV infection significantly upregulated the expression of NbSGT1 gene and transient overexpression of NbSGT1 in N.benthamiana leaves accelerated TSWV infection. In contrast, silencing the NbSGT1 gene expression using a virus-induced gene silencing (VIGS) approach strongly inhibited TSWV NSm cell-to-cell movement, as well as TSWV local and systemic infection in N.benthamiana plants. Furthermore, NbSGT1 was found to regulate the infection of both American and Euro/Asia type tospoviruses in N.benthamiana plant. Collectively, our findings presented in this paper and the results published previously indicated that molecular co-chaperone NbSGT1 plays important roles in modulating both positive stranded and tripartite negative stranded RNA virus infection in plants.
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Affiliation(s)
- Xin Qian
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qing Xiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tongqing Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Hongyu Ma
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xin Shun Ding
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaorong Tao
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China.
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Etienne H, Breton D, Breitler JC, Bertrand B, Déchamp E, Awada R, Marraccini P, Léran S, Alpizar E, Campa C, Courtel P, Georget F, Ducos JP. Coffee Somatic Embryogenesis: How Did Research, Experience Gained and Innovations Promote the Commercial Propagation of Elite Clones From the Two Cultivated Species? FRONTIERS IN PLANT SCIENCE 2018; 9:1630. [PMID: 30483287 PMCID: PMC6240679 DOI: 10.3389/fpls.2018.01630] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/19/2018] [Indexed: 05/09/2023]
Abstract
Since the 1990s, somatic embryogenesis (SE) has enabled the propagation of selected varieties, Arabica F1 hybrid and Robusta clones, originating from the two cultivated coffee species, Coffea arabica and Coffea canephora, respectively. This paper shows how mostly empirical research has led to successful industrial transfers launched in the 2000s in Latin America, Africa, and Asia. Coffee SE can be considered as a model for other woody perennial crops for the following reasons: (i) a high biological efficiency has been demonstrated for propagated varieties at all developmental stages, and (ii) somaclonal variation is understood and mastered thanks to intensive research combining molecular markers and field observations. Coffee SE is also a useful model given the strong economic constraints that are specific to this species. In brief, SE faced four difficulties: (i) the high cost of SE derived plants compared to the cost of seedlings of conventional varieties, (ii) the logistic problems involved in reaching small-scale coffee growers, (iii) the need for certification, and (iv) the lack of solvency among small-scale producers. Nursery activities were professionalized by introducing varietal certification, quality control with regard to horticultural problems and somaclonal variation, and sanitary control for Xylella fastidiosa. In addition, different technology transfers were made to ensure worldwide dissemination of improved F1 Arabica hybrids and Robusta clones. Innovations have been decisive for successful scaling-up and reduction of production costs, such as the development of temporary immersion bioreactors for the mass production of pre-germinated embryos, their direct sowing on horticultural soil, and the propagation of rejuvenated SE plants by rooted mini-cuttings. Today, SE is a powerful tool that is widely used in coffee for biotechnological applications including propagation and genetic transformation. Basic research has recently started taking advantage of optimized SE protocols. Based on -omics methodologies, research aims to decipher the molecular events involved in the key developmental switches of coffee SE. In parallel, a high-throughput screening of active molecules on SE appears to be a promising tool to speed-up the optimization of SE protocols.
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Affiliation(s)
- Hervé Etienne
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - David Breton
- Nestlé R&D Center Tours – Plant Science Research Unit, Tours, France
| | - Jean-Christophe Breitler
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Benoît Bertrand
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Eveline Déchamp
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Rayan Awada
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
- Nestlé R&D Center Tours – Plant Science Research Unit, Tours, France
| | - Pierre Marraccini
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Sophie Léran
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | | | - Claudine Campa
- IRD, CIRAD, Université de Montpellier, IPME, Montpellier, France
| | | | - Frédéric Georget
- CIRAD, UMR IPME, Montpellier, France
- IPME, Université de Montpellier, IRD, CIRAD, Montpellier, France
| | - Jean-Paul Ducos
- Nestlé R&D Center Tours – Plant Science Research Unit, Tours, France
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40
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Zhou J, Wang G, Liu Z. Efficient genome editing of wild strawberry genes, vector development and validation. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1868-1877. [PMID: 29577545 PMCID: PMC6181217 DOI: 10.1111/pbi.12922] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 03/06/2018] [Accepted: 03/15/2018] [Indexed: 05/18/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system is an effective genome editing tool for plant and animal genomes. However, there are still few reports on the successful application of CRISPR-Cas9 to horticultural plants, especially with regard to germ-line transmission of targeted mutations. Here, we report high-efficiency genome editing in the wild strawberry Fragaria vesca and its successful application to mutate the auxin biosynthesis gene TAA1 and auxin response factor 8 (ARF8). In our CRISPR system, the Arabidopsis U6 promoter AtU6-26 and the wild strawberry U6 promoter FveU6-2 were each used to drive the expression of sgRNA, and both promoters were shown to lead to high-efficiency genome editing in strawberry. To test germ-line transmission of the edited mutations and new mutations induced in the next generation, the progeny of the primary (T0) transgenic plants carrying the CRISPR construct was analysed. New mutations were detected in the progeny plants at a high efficiency, including large deletions between the two PAM sites. Further, T1 plants harbouring arf8 homozygous knockout mutations grew considerably faster than wild-type plants. The results indicate that our CRISPR vectors can be used to edit the wild strawberry genome at a high efficiency and that both sgRNA design and appropriate U6 promoters contribute to the success of genomic editing. Our results open up exciting opportunities for engineering strawberry and related horticultural crops to improve traits of economic importance.
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Affiliation(s)
- Junhui Zhou
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMDUSA
| | - Guoming Wang
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMDUSA
- State Key Laboratory of Crop Genetics and Germplasm EnhancementCentre of Pear Engineering Technology ResearchNanjing Agricultural UniversityNanjingJiangsuChina
| | - Zhongchi Liu
- Department of Cell Biology and Molecular GeneticsUniversity of MarylandCollege ParkMDUSA
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41
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Kadam US, Shelake RM, Chavhan RL, Suprasanna P. Concerns regarding 'off-target' activity of genome editing endonucleases. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:22-30. [PMID: 29653762 DOI: 10.1016/j.plaphy.2018.03.027] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2017] [Revised: 03/21/2018] [Accepted: 03/23/2018] [Indexed: 05/15/2023]
Abstract
Genome editing (GE) tools ensure targeted mutagenesis and sequence-specific modification in plants using a wide resource of customized endonucleases; namely, zinc-finger nucleases (ZFNs), and transcription activator-like effector nucleases (TALENs), and the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated protein) system. Among these, in recent times CRISPR/Cas9 has been widely used in functional genomics and plant genetic modification. A significant concern in the application of GE tools is the occurrence of 'off-target' activity and induced mutations, which may impede functional analysis and gene activity studies. Moreover, the 'off-target' activity results in either not reported or unknown, difficult to detect, produce non-quantifiable cellular signaling and physiological effects. In the past few years, several experimental methods have been developed to identify undesired mutations and to curtail 'off-target' cleavage. Improvement in target specificity and minimizing 'off-target' activity will offer better applications of GE technology in plant biology and crop improvement.
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Affiliation(s)
- Ulhas Sopanrao Kadam
- VD College of Agricultural Biotechnology, Latur, Maharashtra, India; Max-Planck Institute of Molecular Plant Physiology, Wissenschaftspark Golm, Am Muhlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Rahul Mahadev Shelake
- Plant Molecular Biology & Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Rahul L Chavhan
- VD College of Agricultural Biotechnology, Latur, Maharashtra, India
| | - Penna Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085 India
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42
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Singh M, Kumar M, Albertsen MC, Young JK, Cigan AM. Concurrent modifications in the three homeologs of Ms45 gene with CRISPR-Cas9 lead to rapid generation of male sterile bread wheat (Triticum aestivum L.). PLANT MOLECULAR BIOLOGY 2018; 97:371-383. [PMID: 29959585 DOI: 10.1007/s11103-018-0749-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 06/02/2018] [Indexed: 05/05/2023]
Abstract
Hexaploid bread wheat is not readily amenable to traditional mutagenesis approaches. In this study, we show efficient utilization of CRISPR-Cas system and Next Generation Sequencing for mutant analysis in wheat. Identification and manipulation of male fertility genes in hexaploid bread wheat is important for understanding the molecular basis of pollen development and to obtain novel sources of nuclear genetic male sterility (NGMS). The maize Male sterile 45 (Ms45) gene encodes a strictosidine synthase-like enzyme and has been shown to be required for male fertility. To investigate the role of Ms45 gene in wheat, mutations in the A, B and D homeologs were produced using CRISPR-Cas9. A variety of mutations in the three homeologs were recovered, including a plant from two different genotypes each with mutations in all three homeologs. Genetic analysis of the mutations demonstrated that all three wheat Ms45 homeologs contribute to male fertility and that triple homozygous mutants are required to abort pollen development and achieve male sterility. Further, it was demonstrated that a wild-type copy of Ms45 gene from rice was able to restore fertility to these wheat mutant plants. Taken together, these observations provide insights into the conservation of MS45 function in a polyploid species. Ms45 based NGMS can be potentially utilized for a Seed Production Technology (SPT)-like hybrid seed production system in wheat.
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Affiliation(s)
| | | | | | | | - A Mark Cigan
- DuPont Pioneer, Johnston, IA, USA
- Genus, DeForest, WI, USA
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Franco-Tormo MJ, Salas-Crisostomo M, Rocha NB, Budde H, Machado S, Murillo-Rodríguez E. CRISPR/Cas9, the Powerful New Genome-Editing Tool for Putative Therapeutics in Obesity. J Mol Neurosci 2018; 65:10-16. [PMID: 29732484 DOI: 10.1007/s12031-018-1076-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 04/20/2018] [Indexed: 12/12/2022]
Abstract
The molecular technology known as clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) is revolutionizing the field of medical research and deepening our understanding of numerous biological processes. The attraction of CRISPR/Cas9 lies in its ability to efficiently edit DNA or modulate gene expression in living eukaryotic cells and organisms, a technology that was once considered either too expensive or scientifically risky. CRISPR/Cas9 has been successfully applied in agriculture to develop the next generation of disease-resistant plants. Now, the capability of gene editing has been translated to the biomedical area, focusing on the future of medicine faced with drug-resistant microbes by selectively targeting genes involved in antibiotic resistance, for example, or finding the ultimate strategy for cancer or HIV. In this regard, it was recently demonstrated that an injection of cancer-fighting CRISPR-modified white blood cells in a patient suffering from metastatic lung cancer could lead to promising results. Researchers and bioethicists are debating questions about the regulation of CRISPR/Cas9 that must be addressed. While legal challenges surround the use of this technique for genetically modifying cell lines in humans, we review the basic understanding of CRISPR/Cas9 and discuss how this technology could represent a candidate for treatment of non-communicable diseases in nutrition, such as obesity.
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Affiliation(s)
- María José Franco-Tormo
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina División Ciencias de la Salud, Universidad Anáhuac Mayab, A.P. 96 Cordemex C.P, 97310, Mérida, Yucatán, Mexico.,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico
| | - Mireille Salas-Crisostomo
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina División Ciencias de la Salud, Universidad Anáhuac Mayab, A.P. 96 Cordemex C.P, 97310, Mérida, Yucatán, Mexico.,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico
| | - Nuno Barbosa Rocha
- Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.,Health School, Polytechnic Institute of Porto, Porto, Portugal
| | - Henning Budde
- Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.,Faculty of Human Sciences, Medical School Hamburg, Hamburg, Germany.,Physical Activity, Physical Education, Health and Sport Research Centre (PAPESH), Sports Science Department, School of Science and Engineering, Reykjavik University, Reykjavik, Iceland.,Lithuanian Sports University, Kaunas, Lithuania
| | - Sérgio Machado
- Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.,Laboratory of Panic and Respiration, Institute of Psychiatry of Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Physical Activity Neuroscience Laboratory, Physical Activity Sciences Postgraduate Program of Salgado de Oliveira University, Niterói, Brazil
| | - Eric Murillo-Rodríguez
- Laboratorio de Neurociencias Moleculares e Integrativas, Escuela de Medicina División Ciencias de la Salud, Universidad Anáhuac Mayab, A.P. 96 Cordemex C.P, 97310, Mérida, Yucatán, Mexico. .,Intercontinental Neuroscience Research Group, Mérida, Yucatán, Mexico.
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Bastiaansen JWM, Bovenhuis H, Groenen MAM, Megens HJ, Mulder HA. The impact of genome editing on the introduction of monogenic traits in livestock. Genet Sel Evol 2018; 50:18. [PMID: 29661133 PMCID: PMC5902981 DOI: 10.1186/s12711-018-0389-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2017] [Accepted: 04/02/2018] [Indexed: 01/11/2023] Open
Abstract
Background Genome editing technologies provide new tools for genetic improvement and have the potential to become the next game changer in animal and plant breeding. The aim of this study was to investigate how genome editing in combination with genomic selection can accelerate the introduction of a monogenic trait in a livestock population as compared to genomic selection alone. Methods A breeding population was simulated under genomic selection for a polygenic trait. After reaching Bulmer equilibrium, the selection objective was to increase the allele frequency of a monogenic trait, with or without genome editing, in addition to improving the polygenic trait. Scenarios were compared for time to fixation of the desired allele, selection response for the polygenic trait, and level of inbreeding. The costs, in terms of number of editing procedures, were compared to the benefits of having more animals with the desired phenotype of the monogenic trait. Effects of reduced editing efficiency were investigated. Results In a population of 20,000 selection candidates per generation, the total number of edited zygotes needed to reach fixation of the desired allele was 22,118, 7072, or 3912 with, no, moderate, or high selection emphasis on the monogenic trait, respectively. Genome editing resulted in up to four-fold faster fixation of the desired allele when efficiency was 100%, while the loss in long-term selection response for the polygenic trait was up to seven-fold less compared to genomic selection alone. With moderate selection emphasis on the monogenic trait, introduction of genome editing led to a four-fold reduction in the total number of animals showing the undesired phenotype before fixation. However, with a currently realistic editing efficiency of 4%, the number of required editing procedures increased by 72% and loss in selection response increased eight-fold compared to 100% efficiency. With low efficiency, loss in selection response was 29% more compared to genomic selection alone. Conclusions Genome editing strongly decreased the time to fixation for a desired allele compared to genomic selection alone. Reduced editing efficiency had a major impact on the number of editing procedures and on the loss in selection response. In addition to ethical and welfare considerations of genome editing, a careful assessment of its technical costs and benefits is required. Electronic supplementary material The online version of this article (10.1186/s12711-018-0389-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John W M Bastiaansen
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Henk Bovenhuis
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Martien A M Groenen
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands
| | - Han A Mulder
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands
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Liang Z, Chen K, Zhang Y, Liu J, Yin K, Qiu JL, Gao C. Genome editing of bread wheat using biolistic delivery of CRISPR/Cas9 in vitro transcripts or ribonucleoproteins. Nat Protoc 2018; 13:413-430. [PMID: 29388938 DOI: 10.1038/nprot.2017.145] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This protocol is an extension to: Nat. Protoc. 9, 2395-2410 (2014); doi:10.1038/nprot.2014.157; published online 18 September 2014In recent years, CRISPR/Cas9 has emerged as a powerful tool for improving crop traits. Conventional plant genome editing mainly relies on plasmid-carrying cassettes delivered by Agrobacterium or particle bombardment. Here, we describe DNA-free editing of bread wheat by delivering in vitro transcripts (IVTs) or ribonucleoprotein complexes (RNPs) of CRISPR/Cas9 by particle bombardment. This protocol serves as an extension of our previously published protocol on genome editing in bread wheat using CRISPR/Cas9 plasmids delivered by particle bombardment. The methods we describe not only eliminate random integration of CRISPR/Cas9 into genomic DNA, but also reduce off-target effects. In this protocol extension article, we present detailed protocols for preparation of IVTs and RNPs; validation by PCR/restriction enzyme (RE) and next-generation sequencing; delivery by biolistics; and recovery of mutants and identification of mutants by pooling methods and Sanger sequencing. To use these protocols, researchers should have basic skills and experience in molecular biology and biolistic transformation. By using these protocols, plants edited without the use of any foreign DNA can be generated and identified within 9-11 weeks.
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Affiliation(s)
- Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Key Laboratory of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, China
| | - Jinxing Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Kangquan Yin
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Jin-Long Qiu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
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Brain lipid binding protein mediates the proliferation of human glioblastoma cells by regulating ERK1/2 signaling pathway in vitro. In Vitro Cell Dev Biol Anim 2017; 54:156-162. [PMID: 29288341 DOI: 10.1007/s11626-017-0220-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/27/2017] [Indexed: 12/20/2022]
Abstract
Brain lipid binding protein (BLBP) is highly expressed in the radial glial cells (RGCs) of the central nervous system (CNS), in glioblastomas, and, in vitro, in U251 cells. In this report, we have demonstrated that increased BLBP expression in glioblastoma is associated with poor survival and used a double-vector CRISPR/Cas9 lentiviral system to deplete endogenous BLBP from U251 cells, we found that loss of BLBP induced cell growth inhibition and S-phase arrest. Moreover, an increase in P53 and a decrease in p-ERK1/2 were observed after BLBP depletion, suggesting a potential mechanism by which loss of BLBP results in growth inhibition.
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Fritsche S, Wang X, Jung C. Recent Advances in our Understanding of Tocopherol Biosynthesis in Plants: An Overview of Key Genes, Functions, and Breeding of Vitamin E Improved Crops. Antioxidants (Basel) 2017; 6:E99. [PMID: 29194404 PMCID: PMC5745509 DOI: 10.3390/antiox6040099] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/19/2017] [Accepted: 11/23/2017] [Indexed: 12/17/2022] Open
Abstract
Tocopherols, together with tocotrienols and plastochromanols belong to a group of lipophilic compounds also called tocochromanols or vitamin E. Considered to be one of the most powerful antioxidants, tocochromanols are solely synthesized by photosynthetic organisms including plants, algae, and cyanobacteria and, therefore, are an essential component in the human diet. Tocochromanols potent antioxidative properties are due to their ability to interact with polyunsaturated acyl groups and scavenge lipid peroxyl radicals and quench reactive oxygen species (ROS), thus protecting fatty acids from lipid peroxidation. In the plant model species Arabidopsis thaliana, the required genes for tocopherol biosynthesis and functional roles of tocopherols were elucidated in mutant and transgenic plants. Recent research efforts have led to new outcomes for the vitamin E biosynthetic and related pathways, and new possible alternatives for the biofortification of important crops have been suggested. Here, we review 30 years of research on tocopherols in model and crop species, with emphasis on the improvement of vitamin E content using transgenic approaches and classical breeding. We will discuss future prospects to further improve the nutritional value of our food.
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Affiliation(s)
- Steffi Fritsche
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany.
| | - Xingxing Wang
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany.
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Christian Jung
- Plant Breeding Institute, Christian-Albrechts-University of Kiel, 24118 Kiel, Germany.
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Barrero-Sicilia C, Silvestre S, Haslam RP, Michaelson LV. Lipid remodelling: Unravelling the response to cold stress in Arabidopsis and its extremophile relative Eutrema salsugineum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2017; 263:194-200. [PMID: 28818375 PMCID: PMC5567406 DOI: 10.1016/j.plantsci.2017.07.017] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 06/20/2017] [Accepted: 07/12/2017] [Indexed: 05/19/2023]
Abstract
Environmental constraints limit the geographic distribution of many economically important crops. Cold stress is an important abiotic stress that affects plant growth and development, resulting in loss of vigour and surface lesions. These symptoms are caused by, among other metabolic processes, the altered physical and chemical composition of cell membranes. As a major component of cell membranes lipids have been recognized as having a significant role in cold stress, both as a mechanical defence through leaf surface protection and plasma membrane remodelling, and as signal transduction molecules. We present an overview integrating gene expression and lipidomic data published so far in Arabidopsis and its relative the extremophile Eutrema salsugineum. This data enables a better understanding of the contribution of the lipidome in determining the ability to tolerate suboptimal temperature conditions. Collectively this information will allow us to identify the key lipids and pathways responsible for resilience, enabling the development of new approaches for crop tolerance to stress.
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Affiliation(s)
| | - Susana Silvestre
- Plant Sciences, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK
| | - Richard P Haslam
- Plant Sciences, Rothamsted Research, West Common, Harpenden, AL5 2JQ, UK.
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Kirchner TW, Niehaus M, Debener T, Schenk MK, Herde M. Efficient generation of mutations mediated by CRISPR/Cas9 in the hairy root transformation system of Brassica carinata. PLoS One 2017; 12:e0185429. [PMID: 28937992 PMCID: PMC5609758 DOI: 10.1371/journal.pone.0185429] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/12/2017] [Indexed: 11/23/2022] Open
Abstract
A protocol for the induction of site-directed deletions and insertions in the genome of Brassica carinata with CRISPR is described. The construct containing the Cas9 nuclease and the guide RNA (gRNA) was delivered by the hairy root transformation technique, and a successful transformation was monitored by GFP fluorescence. PAGE analysis of an amplified region, presumably containing the deletions and insertions, demonstrated up to seven different indels in one transgenic root and in all analyzed roots a wildtype allele of the modified gene was not detectable. Interestingly, many of these mutations consisted of relatively large indels with up to 112 bp. The exact size of the deletions was determined to allow an estimation whether the targeted gene was not functional due to a considerable deletion or a frame shift within the open reading frame. This allowed a direct phenotypic assessment of the previously characterized roots and, in fact, deletions in FASCICLIN-LIKE ARABINOGALACTAN PROTEIN 1 (BcFLA1)-a gene with an expression pattern consistent with a role in root hair architecture-resulted in shorter root hairs compared to control roots ectopically expressing an allele of the gene that cannot be targeted by the gRNA in parallel to the CRISPR construct. As an additional line of evidence, we monitored BcFLA1 expression with qPCR and detected a significant reduction of the transcript in roots with an active CRISPR construct compared to the control, although residual amounts of the transcript were detected, possibly due to inefficient nonsense-mediated mRNA decay. Additionally, the presence of deletions and insertions were verified by Sanger sequencing of the respective amplicons. In summary we demonstrate the successful application of CRISPR/Cas9 in hairy roots of B. carinata, the proof of its effectiveness and its effect on the root hair phenotype. This study paves the way for experimental strategies involving the phenotypic assessment of gene lesions by CRISPR which do not require germline transmission.
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Affiliation(s)
- Thomas W. Kirchner
- Institute of Plant Nutrition, Leibniz Universitaet Hannover, Hannover, Germany
| | - Markus Niehaus
- Institute of Plant Nutrition, Leibniz Universitaet Hannover, Hannover, Germany
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz Universitaet Hannover, Hannover, Germany
| | - Manfred K. Schenk
- Institute of Plant Nutrition, Leibniz Universitaet Hannover, Hannover, Germany
| | - Marco Herde
- Institute of Plant Nutrition, Leibniz Universitaet Hannover, Hannover, Germany
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50
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Sattar MN, Iqbal Z, Tahir MN, Shahid MS, Khurshid M, Al-Khateeb AA, Al-Khateeb SA. CRISPR/Cas9: A Practical Approach in Date Palm Genome Editing. FRONTIERS IN PLANT SCIENCE 2017; 8:1469. [PMID: 28878801 PMCID: PMC5572371 DOI: 10.3389/fpls.2017.01469] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/07/2017] [Indexed: 05/22/2023]
Abstract
The genetic modifications through breeding of crop plants have long been used to improve the yield and quality. However, precise genome editing (GE) could be a very useful supplementary tool for improvement of crop plants by targeted genome modifications. Various GE techniques including ZFNs (zinc finger nucleases), TALENs (transcription activator-like effector nucleases), and most recently clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 (CRISPR-associated protein 9)-based approaches have been successfully employed for various crop plants including fruit trees. CRISPR/Cas9-based approaches hold great potential in GE due to their simplicity, competency, and versatility over other GE techniques. However, to the best of our knowledge no such genetic improvement has ever been developed in date palm-an important fruit crop in Oasis agriculture. The applications of CRISPR/Cas9 can be a challenging task in date palm GE due to its large and complex genome, high rate of heterozygosity and outcrossing, in vitro regeneration and screening of mutants, high frequency of single-nucleotide polymorphism in the genome and ultimately genetic instability. In this review, we addressed the potential application of CRISPR/Cas9-based approaches in date palm GE to improve the sustainable date palm production. The availability of the date palm whole genome sequence has made it feasible to use CRISPR/Cas9 GE approach for genetic improvement in this species. Moreover, the future prospects of GE application in date palm are also addressed in this review.
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Affiliation(s)
- Muhammad N. Sattar
- Department of Environment and Natural Resources, Faculty of Agriculture and Food Sciences, King Faisal UniversityAl-Ahsa, Saudi Arabia
| | - Zafar Iqbal
- Akhuwat-Faisalabad Institute of Research, Science and TechnologyFaisalabad, Pakistan
| | - Muhammad N. Tahir
- National Institute for Biotechnology and Genetic EngineeringFaisalabad, Pakistan
| | - Muhammad S. Shahid
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos UniversityAl-Khoud, Oman
| | - Muhammad Khurshid
- Institute of Biochemistry and Biotechnology, University of the PunjabLahore, Pakistan
| | - Abdullatif A. Al-Khateeb
- Plant Biotechnology Department, Faculty of Agricultural and Food Sciences, King Faisal UniversityAl-Ahsa, Saudi Arabia
| | - Suliman A. Al-Khateeb
- Department of Environment and Natural Resources, Faculty of Agriculture and Food Sciences, King Faisal UniversityAl-Ahsa, Saudi Arabia
- Ministry of Environment, Water and AgricultureRiyadh, Saudi Arabia
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