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Azizi-Dargahlou S, Pouresmaeil M. Agrobacterium tumefaciens-Mediated Plant Transformation: A Review. Mol Biotechnol 2024; 66:1563-1580. [PMID: 37340198 DOI: 10.1007/s12033-023-00788-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 06/07/2023] [Indexed: 06/22/2023]
Abstract
Agrobacterium tumefaciens-mediated plant transformation is the most dominant technique for the transformation of plants. It is used to transform monocotyledonous and dicotyledonous plants. A. tumefaciens apply for stable and transient transformation, random and targeted integration of foreign genes, as well as genome editing of plants. The Advantages of this method include cheapness, uncomplicated operation, high reproducibility, a low copy number of integrated transgenes, and the possibility of transferring larger DNA fragments. Engineered endonucleases such as CRISPR/Cas9 systems, TALENs, and ZFNs can be delivered with this method. Nowadays, Agrobacterium-mediated transformation is used for the Knock in, Knock down, and Knock out of genes. The transformation effectiveness of this method is not always desirable. Researchers applied various strategies to improve the effectiveness of this method. Here, a general overview of the characteristics and mechanism of gene transfer with Agrobacterium is presented. Advantages, updated data on the factors involved in optimizing this method, and other useful materials that lead to maximum exploitation as well as overcoming obstacles of this method are discussed. Moreover, the application of this method in the generation of genetically edited plants is stated. This review can help researchers to establish a rapid and highly effective Agrobacterium-mediated transformation protocol for any plant species.
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Affiliation(s)
| | - Mahin Pouresmaeil
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
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2
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Patel A, Sinha S, Arantes P, Palermo G. Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.21.600075. [PMID: 38948825 PMCID: PMC11213026 DOI: 10.1101/2024.06.21.600075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
Cascade is a class 1, type 1 CRISPR-Cas system with a variety of roles in prokaryote defense, specifically against DNA-based viruses. The Vibrio Cholerae transposon, Tn6677, encodes a variant of the type 1F Cascade known as type 1F-3. This Cascade variant complexes with a homodimer of the transposition protein TniQ and leverages the sequence specificity of Cascade to direct the integration activity of the heteromeric transposase tnsA/B, resulting in site-specific transposition of Tn6677. We desire to uncover the molecular details behind R Loop formation of 'Cascade-TniQ.' Due to the lack of a complete model of Cascade-TniQ available at atom-level resolution, we first build a complete model using AlphaFold V2.1. We then simulate this model via classical molecular dynamics and umbrella sampling to study an important regulatory component within Cascade-TniQ, known as the Cas8 'bundle.' Particularly, we show that this alpha helical bundle experiences a free energy barrier to its large-scale translatory motions and relative free energies of its states primarily dependent on a loop within a Cas7 subunit in Cascade-TniQ. Further, we comment on additional structural and dynamical regulatory points of Cascade-TniQ during R Loop formation, such as Cascade-TniQ backbone rigidity, and the potential role TniQ plays in regulating bundle dynamics. In summary, our outcomes provide the first all-atom dynamic representation of one of the largest CRISPR systems, with information that can contribute to understanding the mechanism of nucleic acid binding and, eventually, to transposase recruitment itself. Such information may prove informative to advance genome engineering efforts.
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Kumari M, Checker VG, Kathpalia R, Srivastava V, Singh IK, Singh A. Metabolic engineering for enhanced terpenoid production: Leveraging new horizons with an old technique. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108511. [PMID: 38593484 DOI: 10.1016/j.plaphy.2024.108511] [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: 12/07/2023] [Revised: 02/06/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Terpenoids are a vast class of plant specialized metabolites (PSMs) manufactured by plants and are involved in their interactions with environment. In addition, they add health benefits to human nutrition and are widely used as pharmaceutically active compounds. However, native plants produce a limited amount of terpenes restricting metabolite yield of terpene-related metabolites. Exponential growth in the plant metabolome data and the requirement of alternative approaches for producing the desired amount of terpenoids, has redirected plant biotechnology research to plant metabolic engineering, which requires in-depth knowledge and precise expertise about dynamic plant metabolic pathways and cellular physiology. Metabolic engineering is an assuring tool for enhancing the concentration of terpenes by adopting specific strategies such as overexpression of the key genes associated with the biosynthesis of targeted metabolites, controlling the modulation of transcription factors, downregulation of competitive pathways (RNAi), co-expression of the biosynthetic pathway genes in heterologous system and other combinatorial approaches. Microorganisms, fast-growing host plants (such as Nicotiana benthamiana), and cell suspension/callus cultures have provided better means for producing valuable terpenoids. Manipulation in the biosynthetic pathways responsible for synthesis of terpenoids can provide opportunities to enhance the content of desired terpenoids and open up new avenues to enhance their production. This review deliberates the worth of metabolic engineering in medicinal plants to resolve issues associated with terpenoid production at a commercial scale. However, to bring the revolution through metabolic engineering, further implementation of genome editing, elucidation of metabolic pathways using omics approaches, system biology approaches, and synthetic biology tactics are essentially needed.
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Affiliation(s)
- Megha Kumari
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | | | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, 110007, India
| | - Vikas Srivastava
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, 181143, India
| | - Indrakant Kumar Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, Dhaula Kuan, New Delhi, 110021, India; Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India; Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India.
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4
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Hwang J, Ye DY, Jung GY, Jang S. Mobile genetic element-based gene editing and genome engineering: Recent advances and applications. Biotechnol Adv 2024; 72:108343. [PMID: 38521283 DOI: 10.1016/j.biotechadv.2024.108343] [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: 10/14/2023] [Revised: 03/14/2024] [Accepted: 03/16/2024] [Indexed: 03/25/2024]
Abstract
Genome engineering has revolutionized several scientific fields, ranging from biochemistry and fundamental research to therapeutic uses and crop development. Diverse engineering toolkits have been developed and used to effectively modify the genome sequences of organisms. However, there is a lack of extensive reviews on genome engineering technologies based on mobile genetic elements (MGEs), which induce genetic diversity within host cells by changing their locations in the genome. This review provides a comprehensive update on the versatility of MGEs as powerful genome engineering tools that offers efficient solutions to challenges associated with genome engineering. MGEs, including DNA transposons, retrotransposons, retrons, and CRISPR-associated transposons, offer various advantages, such as a broad host range, genome-wide mutagenesis, efficient large-size DNA integration, multiplexing capabilities, and in situ single-stranded DNA generation. We focused on the components, mechanisms, and features of each MGE-based tool to highlight their cellular applications. Finally, we discussed the current challenges of MGE-based genome engineering and provided insights into the evolving landscape of this transformative technology. In conclusion, the combination of genome engineering with MGE demonstrates remarkable potential for addressing various challenges and advancing the field of genetic manipulation, and promises to revolutionize our ability to engineer and understand the genomes of diverse organisms.
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Affiliation(s)
- Jaeseong Hwang
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Dae-Yeol Ye
- Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea
| | - Gyoo Yeol Jung
- School of Interdisciplinary Bioscience and Bioengineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea; Department of Chemical Engineering, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-gu, Pohang, Gyeongbuk 37673, Republic of Korea.
| | - Sungho Jang
- Department of Bioengineering and Nano-Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Division of Bioengineering, College of Life Sciences and Bioengineering, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea; Research Center for Bio Materials & Process Development, Incheon National University, 119 Academy-ro, Yeonsu-gu, Incheon 22012, Republic of Korea.
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5
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Vondracek K, Altpeter F, Liu T, Lee S. Advances in genomics and genome editing for improving strawberry ( Fragaria ×ananassa). Front Genet 2024; 15:1382445. [PMID: 38706796 PMCID: PMC11066249 DOI: 10.3389/fgene.2024.1382445] [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: 02/05/2024] [Accepted: 04/04/2024] [Indexed: 05/07/2024] Open
Abstract
The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.
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Affiliation(s)
- Kaitlyn Vondracek
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Fredy Altpeter
- University of Florida, Agronomy Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Tie Liu
- University of Florida, Horticultural Sciences Department, Institute of Food and Agricultural Sciences, Gainesville, FL, United States
| | - Seonghee Lee
- Gulf Coast Research and Education Center, Institute of Food and Agricultural Sciences, University of Florida, Wimauma, FL, United States
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6
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Shumega AR, Pavlov YI, Chirinskaite AV, Rubel AA, Inge-Vechtomov SG, Stepchenkova EI. CRISPR/Cas9 as a Mutagenic Factor. Int J Mol Sci 2024; 25:823. [PMID: 38255897 PMCID: PMC10815272 DOI: 10.3390/ijms25020823] [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: 11/15/2023] [Revised: 12/23/2023] [Accepted: 01/03/2024] [Indexed: 01/24/2024] Open
Abstract
The discovery of the CRISPR/Cas9 microbial adaptive immune system has revolutionized the field of genetics, by greatly enhancing the capacity for genome editing. CRISPR/Cas9-based editing starts with DNA breaks (or other lesions) predominantly at target sites and, unfortunately, at off-target genome sites. DNA repair systems differing in accuracy participate in establishing desired genetic changes but also introduce unwanted mutations, that may lead to hereditary, oncological, and other diseases. New approaches to alleviate the risks associated with genome editing include attenuating the off-target activity of editing complex through the use of modified forms of Cas9 nuclease and single guide RNA (sgRNA), improving delivery methods for sgRNA/Cas9 complex, and directing DNA lesions caused by the sgRNA/Cas9 to non-mutagenic repair pathways. Here, we have described CRISPR/Cas9 as a new powerful mutagenic factor, discussed its mutagenic properties, and reviewed factors influencing the mutagenic activity of CRISPR/Cas9.
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Affiliation(s)
- Andrey R. Shumega
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA;
- Departments of Biochemistry and Molecular Biology, Pathology and Microbiology, Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Angelina V. Chirinskaite
- Center of Transgenesis and Genome Editing, St. Petersburg State University, Universitetskaja Emb., 7/9, 199034 St. Petersburg, Russia;
| | - Aleksandr A. Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, 199034 St. Petersburg, Russia;
| | - Sergey G. Inge-Vechtomov
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, St. Petersburg State University, 199034 St. Petersburg, Russia; (A.R.S.); (S.G.I.-V.)
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, 199034 St. Petersburg, Russia
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7
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Prado GS, Rocha DC, dos Santos LN, Contiliani DF, Nobile PM, Martinati-Schenk JC, Padilha L, Maluf MP, Lubini G, Pereira TC, Monteiro-Vitorello CB, Creste S, Boscariol-Camargo RL, Takita MA, Cristofani-Yaly M, de Souza AA. CRISPR technology towards genome editing of the perennial and semi-perennial crops citrus, coffee and sugarcane. FRONTIERS IN PLANT SCIENCE 2024; 14:1331258. [PMID: 38259920 PMCID: PMC10801916 DOI: 10.3389/fpls.2023.1331258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
Gene editing technologies have opened up the possibility of manipulating the genome of any organism in a predicted way. CRISPR technology is the most used genome editing tool and, in agriculture, it has allowed the expansion of possibilities in plant biotechnology, such as gene knockout or knock-in, transcriptional regulation, epigenetic modification, base editing, RNA editing, prime editing, and nucleic acid probing or detection. This technology mostly depends on in vitro tissue culture and genetic transformation/transfection protocols, which sometimes become the major challenges for its application in different crops. Agrobacterium-mediated transformation, biolistics, plasmid or RNP (ribonucleoprotein) transfection of protoplasts are some of the commonly used CRISPR delivery methods, but they depend on the genotype and target gene for efficient editing. The choice of the CRISPR system (Cas9, Cas12), CRISPR mechanism (plasmid or RNP) and transfection technique (Agrobacterium spp., PEG solution, lipofection) directly impacts the transformation efficiency and/or editing rate. Besides, CRISPR/Cas technology has made countries rethink regulatory frameworks concerning genetically modified organisms and flexibilize regulatory obstacles for edited plants. Here we present an overview of the state-of-the-art of CRISPR technology applied to three important crops worldwide (citrus, coffee and sugarcane), considering the biological, methodological, and regulatory aspects of its application. In addition, we provide perspectives on recently developed CRISPR tools and promising applications for each of these crops, thus highlighting the usefulness of gene editing to develop novel cultivars.
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Affiliation(s)
- Guilherme Souza Prado
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
| | - Dhiôvanna Corrêia Rocha
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Lucas Nascimento dos Santos
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
- Institute of Biology, State University of Campinas (Unicamp), Campinas, Brazil
| | - Danyel Fernandes Contiliani
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Paula Macedo Nobile
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
| | | | - Lilian Padilha
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Mirian Perez Maluf
- Coffee Center of the Agronomic Institute of Campinas (IAC), Campinas, Brazil
- Embrapa Coffee, Brazilian Agricultural Research Corporation, Brasília, Federal District, Brazil
| | - Greice Lubini
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | - Tiago Campos Pereira
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão Preto, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Silvana Creste
- Sugarcane Research Center – Agronomic Institute (IAC), Ribeirão Preto, Brazil
- Ribeirão Preto Medical School, University of São Paulo (USP), Ribeirão Preto, Brazil
| | | | - Marco Aurélio Takita
- Citrus Research Center “Sylvio Moreira” – Agronomic Institute (IAC), Cordeirópolis, Brazil
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Kharbikar L, Konwarh R, Chakraborty M, Nandanwar S, Marathe A, Yele Y, Ghosh PK, Sanan-Mishra N, Singh AP. 3Bs of CRISPR-Cas mediated genome editing in plants: exploring the basics, bioinformatics and biosafety landscape. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1825-1850. [PMID: 38222286 PMCID: PMC10784264 DOI: 10.1007/s12298-023-01397-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/16/2024]
Abstract
The recent thrust in research has projected the type II clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR-Cas9) system as an avant-garde plant genome editing tool. It facilitates the induction of site-specific double-stranded DNA cleavage by the RNA-guided DNA endonuclease (RGEN), Cas9. Elimination, addition, or alteration of sections in DNA sequence besides the creation of a knockout genotype (CRISPRko) is aided by the CRISPR-Cas9 system in its wild form (wtCas9). The inactivation of the nuclease domain generates a dead Cas9 (dCas9), which is capable of targeting genomic DNA without scissoring it. The dCas9 system can be engineered by fusing it with different effectors to facilitate transcriptional activation (CRISPRa) and transcriptional interference (CRISPRi). CRISPR-Cas thus holds tremendous prospects as a genome-manipulating stratagem for a wide gamut of crops. In this article, we present a brief on the fundamentals and the general workflow of the CRISPR-Cas system followed by an overview of the prospects of bioinformatics in propelling CRISPR-Cas research with a special thrust on the available databases and algorithms/web-accessible applications that have aided in increasing the usage and efficiency of editing. The article also provides an update on the current regulatory landscape in different countries on the CRISPR-Cas edited plants to emphasize the far-reaching impact of the genomic editing technology. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01397-3.
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Affiliation(s)
- Lalit Kharbikar
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Rocktotpal Konwarh
- Department of Biotechnology, Addis Ababa Science and Technology University, Addis Ababa, Ethiopia
- Baba Kinaram Research Foundation (BKRF), Bramsthan, Mau, Uttar Pradesh India
| | - Monoswi Chakraborty
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Bengaluru, Karnataka India
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shweta Nandanwar
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Ashish Marathe
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Yogesh Yele
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Probir Kumar Ghosh
- ICAR - National Institute of Biotic Stress Management (NIBSM), Raipur, India
| | - Neeti Sanan-Mishra
- International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Anand Pratap Singh
- Baba Kinaram Research Foundation (BKRF), Bramsthan, Mau, Uttar Pradesh India
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Movahedi A, Aghaei-Dargiri S, Li H, Zhuge Q, Sun W. CRISPR Variants for Gene Editing in Plants: Biosafety Risks and Future Directions. Int J Mol Sci 2023; 24:16241. [PMID: 38003431 PMCID: PMC10671001 DOI: 10.3390/ijms242216241] [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: 09/27/2023] [Revised: 10/25/2023] [Accepted: 11/09/2023] [Indexed: 11/26/2023] Open
Abstract
The CRISPR genome editing technology is a crucial tool for enabling revolutionary advancements in plant genetic improvement. This review shows the latest developments in CRISPR/Cas9 genome editing system variants, discussing their benefits and limitations for plant improvement. While this technology presents immense opportunities for plant breeding, it also raises serious biosafety concerns that require careful consideration, including potential off-target effects and the unintended transfer of modified genes to other organisms. This paper highlights strategies to mitigate biosafety risks and explores innovative plant gene editing detection methods. Our review investigates the international biosafety guidelines for gene-edited crops, analyzing their broad implications for agricultural and biotechnology research and advancement. We hope to provide illuminating and refined perspectives for industry practitioners and policymakers by evaluating CRISPR genome enhancement in plants.
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Affiliation(s)
- Ali Movahedi
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Soheila Aghaei-Dargiri
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research Education and Extension Organization (AREEO), Tehran 19858-13111, Iran
| | - Hongyan Li
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Qiang Zhuge
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
| | - Weibo Sun
- Department of Biology and the Environment, College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
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Suprasanna P, Klimek-Chodacka M, Jain SM. Editorial: CRISPR tools, technology development, and application. FRONTIERS IN PLANT SCIENCE 2023; 14:1329780. [PMID: 38023829 PMCID: PMC10679726 DOI: 10.3389/fpls.2023.1329780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023]
Affiliation(s)
- Penna Suprasanna
- Amity Centre for Nuclear Biotechnology, Amity Institute of Biotechnology, Amity University of Maharashtra, Mumbai, India
| | | | - Shri Mohan Jain
- Department of Plant Production, University of Helsinki, Helsinki, Finland
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Vu BN, Vu TV, Yoo JY, Nguyen NT, Ko KS, Kim JY, Lee KO. CRISPR-Cas-mediated unfolded protein response control for enhancing plant stress resistance. FRONTIERS IN PLANT SCIENCE 2023; 14:1271368. [PMID: 37908833 PMCID: PMC10613997 DOI: 10.3389/fpls.2023.1271368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/02/2023] [Indexed: 11/02/2023]
Abstract
Plants consistently encounter environmental stresses that negatively affect their growth and development. To mitigate these challenges, plants have developed a range of adaptive strategies, including the unfolded protein response (UPR), which enables them to manage endoplasmic reticulum (ER) stress resulting from various adverse conditions. The CRISPR-Cas system has emerged as a powerful tool for plant biotechnology, with the potential to improve plant tolerance and resistance to biotic and abiotic stresses, as well as enhance crop productivity and quality by targeting specific genes, including those related to the UPR. This review highlights recent advancements in UPR signaling pathways and CRISPR-Cas technology, with a particular focus on the use of CRISPR-Cas in studying plant UPR. We also explore prospective applications of CRISPR-Cas in engineering UPR-related genes for crop improvement. The integration of CRISPR-Cas technology into plant biotechnology holds the promise to revolutionize agriculture by producing crops with enhanced resistance to environmental stresses, increased productivity, and improved quality traits.
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Affiliation(s)
- Bich Ngoc Vu
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
| | - Tien Van Vu
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Jae Yong Yoo
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Ngan Thi Nguyen
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Seong Ko
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Jae-Yean Kim
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
- Nulla Bio Inc., Jinju, Republic of Korea
| | - Kyun Oh Lee
- Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Division of Applied Life Science (BK21 Four), Gyeongsang National University, Jinju, Republic of Korea
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Yadav B, Majhi A, Phagna K, Meena MK, Ram H. Negative regulators of grain yield and mineral contents in rice: potential targets for CRISPR-Cas9-mediated genome editing. Funct Integr Genomics 2023; 23:317. [PMID: 37837547 DOI: 10.1007/s10142-023-01244-4] [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: 07/31/2023] [Revised: 09/27/2023] [Accepted: 09/29/2023] [Indexed: 10/16/2023]
Abstract
Rice is a major global staple food crop, and improving its grain yield and nutritional quality has been a major thrust research area since last decades. Yield and nutritional quality are complex traits which are controlled by multiple signaling pathways. Sincere efforts during past decades of research have identified several key genetic and molecular regulators that governed these complex traits. The advent of clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9)-mediated gene knockout approaches has accelerated the development of improved varieties; however, finding out target gene with negative regulatory function in particular trait without giving any pleiotropic effect remains a challenge. Here, we have reviewed past and recent literature and identified important negative regulators of grain yield and mineral contents which could be potential targets for CRISPR-Cas9-mediated gene knockout. Additionally, we have also compiled a list of microRNAs (miRNAs), which target positive regulators of grain yield, plant stress tolerance, and grain mineral contents. Knocking out these miRNAs could help to increase expression of such positive regulators and thus improve the plant trait. The knowledge presented in this review would help to further accelerate the CRISPR-Cas9-mediated trait improvement in rice.
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Affiliation(s)
- Banita Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Ashis Majhi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Kanika Phagna
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mukesh Kumar Meena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
| | - Hasthi Ram
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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13
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Yadav S, Kalwan G, Meena S, Gill SS, Yadava YK, Gaikwad K, Jain PK. Unravelling the due importance of pseudogenes and their resurrection in plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108062. [PMID: 37778114 DOI: 10.1016/j.plaphy.2023.108062] [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: 07/20/2023] [Revised: 09/22/2023] [Accepted: 09/26/2023] [Indexed: 10/03/2023]
Abstract
The complexities of a genome are underpinned to the vast expanses of the intergenic region, which constitutes ∼97-98% of the genome. This region is essentially composed of what is colloquially referred to as the "junk DNA" and is composed of various elements like transposons, repeats, pseudogenes, etc. The latter have long been considered as dead elements merely contributing to transcriptional noise in the genome. Many studies now describe the previously unknown regulatory functions of these genes. Recent advances in the Next-generation sequencing (NGS) technologies have allowed unprecedented access to these regions. With the availability of whole genome sequences of more than 788 different plant species in past 20 years, genome annotation has become feasible like never before. Different bioinformatic pipelines are available for the identification of pseudogenes. However, still little is known about their biological functions. The functional validation of these genes remains challenging and research in this area is still in infancy, particularly in plants. CRISPR/Cas-based genome editing could provide solutions to understand the biological roles of these genes by allowing creation of precise edits within these genes. The possibility of pseudogene reactivation or resurrection as has been demonstrated in a few studies might open new avenues of genetic manipulation to yield a desirable phenotype. This review aims at comprehensively summarizing the progress made with regards to the identification of pseudogenes and understanding their biological functions in plants.
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Affiliation(s)
- Sheel Yadav
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gopal Kalwan
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India; PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Shashi Meena
- PG School, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India; Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sarvajeet Singh Gill
- Stress Physiology & Molecular Biology Lab, Centre for Biotechnology, Maharshi Dayanand University, Rohtak, 124 001, Haryana, India
| | - Yashwant K Yadava
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India
| | - P K Jain
- ICAR-National Institute for Plant Biotechnology, New Delhi, 110012, India.
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Sabnam N, Hussain A, Saha P. The secret password: Cell death-inducing proteins in filamentous phytopathogens - As versatile tools to develop disease-resistant crops. Microb Pathog 2023; 183:106276. [PMID: 37541554 DOI: 10.1016/j.micpath.2023.106276] [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: 05/05/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/06/2023]
Abstract
Cell death-inducing proteins (CDIPs) are some of the secreted effector proteins manifested by filamentous oomycetes and fungal pathogens to invade the plant tissue and facilitate infection. Along with their involvement in different developmental processes and virulence, CDIPs play a crucial role in plant-pathogen interactions. As the name implies, CDIPs cause necrosis and trigger localised cell death in the infected host tissues by the accumulation of higher concentrations of hydrogen peroxide (H2O2), oxidative burst, accumulation of nitric oxide (NO), and electrolyte leakage. They also stimulate the biosynthesis of defense-related phytohormones such as salicylic acid (SA), jasmonic acid (JA), abscisic acid (ABA), and ethylene (ET), as well as the expression of pathogenesis-related (PR) genes that are important in disease resistance. Altogether, the interactions result in the hypersensitive response (HR) in the host plant, which might confer systemic acquired resistance (SAR) in some cases against a vast array of related and unrelated pathogens. The CDIPs, due to their capability of inducing host resistance, are thus unique among the array of proteins secreted by filamentous plant pathogens. More interestingly, a few transgenic plant lines have also been developed expressing the CDIPs with added resistance. Thus, CDIPs have opened an interesting hot area of research. The present study critically reviews the current knowledge of major types of CDIPs identified across filamentous phytopathogens and their modes of action in the last couple of years. This review also highlights the recent breakthrough technologies in studying plant-pathogen interactions as well as crop improvement by enhancing disease resistance through CDIPs.
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Affiliation(s)
- Nazmiara Sabnam
- Department of Life Sciences, Presidency University, Kolkata, India.
| | - Afzal Hussain
- Department of Bioinformatics, Maulana Azad National Institute of Technology, Bhopal, India
| | - Pallabi Saha
- Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota, 55108, United States; Department of Biotechnology, National Institute of Technology, Durgapur, India
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KhokharVoytas A, Shahbaz M, Maqsood MF, Zulfiqar U, Naz N, Iqbal UZ, Sara M, Aqeel M, Khalid N, Noman A, Zulfiqar F, Al Syaad KM, AlShaqhaa MA. Genetic modification strategies for enhancing plant resilience to abiotic stresses in the context of climate change. Funct Integr Genomics 2023; 23:283. [PMID: 37642792 DOI: 10.1007/s10142-023-01202-0] [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: 05/08/2023] [Revised: 07/18/2023] [Accepted: 08/02/2023] [Indexed: 08/31/2023]
Abstract
Enhancing the resilience of plants to abiotic stresses, such as drought, salinity, heat, and cold, is crucial for ensuring global food security challenge in the context of climate change. The adverse effects of climate change, characterized by rising temperatures, shifting rainfall patterns, and increased frequency of extreme weather events, pose significant threats to agricultural systems worldwide. Genetic modification strategies offer promising approaches to develop crops with improved abiotic stress tolerance. This review article provides a comprehensive overview of various genetic modification techniques employed to enhance plant resilience. These strategies include the introduction of stress-responsive genes, transcription factors, and regulatory elements to enhance stress signaling pathways. Additionally, the manipulation of hormone signaling pathways, osmoprotectant accumulation, and antioxidant defense mechanisms is discussed. The use of genome editing tools, such as CRISPR-Cas9, for precise modification of target genes related to stress tolerance is also explored. Furthermore, the challenges and future prospects of genetic modification for abiotic stress tolerance are highlighted. Understanding and harnessing the potential of genetic modification strategies can contribute to the development of resilient crop varieties capable of withstanding adverse environmental conditions caused by climate change, thereby ensuring sustainable agricultural productivity and food security.
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Affiliation(s)
| | - Muhammad Shahbaz
- Department of Botany, University of Agriculture, Faisalabad, Pakistan.
| | | | - Usman Zulfiqar
- Department of Agronomy, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan.
| | - Nargis Naz
- Department of Botany, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Usama Zafar Iqbal
- Department of Botany, University of Agriculture, Faisalabad, Pakistan
| | - Maheen Sara
- Department of Nutritional Sciences, Government College Women University, Faisalabad, Pakistan
| | - Muhammad Aqeel
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems (SKLHIGA), College of Ecology, Lanzhou University, Lanzhou, 730000, Gansu, People's Republic of China
| | - Noreen Khalid
- Department of Botany, Government College Women University Sialkot, Sialkot, Pakistan
| | - Ali Noman
- Department of Botany, Government College University, Faisalabad, Pakistan
| | - Faisal Zulfiqar
- Department of Horticultural Sciences, Faculty of Agriculture and Environment, The Islamia University of Bahawalpur, Bahawalpur, 63100, Pakistan
| | - Khalid M Al Syaad
- Department of Biology, College of Science, King Khalid University, Abha, 61413, Saudi Arabia
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Qureshi A, Connolly JB. Bioinformatic and literature assessment of toxicity and allergenicity of a CRISPR-Cas9 engineered gene drive to control Anopheles gambiae the mosquito vector of human malaria. Malar J 2023; 22:234. [PMID: 37580703 PMCID: PMC10426224 DOI: 10.1186/s12936-023-04665-5] [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: 12/02/2022] [Accepted: 08/07/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Population suppression gene drive is currently being evaluated, including via environmental risk assessment (ERA), for malaria vector control. One such gene drive involves the dsxFCRISPRh transgene encoding (i) hCas9 endonuclease, (ii) T1 guide RNA (gRNA) targeting the doublesex locus, and (iii) DsRed fluorescent marker protein, in genetically-modified mosquitoes (GMMs). Problem formulation, the first stage of ERA, for environmental releases of dsxFCRISPRh previously identified nine potential harms to the environment or health that could occur, should expressed products of the transgene cause allergenicity or toxicity. METHODS Amino acid sequences of hCas9 and DsRed were interrogated against those of toxins or allergens from NCBI, UniProt, COMPARE and AllergenOnline bioinformatic databases and the gRNA was compared with microRNAs from the miRBase database for potential impacts on gene expression associated with toxicity or allergenicity. PubMed was also searched for any evidence of toxicity or allergenicity of Cas9 or DsRed, or of the donor organisms from which these products were originally derived. RESULTS While Cas9 nuclease activity can be toxic to some cell types in vitro and hCas9 was found to share homology with the prokaryotic toxin VapC, there was no evidence from previous studies of a risk of toxicity to humans and other animals from hCas9. Although hCas9 did contain an 8-mer epitope found in the latex allergen Hev b 9, the full amino acid sequence of hCas9 was not homologous to any known allergens. Combined with a lack of evidence in the literature of Cas9 allergenicity, this indicated negligible risk to humans of allergenicity from hCas9. No matches were found between the gRNA and microRNAs from either Anopheles or humans. Moreover, potential exposure to dsxFCRISPRh transgenic proteins from environmental releases was assessed as negligible. CONCLUSIONS Bioinformatic and literature assessments found no convincing evidence to suggest that transgenic products expressed from dsxFCRISPRh were allergens or toxins, indicating that environmental releases of this population suppression gene drive for malaria vector control should not result in any increased allergenicity or toxicity in humans or animals. These results should also inform evaluations of other GMMs being developed for vector control and in vivo clinical applications of CRISPR-Cas9.
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Affiliation(s)
- Alima Qureshi
- Department of Life Sciences, Imperial College London, Silwood Park, Sunninghill, Ascot, UK
| | - John B Connolly
- Department of Life Sciences, Imperial College London, Silwood Park, Sunninghill, Ascot, UK.
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Chauhan S, Tiwari PN, Payasi DK. Genome Editing and Improvement of Abiotic Stress Tolerance in Crop Plants. Life (Basel) 2023; 13:1456. [PMID: 37511831 PMCID: PMC10381907 DOI: 10.3390/life13071456] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/25/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023] Open
Abstract
Genome editing aims to revolutionise plant breeding and could assist in safeguarding the global food supply. The inclusion of a 12-40 bp recognition site makes mega nucleases the first tools utilized for genome editing and first generation gene-editing tools. Zinc finger nucleases (ZFNs) are the second gene-editing technique, and because they create double-stranded breaks, they are more dependable and effective. ZFNs were the original designed nuclease-based approach of genome editing. The Cys2-His2 zinc finger domain's discovery made this technique possible. Clustered regularly interspaced short palindromic repeats (CRISPR) are utilized to improve genetics, boost biomass production, increase nutrient usage efficiency, and develop disease resistance. Plant genomes can be effectively modified using genome-editing technologies to enhance characteristics without introducing foreign DNA into the genome. Next-generation plant breeding will soon be defined by these exact breeding methods. There is abroad promise that genome-edited crops will be essential in the years to come for improving the sustainability and climate-change resilience of food systems. This method also has great potential for enhancing crops' resistance to various abiotic stressors. In this review paper, we summarize the most recent findings about the mechanism of abiotic stress response in crop plants and the use of the CRISPR/Cas mediated gene-editing systems to improve tolerance to stresses including drought, salinity, cold, heat, and heavy metals.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Shailja Chauhan
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Prakash Narayan Tiwari
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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Bishnoi R, Kaur S, Sandhu JS, Singla D. Genome engineering of disease susceptibility genes for enhancing resistance in plants. Funct Integr Genomics 2023; 23:207. [PMID: 37338599 DOI: 10.1007/s10142-023-01133-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 06/21/2023]
Abstract
Introgression of disease resistance genes (R-genes) to fight against an array of phytopathogens takes several years using conventional breeding approaches. Pathogens develop mechanism(s) to escape plants immune system by evolving new strains/races, thus making them susceptible to disease. Conversely, disruption of host susceptibility factors (or S-genes) provides opportunities for resistance breeding in crops. S-genes are often exploited by phytopathogens to promote their growth and infection. Therefore, identification and targeting of disease susceptibility genes (S-genes) are gaining more attention for the acquisition of resistance in plants. Genome engineering of S-genes results in targeted, transgene-free gene modification through CRISPR-Cas-mediated technology and has been reported in several agriculturally important crops. In this review, we discuss the defense mechanism in plants against phytopathogens, tug of war between R-genes and S-genes, in silico techniques for identification of host-target (S-) genes and pathogen effector molecule(s), CRISPR-Cas-mediated S-gene engineering, its applications, challenges, and future prospects.
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Affiliation(s)
- Ritika Bishnoi
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
| | - Sehgeet Kaur
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Jagdeep Singh Sandhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Deepak Singla
- Bioinformatics Centre, School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India.
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Ahmad N, Fatima S, Mehmood MA, Zaman QU, Atif RM, Zhou W, Rahman MU, Gill RA. Targeted genome editing in polyploids: lessons from Brassica. FRONTIERS IN PLANT SCIENCE 2023; 14:1152468. [PMID: 37409308 PMCID: PMC10318174 DOI: 10.3389/fpls.2023.1152468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 04/11/2023] [Indexed: 07/07/2023]
Abstract
CRISPR-mediated genome editing has emerged as a powerful tool for creating targeted mutations in the genome for various applications, including studying gene functions, engineering resilience against biotic and abiotic stresses, and increasing yield and quality. However, its utilization is limited to model crops for which well-annotated genome sequences are available. Many crops of dietary and economic importance, such as wheat, cotton, rapeseed-mustard, and potato, are polyploids with complex genomes. Therefore, progress in these crops has been hampered due to genome complexity. Excellent work has been conducted on some species of Brassica for its improvement through genome editing. Although excellent work has been conducted on some species of Brassica for genome improvement through editing, work on polyploid crops, including U's triangle species, holds numerous implications for improving other polyploid crops. In this review, we summarize key examples from genome editing work done on Brassica and discuss important considerations for deploying CRISPR-mediated genome editing more efficiently in other polyploid crops for improvement.
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Affiliation(s)
- Niaz Ahmad
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Samia Fatima
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Aamer Mehmood
- Department of Bioinformatics & Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Qamar U. Zaman
- Hainan Yazhou Bay Seed Laboratory, Sanya Nanfan Research Institute of Hainan University, Sanya, China
- College of Tropical Crops, Hainan University, Haikou, China
| | - Rana Muhammad Atif
- National Center of Genome Editing, Center of Advanced Studies, Agriculture and Food Security, University of Agriculture, Faisalabad, Pakistan
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Weijun Zhou
- Ministry of Agriculture and Rural Affairs Key Lab of Spectroscopy Sensing, Institute of Crop Science, Zhejiang University, Hangzhou, China
| | - Mehboob-ur Rahman
- National Institute for Biotechnology and Genetic Engineering College, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Rafaqat Ali Gill
- Key Laboratory for Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Suputri NPAEO, Prasojo IS, Prabowo LAT, Purwestri YA, Semiarti E. Identification of early flowering mutant gene in Phalaenopsis amabilis (L.) Blume for sgRNA construction in CRISPR/Cas9 genome editing system. BRAZ J BIOL 2023; 84:e268133. [PMID: 37283391 DOI: 10.1590/1519-6984.268133] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 04/12/2023] [Indexed: 06/08/2023] Open
Abstract
Phalaenopsis amabilis (L.) Blume commonly called Moth Orchid (Orchidaceae) is a natural orchid species designated as the National Flower of Indonesia for its beautiful flower shape and long-lasting flowering period. Basically, P. amabilis has a long vegetative phase that cause late flowering, about 2 to 3 years for flowering, hence a method to shorten vegetative period is desired. The latest technological approach that can be used to accelerate flowering of P. amabilis is the CRISPR/Cas9 genome editing method to inactivate the GAI (Gibberellic Acid Insensitive) gene as a mutant gene that can accelerate the regulation of FLOWERING TIME (FT) genes flowering biosynthesis pathway. The approach that needs to be taken is to silence the GAI gene with a knockout system which begins with identifying and characterizing the GAI target gene in the P. amabilis which will be used as a single guide RNA. CRISPR/Cas9 mediated knockout efficiency is highly dependent on the properties of the sgRNA used. SgRNA consists of a target sequence, determining its specificity performance. We executed phylogenetic clustering for the PaGAI protein with closely related orchid species such as Dendrobium capra, Dendrobium cultivars and Cymbidium sinensis. SWISS-Model as tool webserver for protein structure homology modeling. Results show that P. amabilis has a specific domain with the occurrence of point mutations in the two conservative domains. Therefore, a single guide RNA reconstruction needs to be implemented.
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Affiliation(s)
- N P A E O Suputri
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - I S Prasojo
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - L A T Prabowo
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - Y A Purwestri
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
| | - E Semiarti
- Universitas Gadjah Mada, Faculty of Biology, Department of Tropical Biology, Yogyakarta, Special Region of Yogyakarta, Indonesia
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Illa-Berenguer E, LaFayette PR, Parrott WA. Editing efficiencies with Cas9 orthologs, Cas12a endonucleases, and temperature in rice. Front Genome Ed 2023; 5:1074641. [PMID: 37032710 PMCID: PMC10080323 DOI: 10.3389/fgeed.2023.1074641] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/07/2023] [Indexed: 03/19/2023] Open
Abstract
The advent of CRISPR-Cas technology has made it the genome editing tool of choice in all kingdoms of life, including plants, which can have large, highly duplicated genomes. As a result, finding adequate target sequences that meet the specificities of a given Cas nuclease on any gene of interest remains challenging in many cases. To assess target site flexibility, we tested five different Cas9/Cas12a endonucleases (SpCas9, SaCas9, St1Cas9, Mb3Cas12a, and AsCas12a) in embryogenic rice calli from Taipei 309 at 37°C (optimal temperature for most Cas9/Cas12a proteins) and 27°C (optimal temperature for tissue culture) and measured their editing rates under regular tissue culture conditions using Illumina sequencing. StCas9 and AsCas12 were not functional as tested, regardless of the temperature used. SpCas9 was the most efficient endonuclease at either temperature, regardless of whether monoallelic or biallelic edits were considered. Mb3Cas12a at 37°C was the next most efficient endonuclease. Monoallelic edits prevailed for both SaCas9 and Mb3Cas12a at 27°C, but biallelic edits prevailed at 37°C. Overall, the use of other Cas9 orthologs, the use of Cas12a endonucleases, and the optimal temperature can expand the range of targetable sequences.
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Affiliation(s)
- Eudald Illa-Berenguer
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- *Correspondence: Eudald Illa-Berenguer,
| | - Peter R. LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
| | - Wayne A. Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, United States
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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22
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AHMAD M. Plant breeding advancements with "CRISPR-Cas" genome editing technologies will assist future food security. FRONTIERS IN PLANT SCIENCE 2023; 14:1133036. [PMID: 36993865 PMCID: PMC10040607 DOI: 10.3389/fpls.2023.1133036] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world's population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic stress response mechanism. Both conventional and molecular breeding techniques have been used to create viable crop types both processes are time-consuming. Recently, plant breeders have shown an interest in genome editing approaches for genetic manipulation that use clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). To ensure the security of the food supply in the future, plant kinds with desired traits must be developed. A completely new era in plant breeding has begun because of the revolution in genome editing techniques based on the CRISPR/CRISPR-associated nuclease (Cas9) systems. All plants may effectively target a particular gene or group of loci using Cas9 and single-guide RNA (sgRNA). CRISPR/Cas9 can thereby save time and labor compared to conventional breeding methods. An easy, quick, and efficient method for directly altering the genetic sequences in cells is with the CRISPR and Cas9 systems. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease. We summarize recent CRISPR/Cas9 plant research findings, investigate potential applications in plant breeding, and make predictions about likely future breakthroughs and approaches to food security through 2050.
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Affiliation(s)
- M. AHMAD
- Department of Plant Sciences, University of Nebraska, Lincoln, NE, United States
- Department of Genetics and Plant Breeding, Sheri-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Srinagar, India
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Lee HJ, Kim HJ, Lee SJ. Miniature CRISPR-Cas12f1-Mediated Single-Nucleotide Microbial Genome Editing Using 3'-Truncated sgRNA. CRISPR J 2023; 6:52-61. [PMID: 36576897 PMCID: PMC9942177 DOI: 10.1089/crispr.2022.0071] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The CRISPR-Cas system has been used as a convenient tool for genome editing because the nuclease that cuts the target DNA and the guide RNA that recognizes the target are separated into modules. Cas12f1, which has a smaller size than that of other Cas nucleases, is easily loaded into vectors and is emerging as a new genome editing tool. In this study, AsCas12f1 was used to negatively select only Escherichia coli cells obtained by oligonucleotide-directed genome editing. Although double-, triple-, and quadruple-base substitutions were accurately and efficiently performed in the genome, the performance of single-base editing was poor. To resolve this limitation, we serially truncated the 3'-end of sgRNAs and determined the maximal truncation required to maintain the target DNA cleavage activity of Cas12f1. Negative selection of single-nucleotide-edited cells was efficiently performed with the maximally 3'-truncated sgRNA-Cas12f1 complex in vivo. Moreover, Sanger sequencing showed that the accuracy of single-nucleotide substitution, insertion, and deletion in the microbial genome was improved. These results demonstrated that a truncated sgRNA approach could be widely used for accurate CRISPR-mediated genome editing.
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Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong, Republic of Korea.,Address correspondence to: Sang Jun Lee, Department of Systems Biotechnology, Institute of Microbiomics, Chung-Ang University, Anseong 17546, Republic of Korea.
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24
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Rahman SU, McCoy E, Raza G, Ali Z, Mansoor S, Amin I. Improvement of Soybean; A Way Forward Transition from Genetic Engineering to New Plant Breeding Technologies. Mol Biotechnol 2023; 65:162-180. [PMID: 35119645 DOI: 10.1007/s12033-022-00456-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/21/2022] [Indexed: 01/18/2023]
Abstract
Soybean is considered one of the important crops among legumes. Due to high nutritional contents in seed (proteins, sugars, oil, fatty acids, and amino acids), soybean is used globally for food, feed, and fuel. The primary consumption of soybean is vegetable oil and feed for chickens and livestock. Apart from this, soybean benefits soil fertility by fixing atmospheric nitrogen through root nodular bacteria. While conventional breeding is practiced for soybean improvement, with the advent of new biotechnological methods scientists have also engineered soybean to improve different traits (herbicide, insect, and disease resistance) to fulfill consumer requirements and to meet the global food deficiency. Genetic engineering (GE) techniques such as transgenesis and gene silencing help to minimize the risks and increase the adaptability of soybean. Recently, new plant breeding technologies (NPBTs) emerged such as zinc-finger nucleases, transcription activator-like effector nucleases, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9), which paved the way for enhanced genetic modification of soybean. These NPBTs have the potential to improve soybean via gene functional characterization precision genome engineering for trait improvement. Importantly, these NPBTs address the ethical and public acceptance issues related to genetic modifications and transgenesis in soybean. In the present review, we summarized the improvement of soybean through GE and NPBTs. The valuable traits that have been improved through GE for different constraints have been discussed. Moreover, the traits that have been improved through NPBTs and potential targets for soybean improvements via NPBTs and solutions for ethical and public acceptance are also presented.
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Affiliation(s)
- Saleem Ur Rahman
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Evan McCoy
- Center for Applied Genetic Technologies (CAGT), University of Georgia, Athens, USA
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Zahir Ali
- Laboratory for Genome Engineering, Center for Desert Agriculture and Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Imran Amin
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan.
- Constituent College Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan.
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25
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Nascimento FDS, Rocha ADJ, Soares JMDS, Mascarenhas MS, Ferreira MDS, Morais Lino LS, Ramos APDS, Diniz LEC, Mendes TADO, Ferreira CF, dos Santos-Serejo JA, Amorim EP. Gene Editing for Plant Resistance to Abiotic Factors: A Systematic Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020305. [PMID: 36679018 PMCID: PMC9860801 DOI: 10.3390/plants12020305] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/02/2023] [Accepted: 01/05/2023] [Indexed: 05/22/2023]
Abstract
Agricultural crops are exposed to various abiotic stresses, such as salinity, water deficits, temperature extremes, floods, radiation, and metal toxicity. To overcome these challenges, breeding programs seek to improve methods and techniques. Gene editing by Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR/Cas-is a versatile tool for editing in all layers of the central dogma with focus on the development of cultivars of plants resistant or tolerant to multiple biotic or abiotic stresses. This systematic review (SR) brings new contributions to the study of the use of CRISPR/Cas in gene editing for tolerance to abiotic stress in plants. Articles deposited in different electronic databases, using a search string and predefined inclusion and exclusion criteria, were evaluated. This SR demonstrates that the CRISPR/Cas system has been applied to several plant species to promote tolerance to the main abiotic stresses. Among the most studied crops are rice and Arabidopsis thaliana, an important staple food for the population, and a model plant in genetics/biotechnology, respectively, and more recently tomato, whose number of studies has increased since 2021. Most studies were conducted in Asia, specifically in China. The Cas9 enzyme is used in most articles, and only Cas12a is used as an additional gene editing tool in plants. Ribonucleoproteins (RNPs) have emerged as a DNA-free strategy for genome editing without exogenous DNA. This SR also identifies several genes edited by CRISPR/Cas, and it also shows that plant responses to stress factors are mediated by many complex-signaling pathways. In addition, the quality of the articles included in this SR was validated by a risk of bias analysis. The information gathered in this SR helps to understand the current state of CRISPR/Cas in the editing of genes and noncoding sequences, which plays a key role in the regulation of various biological processes and the tolerance to multiple abiotic stresses, with potential for use in plant genetic improvement programs.
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Affiliation(s)
| | - Anelita de Jesus Rocha
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | - Mileide dos Santos Ferreira
- Department of Biological Sciences, Feira de Santana State University, Feira de Santana 44036-900, BA, Brazil
| | | | | | | | | | | | | | - Edson Perito Amorim
- Embrapa Mandioca e Fruticultura, Cruz das Almas 44380-000, BA, Brazil
- Correspondence: ; Tel.: +55-75-3312-8058; Fax: +55-75-3312-8097
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Park I, Seo YS, Mannaa M. Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential. Front Microbiol 2023; 14:1163832. [PMID: 37213524 PMCID: PMC10196466 DOI: 10.3389/fmicb.2023.1163832] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/11/2023] [Indexed: 05/23/2023] Open
Abstract
The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.
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Affiliation(s)
- Inmyoung Park
- School of Food and Culinary Arts, Youngsan University, Busan, Republic of Korea
| | - Young-Su Seo
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- *Correspondence: Young-Su Seo
| | - Mohamed Mannaa
- Department of Integrated Biological Science, Pusan National University, Busan, Republic of Korea
- Department of Plant Pathology, Faculty of Agriculture, Cairo University, Giza, Egypt
- Mohamed Mannaa
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Wu FH, Hsu CT, Lin CS. Targeted Insertion in Nicotiana benthamiana Genomes via Protoplast Regeneration. Methods Mol Biol 2023; 2653:297-315. [PMID: 36995634 DOI: 10.1007/978-1-0716-3131-7_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Insertion of a specific sequence in a targeted region for precise editing is still a major challenge in plants. Current protocols rely on inefficient homology-directed repair or non-homologous end-joining with modified double-stranded oligodeoxyribonucleotides (dsODNs) as donors. We developed a simple protocol that eliminates the need for expensive equipment, chemicals, modifications of donor DNA, and complicated vector construction. The protocol uses polyethylene glycol (PEG)-calcium to deliver low-cost, unmodified single-stranded oligodeoxyribonucleotides (ssODNs) and CRISPR/Cas9 ribonucleoprotein (RNP) complexes into Nicotiana benthamiana protoplasts. Regenerated plants were obtained from edited protoplasts with an editing frequency of up to 50% at the target locus. The inserted sequence was inherited to the next generation; this method thus opens the possibility for the future exploration of genomes by targeted insertion in plants.
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Affiliation(s)
- Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
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28
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Ul Haq SI, Zheng D, Feng N, Jiang X, Qiao F, He JS, Qiu QS. Progresses of CRISPR/Cas9 genome editing in forage crops. JOURNAL OF PLANT PHYSIOLOGY 2022; 279:153860. [PMID: 36371870 DOI: 10.1016/j.jplph.2022.153860] [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: 10/18/2022] [Accepted: 11/02/2022] [Indexed: 06/16/2023]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mediated-genome editing has evolved into a powerful tool that is widely used in plant species to induce editing in the genome for analyzing gene function and crop improvement. CRISPR/Cas9 is an RNA-guided genome editing tool consisting of a Cas9 nuclease and a single-guide RNA (sgRNA). The CRISPR/Cas9 system enables more accurate and efficient genome editing in crops. In this review, we summarized the advances of the CRISPR/Cas9 technology in plant genome editing and its applications in forage crops. We described briefly about the development of CRISPR/Cas9 technology in plant genome editing. We assessed the progress of CRISPR/Cas9-mediated targeted-mutagenesis in various forage crops, including alfalfa, Medicago truncatula, Hordeum vulgare, Sorghum bicolor, Setaria italica and Panicum virgatum. The potentials and challenges of CRISPR/Cas9 in forage breeding were discussed.
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Affiliation(s)
- Syed Inzimam Ul Haq
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Naijie Feng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China
| | - Feng Qiao
- Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China
| | - Jin-Sheng He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China
| | - Quan-Sheng Qiu
- MOE Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, 730000, China; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, Lanzhou University, Lanzhou, Gansu, 730000, China; Academy of Plateau Science and Sustainability, School of Life Sciences, Qinghai Normal University, Xining, Qinghai, 810016, China; College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, China.
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29
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Ke G, Zhang J, Gao W, Chen J, Liu L, Wang S, Zhang H, Yan G. Application of advanced technology in traditional Chinese medicine for cancer therapy. Front Pharmacol 2022; 13:1038063. [PMID: 36313284 PMCID: PMC9606699 DOI: 10.3389/fphar.2022.1038063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Although cancer has seriously threatened people’s health, it is also identified by the World Health Organization as a controllable, treatable and even curable chronic disease. Traditional Chinese medicine (TCM) has been extensively used to treat cancer due to its multiple targets, minimum side effects and potent therapeutic effects, and thus plays an important role in all stages of tumor therapy. With the continuous progress in cancer treatment, the overall efficacy of cancer therapy has been significantly improved, and the survival time of patients has been dramatically prolonged. In recent years, a series of advanced technologies, including nanotechnology, gene editing technology, real-time cell-based assay (RTCA) technology, and flow cytometry analysis technology, have been developed and applied to study TCM for cancer therapy, which efficiently improve the medicinal value of TCM and accelerate the research progress of TCM in cancer therapy. Therefore, the applications of these advanced technologies in TCM for cancer therapy are summarized in this review. We hope this review will provide a good guidance for TCM in cancer therapy.
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Affiliation(s)
- Gaofeng Ke
- Department of Rehabilitation Medicine, The Affiliated Wenling Hospital of Wenzhou Medical University, Wenling, China
| | - Jia Zhang
- School of Pharmacy, Jiangsu Provincial Engineering Research Center of Traditional Chinese Medicine External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China
| | - Wufeng Gao
- School of Pharmacy, Jiangsu Provincial Engineering Research Center of Traditional Chinese Medicine External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jiayi Chen
- School of Life Sciences, Jilin University, Changchun, China
| | - Luotong Liu
- School of Life Sciences, Jilin University, Changchun, China
| | - Simiao Wang
- School of Life Sciences, Jilin University, Changchun, China
| | - Huan Zhang
- School of Life Sciences, Jilin University, Changchun, China
- *Correspondence: Huan Zhang, ; Guojun Yan,
| | - Guojun Yan
- School of Pharmacy, Jiangsu Provincial Engineering Research Center of Traditional Chinese Medicine External Medication Development and Application, Nanjing University of Chinese Medicine, Nanjing, China
- *Correspondence: Huan Zhang, ; Guojun Yan,
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30
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Sharma KK, Palakolanu SR, Bhattacharya J, Shankhapal AR, Bhatnagar-Mathur P. CRISPR for accelerating genetic gains in under-utilized crops of the drylands: Progress and prospects. Front Genet 2022; 13:999207. [PMID: 36276961 PMCID: PMC9582247 DOI: 10.3389/fgene.2022.999207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/09/2022] [Indexed: 12/12/2022] Open
Abstract
Technologies and innovations are critical for addressing the future food system needs where genetic resources are an essential component of the change process. Advanced breeding tools like "genome editing" are vital for modernizing crop breeding to provide game-changing solutions to some of the "must needed" traits in agriculture. CRISPR/Cas-based tools have been rapidly repurposed for editing applications based on their improved efficiency, specificity and reduced off-target effects. Additionally, precise gene-editing tools such as base editing, prime editing, and multiplexing provide precision in stacking of multiple traits in an elite variety, and facilitating specific and targeted crop improvement. This has helped in advancing research and delivery of products in a short time span, thereby enhancing the rate of genetic gains. A special focus has been on food security in the drylands through crops including millets, teff, fonio, quinoa, Bambara groundnut, pigeonpea and cassava. While these crops contribute significantly to the agricultural economy and resilience of the dryland, improvement of several traits including increased stress tolerance, nutritional value, and yields are urgently required. Although CRISPR has potential to deliver disruptive innovations, prioritization of traits should consider breeding product profiles and market segments for designing and accelerating delivery of locally adapted and preferred crop varieties for the drylands. In this context, the scope of regulatory environment has been stated, implying the dire impacts of unreasonable scrutiny of genome-edited plants on the evolution and progress of much-needed technological advances.
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Affiliation(s)
- Kiran K. Sharma
- Sustainable Agriculture Programme, The Energy and Resources Institute (TERI), India Habitat Center, New Delhi, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Sudhakar Reddy Palakolanu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Joorie Bhattacharya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, Telangana, India
| | - Aishwarya R. Shankhapal
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Nottingham, United Kingdom
- Plant Sciences and the Bioeconomy, Rothamsted Research, Harpenden, Hertfordshire, United Kingdom
| | - Pooja Bhatnagar-Mathur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- International Maize and Wheat Improvement Center (CIMMYT), México, United Kingdom
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31
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Advances in CRISPR/Cas9. BIOMED RESEARCH INTERNATIONAL 2022; 2022:9978571. [PMID: 36193328 PMCID: PMC9525763 DOI: 10.1155/2022/9978571] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 11/30/2022]
Abstract
CRISPR/Cas9 technology has become the most examined gene editing technology in recent years due to its simple design, yet low cost, high efficiency, and simple operation, which can also achieve simultaneous editing of multiple loci. It can also be carried out without using plasmids, saving lots of troubles caused by plasmids. CRISPR/Cas9 has shown great potential in the study of genes or genomic functions in microorganisms, plants, animals, and human beings. In this review, we will examine the history, structure, and basic mechanisms of the CRISPR/Cas9 system, describe its great value in precision medicine and sgRNA library screening, and dig its great potential in a new field: DNA information storage.
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32
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David SR, Maheshwaram SK, Shet D, Lakshminarayana MB, Soni GV. Temperature dependent in vitro binding and release of target DNA by Cas9 enzyme. Sci Rep 2022; 12:15243. [PMID: 36085316 PMCID: PMC9463129 DOI: 10.1038/s41598-022-19485-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/30/2022] [Indexed: 11/08/2022] Open
Abstract
The CRISPR-associated protein 9 (Cas9) system has proven to be a powerful technology for genome editing in a wide variety of in vivo and in vitro applications. CRISPR-Cas9, when loaded with the guide RNA, cleaves the DNA at the target position as recognized by the guide RNA sequence. For successful application of this technology, it is important to study the biophysical parameters affecting its function. Temperature dependence of the Cas9 binding as well as energetics of product release after cleavage has not been well reported in the literature. In this work, we study the binding properties of Cas9 enzyme to the sequence specific target DNA at a range of temperatures and, surprisingly, find that the Cas9 enzyme, in our study, can find and bind its target DNA with 90 ± 20% efficiency at temperatures as low as 4 °C. Further, we show that the cleaved DNA products remain bound to the Cas9 enzyme strongly and is released from the enzyme only at higher temperatures. Using the gel shift assays, we quantify the rate of Cas9 binding to target DNA to be 0.8 ± 0.2 min-1 at 37 °C. We also tested denaturant (SDS) dependent release of cleaved product which showed a similar release pattern with a dissociation constant of 0.23 ± 0.04 mM. Our results of heat and denaturant dependence on Cas9-DNA binding and release mechanics will provide valuable insights for developing temperature dependent applications of the CRISPR-Cas9 technology.
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Affiliation(s)
| | | | - Divya Shet
- Raman Research Institute, Bangalore, Karnataka, 560080, India
| | | | - Gautam V Soni
- Raman Research Institute, Bangalore, Karnataka, 560080, India.
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33
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Mayta ML, Dotto M, Orellano EG, Krapp AR. An experimental protocol for teaching CRISPR/Cas9 in a post-graduate plant laboratory course: An analysis of mutant-edited plants without sequencing. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:537-546. [PMID: 35894125 DOI: 10.1002/bmb.21659] [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: 02/23/2021] [Revised: 02/08/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The CRISPR/Cas9 system is widely used for editing genes in various organisms and is a very useful tool due to its versatility, simplicity, and efficiency. To teach its principles to post-graduate students we designed a laboratory activity to obtain and analyze PDS3 mutants in Arabidopsis thaliana plants consisting of: 1) Design of guide RNAs using bioinformatics tools; 2) plant transformation (which is optional depending on the length of the course); 3) observation and evaluation of the mutant's phenotypes in the Phytoene desaturase (PDS3) gene, which exhibit an albino phenotype and different degrees of mosaicism in the editing events we evaluated; 4) PCR amplification of a fragment that includes the mutated region followed by analysis of single-stranded DNA conformation polymorphisms (SSCP) using native polyacrylamide gel electrophoresis and silver nitrate staining to detect changes in the amplicon sequence due to gene editing. Through SSCP, the students were able to distinguish between homozygous and heterozygous edited plants. A highlight feature of this protocol is the visualization and detection of the mutation/edition without sequencing the edited fragment.
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Affiliation(s)
- Martín L Mayta
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Centro para la Investigación en Ciencias de la Salud, Facultad de Ciencias de la Salud, Universidad Adventista del Plata, Entre Ríos, Argentina
| | - Marcela Dotto
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Ciencias Agropecuarias del Litoral (ICiAgro L.), Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
| | - Elena G Orellano
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana R Krapp
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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34
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Singh J, Sharma D, Brar GS, Sandhu KS, Wani SH, Kashyap R, Kour A, Singh S. CRISPR/Cas tool designs for multiplex genome editing and its applications in developing biotic and abiotic stress-resistant crop plants. Mol Biol Rep 2022; 49:11443-11467. [PMID: 36002653 DOI: 10.1007/s11033-022-07741-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 05/22/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022]
Abstract
Crop plants are prone to several yield-reducing biotic and abiotic stresses. The crop yield reductions due to these stresses need addressing to maintain an adequate balance between the increasing world population and food production to avoid food scarcities in the future. It is impossible to increase the area under food crops proportionately to meet the rising food demand. In such an adverse scenario overcoming the biotic and abiotic stresses through biotechnological interventions may serve as a boon to help meet the globe's food requirements. Under the current genomic era, the wide availability of genomic resources and genome editing technologies such as Transcription Activator-Like Effector Nucleases (TALENs), Zinc Finger Nucleases (ZFNs), and Clustered-Regularly Interspaced Palindromic Repeats/CRISPR-associated proteins (CRISPR/Cas) has widened the scope of overcoming these stresses for several food crops. These techniques have made gene editing more manageable and accessible with changes at the embryo level by adding or deleting DNA sequences of the target gene(s) from the genome. The CRISPR construct consists of a single guide RNA having complementarity with the nucleotide fragments of the target gene sequence, accompanied by a protospacer adjacent motif. The target sequence in the organism's genome is then cleaved by the Cas9 endonuclease for obtaining a desired trait of interest. The current review describes the components, mechanisms, and types of CRISPR/Cas techniques and how this technology has helped to functionally characterize genes associated with various biotic and abiotic stresses in a target organism. This review also summarizes the application of CRISPR/Cas technology targeting these stresses in crops through knocking down/out of associated genes.
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Affiliation(s)
- Jagmohan Singh
- Division of Plant Pathology, Indian Agricultural Research Institute, 110012, New Delhi, India.,Guru Angad Dev Veterinary and Animal Science University, KVK, Barnala, India
| | - Dimple Sharma
- Department of Food Science and Human Nutrition, Michigan State University, 48824, East Lansing, MI, USA
| | - Gagandeep Singh Brar
- Department of Biological Sciences, North Dakota State University, 58102, Fargo, ND, USA
| | - Karansher Singh Sandhu
- Department of Crop and Soil Sciences, Washington State University, 99163, Pullman, WA, USA
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology Srinagar, Khudwani, Srinagar, Jammu, Kashmir, India
| | - Ruchika Kashyap
- Department of Agronomy, Horticulture, and Plant Sciences, South Dakota State University, 57007, Brookings, SD, USA
| | - Amardeep Kour
- Regional Research Station, Punjab Agricultural University, 151001, Bathinda, Punjab, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, 151203, Faridkot, Punjab, India.
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Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front Bioeng Biotechnol 2022; 10:913728. [PMID: 35837551 PMCID: PMC9274005 DOI: 10.3389/fbioe.2022.913728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen Ofuji Osiro
- Department of Phytopathology, University of Brasília, Brasília, Brazil
- Embrapa Agroenergy, Brasília, Brazil
| | | | | | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States
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Beernink BM, Lappe RR, Bredow M, Whitham SA. Impacts of RNA Mobility Signals on Virus Induced Somatic and Germline Gene Editing. Front Genome Ed 2022; 4:925088. [PMID: 35755451 PMCID: PMC9219249 DOI: 10.3389/fgeed.2022.925088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Viral vectors are being engineered to deliver CRISPR/Cas9 components systemically in plants to induce somatic or heritable site-specific mutations. It is hypothesized that RNA mobility signals facilitate entry of viruses or single guide RNAs (sgRNAs) into the shoot apical meristem where germline mutations can occur. Our objective was to understand the impact of RNA mobility signals on virus-induced somatic and germline gene editing in Nicotiana benthamiana and Zea mays. Previously, we showed that foxtail mosaic virus (FoMV) expressing sgRNA induced somatic mutations in N. benthamiana and Z. mays expressing Cas9. Here, we fused RNA mobility signals to sgRNAs targeting the genes encoding either N. benthamiana phytoene desaturase (PDS) or Z. mays high affinity potassium transporter 1 (HKT1). Addition of Arabidopsis thaliana Flowering Locus T (AtFT) and A. thaliana tRNA-Isoleucine (AttRNAIle) did not improve FoMV-induced somatic editing, and neither were sufficient to facilitate germline mutations in N. benthamiana. Maize FT homologs, Centroradialus 16 (ZCN16) and ZCN19, as well as AttRNAIle were found to aid somatic editing in maize but did not enable sgRNAs delivered by FoMV to induce germline mutations. Additional viral guide RNA delivery systems were assessed for somatic and germline mutations in N. benthamiana with the intention of gaining a better understanding of the specificity of mobile signal-facilitated germline editing. Potato virus X (PVX), barley stripe mosaic virus (BSMV), and tobacco rattle virus (TRV) were included in this comparative study, and all three of these viruses delivering sgRNA were able to induce somatic and germline mutations. Unexpectedly, PVX, a potexvirus closely related to FoMV, expressing sgRNA alone induced biallelic edited progeny, indicating that mobility signals are dispensable in virus-induced germline editing. These results show that PVX, BSMV, and TRV expressing sgRNA all have an innate ability to induce mutations in the germline. Our results indicate that mobility signals alone may not be sufficient to enable virus-based delivery of sgRNAs using the viruses, FoMV, PVX, BSMV, and TRV into cell types that result in germline mutations.
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Ankit A, Kamali S, Singh A. Genomic & structural diversity and functional role of potassium (K +) transport proteins in plants. Int J Biol Macromol 2022; 208:844-857. [PMID: 35367275 DOI: 10.1016/j.ijbiomac.2022.03.179] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 03/11/2022] [Accepted: 03/25/2022] [Indexed: 01/03/2023]
Abstract
Potassium (K+) is an essential macronutrient for plant growth and productivity. It is the most abundant cation in plants and is involved in various cellular processes. Variable K+ availability is sensed by plant roots, consequently K+ transport proteins are activated to optimize K+ uptake. In addition to K+ uptake and translocation these proteins are involved in other important physiological processes like transmembrane voltage regulation, polar auxin transport, maintenance of Na+/K+ ratio and stomata movement during abiotic stress responses. K+ transport proteins display tremendous genomic and structural diversity in plants. Their key structural features, such as transmembrane domains, N-terminal domains, C-terminal domains and loops determine their ability of K+ uptake and transport and thus, provide functional diversity. Most K+ transporters are regulated at transcriptional and post-translational levels. Genetic manipulation of key K+ transporters/channels could be a prominent strategy for improving K+ utilization efficiency (KUE) in plants. This review discusses the genomic and structural diversity of various K+ transport proteins in plants. Also, an update on the function of K+ transport proteins and their regulatory mechanism in response to variable K+ availability, in improving KUE, biotic and abiotic stresses is provided.
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Affiliation(s)
- Ankit Ankit
- National Institute of Plant Genome Research, New Delhi 110067, India
| | | | - Amarjeet Singh
- National Institute of Plant Genome Research, New Delhi 110067, India.
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Systemic Signaling: A Role in Propelling Crop Yield. PLANTS 2022; 11:plants11111400. [PMID: 35684173 PMCID: PMC9182853 DOI: 10.3390/plants11111400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022]
Abstract
Food security has become a topic of great concern in many countries. Global food security depends heavily on agriculture that has access to proper resources and best practices to generate higher crop yields. Crops, as with other plants, have a variety of strategies to adapt their growth to external environments and internal needs. In plants, the distal organs are interconnected through the vascular system and intricate hierarchical signaling networks, to communicate and enhance survival within fluctuating environments. Photosynthesis and carbon allocation are fundamental to crop production and agricultural outputs. Despite tremendous progress achieved by analyzing local responses to environmental cues, and bioengineering of critical enzymatic processes, little is known about the regulatory mechanisms underlying carbon assimilation, allocation, and utilization. This review provides insights into vascular-based systemic regulation of photosynthesis and resource allocation, thereby opening the way for the engineering of source and sink activities to optimize the yield performance of major crops.
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John Martin JJ, Yarra R, Wei L, Cao H. Oil Palm Breeding in the Modern Era: Challenges and Opportunities. PLANTS 2022; 11:plants11111395. [PMID: 35684168 PMCID: PMC9183044 DOI: 10.3390/plants11111395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 05/15/2022] [Accepted: 05/19/2022] [Indexed: 11/30/2022]
Abstract
Oil palm, a cross-pollinated crop with long generation time, poses a lot of challenges in achieving sustainable oil palm with high yield and quality. The African oil palm (Elaeis guineensis Jacq.) is the most productive and versatile oil-yielding crop in the world, producing more than any other oil-yielding crop. Despite recent challenges, such as stress tolerance, superior oil quality, disease tolerance, and the need for new market niches, there is a growing need to explore and develop new varieties with high yield potential and the genetic diversity required to maintain oil palm yield stability. Breeding is an indispensable part of producing high-quality planting materials to increase oil palm yield. Biotechnological technologies have transformed conventional plant breeding approaches by introducing novel genotypes for breeding. Innovative pre-breeding and breeding approaches, such as identifying candidate genes in wild or land races using genomics tools, can pave the way for genetic improvement in oil palm. In this review, we highlighted the modern breeding tools, including genomics, marker-assisted breeding, genetic engineering, and genome editing techniques in oil palm crops, and we explored certain concerns connected to the techniques and their applications in practical breeding.
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Affiliation(s)
- Jerome Jeyakumar John Martin
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Rajesh Yarra
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Lu Wei
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
| | - Hongxing Cao
- Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang 571339, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Wenchang 571339, China
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40
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Infante-López DV, Céspedes-Galvis MF, Wilches-Flórez ÁM. CRISPR-Cas9: el debate bioético más allá de la línea germinal. PERSONA Y BIOÉTICA 2022. [DOI: 10.5294/pebi.2021.25.2.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
El sistema CRISPR-Cas9 es una tecnología de edición genética que, además de ampliar las posibilidades en investigación científica, despierta reflexiones asociadas a la dignidad humana, el control biológico, la terapia y la mejora genética. Se revisaron las discusiones bioéticas asociadas a los desafíos y las repercusiones que suscita su aplicación. Como resultado, los cuestionamientos bioéticos tienden a problematizar la aplicación en organismos no humanos, en la investigación básica y en la línea somática y germinal humana. Para concluir, falta incrementar los niveles de seguridad y efectividad para que los beneficios superen los riesgos y, de esta forma, sea posible disminuir las preocupaciones bioéticas y aumentar la credibilidad en el uso de la técnica.
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Naik BJ, Shimoga G, Kim SC, Manjulatha M, Subramanyam Reddy C, Palem RR, Kumar M, Kim SY, Lee SH. CRISPR/Cas9 and Nanotechnology Pertinence in Agricultural Crop Refinement. FRONTIERS IN PLANT SCIENCE 2022; 13:843575. [PMID: 35463432 PMCID: PMC9024397 DOI: 10.3389/fpls.2022.843575] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Accepted: 02/07/2022] [Indexed: 05/08/2023]
Abstract
The CRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated protein 9) method is a versatile technique that can be applied in crop refinement. Currently, the main reasons for declining agricultural yield are global warming, low rainfall, biotic and abiotic stresses, in addition to soil fertility issues caused by the use of harmful chemicals as fertilizers/additives. The declining yields can lead to inadequate supply of nutritional food as per global demand. Grains and horticultural crops including fruits, vegetables, and ornamental plants are crucial in sustaining human life. Genomic editing using CRISPR/Cas9 and nanotechnology has numerous advantages in crop development. Improving crop production using transgenic-free CRISPR/Cas9 technology and produced fertilizers, pesticides, and boosters for plants by adopting nanotechnology-based protocols can essentially overcome the universal food scarcity. This review briefly gives an overview on the potential applications of CRISPR/Cas9 and nanotechnology-based methods in developing the cultivation of major agricultural crops. In addition, the limitations and major challenges of genome editing in grains, vegetables, and fruits have been discussed in detail by emphasizing its applications in crop refinement strategy.
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Affiliation(s)
- Banavath Jayanna Naik
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | - Ganesh Shimoga
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Seong-Cheol Kim
- Research Institute of Climate Change and Agriculture, National Institute of Horticultural and Herbal Science, Rural Development Administration (RDA), Jeju, South Korea
| | | | | | | | - Manu Kumar
- Department of Life Science, College of Life Science and Biotechnology, Dongguk University, Seoul, South Korea
| | - Sang-Youn Kim
- Interaction Laboratory, Future Convergence Engineering, Advanced Technology Research Center, Korea University of Technology and Education, Cheonan-si, South Korea
| | - Soo-Hong Lee
- Department of Medical Biotechnology, Dongguk University, Seoul, South Korea
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Sharma P, Singh SP, Iqbal HM, Parra-Saldivar R, Varjani S, Tong YW. Genetic modifications associated with sustainability aspects for sustainable developments. Bioengineered 2022; 13:9508-9520. [PMID: 35389819 PMCID: PMC9161841 DOI: 10.1080/21655979.2022.2061146] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Sustainable development serves as the foundation for a range of international and national policymaking. Traditional breeding methods have been used to modify plant genomes and production. Genetic engineering is the practice of assisting agricultural systems in adapting to rapidly changing global growth by hastening the breeding of new varieties. On the other hand, the development of genetic engineering has enabled more precise control over the genomic alterations made in recent decades. Genetic changes from one species can now be introduced into a completely unrelated species, increasing agricultural output or making certain elements easier to manufacture. Harvest plants and soil microorganisms are just a few of the more well-known genetically modified creatures. Researchers assess current studies and illustrate the possibility of genetically modified organisms (GMOs) from the perspectives of various stakeholders. GMOs increase yields, reduce costs, and reduce agriculture's terrestrial and ecological footprint. Modern technology benefits innovators, farmers, and consumers alike. Agricultural biotechnology has numerous applications, each with its own set of potential consequences. This will be able to reach its full potential if more people have access to technology and excessive regulation is avoided. This paper covers the regulations for genetically modified crops (GMCs) as well as the economic implications. It also includes sections on biodiversity and environmental impact, as well as GMCs applications. This recounts biotechnological interventions for long-term sustainability in the field of GMCs, as well as the challenges and opportunities in this field of research.Abbreviations: GMCs-Genetically modified crops; GMOs- Genetically modified organisms; GE- Genetic engineering; Bt- Bacillus thuringiensisNIH- National Institutes of Health; FDA- Food and Drug Administration; HGT- Horizontal gene transfer; GM- Genetically modified; rDNA- Ribosomal deoxyribonucleic acid; USDA- United States Department of Agriculture; NIH- National Institutes of Health.
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Affiliation(s)
- Pooja Sharma
- Environmental Research Institute, National University of Singapore, Singapore
- Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
| | - Surendra Pratap Singh
- Plant Molecular Biology Laboratory, Department of Botany, D.A.V. College, Chhatrapati Shahu Ji Maharaj University, Kanpur, India
| | - Hafiz M.N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey, Mexico
| | - Roberto Parra-Saldivar
- FEMSA, Tecnológico de MonterreyEscuela de Ingeniería y Ciencias- Centro de Biotecnología-, Monterrey, Mexico
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar, India
- CONTACT Sunita Varjani ; Yen Wah Tong Environmental Research Institute, National University of Singapore, 1 Create Way, 138602, Singapore
| | - Yen Wah Tong
- Environmental Research Institute, National University of Singapore, Singapore
- Energy and Environmental Sustainability for Megacities (E2S2) Phase II, Campus for Research Excellence and Technological Enterprise (CREATE), Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
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He Y, Mudgett M, Zhao Y. Advances in gene editing without residual transgenes in plants. PLANT PHYSIOLOGY 2022; 188:1757-1768. [PMID: 34893903 PMCID: PMC8968301 DOI: 10.1093/plphys/kiab574] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/09/2021] [Indexed: 05/24/2023]
Abstract
Transgene residuals in edited plants affect genetic analysis, pose off-target risks, and cause regulatory concerns. Several strategies have been developed to efficiently edit target genes without leaving any transgenes in plants. Some approaches directly address this issue by editing plant genomes with DNA-free reagents. On the other hand, DNA-based techniques require another step for ensuring plants are transgene-free. Fluorescent markers, pigments, and chemical treatments have all been employed as tools to distinguish transgenic plants from transgene-free plants quickly and easily. Moreover, suicide genes have been used to trigger self-elimination of transgenic plants, greatly improving the efficiency of isolating the desired transgene-free plants. Transgenes can also be excised from plant genomes using site-specific recombination, transposition or gene editing nucleases, providing a strategy for editing asexually produced plants. Finally, haploid induction coupled with gene editing may make it feasible to edit plants that are recalcitrant to transformation. Here, we evaluate the strengths and weaknesses of recently developed approaches for obtaining edited plants without transgene residuals.
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Affiliation(s)
- Yubing He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Michael Mudgett
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116, USA
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Chennakesavulu K, Singh H, Trivedi PK, Jain M, Yadav SR. State-of-the-Art in CRISPR Technology and Engineering Drought, Salinity, and Thermo-tolerant crop plants. PLANT CELL REPORTS 2022; 41:815-831. [PMID: 33742256 DOI: 10.1007/s00299-021-02681-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/04/2021] [Indexed: 05/28/2023]
Abstract
Our review has described principles and functional importance of CRISPR-Cas9 with emphasis on the recent advancements, such as CRISPR-Cpf1, base editing (BE), prime editing (PE), epigenome editing, tissue-specific (CRISPR-TSKO), and inducible genome editing and their potential applications in generating stress-tolerant plants. Improved agricultural practices and enhanced food crop production using innovative crop breeding technology is essential for increasing access to nutritious foods across the planet. The crop plants play a pivotal role in energy and nutrient supply to humans. The abiotic stress factors, such as drought, heat, and salinity cause a substantial yield loss in crop plants and threaten food security. The most sustainable and eco-friendly way to overcome these challenges are the breeding of crop cultivars with improved tolerance against abiotic stress factors. The conventional plant breeding methods have been highly successful in developing abiotic stress-tolerant crop varieties, but usually cumbersome and time-consuming. Alternatively, the CRISPR/Cas genome editing has emerged as a revolutionary tool for making efficient and precise genetic manipulations in plant genomes. Here, we provide a comprehensive review of the CRISPR/Cas genome editing (GE) technology with an emphasis on recent advances in the plant genome editing, including base editing (BE), prime editing (PE), epigenome editing, tissue-specific (CRISPR-TSKO), and inducible genome editing (CRISPR-IGE), which can be used for obtaining cultivars with enhanced tolerance to various abiotic stress factors. We also describe tissue culture-free, DNA-free GE technology, and some of the CRISPR-based tools that can be modified for their use in crop plants.
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Affiliation(s)
- Kunchapu Chennakesavulu
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Harshita Singh
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India
| | - Prabodh Kumar Trivedi
- CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), Near Kukrail Picnic Spot, Lucknow, 226015, India
| | - Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Shri Ram Yadav
- Department of Biotechnology, Indian Institute of Technology, Roorkee, Uttarakhand, 247667, India.
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Deb S, Choudhury A, Kharbyngar B, Satyawada RR. Applications of CRISPR/Cas9 technology for modification of the plant genome. Genetica 2022; 150:1-12. [PMID: 35018532 DOI: 10.1007/s10709-021-00146-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022]
Abstract
The CRISPR/Cas (Clustered regularly interspaced short palindromic repeats/ CRISPR associated protein 9) system was discovered in bacteria and archea as an acquired immune response to protect the cells from infection. This technology has now evolved to become an efficient genome editing tool, and is replacing older gene editing technologies. This technique uses programmable sgRNAs to guide the Cas9 endonuclease to the target DNA location. sgRNA is a vital component of the CRISPR technology, since without it the Cas nuclease cannot reach to its target location. Over the years, many tools have been developed for designing sgRNAs, the details of which have been extensively reviewed here. It has proven to be a promising tool in the field of genetic engineering and has successfully generated many plant varieties with better and desirable qualities. In the present review, we attempted to collect,collate and summarize information related to the development of CRISPR/Cas9 system as a tool and subsequently into a technique having a wide array of applications in the field of plant genome editing in attaining desirable traits like resistance to various diseases, nutritional enhancement etc. In addition, the probable future prospects and the various bio-safety concerns associated with CRISPR gene editing technology have been discussed in detail.
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Affiliation(s)
- Sohini Deb
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Amrita Choudhury
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Banridor Kharbyngar
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India
| | - Rama Rao Satyawada
- Plant Biotechnology Laboratory, Department of Biotechnology and Bioinformatics, North-Eastern Hill University, Shillong, Meghalaya, 793022, India.
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46
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Gentzel IN, Ohlson EW, Redinbaugh MG, Wang GL. VIGE: virus-induced genome editing for improving abiotic and biotic stress traits in plants. STRESS BIOLOGY 2022; 2:2. [PMID: 37676518 PMCID: PMC10441944 DOI: 10.1007/s44154-021-00026-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 12/12/2021] [Indexed: 09/08/2023]
Abstract
Agricultural production is hampered by disease, pests, and environmental stresses. To minimize yield loss, it is important to develop crop cultivars with resistance or tolerance to their respective biotic and abiotic constraints. Transformation techniques are not optimized for many species and desirable cultivars may not be amenable to genetic transformation, necessitating inferior cultivar usage and time-consuming introgression through backcrossing to the preferred variety. Overcoming these limitations will greatly facilitate the development of disease, insect, and abiotic stress tolerant crops. One such avenue for rapid crop improvement is the development of viral systems to deliver CRISPR/Cas-based genome editing technology to plants to generate targeted beneficial mutations. Viral delivery of genomic editing constructs can theoretically be applied to span the entire host range of the virus utilized, circumventing the challenges associated with traditional transformation and breeding techniques. Here we explore the types of viruses that have been optimized for CRISPR/Cas9 delivery, the phenotypic outcomes achieved in recent studies, and discuss the future potential of this rapidly advancing technology.
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Affiliation(s)
- Irene N Gentzel
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
| | - Erik W Ohlson
- USDA, Agricultural Research Service, Corn, Soybean and Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | | | - Guo-Liang Wang
- Department of Plant Pathology, The Ohio State University, Columbus, OH, 43210, USA.
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Wu FH, Yuan YH, Hsu CT, Cheng QW, Lin CS. Application of Protoplast Regeneration to CRISPR/Cas9 Mutagenesis in Nicotiana tabacum. Methods Mol Biol 2022; 2464:49-64. [PMID: 35258824 DOI: 10.1007/978-1-0716-2164-6_4] [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: 06/14/2023]
Abstract
Protoplast transfection is widely used in plant research to rapidly evaluate RNA degradation, reporter assay, gene expression, subcellular localization, and protein-protein interactions. In order to successfully use protoplast transfection with the newly emerging clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) protein editing platform, high yield of protoplasts, stable transfection efficiency, and reliable regeneration protocols are necessary. The Nicotiana tabacum transient protoplast transfection and regeneration system can effectively obtain target gene mutations in regenerated plants without transgenes and is thus a very attractive technique for evaluating gene editing reagents using CRISPR/Cas-based systems. Here, we describe in detail sterilized seed germination, culture conditions, isolation of Nicotiana tabacum protoplasts from tissue culture explants, construction of a vector containing the Cas protein and sgRNA cassette, highly efficient polyethylene glycol-calcium transient transfection of plasmids delivered into protoplasts, evaluation of mutagenesis efficiency and genotype analysis from protoplasts and regenerated plants, and the regeneration conditions to obtain CRISPR-edited plants from single protoplasts.
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Affiliation(s)
- Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan.
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Baci GM, Cucu AA, Giurgiu AI, Muscă AS, Bagameri L, Moise AR, Bobiș O, Rațiu AC, Dezmirean DS. Advances in Editing Silkworms ( Bombyx mori) Genome by Using the CRISPR-Cas System. INSECTS 2021; 13:28. [PMID: 35055871 PMCID: PMC8777690 DOI: 10.3390/insects13010028] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/18/2021] [Accepted: 12/23/2021] [Indexed: 12/12/2022]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) represents a powerful genome editing technology that revolutionized in a short period of time numerous natural sciences branches. Therefore, extraordinary progress was made in various fields, such as entomology or biotechnology. Bombyx mori is one of the most important insects, not only for the sericulture industry, but for numerous scientific areas. The silkworms play a key role as a model organism, but also as a bioreactor for the recombinant protein production. Nowadays, the CRISPR-Cas genome editing system is frequently used in order to perform gene analyses, to increase the resistance against certain pathogens or as an imaging tool in B. mori. Here, we provide an overview of various studies that made use of CRISPR-Cas for B. mori genome editing, with a focus on emphasizing the high applicability of this system in entomology and biological sciences.
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Affiliation(s)
- Gabriela-Maria Baci
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Alexandra-Antonia Cucu
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Alexandru-Ioan Giurgiu
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Adriana-Sebastiana Muscă
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Lilla Bagameri
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Adela Ramona Moise
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | - Otilia Bobiș
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
| | | | - Daniel Severus Dezmirean
- Faculty of Animal Science and Biotechnology, University of Animal Sciences and Veterinary Medicine Cluj-Napoca, 400372 Cluj-Napoca, Romania; (G.-M.B.); (A.-A.C.); (A.-I.G.); (A.-S.M.); (L.B.); (O.B.); (D.S.D.)
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Hoshikawa K, Pham D, Ezura H, Schafleitner R, Nakashima K. Genetic and Molecular Mechanisms Conferring Heat Stress Tolerance in Tomato Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:786688. [PMID: 35003175 PMCID: PMC8739973 DOI: 10.3389/fpls.2021.786688] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/29/2021] [Indexed: 05/17/2023]
Abstract
Climate change is a major threat to global food security. Changes in climate can directly impact food systems by reducing the production and genetic diversity of crops and their wild relatives, thereby restricting future options for breeding improved varieties and reducing the ability to adapt crops to future challenges. The global surface temperature is predicted to rise by an average of 0.3°C during the next decade, and the Paris Agreement (Paris Climate Accords) aims to limit global warming to below an average of 2°C, preferably to 1.5°C compared to pre-industrial levels. Even if the goal of the Paris Agreement can be met, the predicted rise in temperatures will increase the likelihood of extreme weather events, including heatwaves, making heat stress (HS) a major global abiotic stress factor for many crops. HS can have adverse effects on plant morphology, physiology, and biochemistry during all stages of vegetative and reproductive development. In fruiting vegetables, even moderate HS reduces fruit set and yields, and high temperatures may result in poor fruit quality. In this review, we emphasize the effects of abiotic stress, especially at high temperatures, on crop plants, such as tomatoes, touching upon key processes determining plant growth and yield. Specifically, we investigated the molecular mechanisms involved in HS tolerance and the challenges of developing heat-tolerant tomato varieties. Finally, we discuss a strategy for effectively improving the heat tolerance of vegetable crops.
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Affiliation(s)
- Ken Hoshikawa
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
- Vegetable Diversity and Improvement, World Vegetable Center, Tainan, Taiwan
| | - Dung Pham
- Faculty of Biotechnology, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Hiroshi Ezura
- Tsukuba Plant Innovation Research Center, University of Tsukuba, Tsukuba, Japan
| | | | - Kazuo Nakashima
- Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
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Shojaei Baghini S, Gardanova ZR, Zekiy AO, Shomali N, Tosan F, Jarahian M. Optimizing sgRNA to Improve CRISPR/Cas9 Knockout Efficiency: Special Focus on Human and Animal Cell. Front Bioeng Biotechnol 2021; 9:775309. [PMID: 34869290 PMCID: PMC8640246 DOI: 10.3389/fbioe.2021.775309] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022] Open
Abstract
During recent years, clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) technologies have been noticed as a rapidly evolving tool to deliver a possibility for modifying target sequence expression and function. The CRISPR/Cas9 tool is currently being used to treat a myriad of human disorders, ranging from genetic diseases and infections to cancers. Preliminary reports have shown that CRISPR technology could result in valued consequences for the treatment of Duchenne muscular dystrophy (DMD), cystic fibrosis (CF), β-thalassemia, Huntington's diseases (HD), etc. Nonetheless, high rates of off-target effects may hinder its application in clinics. Thereby, recent studies have focused on the finding of the novel strategies to ameliorate these off-target effects and thereby lead to a high rate of fidelity and accuracy in human, animals, prokaryotes, and also plants. Meanwhile, there is clear evidence indicating that the design of the specific sgRNA with high efficiency is of paramount importance. Correspondingly, elucidation of the principal parameters that contributed to determining the sgRNA efficiencies is a prerequisite. Herein, we will deliver an overview regarding the therapeutic application of CRISPR technology to treat human disorders. More importantly, we will discuss the potent influential parameters (e.g., sgRNA structure and feature) implicated in affecting the sgRNA efficacy in CRISPR/Cas9 technology, with special concentration on human and animal studies.
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Affiliation(s)
- Sadegh Shojaei Baghini
- Plant Biotechnology Department, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Zhanna R. Gardanova
- Department of Psychotherapy, Pirogov Russian National Research Medical University, Moscow, Russia
- Medical Faculty, Russian State Social University, Moscow, Russia
| | - Angelina Olegovna Zekiy
- Department of Prosthetic Dentistry, I. M. Sechenov First Moscow State Medical University (Sechenov University), Moscow, Russia
| | - Navid Shomali
- Immunology Research Center (IRC), Tabriz University of Medical Sciences, Tabriz, Iran
| | - Foad Tosan
- Student Research Committee, Semnan University of Medical Sciences, Semnan, Iran
| | - Mostafa Jarahian
- German Cancer Research Center, Toxicology and Chemotherapy Unit (G401), Heidelberg, Germany
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