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Yong J, Wu M, Carroll BJ, Xu ZP, Zhang R. Enhancing plant biotechnology by nanoparticle delivery of nucleic acids. Trends Genet 2024; 40:352-363. [PMID: 38320883 DOI: 10.1016/j.tig.2024.01.005] [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: 11/30/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/08/2024]
Abstract
Plant biotechnology plays a crucial role in developing modern agriculture and plant science research. However, the delivery of exogenous genetic material into plants has been a long-standing obstacle. Nanoparticle-based delivery systems are being established to address this limitation and are proving to be a feasible, versatile, and efficient approach to facilitate the internalization of functional RNA and DNA by plants. The nanoparticle-based delivery systems can also be designed for subcellular delivery and controlled release of the biomolecular cargo. In this review, we provide a concise overview of the recent advances in nanocarriers for the delivery of biomolecules into plants, with a specific focus on applications to enhance RNA interference, foreign gene transfer, and genome editing in plants.
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Affiliation(s)
- Jiaxi Yong
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Miaomiao Wu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Bernard J Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhi Ping Xu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Institute of Biomedical Health Technology and Engineering and Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, P. R. China 518107
| | - Run Zhang
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia; Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Indooroopilly, Queensland 4068, Australia.
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2
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Cui Y, Zhao H, Zhang C. Zinc oxide nanoparticles enhance plasmid transfer among growth-promoting endophytes in Arabidopsis thaliana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169682. [PMID: 38163607 DOI: 10.1016/j.scitotenv.2023.169682] [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: 11/19/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Nanoparticles (NPs) hold great promise for agricultural applications, yet their potential impact on exogenous gene transfer within plant remains poorly understood. In this study, we utilized the non-conjugative plasmid pCAMBIA1300, harboring the bialaphos resistance (bar) gene expressed in plant and the kanamycin resistance (kanR) gene as selectable marker in bacteria. Our results revealed a significant increase in the transfer of plasmid (via carrier Escherichia coli DH5α), both intra- and inter-species within the endophyte, when Arabidopsis thaliana was exposed to environmentally relevant level of zinc oxide (ZnO) NPs at a concentration of 0.7 μg/mL throughout its lifespan. Intriguingly, the plasmid exhibited selective transfer to growth-promoting endophytes, such as Enterobacter, Serratia, and Achromobacter, with the presence of ZnO NPs expanding the pool of potential recipients. This result is due to the facilitation of an endophytic and mutualistic lifestyle of invasive E. coli DH5α and the enrichment of beneficial bacteria aided by ZnO NPs. The plant's descendant generations did not express the bar gene, and the endophytes carrying the exogenous plasmid did not transmit it to sub sequent generation. This research provides crucial insights for assessing the potential risks associated with gene contamination and ensuring the safe and sustainable use of NPs in agriculture.
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Affiliation(s)
- Yueting Cui
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Huiru Zhao
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100857, China.
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3
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Das S, Kwon M, Kim JY. Enhancement of specialized metabolites using CRISPR/Cas gene editing technology in medicinal plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1279738. [PMID: 38450402 PMCID: PMC10915232 DOI: 10.3389/fpls.2024.1279738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Plants are the richest source of specialized metabolites. The specialized metabolites offer a variety of physiological benefits and many adaptive evolutionary advantages and frequently linked to plant defense mechanisms. Medicinal plants are a vital source of nutrition and active pharmaceutical agents. The production of valuable specialized metabolites and bioactive compounds has increased with the improvement of transgenic techniques like gene silencing and gene overexpression. These techniques are beneficial for decreasing production costs and increasing nutritional value. Utilizing biotechnological applications to enhance specialized metabolites in medicinal plants needs characterization and identification of genes within an elucidated pathway. The breakthrough and advancement of CRISPR/Cas-based gene editing in improving the production of specific metabolites in medicinal plants have gained significant importance in contemporary times. This article imparts a comprehensive recapitulation of the latest advancements made in the implementation of CRISPR-gene editing techniques for the purpose of augmenting specific metabolites in medicinal plants. We also provide further insights and perspectives for improving metabolic engineering scenarios in medicinal plants.
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Affiliation(s)
- Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
| | - Moonhyuk Kwon
- Division of Life Science, Anti-aging Bio Cell Factory Regional Leading Research Center (ABC-RLRC), Research Institute of Molecular Alchemy (RIMA), Gyeongsang National University, Jinju, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Republic of Korea
- Nulla Bio R&D Center, Nulla Bio Inc., Jinju, Republic of Korea
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4
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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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Bhuyan SJ, Kumar M, Ramrao Devde P, Rai AC, Mishra AK, Singh PK, Siddique KHM. Progress in gene editing tools, implications and success in plants: a review. Front Genome Ed 2023; 5:1272678. [PMID: 38144710 PMCID: PMC10744593 DOI: 10.3389/fgeed.2023.1272678] [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: 08/07/2023] [Accepted: 11/13/2023] [Indexed: 12/26/2023] Open
Abstract
Genetic modifications are made through diverse mutagenesis techniques for crop improvement programs. Among these mutagenesis tools, the traditional methods involve chemical and radiation-induced mutagenesis, resulting in off-target and unintended mutations in the genome. However, recent advances have introduced site-directed nucleases (SDNs) for gene editing, significantly reducing off-target changes in the genome compared to induced mutagenesis and naturally occurring mutations in breeding populations. SDNs have revolutionized genetic engineering, enabling precise gene editing in recent decades. One widely used method, homology-directed repair (HDR), has been effective for accurate base substitution and gene alterations in some plant species. However, its application has been limited due to the inefficiency of HDR in plant cells and the prevalence of the error-prone repair pathway known as non-homologous end joining (NHEJ). The discovery of CRISPR-Cas has been a game-changer in this field. This system induces mutations by creating double-strand breaks (DSBs) in the genome and repairing them through associated repair pathways like NHEJ. As a result, the CRISPR-Cas system has been extensively used to transform plants for gene function analysis and to enhance desirable traits. Researchers have made significant progress in genetic engineering in recent years, particularly in understanding the CRISPR-Cas mechanism. This has led to various CRISPR-Cas variants, including CRISPR-Cas13, CRISPR interference, CRISPR activation, base editors, primes editors, and CRASPASE, a new CRISPR-Cas system for genetic engineering that cleaves proteins. Moreover, gene editing technologies like the prime editor and base editor approaches offer excellent opportunities for plant genome engineering. These cutting-edge tools have opened up new avenues for rapidly manipulating plant genomes. This review article provides a comprehensive overview of the current state of plant genetic engineering, focusing on recently developed tools for gene alteration and their potential applications in plant research.
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Affiliation(s)
- Suman Jyoti Bhuyan
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Manoj Kumar
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | - Pandurang Ramrao Devde
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
| | - Avinash Chandra Rai
- Institute of Plant Sciences, Agricultural Research Organization, Volcani Center, Rishon LeZion, Israel
| | | | - Prashant Kumar Singh
- Department of Biotechnology, Mizoram University (A Central University), Pachhunga University College Campus, Aizawl, Mizoram, India
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6
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Liu J, Wang FZ, Li C, Li Y, Li JF. Hidden prevalence of deletion-inversion bi-alleles in CRISPR-mediated deletions of tandemly arrayed genes in plants. Nat Commun 2023; 14:6787. [PMID: 37880225 PMCID: PMC10600118 DOI: 10.1038/s41467-023-42490-1] [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: 01/25/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023] Open
Abstract
Tandemly arrayed genes (TAGs) with functional redundancy and chromosomal linkage constitute 14 ~ 35% in sequenced plant genomes. The multiplex CRISPR system is the tool of choice for creating targeted TAG deletions. Here, we show that up to ~80% of CRISPR-mediated TAG knockout alleles in Arabidopsis and rice are deletion-inversion (delinver) bi-alleles, which are easily misidentified as homozygous deletion alleles by routine PCR-based genotyping. This can lead to misinterpretation of experimental data and production of progenies with genetic heterogeneity in an unnoticed manner. In ~2,650 transgenic events, delinver mutation frequencies are predominantly correlated with deletion frequencies but unrelated to chromosomal locations or deletion sizes. Delinver mutations also occur frequently at genomic non-TAG loci during multiplexed CRISPR editing. Our work raises the alarm about delinver mutations as common unwanted products of targeted TAG deletions in plants and helps prevent false interpretation of plant TAG functions due to this hidden genotype issue.
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Affiliation(s)
- Jiuer Liu
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Feng-Zhu Wang
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Chong Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yujia Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China
| | - Jian-Feng Li
- State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resources, MOE Key Laboratory of Gene Function and Regulation, School of Life Sciences, Sun Yat-sen University, Guangzhou, 510275, China.
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Ali A, Zafar MM, Farooq Z, Ahmed SR, Ijaz A, Anwar Z, Abbas H, Tariq MS, Tariq H, Mustafa M, Bajwa MH, Shaukat F, Razzaq A, Maozhi R. Breakthrough in CRISPR/Cas system: Current and future directions and challenges. Biotechnol J 2023; 18:e2200642. [PMID: 37166088 DOI: 10.1002/biot.202200642] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/12/2023]
Abstract
Targeted genome editing (GE) technology has brought a significant revolution in fictional genomic research and given hope to plant scientists to develop desirable varieties. This technology involves inducing site-specific DNA perturbations that can be repaired through DNA repair pathways. GE products currently include CRISPR-associated nuclease DNA breaks, prime editors generated DNA flaps, single nucleotide-modifications, transposases, and recombinases. The discovery of double-strand breaks, site-specific nucleases (SSNs), and repair mechanisms paved the way for targeted GE, and the first-generation GE tools, ZFNs and TALENs, were successfully utilized in plant GE. However, CRISPR-Cas has now become the preferred tool for GE due to its speed, reliability, and cost-effectiveness. Plant functional genomics has benefited significantly from the widespread use of CRISPR technology for advancements and developments. This review highlights the progress made in CRISPR technology, including multiplex editing, base editing (BE), and prime editing (PE), as well as the challenges and potential delivery mechanisms.
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Affiliation(s)
- Ahmad Ali
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | | | - Zunaira Farooq
- National Center for Soybean Improvement, Key Laboratory of Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, China
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Aqsa Ijaz
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Zunaira Anwar
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Huma Abbas
- Department of Plant Pathology, University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College (NIAB-C), Pakistan Institute of Engineering and Applied Science (PIEAS), Nilore, Pakistan
| | - Hala Tariq
- Institute of Soil and Environmental Sciences, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Mahwish Mustafa
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | | | - Fiza Shaukat
- Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
| | - Abdul Razzaq
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Ren Maozhi
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Institute of, Urban Agriculture, Chinese Academy of Agriculture Science, Chengdu, China
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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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9
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Su W, Xu M, Radani Y, Yang L. Technological Development and Application of Plant Genetic Transformation. Int J Mol Sci 2023; 24:10646. [PMID: 37445824 DOI: 10.3390/ijms241310646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/07/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Genetic transformation is an important strategy for enhancing plant biomass or resistance in response to adverse environments and population growth by imparting desirable genetic characteristics. Research on plant genetic transformation technology can promote the functional analysis of plant genes, the utilization of excellent traits, and precise breeding. Various technologies of genetic transformation have been continuously discovered and developed for convenient manipulation and high efficiency, mainly involving the delivery of exogenous genes and regeneration of transformed plants. Here, currently developed genetic transformation technologies were expounded and compared. Agrobacterium-mediated gene delivery methods are commonly used as direct genetic transformation, as well as external force-mediated ways such as particle bombardment, electroporation, silicon carbide whiskers, and pollen tubes as indirect ones. The regeneration of transformed plants usually involves the de novo organogenesis or somatic embryogenesis pathway of the explants. Ectopic expression of morphogenetic transcription factors (Bbm, Wus2, and GRF-GIF) can significantly improve plant regeneration efficiency and enable the transformation of some hard-to-transform plant genotypes. Meanwhile, some limitations in these gene transfer methods were compared including genotype dependence, low transformation efficiency, and plant tissue damage, and recently developed flexible approaches for plant genotype transformation are discussed regarding how gene delivery and regeneration strategies can be optimized to overcome species and genotype dependence. This review summarizes the principles of various techniques for plant genetic transformation and discusses their application scope and limiting factors, which can provide a reference for plant transgenic breeding.
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Affiliation(s)
- Wenbin Su
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Mingyue Xu
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Yasmina Radani
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Liming Yang
- State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
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10
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Kumari R, Suman K, Karmakar S, Mishra V, Lakra SG, Saurav GK, Mahto BK. Regulation and safety measures for nanotechnology-based agri-products. Front Genome Ed 2023; 5:1200987. [PMID: 37415849 PMCID: PMC10320728 DOI: 10.3389/fgeed.2023.1200987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/09/2023] [Indexed: 07/08/2023] Open
Abstract
There is a wide range of application for nanotechnology in agriculture, including fertilizers, aquaculture, irrigation, water filtration, animal feed, animal vaccines, food processing, and packaging. In recent decades, nanotechnology emerged as a prospective and promising approach for the advancement of Agri-sector such as pest/disease prevention, fertilizers, agrochemicals, biofertilizers, bio-stimulants, post-harvest storage, pheromones-, and nutrient-delivery, and genetic manipulation in plants for crop improvement by using nanomaterial as a carrier system. Exponential increase in global population has enhanced food demand, so to fulfil the demand markets already included nano-based product likewise nano-encapsulated nutrients/agrochemicals, antimicrobial and packaging of food. For the approval of nano-based product, applicants for a marketing approval must show that such novel items can be used safely without endangering the consumer and environment. Several nations throughout the world have been actively looking at whether their regulatory frameworks are suitable for handling nanotechnologies. As a result, many techniques to regulate nano-based products in agriculture, feed, and food have been used. Here, we have contextualized different regulatory measures of several countries for nano-based products in agriculture, from feed to food, including guidance and legislation for safety assessment worldwide.
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Affiliation(s)
- Ritika Kumari
- University Department of Botany, Ranchi University, Ranchi, Jharkhand, India
| | - Kalpana Suman
- University Department of Botany, Ranchi University, Ranchi, Jharkhand, India
| | - Swagata Karmakar
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, India
- Department of Environmental Studies, Ram Lal Anand College, University of Delhi, Delhi, India
| | - Vandana Mishra
- Bioresources and Environmental Biotechnology Laboratory, Department of Environmental Studies, University of Delhi, Delhi, India
| | | | - Gunjan Kumar Saurav
- Department of Zoology, Rajiv Gandhi University, Doimukh, Arunachal Pradesh, India
- Gut Biology Laboratory, Department of Zoology, University of Delhi, Delhi, India
| | - Binod Kumar Mahto
- University Department of Botany, Ranchi University, Ranchi, Jharkhand, India
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [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: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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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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Li R, Han Z, Yin Q, Li M, Zhang M, Li Z, Wang P, Jiang L, Ow DW. Target Lines for in Planta Gene Stacking in Japonica Rice. Int J Mol Sci 2022; 23:ijms23169385. [PMID: 36012650 PMCID: PMC9409015 DOI: 10.3390/ijms23169385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/11/2022] [Accepted: 08/11/2022] [Indexed: 12/02/2022] Open
Abstract
The clustering of transgenes at a chromosome location minimizes the number of segregating loci that needs to be introgressed to field cultivars. Transgenes could be efficiently stacked through site-specific recombination and a recombinase-mediated in planta gene stacking process was described previously in tobacco based on the Mycobacteriophage Bxb1 site-specific integration system. Since this process requires a recombination site in the genome, this work describes the generation of target sites in the Japonica rice genome. Agrobacterium-mediated gene transfer yielded ~4000 random-insertion lines. Seven lines met the criteria of being single copy, not close to a centromere, not inserted within or close to a known gene or repetitive DNA, having precise recombination site sequences on both ends, and able to express the reporter gene. Each target line tested was able to accept the site-specific integration of a new gfp-containing plasmid and in three of those lines, we regenerated fertile plants. These target lines could be used as foundation lines for stacking new traits into Japonica rice.
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Affiliation(s)
- Ruyu Li
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: (R.L.); (D.W.O.)
| | - Zhiguo Han
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Qian Yin
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Meiru Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Mingyong Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Zhenzhen Li
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - Ping Wang
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Li Jiang
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, China
| | - David W. Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences, Guangzhou 510650, China
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- Correspondence: (R.L.); (D.W.O.)
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Piskunen P, Latham R, West CE, Castronovo M, Linko V. Integrating CRISPR/Cas systems with programmable DNA nanostructures for delivery and beyond. iScience 2022; 25:104389. [PMID: 35633938 PMCID: PMC9130510 DOI: 10.1016/j.isci.2022.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Precise genome editing with CRISPR/Cas paves the way for many biochemical, biotechnological, and medical applications, and consequently, it may enable treatment of already known and still-to-be-found genetic diseases. Meanwhile, another rapidly emerging field—structural DNA nanotechnology—provides a customizable and modular platform for accurate positioning of nanoscopic materials, for e.g., biomedical uses. This addressability has just recently been applied in conjunction with the newly developed gene engineering tools to enable impactful, programmable nanotechnological applications. As of yet, self-assembled DNA nanostructures have been mainly employed to enhance and direct the delivery of CRISPR/Cas, but lately the groundwork has also been laid out for other intriguing and complex functions. These recent advances will be described in this perspective.
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15
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Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
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Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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16
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Das D, Singha DL, Paswan RR, Chowdhury N, Sharma M, Reddy PS, Chikkaputtaiah C. Recent advancements in CRISPR/Cas technology for accelerated crop improvement. PLANTA 2022; 255:109. [PMID: 35460444 DOI: 10.1007/s00425-022-03894-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/29/2022] [Indexed: 06/14/2023]
Abstract
Precise genome engineering approaches could be perceived as a second paradigm for targeted trait improvement in crop plants, with the potential to overcome the constraints imposed by conventional CRISPR/Cas technology. The likelihood of reduced agricultural production due to highly turbulent climatic conditions increases as the global population expands. The second paradigm of stress-resilient crops with enhanced tolerance and increased productivity against various stresses is paramount to support global production and consumption equilibrium. Although traditional breeding approaches have substantially increased crop production and yield, effective strategies are anticipated to restore crop productivity even further in meeting the world's increasing food demands. CRISPR/Cas, which originated in prokaryotes, has surfaced as a coveted genome editing tool in recent decades, reshaping plant molecular biology in unprecedented ways and paving the way for engineering stress-tolerant crops. CRISPR/Cas is distinguished by its efficiency, high target specificity, and modularity, enables precise genetic modification of crop plants, allowing for the creation of allelic variations in the germplasm and the development of novel and more productive agricultural practices. Additionally, a slew of advanced biotechnologies premised on the CRISPR/Cas methodologies have augmented fundamental research and plant synthetic biology toolkits. Here, we describe gene editing tools, including CRISPR/Cas and its imitative tools, such as base and prime editing, multiplex genome editing, chromosome engineering followed by their implications in crop genetic improvement. Further, we comprehensively discuss the latest developments of CRISPR/Cas technology including CRISPR-mediated gene drive, tissue-specific genome editing, dCas9 mediated epigenetic modification and programmed self-elimination of transgenes in plants. Finally, we highlight the applicability and scope of advanced CRISPR-based techniques in crop genetic improvement.
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Affiliation(s)
- Debajit Das
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Dhanawantari L Singha
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Ricky Raj Paswan
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Naimisha Chowdhury
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Monica Sharma
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India
| | - Palakolanu Sudhakar Reddy
- International Crop Research Institute for the Semi Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502 324, India
| | - Channakeshavaiah Chikkaputtaiah
- Biological Sciences and Technology Division, CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, 785006, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201 002, India.
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Sharma P, Lew TTS. Principles of Nanoparticle Design for Genome Editing in Plants. Front Genome Ed 2022; 4:846624. [PMID: 35330692 PMCID: PMC8940305 DOI: 10.3389/fgeed.2022.846624] [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: 12/31/2021] [Accepted: 02/15/2022] [Indexed: 12/04/2022] Open
Abstract
Precise plant genome editing technologies have provided new opportunities to accelerate crop improvement and develop more sustainable agricultural systems. In particular, the prokaryote-derived CRISPR platforms allow precise manipulation of the crop genome, enabling the generation of high-yielding and stress-tolerant crop varieties. Nanotechnology has the potential to catalyze the development of a novel molecular toolbox even further by introducing the possibility of a rapid, universal delivery method to edit the plant genome in a species-independent manner. In this Perspective, we highlight how nanoparticles can help unlock the full potential of CRISPR/Cas technology in targeted manipulation of the plant genome to improve agricultural output. We discuss current challenges hampering progress in nanoparticle-enabled plant gene-editing research and application in the field, and highlight how rational nanoparticle design can overcome them. Finally, we examine the implications of the regulatory frameworks and social acceptance for the future of nano-enabled precision breeding in the developing world.
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Affiliation(s)
- Pushkal Sharma
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Tedrick Thomas Salim Lew
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore, Singapore
- Institute of Materials Research and Engineering, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- *Correspondence: Tedrick Thomas Salim Lew, , orcid.org/0000-0002-4815-9921
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Yin Q, Li R, Ow DW. Site-Specific Sequence Exchange Between Homologous and Non-homologous Chromosomes. FRONTIERS IN PLANT SCIENCE 2022; 13:828960. [PMID: 35185992 PMCID: PMC8850970 DOI: 10.3389/fpls.2022.828960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
Transgene integration typically takes place in an easy-to-transform laboratory variety before the transformation event is introgressed through backcrosses to elite cultivars. As new traits are added to existing transgenic lines, site-specific integration can stack new transgenes into a previously created transgenic locus. In planta site-specific integration minimizes the number of segregating loci to assemble into a breeding line, but cannot break genetic linkage between the transgenic locus and nearby undesirable traits. In this study, we describe an additional feature of an in planta gene-stacking scheme, in which the Cre (control of recombination) recombinase not only deletes transgenic DNA no longer needed after transformation but also mediates recombination between homologous or non-homologous chromosomes. Although the target site must first be introgressed through conventional breeding, subsequent transgenes inserted into the same locus would be able to use Cre-mediated translocation to expedite a linkage drag-free introgression to field cultivars.
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Affiliation(s)
- Qian Yin
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangdong Key Laboratory of Applied Botany, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ruyu Li
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangdong Key Laboratory of Applied Botany, Guangzhou, China
| | - David W. Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangdong Key Laboratory of Applied Botany, Guangzhou, China
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Miki D, Wang R, Li J, Kong D, Zhang L, Zhu JK. Gene Targeting Facilitated by Engineered Sequence-Specific Nucleases: Potential Applications for Crop Improvement. PLANT & CELL PHYSIOLOGY 2021; 62:752-765. [PMID: 33638992 PMCID: PMC8484935 DOI: 10.1093/pcp/pcab034] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/09/2021] [Accepted: 02/23/2021] [Indexed: 05/04/2023]
Abstract
Humans are currently facing the problem of how to ensure that there is enough food to feed all of the world's population. Ensuring that the food supply is sufficient will likely require the modification of crop genomes to improve their agronomic traits. The development of engineered sequence-specific nucleases (SSNs) paved the way for targeted gene editing in organisms, including plants. SSNs generate a double-strand break (DSB) at the target DNA site in a sequence-specific manner. These DSBs are predominantly repaired via error-prone non-homologous end joining and are only rarely repaired via error-free homology-directed repair if an appropriate donor template is provided. Gene targeting (GT), i.e. the integration or replacement of a particular sequence, can be achieved with combinations of SSNs and repair donor templates. Although its efficiency is extremely low, GT has been achieved in some higher plants. Here, we provide an overview of SSN-facilitated GT in higher plants and discuss the potential of GT as a powerful tool for generating crop plants with desirable features.
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Affiliation(s)
- Daisuke Miki
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Rui Wang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jing Li
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dali Kong
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Zhang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA
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Mbinda W, Mukami A. A Review of Recent Advances and Future Directions in the Management of Salinity Stress in Finger Millet. FRONTIERS IN PLANT SCIENCE 2021; 12:734798. [PMID: 34603359 PMCID: PMC8481900 DOI: 10.3389/fpls.2021.734798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Salinity stress is a major environmental impediment affecting the growth and production of crops. Finger millet is an important cereal grown in many arid and semi-arid areas of the world characterized by erratic rainfall and scarcity of good-quality water. Finger millet salinity stress is caused by the accumulation of soluble salts due to irrigation without a proper drainage system, coupled with the underlying rocks having a high salt content, which leads to the salinization of arable land. This problem is projected to be exacerbated by climate change. The use of new and efficient strategies that provide stable salinity tolerance across a wide range of environments can guarantee sustainable production of finger millet in the future. In this review, we analyze the strategies that have been used for salinity stress management in finger millet production and discuss potential future directions toward the development of salt-tolerant finger millet varieties. This review also describes how advanced biotechnological tools are being used to develop salt-tolerant plants. The biotechnological techniques discussed in this review are simple to implement, have design flexibility, low cost, and highly efficient. This information provides insights into enhancing finger millet salinity tolerance and improving production.
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Affiliation(s)
- Wilton Mbinda
- Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
- Pwani University Biosciences Research Centre (PUBReC), Pwani University, Kilifi, Kenya
| | - Asunta Mukami
- Department of Life Sciences, South Eastern Kenya University, Kitui, Kenya
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Vu TV, Doan DTH, Tran MT, Sung YW, Song YJ, Kim JY. Improvement of the LbCas12a-crRNA System for Efficient Gene Targeting in Tomato. FRONTIERS IN PLANT SCIENCE 2021; 12:722552. [PMID: 34447405 PMCID: PMC8383147 DOI: 10.3389/fpls.2021.722552] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/16/2021] [Indexed: 05/03/2023]
Abstract
Plant gene targeting (GT) can be utilized to precisely replace up to several kilobases of a plant genome. Recent studies using the powerful clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) nucleases significantly improved plant GT efficiency. However, GT for loci without associated selection markers is still inefficient. We previously utilized Lachnospiraceae bacterium Cas12a (LbCas12a) in combination with a replicon for tomato GT and obtained high GT efficiency with some selection markers. In this study, we advance our GT system by inhibiting the cNHEJ pathway with small chemical molecules such as NU7441. Further optimization of the GT is also possible with the treatment of silver nitrate possibly via its pronounced actions in ethylene inhibition and polyamine production. Importantly, the GT efficiency is significantly enhanced with the use of a temperature-tolerant LbCas12a (ttLbCas12a) that is capable of performing target cleavage even at low temperatures. Targeted deep sequencing, as well as conventional methods, are used for the assessment of the editing efficiency at both cell and plant levels. Our work demonstrates the significance of the selection of gene scissors, the appropriate design and number of LbCas12a crRNAs, the use of chemical treatments, and the establishment of favorable experimental conditions for further enhancement of plant HDR to enable efficient GT in tomato.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Hanoi, Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Crop Science and Rural Development Division, College of Agriculture, Bac Lieu University, Bạc Liêu, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 FOUR Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
- Division of Life Science, Gyeongsang National University, Jinju, South Korea
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22
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Ahmar S, Mahmood T, Fiaz S, Mora-Poblete F, Shafique MS, Chattha MS, Jung KH. Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:663849. [PMID: 34122485 PMCID: PMC8194497 DOI: 10.3389/fpls.2021.663849] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 05/05/2023]
Abstract
Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, Universidad de Talca, Talca, Chile
| | - Tahir Mahmood
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | | | | | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
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Abstract
Conventional methods of DNA sequence insertion into plants, using Agrobacterium-mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.
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Amritha PP, Shah JM. Can genetic engineering-based methods for gene function identification be eclipsed by genome editing in plants? A comparison of methodologies. Mol Genet Genomics 2021; 296:485-500. [PMID: 33751237 DOI: 10.1007/s00438-021-01769-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Finding and explaining the functions of genes in plants have promising applications in crop improvement and bioprospecting and hence, it is important to compare various techniques available for gene function identification in plants. Today, the most popular technology among researchers to identify the functions of genes is the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9)-based genome editing method. But by no means can we say that CRISPR/Cas9 is the go-to method for all purposes. It comes with its own baggage. Researchers will agree and have lived through at least seven more technologies deployed to find the functions of genes, which come under three umbrellas: 1. genetic engineering, 2. transient expression, and 3. chemical/physical mutagenesis. Each of the methods evolved when the previous one ran into an insurmountable problem. In this review, we compare the eight technologies against one another on 14 parameters. This review lays bare the pros and cons, and similarities and dissimilarities of various methods. Every method comes with its advantages and disadvantages. For example, the CRISPR/Cas9-based genome editing is an excellent method for modifying gene sequences, creating allelic versions of genes, thereby aiding the understanding of gene function. But it comes with the baggage of unwanted or off-target mutations. Then, we have methods based on random or targeted knockout of the gene, knockdown, and overexpression of the gene. Targeted disruption of genes is required for complete knockout of gene function, which may not be accomplished by editing. We have also discussed the strategies to overcome the shortcomings of the targeted gene-knockout and the CRISPR/Cas9-based methods. This review serves as a comprehensive guide towards the understanding and comparison of various technologies available for gene function identification in plants and hence, it will find application for crop improvement and bioprospecting related research.
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Affiliation(s)
- P P Amritha
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Periya, Kasaragod, Kerala, 671320, India.
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Alotaibi F, Alharbi S, Alotaibi M, Al Mosallam M, Motawei M, Alrajhi A. Wheat omics: Classical breeding to new breeding technologies. Saudi J Biol Sci 2021; 28:1433-1444. [PMID: 33613071 PMCID: PMC7878716 DOI: 10.1016/j.sjbs.2020.11.083] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 11/26/2020] [Accepted: 11/29/2020] [Indexed: 12/26/2022] Open
Abstract
Wheat is an important cereal crop, and its significance is more due to compete for dietary products in the world. Many constraints facing by the wheat crop due to environmental hazardous, biotic, abiotic stress and heavy matters factors, as a result, decrease the yield. Understanding the molecular mechanism related to these factors is significant to figure out genes regulate under specific conditions. Classical breeding using hybridization has been used to increase the yield but not prospered at the desired level. With the development of newly emerging technologies in biological sciences i.e., marker assisted breeding (MAB), QTLs mapping, mutation breeding, proteomics, metabolomics, next-generation sequencing (NGS), RNA_sequencing, transcriptomics, differential expression genes (DEGs), computational resources and genome editing techniques i.e. (CRISPR cas9; Cas13) advances in the field of omics. Application of new breeding technologies develops huge data; considerable development is needed in bioinformatics science to interpret the data. However, combined omics application to address physiological questions linked with genetics is still a challenge. Moreover, viroid discovery opens the new direction for research, economics, and target specification. Comparative genomics important to figure gene of interest processes are further discussed about considering the identification of genes, genomic loci, and biochemical pathways linked with stress resilience in wheat. Furthermore, this review extensively discussed the omics approaches and their effective use. Integrated plant omics technologies have been used viroid genomes associated with CRISPR and CRISPR-associated Cas13a proteins system used for engineering of viroid interference along with high-performance multidimensional phenotyping as a significant limiting factor for increasing stress resistance in wheat.
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Affiliation(s)
- Fahad Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Saif Alharbi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Majed Alotaibi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Mobarak Al Mosallam
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | | | - Abdullah Alrajhi
- King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
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26
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Capdeville N, Merker L, Schindele P, Puchta H. Sophisticated CRISPR/Cas tools for fine-tuning plant performance. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153332. [PMID: 33383400 DOI: 10.1016/j.jplph.2020.153332] [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: 11/02/2020] [Revised: 12/02/2020] [Accepted: 12/03/2020] [Indexed: 05/03/2023]
Abstract
Over the last years, the discovery of various natural and the development of a row of engineered CRISPR/Cas nucleases have made almost every site of plant genomes accessible for the induction of specific changes. Newly developed tools open up a wide range of possibilities for the induction of genetic variability, from changing a single bp to Mbps, and thus to fine-tune plant performance. Whereas early approaches focused on targeted mutagenesis, recently developed tools enable the induction of precise and predefined genomic modifications. The use of base editors allows the substitution of single nucleotides, whereas the use of prime editors and gene targeting methods enables the induction of larger sequence modifications from a few bases to several kbp. Recently, through CRISPR/Cas-mediated chromosome engineering, it became possible to induce heritable inversions and translocations in the Mbp range. Thus, a novel way of breaking and fixing genetic linkages has come into reach for breeders. In addition, sequence-specific recruitment of various factors involved in transcriptional and post-transcriptional regulation has been shown to provide an additional class of methods for the fine tuning of plant performance. In this review, we provide an overview of the most recent progress in the field of CRISPR/Cas-based tool development for plant genome engineering and try to evaluate the importance of these developments for breeding and biotechnological applications.
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Affiliation(s)
- Niklas Capdeville
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Molecular Biology and Biochemistry, Fritz-Haber-Weg 4, 76135, Karlsruhe, Germany
| | - Laura Merker
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Molecular Biology and Biochemistry, Fritz-Haber-Weg 4, 76135, Karlsruhe, Germany
| | - Patrick Schindele
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Molecular Biology and Biochemistry, Fritz-Haber-Weg 4, 76135, Karlsruhe, Germany
| | - Holger Puchta
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Molecular Biology and Biochemistry, Fritz-Haber-Weg 4, 76135, Karlsruhe, Germany.
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27
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Van Vu T, Thi Hai Doan D, Kim J, Sung YW, Thi Tran M, Song YJ, Das S, Kim J. CRISPR/Cas-based precision genome editing via microhomology-mediated end joining. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:230-239. [PMID: 33047464 PMCID: PMC7868975 DOI: 10.1111/pbi.13490] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 09/11/2020] [Accepted: 10/03/2020] [Indexed: 05/05/2023]
Abstract
Gene editing and/or allele introgression with absolute precision and control appear to be the ultimate goals of genetic engineering. Precision genome editing in plants has been developed through various approaches, including oligonucleotide-directed mutagenesis (ODM), base editing, prime editing and especially homologous recombination (HR)-based gene targeting. With the advent of CRISPR/Cas for the targeted generation of DNA breaks (single-stranded breaks (SSBs) or double-stranded breaks (DSBs)), a substantial advancement in HR-mediated precise editing frequencies has been achieved. Nonetheless, further research needs to be performed for commercially viable applications of precise genome editing; hence, an alternative innovative method for genome editing may be required. Within this scope, we summarize recent progress regarding precision genome editing mediated by microhomology-mediated end joining (MMEJ) and discuss their potential applications in crop improvement.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- National Key Laboratory for Plant Cell BiotechnologyAgricultural Genetics InstituteKm 02, Pham Van Dong RoadCo Nhue 1, Bac Tu Liem, Hanoi11917Vietnam
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Young Jong Song
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Swati Das
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
| | - Jae‐Yean Kim
- Division of Applied Life Science (BK21 Plus Program)Plant Molecular Biology and Biotechnology Research CenterGyeongsang National UniversityJinju 660‐701Republic of Korea
- Division of Life ScienceGyeongsang National University501 Jinju‐daeroJinju52828Republic of Korea
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28
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Zhan X, Lu Y, Zhu JK, Botella JR. Genome editing for plant research and crop improvement. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:3-33. [PMID: 33369120 DOI: 10.1111/jipb.13063] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 12/22/2020] [Indexed: 05/27/2023]
Abstract
The advent of clustered regularly interspaced short palindromic repeat (CRISPR) has had a profound impact on plant biology, and crop improvement. In this review, we summarize the state-of-the-art development of CRISPR technologies and their applications in plants, from the initial introduction of random small indel (insertion or deletion) mutations at target genomic loci to precision editing such as base editing, prime editing and gene targeting. We describe advances in the use of class 2, types II, V, and VI systems for gene disruption as well as for precise sequence alterations, gene transcription, and epigenome control.
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Affiliation(s)
- Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Horticulture, Northwest A&F University, Xianyang, 712100, China
| | - Yuming Lu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, CAS Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Jose Ramon Botella
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, Queensland, 4072, Australia
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29
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Pearl Millet Blast Resistance: Current Status and Recent Advancements in Genomic Selection and Genome Editing Approaches. Fungal Biol 2021. [DOI: 10.1007/978-3-030-60585-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Xu H, Zhang L, Zhang K, Ran Y. Progresses, Challenges, and Prospects of Genome Editing in Soybean ( Glycine max). FRONTIERS IN PLANT SCIENCE 2020; 11:571138. [PMID: 33193504 PMCID: PMC7642200 DOI: 10.3389/fpls.2020.571138] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/28/2020] [Indexed: 05/17/2023]
Abstract
Soybean is grown worldwide for oil and protein source as food, feed and industrial raw material for biofuel. Steady increase in soybean production in the past century mainly attributes to genetic mediation including hybridization, mutagenesis and transgenesis. However, genetic resource limitation and intricate social issues in use of transgenic technology impede soybean improvement to meet rapid increases in global demand for soybean products. New approaches in genomics and development of site-specific nucleases (SSNs) based genome editing technologies have expanded soybean genetic variations in its germplasm and have potential to make precise modification of genes controlling the important agronomic traits in an elite background. ZFNs, TALENS and CRISPR/Cas9 have been adapted in soybean improvement for targeted deletions, additions, replacements and corrections in the genome. The availability of reference genome assembly and genomic resources increases feasibility in using current genome editing technologies and their new development. This review summarizes the status of genome editing in soybean improvement and future directions in this field.
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Affiliation(s)
| | | | | | - Yidong Ran
- Tianjin Genovo Biotechnology Co., Ltd., Tianjin, China
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31
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Applications of CRISPR-Cas in agriculture and plant biotechnology. Nat Rev Mol Cell Biol 2020; 21:661-677. [PMID: 32973356 DOI: 10.1038/s41580-020-00288-9] [Citation(s) in RCA: 306] [Impact Index Per Article: 76.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/11/2020] [Indexed: 12/26/2022]
Abstract
The prokaryote-derived CRISPR-Cas genome editing technology has altered plant molecular biology beyond all expectations. Characterized by robustness and high target specificity and programmability, CRISPR-Cas allows precise genetic manipulation of crop species, which provides the opportunity to create germplasms with beneficial traits and to develop novel, more sustainable agricultural systems. Furthermore, the numerous emerging biotechnologies based on CRISPR-Cas platforms have expanded the toolbox of fundamental research and plant synthetic biology. In this Review, we first briefly describe gene editing by CRISPR-Cas, focusing on the newest, precise gene editing technologies such as base editing and prime editing. We then discuss the most important applications of CRISPR-Cas in increasing plant yield, quality, disease resistance and herbicide resistance, breeding and accelerated domestication. We also highlight the most recent breakthroughs in CRISPR-Cas-related plant biotechnologies, including CRISPR-Cas reagent delivery, gene regulation, multiplexed gene editing and mutagenesis and directed evolution technologies. Finally, we discuss prospective applications of this game-changing technology.
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Ahmar S, Saeed S, Khan MHU, Ullah Khan S, Mora-Poblete F, Kamran M, Faheem A, Maqsood A, Rauf M, Saleem S, Hong WJ, Jung KH. A Revolution toward Gene-Editing Technology and Its Application to Crop Improvement. Int J Mol Sci 2020; 21:E5665. [PMID: 32784649 PMCID: PMC7461041 DOI: 10.3390/ijms21165665] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/05/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing is a relevant, versatile, and preferred tool for crop improvement, as well as for functional genomics. In this review, we summarize the advances in gene-editing techniques, such as zinc-finger nucleases (ZFNs), transcription activator-like (TAL) effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR) associated with the Cas9 and Cpf1 proteins. These tools support great opportunities for the future development of plant science and rapid remodeling of crops. Furthermore, we discuss the brief history of each tool and provide their comparison and different applications. Among the various genome-editing tools, CRISPR has become the most popular; hence, it is discussed in the greatest detail. CRISPR has helped clarify the genomic structure and its role in plants: For example, the transcriptional control of Cas9 and Cpf1, genetic locus monitoring, the mechanism and control of promoter activity, and the alteration and detection of epigenetic behavior between single-nucleotide polymorphisms (SNPs) investigated based on genetic traits and related genome-wide studies. The present review describes how CRISPR/Cas9 systems can play a valuable role in the characterization of the genomic rearrangement and plant gene functions, as well as the improvement of the important traits of field crops with the greatest precision. In addition, the speed editing strategy of gene-family members was introduced to accelerate the applications of gene-editing systems to crop improvement. For this, the CRISPR technology has a valuable advantage that particularly holds the scientist's mind, as it allows genome editing in multiple biological systems.
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Affiliation(s)
- Sunny Ahmar
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Sumbul Saeed
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Muhammad Hafeez Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Shahid Ullah Khan
- College of Plant Sciences and Technology Huazhong Agricultural University, Wuhan 430070, China; (S.A.); (S.S.); (M.H.U.K.); (S.U.K.)
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile;
| | - Muhammad Kamran
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China;
| | - Aroosha Faheem
- Sate Key Laboratory of Agricultural Microbiology and State Key Laboratory of Microbial Biosensor, College of Life Sciences Huazhong Agriculture University Wuhan, Wuhan 430070, China;
| | - Ambreen Maqsood
- Department of Plant Pathology, University College of Agriculture and Environmental Sciences, The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan;
| | - Muhammad Rauf
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan;
| | - Saba Saleem
- Department of Bioscience, COMSATS Institute of Information Technology, Islamabad 45550, Pakistan;
| | - Woo-Jong Hong
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
| | - Ki-Hong Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea;
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Hassan MM, Yuan G, Chen JG, Tuskan GA, Yang X. Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. BIODESIGN RESEARCH 2020; 2020:9350905. [PMID: 37849904 PMCID: PMC10530660 DOI: 10.34133/2020/9350905] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 10/19/2023] Open
Abstract
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
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Affiliation(s)
- Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Hrbáčková M, Dvořák P, Takáč T, Tichá M, Luptovčiak I, Šamajová O, Ovečka M, Šamaj J. Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa. FRONTIERS IN PLANT SCIENCE 2020; 11:592. [PMID: 32508859 PMCID: PMC7253590 DOI: 10.3389/fpls.2020.00592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 04/20/2020] [Indexed: 05/07/2023]
Abstract
For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Jozef Šamaj
- Department of Cell Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University Olomouc, Olomouc, Czechia
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35
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Ramkumar TR, Lenka SK, Arya SS, Bansal KC. A Short History and Perspectives on Plant Genetic Transformation. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2020; 2124:39-68. [PMID: 32277448 DOI: 10.1007/978-1-0716-0356-7_3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plant genetic transformation is an important technological advancement in modern science, which has not only facilitated gaining fundamental insights into plant biology but also started a new era in crop improvement and commercial farming. However, for many crop plants, efficient transformation and regeneration still remain a challenge even after more than 30 years of technical developments in this field. Recently, FokI endonuclease-based genome editing applications in plants offered an exciting avenue for augmenting crop productivity but it is mainly dependent on efficient genetic transformation and regeneration, which is a major roadblock for implementing genome editing technology in plants. In this chapter, we have outlined the major historical developments in plant genetic transformation for developing biotech crops. Overall, this field needs innovations in plant tissue culture methods for simplification of operational steps for enhancing the transformation efficiency. Similarly, discovering genes controlling developmental reprogramming and homologous recombination need considerable attention, followed by understanding their role in enhancing genetic transformation efficiency in plants. Further, there is an urgent need for exploring new and low-cost universal delivery systems for DNA/RNA and protein into plants. The advancements in synthetic biology, novel vector systems for precision genome editing and gene integration could potentially bring revolution in crop-genetic potential enhancement for a sustainable future. Therefore, efficient plant transformation system standardization across species holds the key for translating advances in plant molecular biology to crop improvement.
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Affiliation(s)
- Thakku R Ramkumar
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, USA
| | - Sangram K Lenka
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Sagar S Arya
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India
| | - Kailash C Bansal
- TERI-Deakin NanoBiotechnology Centre, The Energy and Resources Institute, New Delhi, India.
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Van Vu T, Sung YW, Kim J, Doan DTH, Tran MT, Kim JY. Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants. RICE (NEW YORK, N.Y.) 2019; 12:95. [PMID: 31858277 PMCID: PMC6923311 DOI: 10.1186/s12284-019-0355-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/04/2019] [Indexed: 05/18/2023]
Abstract
Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging conditions such as climate change and the reduction in arable lands. Monocotyledonous crops are not only responsible for approximately 70% of total global crop production, indicating their important roles in human life, but also the first crops to be challenged with the abovementioned hurdles; hence, monocot crops should be the first to be engineered and/or de novo domesticated/redomesticated. A long time has passed since the first green revolution; the world is again facing the challenge of feeding a predicted 9.7 billion people in 2050, since the decline in world hunger was reversed in 2015. One of the major lessons learned from the first green revolution is the importance of novel and advanced trait-carrying crop varieties that are ideally adapted to new agricultural practices. New plant breeding techniques (NPBTs), such as genome editing, could help us succeed in this mission to create novel and advanced crops. Considering the importance of NPBTs in crop genetic improvement, we attempt to summarize and discuss the latest progress with major approaches, such as site-directed mutagenesis using molecular scissors, base editors and especially homology-directed gene targeting (HGT), a very challenging but potentially highly precise genome modification approach in plants. We therefore suggest potential approaches for the improvement of practical HGT, focusing on monocots, and discuss a potential approach for the regulation of genome-edited products.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, Km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Vats S, Kumawat S, Kumar V, Patil GB, Joshi T, Sonah H, Sharma TR, Deshmukh R. Genome Editing in Plants: Exploration of Technological Advancements and Challenges. Cells 2019; 8:E1386. [PMID: 31689989 PMCID: PMC6912757 DOI: 10.3390/cells8111386] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 10/04/2019] [Accepted: 10/12/2019] [Indexed: 12/19/2022] Open
Abstract
Genome-editing, a recent technological advancement in the field of life sciences, is one of the great examples of techniques used to explore the understanding of the biological phenomenon. Besides having different site-directed nucleases for genome editing over a decade ago, the CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein) based genome editing approach has become a choice of technique due to its simplicity, ease of access, cost, and flexibility. In the present review, several CRISPR/Cas based approaches have been discussed, considering recent advances and challenges to implicate those in the crop improvement programs. Successful examples where CRISPR/Cas approach has been used to improve the biotic and abiotic stress tolerance, and traits related to yield and plant architecture have been discussed. The review highlights the challenges to implement the genome editing in polyploid crop plants like wheat, canola, and sugarcane. Challenges for plants difficult to transform and germline-specific gene expression have been discussed. We have also discussed the notable progress with multi-target editing approaches based on polycistronic tRNA processing, Csy4 endoribonuclease, intron processing, and Drosha ribonuclease. Potential to edit multiple targets simultaneously makes it possible to take up more challenging tasks required to engineer desired crop plants. Similarly, advances like precision gene editing, promoter bashing, and methylome-editing will also be discussed. The present review also provides a catalog of available computational tools and servers facilitating designing of guide-RNA targets, construct designs, and data analysis. The information provided here will be useful for the efficient exploration of technological advances in genome editing field for the crop improvement programs.
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Affiliation(s)
- Sanskriti Vats
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Virender Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Gunvant B Patil
- Department of Agronomy and Plant Genetics University of Minnesota, St. Paul, MN 55108-6026, USA.
| | - Trupti Joshi
- Department of Health Management and Informatics; Informatics Institute; Christopher S Bond Life Science Center, University of Missouri, Columbia, MO 65211-7310, USA.
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab 140306, India.
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Cody WB, Scholthof HB. Plant Virus Vectors 3.0: Transitioning into Synthetic Genomics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2019; 57:211-230. [PMID: 31185187 DOI: 10.1146/annurev-phyto-082718-100301] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plant viruses were first implemented as heterologous gene expression vectors more than three decades ago. Since then, the methodology for their use has varied, but we propose it was the merging of technologies with virology tools, which occurred in three defined steps discussed here, that has driven viral vector applications to date. The first was the advent of molecular biology and reverse genetics, which enabled the cloning and manipulation of viral genomes to express genes of interest (vectors 1.0). The second stems from the discovery of RNA silencing and the development of high-throughput sequencing technologies that allowed the convenient and widespread use of virus-induced gene silencing (vectors 2.0). Here, we briefly review the events that led to these applications, but this treatise mainly concentrates on the emerging versatility of gene-editing tools, which has enabled the emergence of virus-delivered genetic queries for functional genomics and virology (vectors 3.0).
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Affiliation(s)
- Will B Cody
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA;
- Shriram Center for Biological and Chemical Engineering, Stanford University, Stanford, California 94305, USA
| | - Herman B Scholthof
- Department of Plant Pathology and Microbiology, Texas A&M University, College Station, Texas 77843, USA;
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Zhang Z, Hua L, Gupta A, Tricoli D, Edwards KJ, Yang B, Li W. Development of an Agrobacterium-delivered CRISPR/Cas9 system for wheat genome editing. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1623-1635. [PMID: 30706614 PMCID: PMC6662106 DOI: 10.1111/pbi.13088] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Revised: 01/19/2019] [Accepted: 01/22/2019] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas9 has been widely used for genome editing in many organisms, including important crops like wheat. Despite the tractability in designing CRISPR/Cas9, efficacy in the application of this powerful genome editing tool also depends on DNA delivery methods. In wheat, the biolistics based transformation is the most used method for delivery of the CRISPR/Cas9 complex. Due to the high frequency of gene silencing associated with co-transferred plasmid backbone and low edit rate in wheat, a large T0 transgenic plant population are required for recovery of desired mutations, which poses a bottleneck for many genome editing projects. Here, we report an Agrobacterium-delivered CRISPR/Cas9 system in wheat, which includes a wheat codon optimized Cas9 driven by a maize ubiquitin gene promoter and a guide RNA cassette driven by wheat U6 promoters in a single binary vector. Using this CRISPR/Cas9 system, we have developed 68 edit mutants for four grain-regulatory genes, TaCKX2-1, TaGLW7, TaGW2, and TaGW8, in T0 , T1 , and T2 generation plants at an average edit rate of 10% without detecting off-target mutations in the most Cas9-active plants. Homozygous mutations can be recovered from a large population in a single generation. Different from most plant species, deletions over 10 bp are the dominant mutation types in wheat. Plants homozygous of 1160-bp deletion in TaCKX2-D1 significantly increased grain number per spikelet. In conclusion, our Agrobacterium-delivered CRISPR/Cas9 system provides an alternative option for wheat genome editing, which requires a small number of transformation events because CRISPR/Cas9 remains active for novel mutations through generations.
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Affiliation(s)
- Zhengzhi Zhang
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Lei Hua
- Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsSDUSA
| | - Ajay Gupta
- Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsSDUSA
| | - David Tricoli
- Plant Transformation FacilityUniversity of CaliforniaDavisCAUSA
| | | | - Bing Yang
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
- Donald Danforth Plant Science CenterSt. LouisMOUSA
| | - Wanlong Li
- Department of Biology and MicrobiologySouth Dakota State UniversityBrookingsSDUSA
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Kok EJ, Glandorf DC, Prins TW, Visser RG. Food and environmental safety assessment of new plant varieties after the European Court decision: Process-triggered or product-based? Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2019.03.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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41
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Mushtaq M, Sakina A, Wani SH, Shikari AB, Tripathi P, Zaid A, Galla A, Abdelrahman M, Sharma M, Singh AK, Salgotra RK. Harnessing Genome Editing Techniques to Engineer Disease Resistance in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:550. [PMID: 31134108 PMCID: PMC6514154 DOI: 10.3389/fpls.2019.00550] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 04/10/2019] [Indexed: 05/21/2023]
Abstract
Modern genome editing (GE) techniques, which include clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) system, transcription activator-like effector nucleases (TALENs), zinc-finger nucleases (ZFNs) and LAGLIDADG homing endonucleases (meganucleases), have so far been used for engineering disease resistance in crops. The use of GE technologies has grown very rapidly in recent years with numerous examples of targeted mutagenesis in crop plants, including gene knockouts, knockdowns, modifications, and the repression and activation of target genes. CRISPR/Cas9 supersedes all other GE techniques including TALENs and ZFNs for editing genes owing to its unprecedented efficiency, relative simplicity and low risk of off-target effects. Broad-spectrum disease resistance has been engineered in crops by GE of either specific host-susceptibility genes (S gene approach), or cleaving DNA of phytopathogens (bacteria, virus or fungi) to inhibit their proliferation. This review focuses on different GE techniques that can potentially be used to boost molecular immunity and resistance against different phytopathogens in crops, ultimately leading to the development of promising disease-resistant crop varieties.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Aafreen Sakina
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Asif B. Shikari
- Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Prateek Tripathi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, United States
| | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany, Aligarh Muslim University, Aligarh, India
| | - Aravind Galla
- Department of Entomology, University of Arkansas, Fayetteville, AR, United States
| | - Mostafa Abdelrahman
- Arid Land Research Center, Tottori University, Tottori, Japan
- Botany Department, Faculty of Sciences, Aswan University, Aswan, Egypt
| | - Manmohan Sharma
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Anil Kumar Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
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42
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 607] [Impact Index Per Article: 121.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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Kausch AP, Nelson-Vasilchik K, Hague J, Mookkan M, Quemada H, Dellaporta S, Fragoso C, Zhang ZJ. Edit at will: Genotype independent plant transformation in the era of advanced genomics and genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 281:186-205. [PMID: 30824051 DOI: 10.1016/j.plantsci.2019.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/07/2018] [Accepted: 01/10/2019] [Indexed: 05/21/2023]
Abstract
The combination of advanced genomics, genome editing and plant transformation biology presents a powerful platform for basic plant research and crop improvement. Together these advances provide the tools to identify genes as targets for direct editing as single base pair changes, deletions, insertions and site specific homologous recombination. Recent breakthrough technologies using morphogenic regulators in plant transformation creates the ability to introduce reagents specific toward their identified targets and recover stably transformed and/or edited plants which are genotype independent. These technologies enable the possibility to alter a trait in any variety, without genetic disruption which would require subsequent extensive breeding, but rather to deliver the same variety with one trait changed. Regulatory issues regarding this technology will predicate how broadly these technologies will be implemented. In addition, education will play a crucial role for positive public acceptance. Taken together these technologies comprise a platform for advanced breeding which is an imperative for future world food security.
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Affiliation(s)
- Albert P Kausch
- Department of Cell and Molecular Biology, University of Rhode Island, RI 02892, USA.
| | | | - Joel Hague
- Department of Cell and Molecular Biology, University of Rhode Island, RI 02892, USA
| | - Muruganantham Mookkan
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | | | - Stephen Dellaporta
- Yale University, New Haven, CT 06520, USA; Verinomics Inc., New Haven, CT 06520, USA
| | | | - Zhanyuan J Zhang
- Plant Transformation Core Facility, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
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44
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Lee K, Eggenberger AL, Banakar R, McCaw ME, Zhu H, Main M, Kang M, Gelvin SB, Wang K. CRISPR/Cas9-mediated targeted T-DNA integration in rice. PLANT MOLECULAR BIOLOGY 2019; 99:317-328. [PMID: 30645710 DOI: 10.1007/s11103-018-00819-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2018] [Accepted: 12/27/2018] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Combining with a CRISPR/Cas9 system, Agrobacterium-mediated transformation can lead to precise targeted T-DNA integration in the rice genome. Agrobacterium-mediated T-DNA integration into the plant genomes is random, which often causes variable transgene expression and insertional mutagenesis. Because T-DNA preferentially integrates into double-strand DNA breaks, we adapted a CRISPR/Cas9 system to demonstrate that targeted T-DNA integration can be achieved in the rice genome. Using a standard Agrobacterium binary vector, we constructed a T-DNA that contains a CRISPR/Cas9 system using SpCas9 and a gRNA targeting the exon of the rice AP2 domain-containing protein gene Os01g04020. The T-DNA also carried a red fluorescent protein and a hygromycin resistance (hptII) gene. One version of the vector had hptII expression driven by an OsAct2 promoter. In an effort to detect targeted T-DNA insertion events, we built another T-DNA with a promoterless hptII gene adjacent to the T-DNA right border such that integration of T-DNA into the targeted exon sequence in-frame with the hptII gene would allow hptII expression. Our results showed that these constructs could produce targeted T-DNA insertions with frequencies ranging between 4 and 5.3% of transgenic callus events, in addition to generating a high frequency (50-80%) of targeted indel mutations. Sequencing analyses showed that four out of five sequenced T-DNA/gDNA junctions carry a single copy of full-length T-DNA at the target site. Our results indicate that Agrobacterium-mediated transformation combined with a CRISPR/Cas9 system can efficiently generate targeted T-DNA insertions.
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MESH Headings
- Agrobacterium/genetics
- Base Sequence
- CRISPR-Associated Proteins/metabolism
- CRISPR-Cas Systems/genetics
- DNA, Bacterial/genetics
- Exons
- Gene Editing
- Gene Expression Regulation, Plant/genetics
- Gene Frequency
- Gene Targeting
- Genes, Plant/genetics
- Genetic Vectors/genetics
- Genome, Plant/genetics
- INDEL Mutation
- Luminescent Proteins/genetics
- Mutagenesis, Insertional/methods
- Oryza/genetics
- Oryza/metabolism
- Plant Proteins/genetics
- Plants, Genetically Modified/genetics
- Promoter Regions, Genetic
- RNA, Guide, CRISPR-Cas Systems/genetics
- RNA, Guide, CRISPR-Cas Systems/metabolism
- Sequence Analysis
- Red Fluorescent Protein
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Affiliation(s)
- Keunsub Lee
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Alan L Eggenberger
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Raviraj Banakar
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Morgan E McCaw
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Huilan Zhu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Plant Transformation Facility, Iowa State University, Ames, IA, 50011, USA
| | - Marcy Main
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Plant Transformation Facility, Iowa State University, Ames, IA, 50011, USA
| | - Minjeong Kang
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, 50011, USA
| | - Stanton B Gelvin
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Kan Wang
- Crop Bioengineering Center, Iowa State University, Ames, IA, 50011, USA.
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
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Ru S, Bernardo R. Targeted recombination to increase genetic gain in self-pollinated species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:289-300. [PMID: 30377704 DOI: 10.1007/s00122-018-3216-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 10/20/2018] [Indexed: 06/08/2023]
Abstract
KEY MESSAGE If we can induce or select for recombination at targeted marker intervals, genetic gains for quantitative traits in self-pollinated species may be doubled. Targeted recombination refers to inducing or selecting for a recombination event at genomic positions that maximize genetic gain in a cross. A previous study indicated that targeted recombination could double the rate of genetic gains in maize (Zea mays L.), a cross-pollinated crop for which historical genetic gains have been large. Our objectives were to determine whether targeted recombination can sufficiently increase predicted gains in self-pollinated species, and whether prospective gains from targeted recombination vary across crops, populations, traits, and chromosomes. Genomewide marker effects were estimated from previously published marker and phenotypic data on 21 biparental populations of soybean [Glycine max (L.) Merr.], wheat (Triticum aestivum L.), barley (Hordeum vulgare L.), and pea (Pisum sativum L.). With the predicted gain from nontargeted recombination as the baseline, the relative gains from creating a doubled haploid with up to one targeted recombination [RG(x ≤ 1)] and two targeted recombinations [RG(x ≤ 2)] per chromosome or linkage group were calculated. Targeted recombination significantly (P = 0.05) increased the predicted genetic gain compared to nontargeted recombination for all traits and all populations, except for plant height in barley. The mean RG(x ≤ 1) was 211%, whereas the mean RG(x ≤ 2) was 243%. The predicted gain varied among traits and populations. For most traits and populations, having targeted recombination on less than a third of all the chromosomes led to the same or higher predicted gain than nontargeted recombination. Together with previous findings in maize, our results suggested that targeted recombination could double the genetic gains in both self- and cross-pollinated crops.
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Affiliation(s)
- Sushan Ru
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA
| | - Rex Bernardo
- Department of Agronomy and Plant Genetics, University of Minnesota, 411 Borlaug Hall, 1991 Upper Buford Circle, Saint Paul, MN, 55108, USA.
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46
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Xu J, Hua K, Lang Z. Genome editing for horticultural crop improvement. HORTICULTURE RESEARCH 2019; 6:113. [PMID: 31645967 PMCID: PMC6804600 DOI: 10.1038/s41438-019-0196-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 07/18/2019] [Accepted: 08/13/2019] [Indexed: 05/06/2023]
Abstract
Horticultural crops provide humans with many valuable products. The improvement of the yield and quality of horticultural crops has been receiving increasing research attention. Given the development and advantages of genome-editing technologies, research that uses genome editing to improve horticultural crops has substantially increased in recent years. Here, we briefly review the different genome-editing systems used in horticultural research with a focus on clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9)-mediated genome editing. We also summarize recent progress in the application of genome editing for horticultural crop improvement. The combination of rapidly advancing genome-editing technology with breeding will greatly increase horticultural crop production and quality.
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Affiliation(s)
- Jiemeng Xu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Kai Hua
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032 China
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47
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Schmidt C, Pacher M, Puchta H. DNA Break Repair in Plants and Its Application for Genome Engineering. Methods Mol Biol 2019; 1864:237-266. [PMID: 30415341 DOI: 10.1007/978-1-4939-8778-8_17] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Genome engineering is a biotechnological approach to precisely modify the genetic code of a given organism in order to change the context of an existing sequence or to create new genetic resources, e.g., for obtaining improved traits or performance. Efficient targeted genome alterations are mainly based on the induction of DNA double-strand breaks (DSBs) or adjacent single-strand breaks (SSBs). Naturally, all organisms continuously have to deal with DNA-damaging factors challenging the genetic integrity, and therefore a wide range of DNA repair mechanisms have evolved. A profound understanding of the different repair pathways is a prerequisite to control and enhance targeted gene modifications. DSB repair can take place by nonhomologous end joining (NHEJ) or homology-dependent repair (HDR). As the main outcome of NHEJ-mediated repair is accompanied by small insertions and deletions, it is applicable to specifically knock out genes or to rearrange linkage groups or whole chromosomes. The basic requirement for HDR is the presence of a homologous template; thus this process can be exploited for targeted integration of ectopic sequences into the plant genome. The development of different types of artificial site-specific nucleases allows for targeted DSB induction in the plant genome. Such synthetic nucleases have been used for both qualitatively studying DSB repair in vivo with respect to mechanistic differences and quantitatively in order to determine the role of key factors for NHEJ and HR, respectively. The conclusions drawn from these studies allow for a better understanding of genome evolution and help identifying synergistic or antagonistic genetic interactions while supporting biotechnological applications for transiently modifying the plant DNA repair machinery in favor of targeted genome engineering.
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Affiliation(s)
- Carla Schmidt
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Michael Pacher
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Karlsruhe Institute of Technology, Karlsruhe, Germany.
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Yamamoto T, Kashojiya S, Kamimura S, Kameyama T, Ariizumi T, Ezura H, Miura K. Application and development of genome editing technologies to the Solanaceae plants. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 131:37-46. [PMID: 29523384 DOI: 10.1016/j.plaphy.2018.02.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 02/16/2018] [Accepted: 02/20/2018] [Indexed: 05/22/2023]
Abstract
Genome editing technology using artificial nucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), and clustered regulatory interspaced short palindromic repeats (CRISPR)-Cas9, can mutagenize the target sites of genes of interest. This technology has been successfully applied in several crops, including the Solanaceae plants, such as tomato, potato, tobacco, and petunia. Among the three nucleases, CRISPR-Cas9 is the best for breeding, crop improvement, and the functional analysis of genes of interest, because of its simplicity and high efficiency. Although the technology is useful for reverse genetics, its use in plants is limited due to a lack of regeneration protocols and sequence information. In this review, the present status of genome editing technology in Solanaceae plants is described, and techniques that may improve genome editing technologies are discussed.
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Affiliation(s)
- Tsuyoshi Yamamoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Sachiko Kashojiya
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Saori Kamimura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Takato Kameyama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Tohru Ariizumi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Hiroshi Ezura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, 305-8572, Japan.
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Piatek AA, Lenaghan SC, Neal Stewart C. Advanced editing of the nuclear and plastid genomes in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:42-49. [PMID: 29907308 DOI: 10.1016/j.plantsci.2018.02.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Genome editing is a powerful suite of technologies utilized in basic and applied plant research. Both nuclear and plastid genomes have been genetically engineered to alter traits in plants. While the most frequent molecular outcome of gene editing has been knockouts resulting in a simple deletion of an endogenous protein of interest from the host's proteome, new genes have been added to plant genomes and, in several instances, the sequence of endogenous genes have been targeted for a few coding changes. Targeted plant characteristics for genome editing range from single gene targets for agronomic input traits to metabolic pathways to endow novel plant function. In this paper, we review the fundamental approaches to editing nuclear and plastid genomes in plants with an emphasis on those utilizing synthetic biology. The differences between the eukaryotic-type nuclear genome and the prokaryotic-type plastid genome (plastome) in plants has profound consequences in the approaches employed to transform, edit, select transformants, and indeed, nearly all aspects of genetic engineering procedures. Thus, we will discuss the two genomes targeted for editing in plants, the toolbox used to make edits, along with strategies for future editing approaches to transform crop production and sustainability. While CRISPR/Cas9 is the current method of choice in editing nuclear genomes, the plastome is typically edited using homologous recombination approaches. A particularly promising synthetic biology approach is to replace the endogenous plastome with a 'synplastome' that is computationally designed, and synthesized and assembled in the lab, then installed into chloroplasts. The editing strategies, transformation methods, characteristics of the novel plant also affect how the genetically engineered plant may be governed and regulated. Each of these components and final products of gene editing affect the future of biotechnology and farming.
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Affiliation(s)
- Agnieszka A Piatek
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Scott C Lenaghan
- Department of Food Science, University of Tennessee, Knoxville, TN, 37996, USA; Department of Mechanical, Aerospace, and Biomedical Engineering, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA.
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Miki D, Zhang W, Zeng W, Feng Z, Zhu JK. CRISPR/Cas9-mediated gene targeting in Arabidopsis using sequential transformation. Nat Commun 2018; 9:1967. [PMID: 29773790 PMCID: PMC5958078 DOI: 10.1038/s41467-018-04416-0] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 04/26/2018] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination-based gene targeting is a powerful tool for precise genome modification and has been widely used in organisms ranging from yeast to higher organisms such as Drosophila and mouse. However, gene targeting in higher plants, including the most widely used model plant Arabidopsis thaliana, remains challenging. Here we report a sequential transformation method for gene targeting in Arabidopsis. We find that parental lines expressing the bacterial endonuclease Cas9 from the egg cell- and early embryo-specific DD45 gene promoter can improve the frequency of single-guide RNA-targeted gene knock-ins and sequence replacements via homologous recombination at several endogenous sites in the Arabidopsis genome. These heritable gene targeting can be identified by regular PCR. Our approach enables routine and fine manipulation of the Arabidopsis genome.
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Affiliation(s)
- Daisuke Miki
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
| | - Wenxin Zhang
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Wenjie Zeng
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Zhengyan Feng
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 200032, Shanghai, China.
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
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