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Panda D, Karmakar S, Dash M, Tripathy SK, Das P, Banerjee S, Qi Y, Samantaray S, Mohapatra PK, Baig MJ, Molla KA. Optimized protoplast isolation and transfection with a breakpoint: accelerating Cas9/sgRNA cleavage efficiency validation in monocot and dicot. ABIOTECH 2024; 5:151-168. [PMID: 38974867 PMCID: PMC11224192 DOI: 10.1007/s42994-024-00139-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/18/2024] [Indexed: 07/09/2024]
Abstract
The CRISPR-Cas genome editing tools are revolutionizing agriculture and basic biology with their simplicity and precision ability to modify target genomic loci. Software-predicted guide RNAs (gRNAs) often fail to induce efficient cleavage at target loci. Many target loci are inaccessible due to complex chromatin structure. Currently, there is no suitable tool available to predict the architecture of genomic target sites and their accessibility. Hence, significant time and resources are spent on performing editing experiments with inefficient guides. Although in vitro-cleavage assay could provide a rough assessment of gRNA efficiency, it largely excludes the interference of native genomic context. Transient in-vivo testing gives a proper assessment of the cleavage ability of editing reagents in a native genomic context. Here, we developed a modified protocol that offers highly efficient protoplast isolation from rice, Arabidopsis, and chickpea, using a sucrose gradient, transfection using PEG (polyethylene glycol), and validation of single guide RNAs (sgRNAs) cleavage efficiency of CRISPR-Cas9. We have optimized various parameters for PEG-mediated protoplast transfection and achieved high transfection efficiency using our protocol in both monocots and dicots. We introduced plasmid vectors containing Cas9 and sgRNAs targeting genes in rice, Arabidopsis, and chickpea protoplasts. Using dual sgRNAs, our CRISPR-deletion strategy offers straightforward detection of genome editing success by simple agarose gel electrophoresis. Sanger sequencing of PCR products confirmed the editing efficiency of specific sgRNAs. Notably, we demonstrated that isolated protoplasts can be stored for up to 24/48 h with little loss of viability, allowing a pause between isolation and transfection. This high-efficiency protocol for protoplast isolation and transfection enables rapid (less than 7 days) validation of sgRNA cleavage efficiency before proceeding with stable transformation. The isolation and transfection method can also be utilized for rapid validation of editing strategies, evaluating diverse editing reagents, regenerating plants from transfected protoplasts, gene expression studies, protein localization and functional analysis, and other applications. Supplementary Information The online version contains supplementary material available at 10.1007/s42994-024-00139-7.
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Affiliation(s)
- Debasmita Panda
- ICAR National Rice Research Institute, Cuttack, Odisha 753006 India
- Department of Botany, Ravenshaw University, Cuttack, Odisha 753003 India
| | | | - Manaswini Dash
- ICAR National Rice Research Institute, Cuttack, Odisha 753006 India
| | | | - Priya Das
- ICAR National Rice Research Institute, Cuttack, Odisha 753006 India
| | - Sagar Banerjee
- ICAR National Rice Research Institute, Cuttack, Odisha 753006 India
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742 USA
| | | | | | - Mirza J. Baig
- ICAR National Rice Research Institute, Cuttack, Odisha 753006 India
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2
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Pavese V, Moglia A, Milani AM, Marino LA, Martinez MT, Torello Marinoni D, Botta R, Corredoira E. Advances in Quercus ilex L. breeding: the CRISPR/Cas9 technology via ribonucleoproteins. FRONTIERS IN PLANT SCIENCE 2024; 15:1323390. [PMID: 38439988 PMCID: PMC10910054 DOI: 10.3389/fpls.2024.1323390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 03/06/2024]
Abstract
The CRISPR/Cas9 ribonucleoprotein (RNP)-mediated technology represents a fascinating tool for modifying gene expression or mutagenesis as this system allows for obtaining transgene-free plants, avoiding exogenous DNA integration. Holm oak (Quercus ilex) has an important social, economic, and ecological role in the Mediterranean climate zones of Western Europe and North Africa and is severely affected by oak decline syndrome. Here we report the first example of the application of the CRISPR/Cas9-RNP technology in holm oak. Firstly, we evaluated the protoplast isolation from both in vitro leaves and proembryogenic masses. Proembryogenic masses represented the best material to get high protoplast yield (11 x 106 protoplasts/ml) and viability. Secondly, the protoplast transfection ability was evaluated through a vector expressing green fluorescence protein as marker gene of transfection, reaching a transfection percentage of 62% after 24 hours. CRISPR/Cas9 RNPs were successfully delivered into protoplasts resulting in 5.6% ± 0.5% editing efficiency at phytoene desaturase (pds) target genomic region. Protoplasts were then cultured in semisolid media and, after 45 days in culture, developed embryogenic calli were observed in a Murashige and Skoog media with half concentration of NH4NO3 and KNO3 supplemented with 0.1 mg/L benzylaminopurine and 0.1 mg/L 2,4-dichlorophenoxyacetic acid.
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Affiliation(s)
- Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Andrea Moglia
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Anna Maria Milani
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Lorenzo Antonio Marino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Maria Teresa Martinez
- Mision Biologica de Galicia, Sede de Santiago, Consejo Superior de Investigaciones Cientificas, Santiago de Compostela, Spain
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-Department of Agricultural, Forest and Food Sciences (DISAFA), Università degli Studi di Torino, Torino, Italy
| | - Elena Corredoira
- Mision Biologica de Galicia, Sede de Santiago, Consejo Superior de Investigaciones Cientificas, Santiago de Compostela, Spain
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Divya K, Thangaraj M, Krishna Radhika N. CRISPR/Cas9: an advanced platform for root and tuber crops improvement. Front Genome Ed 2024; 5:1242510. [PMID: 38312197 PMCID: PMC10836405 DOI: 10.3389/fgeed.2023.1242510] [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: 06/19/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024] Open
Abstract
Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.
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Affiliation(s)
- K Divya
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | | | - N Krishna Radhika
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
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Xue Y, Hiti-Bandaralage JCA, Hu Z, Zhao Z, Mitter N. First Report on Mesophyll Protoplast Isolation and Regeneration System for the Duboisia Species. PLANTS (BASEL, SWITZERLAND) 2023; 13:40. [PMID: 38202348 PMCID: PMC10780843 DOI: 10.3390/plants13010040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/05/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]
Abstract
The Duboisia species, a group of plants native to Australia, have been historically valued for their pharmacological properties and have played a significant role in traditional medicine and pharmaceutical research. Persistent efforts are underway to enhance the efficacy of the active ingredient scopolamine, employing both conventional breeding methods and advanced biotechnology tools. The primary objective of this research was to establish a highly efficient method for isolating mesophyll protoplasts and facilitating their regeneration, thereby laying a robust foundation for the application of various advanced plant biotechnology tools in the pursuit of genetic enhancement. The mesophyll protoplast isolation process was developed for hybrid D. myoporoides × D. hopwoodii with careful optimisation of the following parameters: leaf strip size; incubation conditions; physical treatment; and enzyme concentration. The optimal parameters were combined in each individual step; the best enzyme concentration was determined to be 2% (w/v) cellulysin and 0.5% (w/v) macerase. Protoplast yield was found to be greatly affected by the enzyme concentrations. The isolated protoplasts were cultured at a density of 0.5 × 105 to best sustain the highest cell division (33.2%) and a microcalli induction frequency of 17.9%. After 40 days of culture in a modified KM8P medium at 25 °C in darkness, visible microcalli were transferred to a solidified Murashige and Skoog (MS) medium with 1 mg L-1 2,4-dichlorophenoxyacetic acid (2,4-D) for callus induction under a 16 h photoperiod. After 30 days of culture, compact organogenic calli were transferred into a solid MS medium with 6-benzylaminopurine (BA) alone or thidiazuron (TDZ) alone or in combination with BA or naphthalene acetic acid (NAA) for shoot regeneration. The maximum shoot regeneration frequency (63.3%) was observed in the medium with 1.5 mg L-1 TDZ alone. For the first time, a reliable protoplast isolation and regeneration system from mesophyll cells was established for Duboisia with high protoplast viability, successful microcalli formation, and intact plant regeneration. This innovation will significantly contribute towards the genetic enhancement of the Duboisia species.
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Affiliation(s)
- Yuxin Xue
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4068, Australia; (Y.X.); (Z.H.)
| | | | - Zhangpan Hu
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4068, Australia; (Y.X.); (Z.H.)
| | - Zizhu Zhao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia;
| | - Neena Mitter
- Centre for Horticultural Science, Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, QLD 4068, Australia; (Y.X.); (Z.H.)
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Pathi KM, Sprink T. From Petri Dish to Field: Plant Tissue Culture and Genetic Engineering of Oats for Improved Agricultural Outcomes. PLANTS (BASEL, SWITZERLAND) 2023; 12:3782. [PMID: 37960138 PMCID: PMC10647551 DOI: 10.3390/plants12213782] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/24/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
Oats (Avena sativa) hold immense economic and nutritional value as a versatile crop. They have long been recognized as an exceptional choice for human consumption and animal feed. Oats' unique components, including proteins, starches, and β-glucans, have led to its widespread use in various food products such as bread, noodles, flakes, and milk. The popularity of oat milk as a vegan alternative to dairy milk has soared due to the increasing number of vegetarians/vegans and growing environmental awareness. Oat milk offers a sustainable option with reduced greenhouse gas emissions during its production, rendering it an appropriate choice for individuals who are lactose-intolerant or have dairy allergies. To ensure improved adaptability and enhanced nutrition, the development of new oat varieties is crucial, considering factors like cultivation, climate, and growing conditions. Plant cell culture plays a crucial role in both traditional and contemporary breeding methods. In classical breeding, plant cell culture facilitates the rapid production of double haploid plants, which can be employed to accelerate the breeding process. In modern breeding methods, it enables genetic manipulation and precise genome editing at the cellular level. This review delves into the importance of oats and their diverse applications, highlighting the advantages of plant cell culture in both classical and modern breeding methods. Specifically, it provides an overview of plant tissue culture, encompassing genetic transformation, haploid technology, protoplast technology, and genome editing.
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Affiliation(s)
- Krishna Mohan Pathi
- Julius Kuehn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
| | - Thorben Sprink
- Julius Kuehn Institute (JKI)—Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, 06484 Quedlinburg, Germany
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Cardi T, Murovec J, Bakhsh A, Boniecka J, Bruegmann T, Bull SE, Eeckhaut T, Fladung M, Galovic V, Linkiewicz A, Lukan T, Mafra I, Michalski K, Kavas M, Nicolia A, Nowakowska J, Sági L, Sarmiento C, Yıldırım K, Zlatković M, Hensel G, Van Laere K. CRISPR/Cas-mediated plant genome editing: outstanding challenges a decade after implementation. TRENDS IN PLANT SCIENCE 2023; 28:1144-1165. [PMID: 37331842 DOI: 10.1016/j.tplants.2023.05.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/09/2023] [Accepted: 05/15/2023] [Indexed: 06/20/2023]
Abstract
The discovery of the CRISPR/Cas genome-editing system has revolutionized our understanding of the plant genome. CRISPR/Cas has been used for over a decade to modify plant genomes for the study of specific genes and biosynthetic pathways as well as to speed up breeding in many plant species, including both model and non-model crops. Although the CRISPR/Cas system is very efficient for genome editing, many bottlenecks and challenges slow down further improvement and applications. In this review we discuss the challenges that can occur during tissue culture, transformation, regeneration, and mutant detection. We also review the opportunities provided by new CRISPR platforms and specific applications related to gene regulation, abiotic and biotic stress response improvement, and de novo domestication of plants.
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Affiliation(s)
- Teodoro Cardi
- Consiglio Nazionale delle Ricerche (CNR), Institute of Biosciences and Bioresources (IBBR), Portici, Italy; CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Jana Murovec
- University of Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Allah Bakhsh
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Justyna Boniecka
- Department of Genetics, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Toruń, Poland; Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University, Toruń, Poland
| | | | - Simon E Bull
- Molecular Plant Breeding, Institute of Agricultural Sciences, Eidgenössische Technische Hochschule (ETH) Zurich, Switzerland; Plant Biochemistry, Institute of Molecular Plant Biology, ETH, Zurich, Switzerland
| | - Tom Eeckhaut
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium
| | | | - Vladislava Galovic
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Anna Linkiewicz
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Tjaša Lukan
- National Institute of Biology, Department of Biotechnology and Systems Biology, Ljubljana, Slovenia
| | - Isabel Mafra
- Rede de Química e Tecnologia (REQUIMTE) Laboratório Associado para a Química Verde (LAQV), Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Krzysztof Michalski
- Plant Breeding and Acclimatization Institute, National Research Institute, Błonie, Poland
| | - Musa Kavas
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Alessandro Nicolia
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano, Italy
| | - Justyna Nowakowska
- Molecular Biology and Genetics Department, Institute of Biological Sciences, Faculty of Biology and Environmental Sciences, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Laszlo Sági
- Centre for Agricultural Research, Loránd Eötvös Research Network, Martonvásár, Hungary
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Kubilay Yıldırım
- Department of Molecular Biology and Genetics, Faculty of Science, Ondokuz Mayis University, Samsun, Turkey
| | - Milica Zlatković
- University of Novi Sad, Institute of Lowland Forestry and Environment (ILFE), Novi Sad, Serbia
| | - Goetz Hensel
- Heinrich-Heine-University, Institute of Plant Biochemistry, Centre for Plant Genome Engineering, Düsseldorf, Germany; Division of Molecular Biology, Centre of the Region Hana for Biotechnological and Agriculture Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Katrijn Van Laere
- Flanders Research Institute for Agricultural, Fisheries and Food, Melle, Belgium.
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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8
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Nakamura A, Yano T, Mitsuda N, Furubayashi M, Ito S, Sugano SS, Terakawa T. The sonication-assisted whisker method enables CRISPR-Cas9 ribonucleoprotein delivery to induce genome editing in rice. Sci Rep 2023; 13:14205. [PMID: 37679413 PMCID: PMC10484913 DOI: 10.1038/s41598-023-40433-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/10/2023] [Indexed: 09/09/2023] Open
Abstract
CRISPR/Cas9-based genome editing represents an unprecedented potential for plant breeding. Unlike animal cells, plant cells contain a rigid cell wall, genome editing tool delivery into plant cells is thus challenging. In particular, the delivery of the Cas9-gRNA ribonucleoprotein (RNP) into plant cells is desired since the transgene insertion into the genome should be avoided for industrial applications in plants. In this study, we present a novel RNP delivery approach in rice. We applied the sonication-assisted whisker method, conventionally developed for DNA delivery in plants, for RNP delivery in rice. Combined with marker gene delivery, we successfully isolated OsLCYβ genome-edited lines generated by RNPs. The calli and regenerated shoot of the OsLCYβ mutant showed abnormal carotenoid accumulation. In addition, we also detected, although at a low frequency, genome editing events in rice calli cells by RNP delivery using the sonication-assisted whisker method without any additional. Therefore, the sonication-assisted whisker method could be an attractive way to create RNP-based genome-edited lines in plants.
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Affiliation(s)
- Akiyoshi Nakamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Japan
| | - Tsubasa Yano
- Inplanta Innovations Inc., 4-5-11, Namamugi, Tsurumi-ku, Yokohama, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | - Maiko Furubayashi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo, Japan
| | | | - Shigeo S Sugano
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1, Higashi, Tsukuba, Japan.
| | - Teruhiko Terakawa
- Inplanta Innovations Inc., 4-5-11, Namamugi, Tsurumi-ku, Yokohama, Japan.
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Nishiguchi M, Futamura N, Endo M, Mikami M, Toki S, Katahata SI, Ohmiya Y, Konagaya KI, Nanasato Y, Taniguchi T, Maruyama TE. CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don). Sci Rep 2023; 13:11779. [PMID: 37479866 PMCID: PMC10361980 DOI: 10.1038/s41598-023-38339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an economically important coniferous tree in Japan. However, abundant sugi pollen grains are dispersed and transported by the wind each spring and cause a severe pollen allergy syndrome (Japanese cedar pollinosis). The use of pollen-free sugi that cannot produce pollen has been thought as a countermeasure to Japanese cedar pollinosis. The sugi CjACOS5 gene is an ortholog of Arabidopsis ACOS5 and rice OsACOS12, which encode an acyl-CoA synthetase that is involved in the synthesis of sporopollenin in pollen walls. To generate pollen-free sugi, we mutated CjACOS5 using the CRISPR/Cas9 system. As a result of sugi transformation mediated by Agrobacterium tumefaciens harboring the CjACOS5-targeted CRISPR/Cas9 vector, 1 bp-deleted homo biallelic mutant lines were obtained. Chimeric mutant lines harboring both mutant and wild-type CjACOS5 genes were also generated. The homo biallelic mutant lines had no-pollen in male strobili, whereas chimeric mutant lines had male strobili with or without pollen grains. Our results suggest that CjACOS5 is essential for the production of pollen in sugi and that its disruption is useful for the generation of pollen-free sugi. In addition to conventional transgenic technology, genome editing technology, including CRISPR/Cas9, can confer new traits on sugi.
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Affiliation(s)
- Mitsuru Nishiguchi
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Masafumi Mikami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Shin-Ichiro Katahata
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Yasunori Ohmiya
- Extension and International Cooperation Department, Forest Tree Breeding Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Ken-Ichi Konagaya
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Toru Taniguchi
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tsuyoshi Emilio Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
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10
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Figueroa-Varela P, Susunaga-Gómez D, Restrepo-Osorio C, Harms C, Villanueva-Mejía D. An efficient method for protoplast-mediated production of transformed castor bean (Ricinus communis) lines. BMC Res Notes 2023; 16:140. [PMID: 37415245 DOI: 10.1186/s13104-023-06414-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: 09/25/2022] [Accepted: 06/20/2023] [Indexed: 07/08/2023] Open
Abstract
OBJECTIVE The purpose of this study was to develop a method for the isolation, culture, and PEG-mediated protoplast transfection from leaves of in vitro-grown plants of Ricinus communis. RESULTS Factors such as the enzymatic composition and the incubation time were evaluated. The enzymatic solution, containing 1.6% Cellulase-R10 and 0.8% Macerozyme-R10, with 16 h of incubation, was the best condition to achieve a high protoplast yield (481.16 × 104 protoplasts/g FW) with a high percentage of viability (95%). The combination and concentration of enzymes have been shown to affect the protoplast isolation efficiency significantly. Furthermore, we found that a higher number of protoplasts (8.5 × 105 protoplast/g FW) was obtained at a longer incubation time, but their viability decreased. We obtained a simple and efficient protocol to isolate protoplast from Ricinus communis leaves and culture. A PEG-mediated protoplast transfection protocol was also established to introduce plasmid DNA into Ricinus communis genotypes cultivated in Colombia. Thus, strengthening advances in the genetic improvement processes for this crop are presented.
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Affiliation(s)
- Paula Figueroa-Varela
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín, Colombia
| | - Danna Susunaga-Gómez
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín, Colombia
| | - Catalina Restrepo-Osorio
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín, Colombia
| | - Carsten Harms
- Bremerhaven Institute for Applied Molecular Biology, University of Applied Sciences Bremerhaven, Bremerhaven, Germany
| | - Diego Villanueva-Mejía
- CIBIOP Research Group, School of Applied Sciences and Engineering, EAFIT University, Medellín, Colombia.
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Tamilselvan-Nattar-Amutha S, Hiekel S, Hartmann F, Lorenz J, Dabhi RV, Dreissig S, Hensel G, Kumlehn J, Heckmann S. Barley stripe mosaic virus-mediated somatic and heritable gene editing in barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1201446. [PMID: 37404527 PMCID: PMC10315673 DOI: 10.3389/fpls.2023.1201446] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
Genome editing strategies in barley (Hordeum vulgare L.) typically rely on Agrobacterium-mediated genetic transformation for the delivery of required genetic reagents involving tissue culture techniques. These approaches are genotype-dependent, time-consuming, and labor-intensive, which hampers rapid genome editing in barley. More recently, plant RNA viruses have been engineered to transiently express short guide RNAs facilitating CRISPR/Cas9-based targeted genome editing in plants that constitutively express Cas9. Here, we explored virus-induced genome editing (VIGE) based on barley stripe mosaic virus (BSMV) in Cas9-transgenic barley. Somatic and heritable editing in the ALBOSTRIANS gene (CMF7) resulting in albino/variegated chloroplast-defective barley mutants is shown. In addition, somatic editing in meiosis-related candidate genes in barley encoding ASY1 (an axis-localized HORMA domain protein), MUS81 (a DNA structure-selective endonuclease), and ZYP1 (a transverse filament protein of the synaptonemal complex) was achieved. Hence, the presented VIGE approach using BSMV enables rapid somatic and also heritable targeted gene editing in barley.
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12
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Fang W, Fasano C, Perrella G. Unlocking the Secret to Higher Crop Yield: The Potential for Histone Modifications. PLANTS (BASEL, SWITZERLAND) 2023; 12:1712. [PMID: 37111933 PMCID: PMC10144255 DOI: 10.3390/plants12081712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/11/2023] [Accepted: 04/14/2023] [Indexed: 06/19/2023]
Abstract
Histone modifications are epigenetic mechanisms, termed relative to genetics, and they refer to the induction of heritable changes without altering the DNA sequence. It is widely known that DNA sequences precisely modulate plant phenotypes to adapt them to the changing environment; however, epigenetic mechanisms also greatly contribute to plant growth and development by altering chromatin status. An increasing number of recent studies have elucidated epigenetic regulations on improving plant growth and adaptation, thus making contributions to the final yield. In this review, we summarize the recent advances of epigenetic regulatory mechanisms underlying crop flowering efficiency, fruit quality, and adaptation to environmental stimuli, especially to abiotic stress, to ensure crop improvement. In particular, we highlight the major discoveries in rice and tomato, which are two of the most globally consumed crops. We also describe and discuss the applications of epigenetic approaches in crop breeding programs.
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Affiliation(s)
- Weiwei Fang
- Department of Biosciences, University of Milan, Via Giovanni Celoria 26, 20133 Milan, MI, Italy;
| | - Carlo Fasano
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Develoment, (ENEA), 75026 Rotondella, MT, Italy;
| | - Giorgio Perrella
- Department of Biosciences, University of Milan, Via Giovanni Celoria 26, 20133 Milan, MI, Italy;
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Joshi T, Sehgal H, Mandal SK, Joshi M, Deepa PR, Sharma PK. Nutraceutical and flavor profiles in underutilized desert legumes of India: gene editing strategies towards sustainable food development. JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2023:1-8. [PMID: 37359892 PMCID: PMC10049905 DOI: 10.1007/s13562-023-00836-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/09/2023] [Indexed: 06/28/2023]
Abstract
Climate change has posed a challenge for food security all over the world in the form of fluctuating crop yields and novel disease outbreaks in plants. Human society's overdependence on a few food crops does not seem a wise precedence. There are numerous underutilized/orphan/neglected legumes growing in the Indian desert regions that can come to the rescue and act as balanced and sustainable sources of nutrients and health-benefitting nutraceuticals. However, challenges such as low plant yield, unidentified metabolic pathways and off-flavor in the food products derived from them prevent the realization of their full potential. Conventional breeding techniques are too slow to achieve the desired modifications and cater to the sharply rising demand for functional foods. The novel gene editing tools like CRISPR-Cas provide more precise tool to manipulate the target genes with or without introduction of foreign DNA and therefore, have better chances to be accepted by governments and societies. The current article reports some of the relevant 'gene editing' success stories with respect to nutraceutical and flavor profiles in the popular legumes. It highlights gaps and future potential, along with areas requiring caution, in underutilized edible legumes of the Indian (semi) arid regions like Prosopis cineraria, Acacia senegal and Cyamopsis tetragonoloba.
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Affiliation(s)
- Tripti Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Sumit Kumar Mandal
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Mukul Joshi
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - P. R. Deepa
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
| | - Pankaj Kumar Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
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AHMAD M. Plant breeding advancements with "CRISPR-Cas" genome editing technologies will assist future food security. FRONTIERS IN PLANT SCIENCE 2023; 14:1133036. [PMID: 36993865 PMCID: PMC10040607 DOI: 10.3389/fpls.2023.1133036] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Genome editing techniques are being used to modify plant breeding, which might increase food production sustainably by 2050. A product made feasible by genome editing is becoming better known, because of looser regulation and widespread acceptance. The world's population and food supply would never have increased proportionally under current farming practices. The development of plants and food production has been greatly impacted by global warming and climate change. Therefore, minimizing these effects is crucial for agricultural production that is sustainable. Crops are becoming more resilient to abiotic stress because of sophisticated agricultural practices and a better understanding of the abiotic stress response mechanism. Both conventional and molecular breeding techniques have been used to create viable crop types both processes are time-consuming. Recently, plant breeders have shown an interest in genome editing approaches for genetic manipulation that use clustered regularly interspaced short palindromic repeats (CRISPR/Cas9). To ensure the security of the food supply in the future, plant kinds with desired traits must be developed. A completely new era in plant breeding has begun because of the revolution in genome editing techniques based on the CRISPR/CRISPR-associated nuclease (Cas9) systems. All plants may effectively target a particular gene or group of loci using Cas9 and single-guide RNA (sgRNA). CRISPR/Cas9 can thereby save time and labor compared to conventional breeding methods. An easy, quick, and efficient method for directly altering the genetic sequences in cells is with the CRISPR and Cas9 systems. The CRISPR-Cas9 system, which was developed from components of the earliest known bacterial immune system, allows for targeted gene breakage and gene editing in a variety of cells/RNA sequences to guide endonuclease cleavage specificity in the CRISPR-Cas9 system. Editing can be directed to practically any genomic site by altering the guide RNA (gRNA) sequence and delivering it to a target cell along with the Cas9 endonuclease. We summarize recent CRISPR/Cas9 plant research findings, investigate potential applications in plant breeding, and make predictions about likely future breakthroughs and approaches to food security through 2050.
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Affiliation(s)
- M. AHMAD
- Department of Plant Sciences, University of Nebraska, Lincoln, NE, United States
- Department of Genetics and Plant Breeding, Sheri-e-Kashmir University of Agricultural Sciences and Technology-Kashmir, Srinagar, India
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15
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Bai S, Han X, Feng D. Shoot-root signal circuit: Phytoremediation of heavy metal contaminated soil. FRONTIERS IN PLANT SCIENCE 2023; 14:1139744. [PMID: 36890896 PMCID: PMC9987563 DOI: 10.3389/fpls.2023.1139744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
High concentrations of heavy metals in the environment will cause serious harm to ecosystems and human health. It is urgent to develop effective methods to control soil heavy metal pollution. Phytoremediation has advantages and potential for soil heavy metal pollution control. However, the current hyperaccumulators have the disadvantages of poor environmental adaptability, single enrichment species and small biomass. Based on the concept of modularity, synthetic biology makes it possible to design a wide range of organisms. In this paper, a comprehensive strategy of "microbial biosensor detection - phytoremediation - heavy metal recovery" for soil heavy metal pollution control was proposed, and the required steps were modified by using synthetic biology methods. This paper summarizes the new experimental methods that promote the discovery of synthetic biological elements and the construction of circuits, and combs the methods of producing transgenic plants to facilitate the transformation of constructed synthetic biological vectors. Finally, the problems that should be paid more attention to in the remediation of soil heavy metal pollution based on synthetic biology were discussed.
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Affiliation(s)
- Shiyan Bai
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Xiao Han
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Dan Feng
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
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16
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Shaigani P, Fuchs T, Graban P, Prem S, Haack M, Masri M, Mehlmer N, Brueck T. Mastering targeted genome engineering of GC-rich oleaginous yeast for tailored plant oil alternatives for the food and chemical sector. Microb Cell Fact 2023; 22:25. [PMID: 36755261 PMCID: PMC9906925 DOI: 10.1186/s12934-023-02033-1] [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: 12/16/2022] [Accepted: 01/31/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Sustainable production of triglycerides for various applications is a major focus of microbial factories. Oleaginous yeast species have been targeted for commercial production of microbial oils. Among all the oleaginous yeasts examined in a previous comparative study, Cutaneotrichosporon oleaginosus showed the highest lipid productivity. Moreover, a new lipid production process for C. oleaginosus with minimal waste generation and energy consumption resulted in the highest lipid productivity in the history of oleaginous yeasts. However, productivity and product diversity are restricted because of the genetic intractability of this yeast. To date, successful targeted genetic engineering of C. oleaginosus has not yet been reported. RESULTS The targeted gene editing was successfully carried out in C. oleaginosus using CRISPR/Cas system. A tailored enzyme system isolated to degrade the C. oleaginosus cell wall enabled the isolation of viable spheroplasts that are amenable to in-cell delivery of nucleic acids and proteins. The employment of both Cas9 protein and Cas mRNA was effective in obtaining strains with URA5 knockout that did not exhibit growth in the absence of uracil. Subsequently, we successfully created several strains with enhanced lipid yield (54% increase compared to that in wild type) or modified fatty acid profiles comparable with those of cocoa butter or sunflower oil compositions. CONCLUSION This study establishes the first targeted engineering technique for C. oleaginosus using the CRISPR/Cas system. The current study creates the foundation for flexible and targeted strain optimizations towards building a robust platform for sustainable microbial lipid production. Moreover, the genetic transformation of eukaryotic microbial cells using Cas9 mRNA was successfully achieved.
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Affiliation(s)
- Pariya Shaigani
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Tobias Fuchs
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Petra Graban
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Sophia Prem
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Martina Haack
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Mahmoud Masri
- grid.6936.a0000000123222966Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany
| | - Norbert Mehlmer
- Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany.
| | - Thomas Brueck
- Department of Chemistry, Werner Siemens-Chair of Synthetic Biotechnology, Technical University of Munich, Garching, Germany.
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17
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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18
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Anders C, Hoengenaert L, Boerjan W. Accelerating wood domestication in forest trees through genome editing: Advances and prospects. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102329. [PMID: 36586396 PMCID: PMC7614060 DOI: 10.1016/j.pbi.2022.102329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The high economic value of wood requires intensive breeding towards multipurpose biomass. However, long breeding cycles hamper the fast development of novel tree varieties that have improved biomass properties, are tolerant to biotic and abiotic stresses, and resilient to climate change. To speed up domestication, the integration of conventional breeding and new breeding techniques is needed. In this review, we discuss recent advances in genome editing and Cas-DNA-free genome engineering of forest trees, and briefly discuss how multiplex editing combined with multi-omics approaches can accelerate the genetic improvement of forest trees, with a focus on wood.
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Affiliation(s)
- Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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19
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Thingnam SS, Lourembam DS, Tongbram PS, Lokya V, Tiwari S, Khan MK, Pandey A, Hamurcu M, Thangjam R. A Perspective Review on Understanding Drought Stress Tolerance in Wild Banana Genetic Resources of Northeast India. Genes (Basel) 2023; 14:genes14020370. [PMID: 36833297 PMCID: PMC9957078 DOI: 10.3390/genes14020370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
The enormous perennial monocotyledonous herb banana (Musa spp.), which includes dessert and cooking varieties, is found in more than 120 countries and is a member of the order Zingiberales and family Musaceae. The production of bananas requires a certain amount of precipitation throughout the year, and its scarcity reduces productivity in rain-fed banana-growing areas due to drought stress. To increase the tolerance of banana crops to drought stress, it is necessary to explore crop wild relatives (CWRs) of banana. Although molecular genetic pathways involved in drought stress tolerance of cultivated banana have been uncovered and understood with the introduction of high-throughput DNA sequencing technology, next-generation sequencing (NGS) techniques, and numerous "omics" tools, unfortunately, such approaches have not been thoroughly implemented to utilize the huge potential of wild genetic resources of banana. In India, the northeastern region has been reported to have the highest diversity and distribution of Musaceae, with more than 30 taxa, 19 of which are unique to the area, accounting for around 81% of all wild species. As a result, the area is regarded as one of the main locations of origin for the Musaceae family. The understanding of the response of the banana genotypes of northeastern India belonging to different genome groups to water deficit stress at the molecular level will be useful for developing and improving drought tolerance in commercial banana cultivars not only in India but also worldwide. Hence, in the present review, we discuss the studies conducted to observe the effect of drought stress on different banana species. Moreover, the article highlights the tools and techniques that have been used or that can be used for exploring and understanding the molecular basis of differentially regulated genes and their networks in different drought stress-tolerant banana genotypes of northeast India, especially wild types, for unraveling their potential novel traits and genes.
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Affiliation(s)
| | | | - Punshi Singh Tongbram
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
| | - Vadthya Lokya
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector 81, Knowledge City, S.A.S. Nagar, Mohali 140306, India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya 42079, Turkey
| | - Robert Thangjam
- Department of Biotechnology, School of Life Sciences, Mizoram University, Aizawl 796004, India
- Department of Life Sciences, School of Life Sciences, Manipur University, Imphal 795003, India
- Correspondence:
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20
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May D, Paldi K, Altpeter F. Targeted mutagenesis with sequence-specific nucleases for accelerated improvement of polyploid crops: Progress, challenges, and prospects. THE PLANT GENOME 2023:e20298. [PMID: 36692095 DOI: 10.1002/tpg2.20298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Many of the world's most important crops are polyploid. The presence of more than two sets of chromosomes within their nuclei and frequently aberrant reproductive biology in polyploids present obstacles to conventional breeding. The presence of a larger number of homoeologous copies of each gene makes random mutation breeding a daunting task for polyploids. Genome editing has revolutionized improvement of polyploid crops as multiple gene copies and/or alleles can be edited simultaneously while preserving the key attributes of elite cultivars. Most genome-editing platforms employ sequence-specific nucleases (SSNs) to generate DNA double-stranded breaks at their target gene. Such DNA breaks are typically repaired via the error-prone nonhomologous end-joining process, which often leads to frame shift mutations, causing loss of gene function. Genome editing has enhanced the disease resistance, yield components, and end-use quality of polyploid crops. However, identification of candidate targets, genotyping, and requirement of high mutagenesis efficiency remain bottlenecks for targeted mutagenesis in polyploids. In this review, we will survey the tremendous progress of SSN-mediated targeted mutagenesis in polyploid crop improvement, discuss its challenges, and identify optimizations needed to sustain further progress.
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Affiliation(s)
- David May
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Katalin Paldi
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
| | - Fredy Altpeter
- Agronomy Department, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, Gainesville, FL, USA
- Plant Cellular and Molecular Biology Program, Genetics Institute, University of Florida Institute of Food and Agricultural Sciences, Gainesville, FL, USA
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21
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Rigoulot SB, Barco B, Zhang Y, Zhang C, Meier KA, Moore M, Fabish J, Whinna R, Park J, Seaberry EM, Gopalan A, Dong S, Chen Z, Que Q. Automated, High-Throughput Protoplast Transfection for Gene Editing and Transgene Expression Studies. Methods Mol Biol 2023; 2653:129-149. [PMID: 36995624 DOI: 10.1007/978-1-0716-3131-7_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
In an era of cost-efficient gene synthesis and high-throughput construct assembly, the onus of scientific experimentation is on the rate of in vivo testing for the identification of top performing candidates or designs. Assay platforms that are relevant to the species of interest and in the tissue of choice are highly desirable. A protoplast isolation and transfection method that is compatible with a large repertoire of species and tissues would be the platform of choice. A necessary aspect of this high-throughput screening approach is the need to handle many delicate protoplast samples at the same time, which is a bottleneck for manual operation. Such bottlenecks can be mitigated with the use of automated liquid handlers for the execution of protoplast transfection steps. The method described within this chapter utilizes a 96-well head for simultaneous, high-throughput initiation of transfection. While initially developed and optimized for use with etiolated maize leaf protoplasts, the automated protocol has also been demonstrated to be compatible with other established protoplast systems, such as soybean immature embryo derived protoplast, similarly described within. This chapter also includes instructions for a sample randomization design to reduce the impact of edge effects, which might be present when microplates are used for fluorescence readout following transfection. We also describe a streamlined, expedient, and cost-effective protocol for determining gene editing efficiencies using the T7E1 endonuclease cleavage assay with a publicly available image analysis tool.
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Affiliation(s)
| | - Brenden Barco
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Yingxiao Zhang
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Chengjin Zhang
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Kerry A Meier
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Matthew Moore
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Jonathan Fabish
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Rachel Whinna
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Jeongmoo Park
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Erin M Seaberry
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Aditya Gopalan
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Shujie Dong
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Zhongying Chen
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA
| | - Qiudeng Que
- Syngenta Crop Protection, LLC, Research Triangle Park, NC, USA.
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22
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Khan FS, Goher F, Zhang D, Shi P, Li Z, Htwe YM, Wang Y. Is CRISPR/Cas9 a way forward to fast-track genetic improvement in commercial palms? Prospects and limits. FRONTIERS IN PLANT SCIENCE 2022; 13:1042828. [PMID: 36578341 PMCID: PMC9791139 DOI: 10.3389/fpls.2022.1042828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Commercially important palms (oil palm, coconut, and date palm) are widely grown perennial trees with tremendous commercial significance due to food, edible oil, and industrial applications. The mounting pressure on the human population further reinforces palms' importance, as they are essential crops to meet vegetable oil needs around the globe. Various conventional breeding methods are used for the genetic improvement of palms. However, adopting new technologies is crucial to accelerate breeding and satisfy the expanding population's demands. CRISPR/Cas9 is an efficient genome editing tool that can incorporate desired traits into the existing DNA of the plant without losing common traits. Recent progress in genome editing in oil palm, coconut and date palm are preliminarily introduced to potential readers. Furthermore, detailed information on available CRISPR-based genome editing and genetic transformation methods are summarized for researchers. We shed light on the possibilities of genome editing in palm crops, especially on the modification of fatty acid biosynthesis in oil palm. Moreover, the limitations in genome editing, including inadequate target gene screening due to genome complexities and low efficiency of genetic transformation, are also highlighted. The prospects of CRISPR/Cas9-based gene editing in commercial palms to improve sustainable production are also addressed in this review paper.
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Affiliation(s)
- Faiza Shafique Khan
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Farhan Goher
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, China
| | - Dapeng Zhang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Peng Shi
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Zhiying Li
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yin Min Htwe
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
| | - Yong Wang
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off-Season Reproduction Regions/Sanya Research Institute of Chinese Academy of Tropical Agricultural Sciences, Sanya, Hainan, China
- Hainan Key Laboratory of Tropical Oil Crops Biology, Coconut Research Institute of Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China
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Abdul Aziz M, Brini F, Rouached H, Masmoudi K. Genetically engineered crops for sustainably enhanced food production systems. FRONTIERS IN PLANT SCIENCE 2022; 13:1027828. [PMID: 36426158 PMCID: PMC9680014 DOI: 10.3389/fpls.2022.1027828] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
Genetic modification of crops has substantially focused on improving traits for desirable outcomes. It has resulted in the development of crops with enhanced yields, quality, and tolerance to biotic and abiotic stresses. With the advent of introducing favorable traits into crops, biotechnology has created a path for the involvement of genetically modified (GM) crops into sustainable food production systems. Although these plants heralded a new era of crop production, their widespread adoption faces diverse challenges due to concerns about the environment, human health, and moral issues. Mitigating these concerns with scientific investigations is vital. Hence, the purpose of the present review is to discuss the deployment of GM crops and their effects on sustainable food production systems. It provides a comprehensive overview of the cultivation of GM crops and the issues preventing their widespread adoption, with appropriate strategies to overcome them. This review also presents recent tools for genome editing, with a special focus on the CRISPR/Cas9 platform. An outline of the role of crops developed through CRSIPR/Cas9 in achieving sustainable development goals (SDGs) by 2030 is discussed in detail. Some perspectives on the approval of GM crops are also laid out for the new age of sustainability. The advancement in molecular tools through plant genome editing addresses many of the GM crop issues and facilitates their development without incorporating transgenic modifications. It will allow for a higher acceptance rate of GM crops in sustainable agriculture with rapid approval for commercialization. The current genetic modification of crops forecasts to increase productivity and prosperity in sustainable agricultural practices. The right use of GM crops has the potential to offer more benefit than harm, with its ability to alleviate food crises around the world.
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Affiliation(s)
- Mughair Abdul Aziz
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
| | - Faical Brini
- Biotechnology and Plant Improvement Laboratory, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Hatem Rouached
- Michigan State University, Plant and Soil Science Building, East Lansing, MI, United States
| | - Khaled Masmoudi
- Department of Integrative Agriculture, College of Agriculture and Veterinary Medicine, United Arab Emirates University, Al−Ain, Abu−Dhabi, United Arab Emirates
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24
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Mullins E, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Naegeli H, Nogué F, Serrano JJS, Savoini G, Veromann E, Veronesi F, Casacuberta J, Dumont AF, Gennaro A, Lenzi P, Lewandowska A, Guajardo IPM, Papadopoulou N, Rostoks N. Updated scientific opinion on plants developed through cisgenesis and intragenesis. EFSA J 2022; 20:e07621. [PMID: 36274982 PMCID: PMC9583739 DOI: 10.2903/j.efsa.2022.7621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
In 2012, EFSA issued an opinion on plants developed through cisgenesis and intragenesis. With the development of New Genomic Techniques (NGTs) in the last decade, cisgenic and intragenic plants can now be obtained with the insertion of a desired sequence in a precise location of the genome. EFSA has been requested by European Commission to provide an updated scientific opinion on the safety and the risk assessment of plants developed through cisgenesis and intragenesis, in order to (i) identify potential risks, comparing them with those posed by plants obtained by conventional breeding and Established Genomic Techniques (EGTs) and (ii) to determine the applicability of current guidelines for the risk assessment of cisgenic and intragenic plants. The conclusions of the previous EFSA opinion were reviewed, taking into consideration the new guidelines and the recent literature. The GMO panel concludes that no new risks are identified in cisgenic and intragenic plants obtained with NGTs, as compared with those already considered for plants obtained with conventional breeding and EGTs. There are no new data since the publication of the 2012 EFSA opinion that would challenge the conclusions raised in that document. The conclusions of the EFSA 2012 Scientific Opinion remain valid. The EFSA GMO Panel reiterates from these conclusions that with respect to the source of DNA and the safety of the gene product, the hazards arising from the use of a related plant‐derived gene by cisgenesis are similar to those from conventional plant breeding, whereas additional hazards may arise for intragenic plants. Furthermore, the EFSA GMO Panel considers that cisgenesis and intragenesis make use of the same transformation techniques as transgenesis, and therefore, with respect to the alterations to the host genome, cisgenic, intragenic and transgenic plants obtained by random insertion do not cause different hazards. Compared to that, the use of NGTs reduces the risks associated with potential unintended modifications of the host genome. Thus, fewer requirements may be needed for the assessment of cisgenic and intragenic plants obtained through NGTs, due to site‐directed integration of the added genetic material. Moreover, the GMO panel concludes that the current guidelines are partially applicable and sufficient. On a case‐by‐case basis, a lesser amount of data might be needed for the risk assessment of cisgenic or intragenic plants obtained through NGTs. This publication is linked to the following EFSA Journal article: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2022.7618/full
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Tiwari JK, A J, Tuteja N, Khurana SMP. Genome editing (CRISPR-Cas)-mediated virus resistance in potato (Solanum tuberosum L.). Mol Biol Rep 2022; 49:12109-12119. [PMID: 35764748 DOI: 10.1007/s11033-022-07704-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Plant viruses are the major pathogens that cause heavy yield loss in potato. The important viruses are potato virus X, potato virus Y and potato leaf roll virus around the world. Besides these three viruses, a novel tomato leaf curl New Delhi virus is serious in India. Conventional cum molecular breeding and transgenics approaches have been applied to develop virus resistant potato genotypes. But progress is slow in developing resistant varieties due to lack of host genes and long breeding process, and biosafety concern with transgenics. Hence, CRISPR-Cas mediated genome editing has emerged as a powerful technology to address these issues. CRISPR-Cas technology has been deployed in potato for several important traits. We highlight here CRISPR-Cas approaches of virus resistance through targeting viral genome (DNA or RNA), host factor gene and multiplexing of target genes simultaneously. Further, advancement in CRISPR-Cas research is presented in the area of DNA-free genome editing, virus-induced genome editing, and base editing. CRISPR-Cas delivery, transformation methods, and challenges in tetraploid potato and possible methods are also discussed.
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Affiliation(s)
- Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, 171001, India.
| | - Jeevalatha A
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, 673012, India
| | - Narendra Tuteja
- International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Road, New Delhi, 110067, India
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Viswan A, Yamagishi A, Hoshi M, Furuhata Y, Kato Y, Makimoto N, Takeshita T, Kobayashi T, Iwata F, Kimura M, Yoshizumi T, Nakamura C. Microneedle Array-Assisted, Direct Delivery of Genome-Editing Proteins Into Plant Tissue. FRONTIERS IN PLANT SCIENCE 2022; 13:878059. [PMID: 35812975 PMCID: PMC9263851 DOI: 10.3389/fpls.2022.878059] [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: 02/17/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Genome editing in plants employing recombinant DNA often results in the incorporation of foreign DNA into the host genome. The direct delivery of genome-editing proteins into plant tissues is desired to prevent undesirable genetic alterations. However, in most currently available methods, the point of entry of the genome-editing proteins cannot be controlled and time-consuming processes are required to select the successfully transferred samples. To overcome these limitations, we considered a novel microneedle array (MNA)-based delivery system, in which the needles are horizontally aligned from the substrate surface, giving it a comb-like configuration. We aimed to deliver genome-editing proteins directly into the inner layers of leaf tissues; palisade, the spongy and subepidermal L2 layers of the shoot apical meristem (SAM) which include cells that can differentiate into germlines. The array with needles 2 μm wide and 60 μm long was effective in inserting into Arabidopsis thaliana leaves and Glycine max (L.) Merr. (soybeans) SAM without the needles buckling or breaking. The setup was initially tested for the delivery of Cre recombinase into the leaves of the reporter plant A. thaliana by quantifying the GUS (β-glucuronidase) expression that occurred by the recombination of the loxP sites. We observed GUS expression at every insertion. Additionally, direct delivery of Cas9 ribonucleoprotein (RNP) targeting the PDS11/18 gene in soybean SAM showed an 11 bp deletion in the Cas9 RNP target site. Therefore, this method effectively delivered genome-editing proteins into plant tissues with precise control over the point of entry.
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Affiliation(s)
- Anchu Viswan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ayana Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masamichi Hoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yuichi Furuhata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Natsumi Makimoto
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Toshihiro Takeshita
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takeshi Kobayashi
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Futoshi Iwata
- Graduate School of Medical Photonics, Shizuoka University, Hamamatsu, Japan
| | - Mitsuhiro Kimura
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Japan
| | - Takeshi Yoshizumi
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Japan
| | - Chikashi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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A Robust Expression and Purification Method for Production of SpCas9-GFP-MBP Fusion Protein for In Vitro Applications. Methods Protoc 2022; 5:mps5030044. [PMID: 35736545 PMCID: PMC9228339 DOI: 10.3390/mps5030044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/16/2022] Open
Abstract
Genome editing using the CRISPR/Cas9 system is one of the trendiest methodologies in the scientific community. Many genome editing approaches require recombinant Streptococcus pyogenes Cas9 (SpCas9) at some point during their application, for instance, for in vitro validation of single guide RNAs (SgRNAs) or for the DNA-free editing of genes of interest. Hereby, we provide a simple and detailed expression and purification protocol for SpCas9 as a protein fused to GFP and MBP. This protocol improves protein yield and simplifies the purification process by overcoming the frequently occurring obstacles such as plasmid loss, inconsistent protein expression levels, or inadequate protein binding to affinity resins. On average, this protocol yields 10 to 30 mg of purified, active, His6−MBP−SpCas9 NLS−GFP protein. The purity addressed through SDS-PAGE is > 80%.
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28
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Van Vu T, Das S, Hensel G, Kim JY. Genome editing and beyond: what does it mean for the future of plant breeding? PLANTA 2022; 255:130. [PMID: 35587292 PMCID: PMC9120101 DOI: 10.1007/s00425-022-03906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
Genome editing offers revolutionized solutions for plant breeding to sustain food production to feed the world by 2050. Therefore, genome-edited products are increasingly recognized via more relaxed legislation and community adoption. The world population and food production are disproportionally growing in a manner that would have never matched each other under the current agricultural practices. The emerging crisis is more evident with the subtle changes in climate and the running-off of natural genetic resources that could be easily used in breeding in conventional ways. Under these circumstances, affordable CRISPR-Cas-based gene-editing technologies have brought hope and charged the old plant breeding machine with the most energetic and powerful fuel to address the challenges involved in feeding the world. What makes CRISPR-Cas the most powerful gene-editing technology? What are the differences between it and the other genetic engineering/breeding techniques? Would its products be labeled as "conventional" or "GMO"? There are so many questions to be answered, or that cannot be answered within the limitations of our current understanding. Therefore, we would like to discuss and answer some of the mentioned questions regarding recent progress in technology development. We hope this review will offer another view on the role of CRISPR-Cas technology in future of plant breeding for food production and beyond.
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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, 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
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371, Olomouc, Czech Republic.
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four 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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Chen Y, Sun W, Tang H, Li Y, Li C, Wang L, Chen J, Lin W, Li S, Fan Z, Cheng Y, Chen C. Interactions Between Immunomodulatory Biomaterials and Immune Microenvironment: Cues for Immunomodulation Strategies in Tissue Repair. Front Bioeng Biotechnol 2022; 10:820940. [PMID: 35646833 PMCID: PMC9140325 DOI: 10.3389/fbioe.2022.820940] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 01/31/2022] [Indexed: 11/13/2022] Open
Abstract
The foreign body response (FBR) caused by biomaterials can essentially be understood as the interaction between the immune microenvironment and biomaterials, which has severely impeded the application of biomaterials in tissue repair. This concrete interaction occurs via cells and bioactive substances, such as proteins and nucleic acids. These cellular and molecular interactions provide important cues for determining which element to incorporate into immunomodulatory biomaterials (IMBs), and IMBs can thus be endowed with the ability to modulate the FBR and repair damaged tissue. In terms of cellular, IMBs are modified to modulate functions of immune cells, such as macrophages and mast cells. In terms of bioactive substances, proteins and nucleic acids are delivered to influence the immune microenvironment. Meanwhile, IMBs are designed with high affinity for spatial targets and the ability to self-adapt over time, which allows for more efficient and intelligent tissue repair. Hence, IMB may achieve the perfect functional integration in the host, representing a breakthrough in tissue repair and regeneration medicine.
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Affiliation(s)
- Yi Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Weiyan Sun
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Hai Tang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Yingze Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
- Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chen Li
- School of Materials Science and Engineering, Tongji University, Shanghai, China
| | - Long Wang
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Jiafei Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Weikang Lin
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Shenghui Li
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Ziwen Fan
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
| | - Yu Cheng
- Institute for Regenerative Medicine, Institute for Translational Nanomedicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- The Institute for Biomedical Engineering and Nano Science, Tongji University School of Medicine, Shanghai, China
- *Correspondence: Yu Cheng, ; Chang Chen,
| | - Chang Chen
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital, Tongji University, Shanghai, China
- *Correspondence: Yu Cheng, ; Chang Chen,
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30
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Muguerza MB, Gondo T, Ishigaki G, Shimamoto Y, Umami N, Nitthaisong P, Rahman MM, Akashi R. Tissue Culture and Somatic Embryogenesis in Warm-Season Grasses—Current Status and Its Applications: A Review. PLANTS 2022; 11:plants11091263. [PMID: 35567264 PMCID: PMC9101205 DOI: 10.3390/plants11091263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]
Abstract
Warm-season grasses are C4 plants and have a high capacity for biomass productivity. These grasses are utilized in many agricultural production systems with their greatest value as feeds for livestock, bioethanol, and turf. However, many important warm-season perennial grasses multiply either by vegetative propagation or form their seeds by an asexual mode of reproduction called apomixis. Therefore, the improvement of these grasses by conventional breeding is difficult and is dependent on the availability of natural genetic variation and its manipulation through breeding and selection. Recent studies have indicated that plant tissue culture system through somatic embryogenesis complements and could further develop conventional breeding programs by micropropagation, somaclonal variation, somatic hybridization, genetic transformation, and genome editing. This review summarizes the tissue culture and somatic embryogenesis in warm-season grasses and focus on current status and above applications including the author’s progress.
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Affiliation(s)
- Melody Ballitoc Muguerza
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
| | - Takahiro Gondo
- Frontier Science Research Center, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan
- Correspondence:
| | - Genki Ishigaki
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
| | - Yasuyo Shimamoto
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
| | - Nafiatul Umami
- Faculty of Animal Science, Universitas Gadjah Mada, Jl Fauna 3, Yogyakarta 55281, Indonesia;
| | - Pattama Nitthaisong
- Faculty of Agricultural Technology, King Mongkut’s Institute of Technology Ladkrabang, Bangkok 10520, Thailand;
| | - Mohammad Mijanur Rahman
- Faculty of Agro-Based Industry, Jeli Campus, Universiti Malaysia Kelantan, Jeli 17600, Kelantan, Malaysia;
| | - Ryo Akashi
- Faculty of Agriculture, University of Miyazaki, 1-1 Gakuenkibanadai-Nishi, Miyazaki 889-2192, Japan; (M.B.M.); (G.I.); (Y.S.); (R.A.)
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31
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Kumari C, Sharma M, Kumar V, Sharma R, Kumar V, Sharma P, Kumar P, Irfan M. Genome Editing Technology for Genetic Amelioration of Fruits and Vegetables for Alleviating Post-Harvest Loss. Bioengineering (Basel) 2022; 9:bioengineering9040176. [PMID: 35447736 PMCID: PMC9028506 DOI: 10.3390/bioengineering9040176] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/02/2022] [Accepted: 04/15/2022] [Indexed: 01/13/2023] Open
Abstract
Food security and crop production are challenged worldwide due to overpopulation, changing environmental conditions, crop establishment failure, and various kinds of post-harvest losses. The demand for high-quality foods with improved nutritional quality is also growing day by day. Therefore, production of high-quality produce and reducing post-harvest losses of produce, particularly of perishable fruits and vegetables, are vital. For many decades, attempts have been made to improve the post-harvest quality traits of horticultural crops. Recently, modern genetic tools such as genome editing emerged as a new approach to manage and overcome post-harvest effectively and efficiently. The different genome editing tools including ZFNs, TALENs, and CRISPR/Cas9 system effectively introduce mutations (In Dels) in many horticultural crops to address and resolve the issues associated with post-harvest storage quality. Henceforth, we provide a broad review of genome editing applications in horticulture crops to improve post-harvest stability traits such as shelf life, texture, and resistance to pathogens without compromising nutritional value. Moreover, major roadblocks, challenges, and their possible solutions for employing genome editing tools are also discussed.
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Affiliation(s)
- Chanchal Kumari
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Megha Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Vinay Kumar
- Department of Physiology and Cell Biology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA;
| | - Parul Sharma
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
- Correspondence: (P.S.); (M.I.)
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh 173230, India; (C.K.); (M.S.); (V.K.); (R.S.); (P.K.)
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY 14853, USA
- Correspondence: (P.S.); (M.I.)
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Rana S, Aggarwal PR, Shukla V, Giri U, Verma S, Muthamilarasan M. Genome Editing and Designer Crops for the Future. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2408:37-69. [PMID: 35325415 DOI: 10.1007/978-1-0716-1875-2_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Domestication spanning over thousands of years led to the evolution of crops that are being cultivated in recent times. Later, selective breeding methods were practiced by human to produce improved cultivars/germplasm. Classical breeding was further transformed into molecular- and genomics-assisted breeding strategies, however, these approaches are labor-intensive and time-consuming. The advent of omics technologies has facilitated the identification of genes and genetic determinants that regulate particular traits allowing the direct manipulation of target genes and genomic regions to achieve desirable phenotype. Recently, genome editing technologies such as meganucleases (MN), zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeats)/CRISPR-Associated protein 9 (Cas9) have gained popularity for precise editing of genes to develop crop varieties with superior agronomic, physiological, climate-resilient, and nutritional traits. Owing to the efficiency and precision, genome editing approaches have been widely used to design the crops that can survive the challenges posed by changing climate, and also cater the food and nutritional requirements for ever-growing population. Here, we briefly review different genome editing technologies deployed for crop improvement, and the fundamental differences between GE technology and transgene-based approach. We also summarize the recent advances in genome editing and how this radical expansion can complement the previously established technologies along with breeding for creating designer crops.
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Affiliation(s)
- Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Varsa Shukla
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Urmi Giri
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Shubham Verma
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
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Huang Y, Shang M, Liu T, Wang K. High-throughput methods for genome editing: the more the better. PLANT PHYSIOLOGY 2022; 188:1731-1745. [PMID: 35134245 PMCID: PMC8968257 DOI: 10.1093/plphys/kiac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/29/2021] [Indexed: 05/04/2023]
Abstract
During the last decade, targeted genome-editing technologies, especially clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) technologies, have permitted efficient targeting of genomes, thereby modifying these genomes to offer tremendous opportunities for deciphering gene function and engineering beneficial traits in many biological systems. As a powerful genome-editing tool, the CRISPR/Cas systems, combined with the development of next-generation sequencing and many other high-throughput techniques, have thus been quickly developed into a high-throughput engineering strategy in animals and plants. Therefore, here, we review recent advances in using high-throughput genome-editing technologies in animals and plants, such as the high-throughput design of targeted guide RNA (gRNA), construction of large-scale pooled gRNA, and high-throughput genome-editing libraries, high-throughput detection of editing events, and high-throughput supervision of genome-editing products. Moreover, we outline perspectives for future applications, ranging from medication using gene therapy to crop improvement using high-throughput genome-editing technologies.
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Affiliation(s)
- Yong Huang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Meiqi Shang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Tingting Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
| | - Kejian Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China
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He Y, Mudgett M, Zhao Y. Advances in gene editing without residual transgenes in plants. PLANT PHYSIOLOGY 2022; 188:1757-1768. [PMID: 34893903 PMCID: PMC8968301 DOI: 10.1093/plphys/kiab574] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 11/09/2021] [Indexed: 05/24/2023]
Abstract
Transgene residuals in edited plants affect genetic analysis, pose off-target risks, and cause regulatory concerns. Several strategies have been developed to efficiently edit target genes without leaving any transgenes in plants. Some approaches directly address this issue by editing plant genomes with DNA-free reagents. On the other hand, DNA-based techniques require another step for ensuring plants are transgene-free. Fluorescent markers, pigments, and chemical treatments have all been employed as tools to distinguish transgenic plants from transgene-free plants quickly and easily. Moreover, suicide genes have been used to trigger self-elimination of transgenic plants, greatly improving the efficiency of isolating the desired transgene-free plants. Transgenes can also be excised from plant genomes using site-specific recombination, transposition or gene editing nucleases, providing a strategy for editing asexually produced plants. Finally, haploid induction coupled with gene editing may make it feasible to edit plants that are recalcitrant to transformation. Here, we evaluate the strengths and weaknesses of recently developed approaches for obtaining edited plants without transgene residuals.
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Affiliation(s)
- Yubing He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Collaborative Innovation Center for Modern Crop Production Co-sponsored by Province and Ministry, Nanjing Agricultural University, Nanjing 210095, China
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Science, Nanjing 210014, China
| | - Michael Mudgett
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, California 92093-0116, USA
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Ali Q, Yu C, Hussain A, Ali M, Ahmar S, Sohail MA, Riaz M, Ashraf MF, Abdalmegeed D, Wang X, Imran M, Manghwar H, Zhou L. Genome Engineering Technology for Durable Disease Resistance: Recent Progress and Future Outlooks for Sustainable Agriculture. FRONTIERS IN PLANT SCIENCE 2022; 13:860281. [PMID: 35371164 PMCID: PMC8968944 DOI: 10.3389/fpls.2022.860281] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/22/2022] [Indexed: 05/15/2023]
Abstract
Crop production worldwide is under pressure from multiple factors, including reductions in available arable land and sources of water, along with the emergence of new pathogens and development of resistance in pre-existing pathogens. In addition, the ever-growing world population has increased the demand for food, which is predicted to increase by more than 100% by 2050. To meet these needs, different techniques have been deployed to produce new cultivars with novel heritable mutations. Although traditional breeding continues to play a vital role in crop improvement, it typically involves long and laborious artificial planting over multiple generations. Recently, the application of innovative genome engineering techniques, particularly CRISPR-Cas9-based systems, has opened up new avenues that offer the prospects of sustainable farming in the modern agricultural industry. In addition, the emergence of novel editing systems has enabled the development of transgene-free non-genetically modified plants, which represent a suitable option for improving desired traits in a range of crop plants. To date, a number of disease-resistant crops have been produced using gene-editing tools, which can make a significant contribution to overcoming disease-related problems. Not only does this directly minimize yield losses but also reduces the reliance on pesticide application, thereby enhancing crop productivity that can meet the globally increasing demand for food. In this review, we describe recent progress in genome engineering techniques, particularly CRISPR-Cas9 systems, in development of disease-resistant crop plants. In addition, we describe the role of CRISPR-Cas9-mediated genome editing in sustainable agriculture.
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Affiliation(s)
- Qurban Ali
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
| | - Amjad Hussain
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Mohsin Ali
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Sunny Ahmar
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Muhammad Aamir Sohail
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Riaz
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, China
| | - Muhammad Furqan Ashraf
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Dyaaaldin Abdalmegeed
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Ministry of Education, Nanjing Agricultural University, Nanjing, China
- Department of Botany and Microbiology, Faculty of Science, Tanta University, Tanta, Egypt
| | - Xiukang Wang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Muhammad Imran
- Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Lei Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Agro-product Safety and Nutrition, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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Prevention of Enzymatic Browning by Natural Extracts and Genome-Editing: A Review on Recent Progress. Molecules 2022; 27:molecules27031101. [PMID: 35164369 PMCID: PMC8839884 DOI: 10.3390/molecules27031101] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 01/23/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022] Open
Abstract
Fresh fruits and vegetable products are easily perishable during postharvest handling due to enzymatic browning reactions. This phenomenon has contributed to a significant loss of food quality and appearance. Thus, a safe and effective alternative method from natural sources is needed to tackle enzymatic browning prevention. The capabilities of natural anti-browning agents derived from plant- and animal-based resources in inhibiting enzymatic activity have been demonstrated in the literature. Some also possess strong antioxidants properties. This review aims to summarize a recent investigation regarding the use of natural anti-browning extracts from different sources for controlling the browning. The potential applications of genome-editing in preventing browning activity and improving postharvest quality is also discussed. Moreover, the patents on the anti-browning extract from natural sources is also presented in this review. The information reviewed here could provide new insights, contributing to the development of natural anti-browning extracts and genome-editing techniques for the prevention of food browning.
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Hüdig M, Laibach N, Hein AC. Genome Editing in Crop Plant Research-Alignment of Expectations and Current Developments. PLANTS (BASEL, SWITZERLAND) 2022; 11:212. [PMID: 35050100 PMCID: PMC8778883 DOI: 10.3390/plants11020212] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/07/2022] [Accepted: 01/08/2022] [Indexed: 06/14/2023]
Abstract
The rapid development of genome editing and other new genomic techniques (NGT) has evoked manifold expectations on purposes of the application of these techniques to crop plants. In this study, we identify and align these expectations with current scientific development. We apply a semi-quantitative text analysis approach on political, economic, and scientific opinion papers to disentangle and extract expectations towards the application of NGT-based plants. Using the sustainable development goals (SDG) of the 2030 agenda as categories, we identify contributions to food security or adaptation to climatic changes as the most frequently mentioned expectations, accompanied by the notion of sustainable agriculture and food systems. We then link SDG with relevant plant traits and review existing research and commercial field trials for genome-edited crop plants. For a detailed analysis we pick as representative traits drought tolerance and resistance against fungal pathogens. Diverse genetic setscrews for both traits have been identified, modified, and tested under laboratory conditions, although there are only a few in the field. All in all, NGT-plants that can withstand more than one stressor or different environments are not documented in advanced development states. We further conclude that developing new plants with modified traits will not be sufficient to reach food security or adaption to climatic changes in a short time frame. Further scientific development of sustainable agricultural systems will need to play an important role to tackle SDG challenges, as well.
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Affiliation(s)
- Meike Hüdig
- Molecular Plant Physiology Division, Institute of Molecular Physiology and Biotechnology of Plants, University of Bonn, Kirschallee 1, 53115 Bonn, Germany
| | - Natalie Laibach
- Centre for Research in Agricultural Genomics (CRAG), Edifici CRAG-Campus UAB, 08193 Cerdanyola del Vallès, Spain
| | - Anke-Christiane Hein
- Federal Agency for Nature Conservation, Assessment of Genetically Modified Organisms, Konstantinstraße 110, 53179 Bonn, Germany
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Subburaj S, Zanatta CB, Nunn JAL, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. A DNA-Free Editing Platform for Genetic Screens in Soybean via CRISPR/Cas9 Ribonucleoprotein Delivery. FRONTIERS IN PLANT SCIENCE 2022; 13:939997. [PMID: 35903231 PMCID: PMC9315425 DOI: 10.3389/fpls.2022.939997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 05/06/2023]
Abstract
CRISPR/Cas9-based ribonucleoprotein (RNP)-mediated system has the property of minimizing the effects related to the unwanted introduction of vector DNA and random integration of recombinant DNA. Here, we describe a platform based on the direct delivery of Cas9 RNPs to soybean protoplasts for genetic screens in knockout gene-edited soybean lines without the transfection of DNA vectors. The platform is based on the isolation of soybean protoplasts and delivery of Cas RNP complex. To empirically test our platform, we have chosen a model gene from the soybean genetic toolbox. We have used five different guide RNA (gRNA) sequences that targeted the constitutive pathogen response 5 (CPR5) gene associated with the growth of trichomes in soybean. In addition, efficient protoplast transformation, concentration, and ratio of Cas9 and gRNAs were optimized for soybean for the first time. Targeted mutagenesis insertion and deletion frequency and sequences were analyzed using both Sanger and targeted deep sequencing strategies. We were able to identify different mutation patterns within insertions and deletions (InDels) between + 5 nt and -30 bp and mutation frequency ranging from 4.2 to 18.1% in the GmCPR5 locus. Our results showed that DNA-free delivery of Cas9 complexes to protoplasts is a useful approach to perform early-stage genetic screens and anticipated analysis of Cas9 activity in soybeans.
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Affiliation(s)
- Saminathan Subburaj
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
| | - Caroline Bedin Zanatta
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Jennifer A. L. Nunn
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Sarah Zanon Agapito-Tenfen
- NORCE Norwegian Research Centre AS, Department of Climate & Environment, Tromsø, Norway
- *Correspondence: Sarah Zanon Agapito-Tenfen,
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Abdallah NA, Hamwieh A, Radwan K, Fouad N, Prakash C. Genome editing techniques in plants: a comprehensive review and future prospects toward zero hunger. GM CROPS & FOOD 2021; 12:601-615. [PMID: 35135438 PMCID: PMC9208631 DOI: 10.1080/21645698.2021.2021724] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Indexed: 12/15/2022]
Abstract
Promoting sustainable agriculture and improving nutrition are the main united nation sustainable development goals by 2030. New technologies are required to achieve zero hunger, and genome editing technology is the most promising one. In the last decade, genome editing (GE) using the CRISPR/Cas system has attracted researchers as a safer and easy tool for genome editing in several living organisms. GE has revolutionized the field of agriculture by improving biotic and abiotic stresses and yield improvement. GE technologies were developed fast lately to avoid the obstacles that face GM crops. GE technology, depending on site directed nuclease (SDN), is divided into three categories according to the modification methods. Developing transgenic-free edited plants without introducing foreign DNA meet the acceptance and regulatory ratification of several countries. There are several ongoing efforts from different countries that are rapidly expanding to adopt the current technological innovations. This review summarizes the different GE technologies and their application as a way to help in ending hunger.
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Affiliation(s)
- Naglaa A. Abdallah
- Department of Genetics Faculty of Agriculture, Cairo University, Cairo, Egypt
- National Biotechnology Network of Expertise, ASRT, Egypt
| | - Aladdin Hamwieh
- Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled Radwan
- National Biotechnology Network of Expertise, ASRT, Egypt
- Department of Biotechnology, Agricultural Genetic Engineering Research Institute (AGERI), ARC, Giza, Egypt
| | - Nourhan Fouad
- Department of Biotechnology, International Centre for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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Tsai AYL, McGee R, Dean GH, Haughn GW, Sawa S. Seed Mucilage: Biological Functions and Potential Applications in Biotechnology. PLANT & CELL PHYSIOLOGY 2021; 62:1847-1857. [PMID: 34195842 DOI: 10.1093/pcp/pcab099] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Revised: 05/16/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
In plants, the diaspore (seed dispersal unit) may include a seed coat and/or pericarp to protect the embryo and assist in dispersion. In many species, the seed coat and/or pericarp secrete a gelatinous mixture of cell wall polysaccharides known as mucilage. In several species, mucilage synthesis, secretion and modification have been studied extensively as model systems for the investigation of plant cell wall structure and function. Despite this, efforts toward understanding the role of mucilage have received less attention. Mucilage has been hypothesized to impact seed dispersal through interaction with soil, protecting the seed in the gut following ingestion by animals or affecting the ability of seeds to sink or float in water. Mucilage has been found to influence seed germination and seedling establishment, most often during abiotic stress, probably by maintaining seed hydration when water is scarce. Finally, mucilage has been documented to mediate interactions with various organisms. Advances in transgenic technology should enable the genetic modification of mucilage structure and function in crop plants. Cells synthesizing mucilage may also be a suitable platform for creating custom polysaccharides or proteins with industrial applications. Thus, in the near future, it is likely that research on seed mucilage will expand well beyond the current focus. Here we summarize our understanding of the biological functions of mucilage and provide an outlook on the future of mucilage research.
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Affiliation(s)
- Allen Yi-Lun Tsai
- International Research Center for Agricultural & Environmental Biology, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo Ward, Kumamoto 860-8555, Japan
| | - Robert McGee
- L'Institut National de la Recherche Scientifique Centre Armand-Frappier Santé Biotechnologie (INRS-CAFSB), 531 des Prairies Blvd, Laval, QC H7V 1B7, Canada
| | - Gillian H Dean
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
| | - George W Haughn
- Department of Botany, University of British Columbia, 6270 University Blvd, Vancouver, BC V6T 1Z4, Canada
| | - Shinichiro Sawa
- International Research Center for Agricultural & Environmental Biology, Faculty of Advanced Science and Technology, Kumamoto University, 2-39-1 Kurokami, Chuo Ward, Kumamoto 860-8555, Japan
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Dalla Costa L, Vinciguerra D, Giacomelli L, Salvagnin U, Piazza S, Spinella K, Malnoy M, Moser C, Marchesi U. Integrated approach for the molecular characterization of edited plants obtained via Agrobacterium tumefaciens-mediated gene transfer. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-021-03881-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
AbstractAgrobacterium tumefaciens-mediated gene transfer—actually the most used method to engineer plants—may lead to integration of multiple copies of T-DNA in the plant genome, as well as to chimeric tissues composed of modified cells and wild type cells. A molecular characterization of the transformed lines is thus a good practice to select the best ones for further investigation. Nowadays, several quantitative and semi-quantitative techniques are available to estimate the copy number (CN) of the T-DNA in genetically modified plants. In this study, we compared three methods based on (1) real-time polymerase chain reaction (qPCR), (2) droplet digital PCR (ddPCR), and (3) next generation sequencing (NGS), to carry out a molecular characterization of grapevine edited lines. These lines contain a knock-out mutation, obtained via CRISPR/Cas9 technology, in genes involved in plant susceptibility to two important mildew diseases of grapevine. According to our results, qPCR and ddPCR outputs are largely in agreement in terms of accuracy, especially for low CN values, while ddPCR resulted more precise than qPCR. With regard to the NGS analysis, the CNs detected with this method were often not consistent with those calculated by qPCR and ddPCR, and NGS was not able to discriminate the integration points in three out of ten lines. Nevertheless, the NGS method can positively identify T-DNA truncations or the presence of tandem/inverted repeats, providing distinct and relevant information about the transgene integration asset. Moreover, the expression analysis of Cas9 and single guide RNA (sgRNA), and the sequencing of the target site added new information to be related to CN data. This work, by reporting a practical case-study on grapevine edited lines, explores pros and cons of the most advanced diagnostic techniques available for the precocious selection of the proper transgenic material. The results may be of interest both to scientists developing new transgenic lines, and to laboratories in charge of GMO control.
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Engineering Properties of Sweet Potato Starch for Industrial Applications by Biotechnological Techniques including Genome Editing. Int J Mol Sci 2021; 22:ijms22179533. [PMID: 34502441 PMCID: PMC8431112 DOI: 10.3390/ijms22179533] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/20/2021] [Accepted: 08/29/2021] [Indexed: 11/25/2022] Open
Abstract
Sweet potato (Ipomoea batatas) is one of the largest food crops in the world. Due to its abundance of starch, sweet potato is a valuable ingredient in food derivatives, dietary supplements, and industrial raw materials. In addition, due to its ability to adapt to a wide range of harsh climate and soil conditions, sweet potato is a crop that copes well with the environmental stresses caused by climate change. However, due to the complexity of the sweet potato genome and the long breeding cycle, our ability to modify sweet potato starch is limited. In this review, we cover the recent development in sweet potato breeding, understanding of starch properties, and the progress in sweet potato genomics. We describe the applicational values of sweet potato starch in food, industrial products, and biofuel, in addition to the effects of starch properties in different industrial applications. We also explore the possibility of manipulating starch properties through biotechnological means, such as the CRISPR/Cas-based genome editing. The ability to target the genome with precision provides new opportunities for reducing breeding time, increasing yield, and optimizing the starch properties of sweet potatoes.
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Dalakouras A, Vlachostergios D. Epigenetic approaches to crop breeding: current status and perspectives. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:5356-5371. [PMID: 34017985 DOI: 10.1093/jxb/erab227] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/18/2021] [Indexed: 05/10/2023]
Abstract
In order to tackle the cumulative adverse effects of global climate change, reduced farmland, and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued agronomical traits, but its potential is gradually being compromised by the menacing decline of genetic variation. Resorting to the epigenome as a source of variation could serve as a promising alternative. Here, we discuss current status of epigenetics-mediated crop breeding (epibreeding), highlight its advances and limitations, outline currently available methodologies, and propose novel RNA-based strategies to modify the epigenome in a gene-specific and transgene-free manner.
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Affiliation(s)
- Athanasios Dalakouras
- Institute of Industrial and Forage Crops, HAO-DEMETER, 41335 Larissa, Greece
- Institute of Plant Breeding and Genetic Resources, HAO-DEMETER, 57001 Thessaloniki, Greece
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Lobato-Gómez M, Hewitt S, Capell T, Christou P, Dhingra A, Girón-Calva PS. Transgenic and genome-edited fruits: background, constraints, benefits, and commercial opportunities. HORTICULTURE RESEARCH 2021; 8:166. [PMID: 34274949 PMCID: PMC8286259 DOI: 10.1038/s41438-021-00601-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 04/14/2021] [Accepted: 05/20/2021] [Indexed: 05/14/2023]
Abstract
Breeding has been used successfully for many years in the fruit industry, giving rise to most of today's commercial fruit cultivars. More recently, new molecular breeding techniques have addressed some of the constraints of conventional breeding. However, the development and commercial introduction of such novel fruits has been slow and limited with only five genetically engineered fruits currently produced as commercial varieties-virus-resistant papaya and squash were commercialized 25 years ago, whereas insect-resistant eggplant, non-browning apple, and pink-fleshed pineapple have been approved for commercialization within the last 6 years and production continues to increase every year. Advances in molecular genetics, particularly the new wave of genome editing technologies, provide opportunities to develop new fruit cultivars more rapidly. Our review, emphasizes the socioeconomic impact of current commercial fruit cultivars developed by genetic engineering and the potential impact of genome editing on the development of improved cultivars at an accelerated rate.
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Affiliation(s)
- Maria Lobato-Gómez
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
| | - Seanna Hewitt
- Department of Horticulture, Washington State University, PO Box, 646414, Pullman, WA, USA
| | - Teresa Capell
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
| | - Paul Christou
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, 08010, Barcelona, Spain
| | - Amit Dhingra
- Department of Horticulture, Washington State University, PO Box, 646414, Pullman, WA, USA
| | - Patricia Sarai Girón-Calva
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio CERCA Center, Lleida, 25198, Spain.
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Fiaz S, Ahmar S, Saeed S, Riaz A, Mora-Poblete F, Jung KH. Evolution and Application of Genome Editing Techniques for Achieving Food and Nutritional Security. Int J Mol Sci 2021; 22:5585. [PMID: 34070430 PMCID: PMC8197453 DOI: 10.3390/ijms22115585] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/16/2021] [Accepted: 05/20/2021] [Indexed: 12/26/2022] Open
Abstract
A world with zero hunger is possible only through a sustainable increase in food production and distribution and the elimination of poverty. Scientific, logistical, and humanitarian approaches must be employed simultaneously to ensure food security, starting with farmers and breeders and extending to policy makers and governments. The current agricultural production system is facing the challenge of sustainably increasing grain quality and yield and enhancing resistance to biotic and abiotic stress under the intensifying pressure of climate change. Under present circumstances, conventional breeding techniques are not sufficient. Innovation in plant breeding is critical in managing agricultural challenges and achieving sustainable crop production. Novel plant breeding techniques, involving a series of developments from genome editing techniques to speed breeding and the integration of omics technology, offer relevant, versatile, cost-effective, and less time-consuming ways of achieving precision in plant breeding. Opportunities to edit agriculturally significant genes now exist as a result of new genome editing techniques. These range from random (physical and chemical mutagens) to non-random meganucleases (MegaN), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), clustered regularly interspaced short palindromic repeats (CRISPR)/associated protein system 9 (CRISPR/Cas9), the CRISPR system from Prevotella and Francisella1 (Cpf1), base editing (BE), and prime editing (PE). Genome editing techniques that promote crop improvement through hybrid seed production, induced apomixis, and resistance to biotic and abiotic stress are prioritized when selecting for genetic gain in a restricted timeframe. The novel CRISPR-associated protein system 9 variants, namely BE and PE, can generate transgene-free plants with more frequency and are therefore being used for knocking out of genes of interest. We provide a comprehensive review of the evolution of genome editing technologies, especially the application of the third-generation genome editing technologies to achieve various plant breeding objectives within the regulatory regimes adopted by various countries. Future development and the optimization of forward and reverse genetics to achieve food security are evaluated.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur 22620, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Sajjad Saeed
- Department of Forestry and Wildlife Management, University of Haripur, Haripur 22620, Pakistan
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 2 Norte 685, Talca 3460000, Chile
| | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin 17104, Korea
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Mushtaq M, Ahmad Dar A, Skalicky M, Tyagi A, Bhagat N, Basu U, Bhat BA, Zaid A, Ali S, Dar TUH, Rai GK, Wani SH, Habib-Ur-Rahman M, Hejnak V, Vachova P, Brestic M, Çığ A, Çığ F, Erman M, EL Sabagh A. CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges. Genes (Basel) 2021; 12:797. [PMID: 34073848 PMCID: PMC8225059 DOI: 10.3390/genes12060797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.
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Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Nancy Bhagat
- School of Biotechnology, University of Jammu, Jammu 180006, India;
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India;
| | | | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany Aligarh Muslim University, Aigarh 202002, India;
| | - Sajad Ali
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India;
| | | | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu 192101, India
| | - Muhammad Habib-Ur-Rahman
- Department of Crop Science, Institute of Crop Science and Resource Conservation (INRES), University Bonn, 53115 Bonn, Germany;
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Arzu Çığ
- Department of Horticulture, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey;
| | - Fatih Çığ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Murat Erman
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
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Korotkov EV, Yakovleva IV, Kamionskaya AM. Use of Mathematical Methods for the Biosafety Assessment of Agricultural Crops. APPL BIOCHEM MICRO+ 2021; 57:271-279. [PMID: 33727728 PMCID: PMC7952145 DOI: 10.1134/s000368382102006x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 12/01/2022]
Abstract
In Russia and around the world, there are important questions regarding the potential threats to national and biological safety created by genetic technologies and the need to improve or introduce new, justified, and adequate measures for their control, regulation, and prevention. The article shows that a significant volume of the global market is occupied by five major transgenic crops, and producers are ready to switch to crops with an edited genome that has been approved in the United States, Argentina, and other countries. We propose a qualitatively new approach to the risk assessment of edited plants, "Safe Design," and we have also developed an extremely important, fundamentally new approach to the development of methods that combine next-generation sequencing (NGS) and Bioinformatics for the assessment of the crop import biosafety. The proposed mathematical approach provides a detailed analysis of the possible insertions of DNA fragments into the genome of edited crops and a clarification of their biological significance. The developed method can be used in the rapid screening of plants for the presence of potentially dangerous genes, viral sequences, and nonspecific promoter sequences.
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Affiliation(s)
- E. V. Korotkov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - I. V. Yakovleva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
| | - A. M. Kamionskaya
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Sciences, 119071 Moscow, Russia
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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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Zhang Y, Iaffaldano B, Qi Y. CRISPR ribonucleoprotein-mediated genetic engineering in plants. PLANT COMMUNICATIONS 2021; 2:100168. [PMID: 33898980 PMCID: PMC8060726 DOI: 10.1016/j.xplc.2021.100168] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 05/15/2023]
Abstract
CRISPR-derived biotechnologies have revolutionized the genetic engineering field and have been widely applied in basic plant research and crop improvement. Commonly used Agrobacterium- or particle bombardment-mediated transformation approaches for the delivery of plasmid-encoded CRISPR reagents can result in the integration of exogenous recombinant DNA and potential off-target mutagenesis. Editing efficiency is also highly dependent on the design of the expression cassette and its genomic insertion site. Genetic engineering using CRISPR ribonucleoproteins (RNPs) has become an attractive approach with many advantages: DNA/transgene-free editing, minimal off-target effects, and reduced toxicity due to the rapid degradation of RNPs and the ability to titrate their dosage while maintaining high editing efficiency. Although RNP-mediated genetic engineering has been demonstrated in many plant species, its editing efficiency remains modest, and its application in many species is limited by difficulties in plant regeneration and selection. In this review, we summarize current developments and challenges in RNP-mediated genetic engineering of plants and provide future research directions to broaden the use of this technology.
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Affiliation(s)
- Yingxiao Zhang
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Brian Iaffaldano
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
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A Roadmap to Modulated Anthocyanin Compositions in Carrots. PLANTS 2021; 10:plants10030472. [PMID: 33801499 PMCID: PMC7999315 DOI: 10.3390/plants10030472] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 02/16/2021] [Accepted: 02/26/2021] [Indexed: 11/16/2022]
Abstract
Anthocyanins extracted from black carrots have received increased interest as natural colorants in recent years. The reason is mainly their high content of acylated anthocyanins that stabilizes the color and thereby increases the shelf-life of products colored with black carrot anthocyanins. Still, the main type of anthocyanins synthesized in all black carrot cultivars is cyanidin limiting their use as colorants due to the narrow color variation. Additionally, in order to be competitive against synthetic colors, a higher percentage of acylated anthocyanins and an increased anthocyanin content in black carrots are needed. However, along with the increased interest in black carrots there has also been an interest in identifying the structural and regulatory genes associated with anthocyanin biosynthesis in black carrots. Thus, huge progress in the identification of genes involved in anthocyanin biosynthesis has recently been achieved. Given this information it is now possible to attempt to modulate anthocyanin compositions in black carrots through genetic modifications. In this review we look into genetic modification opportunities for generating taproots of black carrots with extended color palettes, with a higher percentage of acylated anthocyanins or a higher total content of anthocyanins.
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