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Abstract
Genome engineering technologies enable targeted mutations to be induced at almost any location in plant genomes. In particular, Cas9 nucleases use easily recoded RNA guides to target user-defined sequences and generate double-stranded breaks (DSB) that are then repaired by the cell's endogenous repair mechanisms. Incorrect repair results in mutations at the target. When the targets are in coding sequences, this often results in loss-of-function mutations. In this chapter, we describe a method to rapidly design and assemble RNA-guided Cas9 constructs for plants and test their ability to induce mutations at their intended targets in rapid assays using both Agrobacterium-mediated transient expression and PEG-mediated DNA delivery to protoplasts, the latter of which can be adapted to a wide range of plant species. We describe a PCR-based method for detecting mutagenesis and outline the steps required to segregate the Cas9 transgene from the targeted mutation to enable the production of transgene-free mutated plants. These techniques are amenable to a range of plant species and should accelerate the application of Cas-9-mediated genome engineering for basic plant science as well as crop development.
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Sheoran S, Kaur Y, Kumar S, Shukla S, Rakshit S, Kumar R. Recent Advances for Drought Stress Tolerance in Maize ( Zea mays L.): Present Status and Future Prospects. FRONTIERS IN PLANT SCIENCE 2022; 13:872566. [PMID: 35707615 PMCID: PMC9189405 DOI: 10.3389/fpls.2022.872566] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
Drought stress has severely hampered maize production, affecting the livelihood and economics of millions of people worldwide. In the future, as a result of climate change, unpredictable weather events will become more frequent hence the implementation of adaptive strategies will be inevitable. Through utilizing different genetic and breeding approaches, efforts are in progress to develop the drought tolerance in maize. The recent approaches of genomics-assisted breeding, transcriptomics, proteomics, transgenics, and genome editing have fast-tracked enhancement for drought stress tolerance under laboratory and field conditions. Drought stress tolerance in maize could be considerably improved by combining omics technologies with novel breeding methods and high-throughput phenotyping (HTP). This review focuses on maize responses against drought, as well as novel breeding and system biology approaches applied to better understand drought tolerance mechanisms and the development of drought-tolerant maize cultivars. Researchers must disentangle the molecular and physiological bases of drought tolerance features in order to increase maize yield. Therefore, the integrated investments in field-based HTP, system biology, and sophisticated breeding methodologies are expected to help increase and stabilize maize production in the face of climate change.
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Tussipkan D, Manabayeva SA. Employing CRISPR/Cas Technology for the Improvement of Potato and Other Tuber Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:747476. [PMID: 34764969 PMCID: PMC8576567 DOI: 10.3389/fpls.2021.747476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 10/04/2021] [Indexed: 05/07/2023]
Abstract
New breeding technologies have not only revolutionized biological science, but have also been employed to generate transgene-free products. Genome editing is a powerful technology that has been used to modify genomes of several important crops. This review describes the basic mechanisms, advantages and disadvantages of genome editing systems, such as ZFNs, TALENs, and CRISPR/Cas. Secondly, we summarize in detail all studies of the CRISPR/Cas system applied to potato and other tuber crops, such as sweet potato, cassava, yam, and carrot. Genes associated with self-incompatibility, abiotic-biotic resistance, nutrient-antinutrient content, and post-harvest factors targeted utilizing the CRISPR/Cas system are analyzed in this review. We hope that this review provides fundamental information that will be useful for future breeding of tuber crops to develop novel cultivars.
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Affiliation(s)
| | - Shuga A. Manabayeva
- Plant Genetic Engineering Laboratory, National Center for Biotechnology, Nur-Sultan, Kazakhstan
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4
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Fiaz S, Wang X, Khan SA, Ahmar S, Noor MA, Riaz A, Ali K, Abbas F, Mora-Poblete F, Figueroa CR, Alharthi B. Novel plant breeding techniques to advance nitrogen use efficiency in rice: A review. GM CROPS & FOOD 2021; 12:627-646. [PMID: 34034628 PMCID: PMC9208628 DOI: 10.1080/21645698.2021.1921545] [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] [Indexed: 12/25/2022]
Abstract
Recently, there has been a remarkable increase in rice production owing to genetic improvement and increase in application of synthetic fertilizers. For sustainable agriculture, there is dire need to maintain a balance between profitability and input cost. To meet the steady growing demands of the farming community, researchers are utilizing all available resources to identify nutrient use efficient germplasm, but with very little success. Therefore, it is essential to understand the underlying genetic mechanism controlling nutrients efficiency, with the nitrogen use efficiency (NUE) being the most important trait. Information regarding genetic factors controlling nitrogen (N) transporters, assimilators, and remobilizers can help to identify candidate germplasms via high-throughput technologies. Large-scale field trials have provided morphological, physiological, and biochemical trait data for the detection of genomic regions controlling NUE. The functional aspects of these attributes are time-consuming, costly, labor-intensive, and less accurate. Therefore, the application of novel plant breeding techniques (NPBTs) with context to genome engineering has opened new avenues of research for crop improvement programs. Most recently, genome editing technologies (GETs) have undergone enormous development with various versions from Cas9, Cpf1, base, and prime editing. These GETs have been vigorously adapted in plant sciences for novel trait development to insure food quantity and quality. Base editing has been successfully applied to improve NUE in rice, demonstrating the potential of GETs to develop germplasms with improved resource use efficiency. NPBTs continue to face regulatory setbacks in some countries due to genome editing being categorized in the same category as genetically modified (GM) crops. Therefore, it is essential to involve all stakeholders in a detailed discussion on NPBTs and to formulate uniform policies tackling biosafety, social, ethical, and environmental concerns. In the current review, we have discussed the genetic mechanism of NUE and NPBTs for crop improvement programs with proof of concepts, transgenic and GET application for the development of NUE germplasms, and regulatory aspects of genome edited crops with future directions considering NUE.
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Affiliation(s)
- Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an, Shaanxi, China
| | - Sher Aslam Khan
- Department of Plant Breeding and Genetics, The University of Haripur 22620, Khyber, Pakhtunkhwa, Pakistan
| | - Sunny Ahmar
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Mehmood Ali Noor
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Crop Physiology and Ecology, Ministry of Agriculture, Beijing, China
| | - Aamir Riaz
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, Zhejiang, China
| | - Kazim Ali
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Islamabad, Pakistan
| | - Farhat Abbas
- Research Center for Ornamental Plants, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Carlos R Figueroa
- Institute of Biological Sciences, Campus Talca, Universidad deTalca, Talca, Chile
| | - Badr Alharthi
- College of Khurma, Taif University, Taif, Saudi Arabia.,College of Science and Engineering, Flinders University, Adelaide, South Australia
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Kaul T, Sony SK, Verma R, Motelb KFA, Prakash AT, Eswaran M, Bharti J, Nehra M, Kaul R. Revisiting CRISPR/Cas-mediated crop improvement: Special focus on nutrition. J Biosci 2020. [DOI: 10.1007/s12038-020-00094-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Joshi RK, Bharat SS, Mishra R. Engineering drought tolerance in plants through CRISPR/Cas genome editing. 3 Biotech 2020; 10:400. [PMID: 32864285 PMCID: PMC7438458 DOI: 10.1007/s13205-020-02390-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
Drought stress is primarily responsible for heavy yield losses and productivity in major crops and possesses the greatest threat to the global food security. While conventional and molecular breeding approaches along with genetic engineering techniques have been instrumental in developing drought-tolerant crop varieties, these methods are cumbersome, time consuming and the genetically modified varieties are not widely accepted due to regulatory concerns. Plant breeders are now increasingly centring towards the recently available genome-editing tools for improvement of agriculturally important traits. The advent of multiple sequence-specific nucleases has facilitated precise gene modification towards development of novel climate ready crop variants. Amongst the available genome-editing platforms, the clustered regularly interspaced short palindromic repeat-Cas (CRISPR/Cas) system has emerged as a revolutionary tool for its simplicity, adaptability, flexibility and wide applicability. In this review, we focus on understanding the molecular mechanism of drought response in plants and the application of CRISPR/Cas genome-editing system towards improved tolerance to drought stress.
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Affiliation(s)
- Raj Kumar Joshi
- Department of Biotechnology, Rama Devi Women’s University, Vidya Vihar, Bhubaneswar, Odisha India
| | - Suhas Sutar Bharat
- National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing, 100081 China
| | - Rukmini Mishra
- School of Applied Sciences, Centurion University of Technology and Management, Bhubaneswar, Odisha India
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Eriksson D, Kershen D, Nepomuceno A, Pogson BJ, Prieto H, Purnhagen K, Smyth S, Wesseler J, Whelan A. A comparison of the EU regulatory approach to directed mutagenesis with that of other jurisdictions, consequences for international trade and potential steps forward. THE NEW PHYTOLOGIST 2019; 222:1673-1684. [PMID: 30548610 DOI: 10.1111/nph.15627] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/02/2018] [Indexed: 05/11/2023]
Abstract
A special regulatory regime applies to products of recombinant nucleic acid modifications. A ruling from the European Court of Justice has interpreted this regulatory regime in a way that it also applies to emerging mutagenesis techniques. Elsewhere regulatory progress is also ongoing. In 2015, Argentina launched a regulatory framework, followed by Chile in 2017 and recently Brazil and Colombia. In March 2018, the USDA announced that it will not regulate genome-edited plants differently if they could have also been developed through traditional breeding. Canada has an altogether different approach with their Plants with Novel Traits regulations. Australia is currently reviewing its Gene Technology Act. This article illustrates the deviation of the European Union's (EU's) approach from the one of most of the other countries studied here. Whereas the EU does not implement a case-by-case approach, this approach is taken by several other jurisdictions. Also, the EU court ruling adheres to a process-based approach while most other countries have a stronger emphasis on the regulation of the resulting product. It is concluded that, unless a functioning identity preservation system for products of directed mutagenesis can be established, the deviation results in a risk of asynchronous approvals and disruptions in international trade.
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Affiliation(s)
- Dennis Eriksson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden
| | - Drew Kershen
- College of Law, University of Oklahoma, 300 Timberdell Road, Norman, OK, 73019-5081, USA
| | - Alexandre Nepomuceno
- Brazilian Agricultural Research Cooperation - Embrapa, Brazilian Biosafety Technical Commission - CTNBio, PO Box 231, ZIP 86001-970, Londrina, PR, Brazil
| | - Barry J Pogson
- Global Plant Council and ARC Centre of Excellence in Plant Energy Biology, Australian National University, Canberra, 2601, ACT, Australia
| | - Humberto Prieto
- Biotechnology Laboratory, La Platina Station, Instituto de Investigaciones Agropecuarias, Santa Rosa 11610, La Pintana, Santiago de Chile, Chile
| | - Kai Purnhagen
- Law and Governance Group, Department of Social Sciences, Wageningen University, Hollandseweg 1, 6706 KN, Wageningen, the Netherlands
- Rotterdam Institute of Law and Economics, Law School, Erasmus University of Rotterdam, Burg. Oudlaan 50, 3062 PA, Rotterdam, the Netherlands
| | - Stuart Smyth
- Department of Agricultural and Resource Economics, University of Saskatchewan, 51 Campus Drive, Saskatoon, Sask., S7N 5A8, Canada
| | - Justus Wesseler
- Agricultural Economics and Rural Policy Group, Department of Social Sciences, Wageningen University, Hollandseweg 1, 6706 KN, Wageningen, the Netherlands
| | - Agustina Whelan
- Biotechnology Directorate, Ministry of AgroIndustry, Buenos Aires, Argentina
- National University of Quilmes, Bernal, Argentina
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Hinchliffe A, Harwood WA. Agrobacterium-Mediated Transformation of Barley Immature Embryos. Methods Mol Biol 2019; 1900:115-126. [PMID: 30460562 DOI: 10.1007/978-1-4939-8944-7_8] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Barley transformation is an essential tool for a range of functional genomics studies as well as for future crop improvement. The demand for efficient crop transformation systems continues to grow, with new genome editing technologies adding to that demand. Here we describe an efficient and routine transformation protocol for the spring barley Golden Promise, based on Agrobacterium-mediated inoculation of immature embryos. This protocol has been widely used for overexpression and RNAi applications and more recently for CRISPR/Cas9 mediated genome editing. Average transformation efficiencies of 25% can be easily achieved.
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Affiliation(s)
- Alison Hinchliffe
- Crop Transformation Group, Department of Crop Genetics, John Innes Centre, Norwich, UK
| | - Wendy A Harwood
- Crop Transformation Group, Department of Crop Genetics, John Innes Centre, Norwich, UK.
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Eriksson D. The Swedish policy approach to directed mutagenesis in a European context. PHYSIOLOGIA PLANTARUM 2018; 164:385-395. [PMID: 29602252 DOI: 10.1111/ppl.12740] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/22/2018] [Accepted: 03/25/2018] [Indexed: 05/29/2023]
Abstract
This review describes the Swedish approach to directed mutagenesis in plants and puts it in a comparative European perspective. Directed mutagenesis is accomplished by a number of genome editing techniques; however, the legal status of these techniques and their resulting products is uncertain in the European Union (EU) as there is no political consensus on whether or not these should be regulated as genetically modified organisms (GMOs). A number of cases have developed over the past few years, putting the GMO regulatory framework to the test. These include oilseed rape developed by oligonucleotide-directed mutagenesis, Arabidopsis developed by clustered regularly interspaced short palindromic repeat-Cas9, and the case on mutagenesis for which the French Court requested a preliminary ruling from the Court of Justice of the EU. In this review, the involvement of the Swedish Government and governmental authorities in these cases is described and compared with that of other EU member states and/or EU entity statements and reports. Various approaches to the definition of recombinant nucleic acids are also discussed, as this is crucial for the EU GMO definition thus affecting the legal status of products developed by directed mutagenesis.
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Affiliation(s)
- Dennis Eriksson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 101, Alnarp, Sweden
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10
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Abstract
Genome-editing tools provide advanced biotechnological techniques that enable the precise and efficient targeted modification of an organism's genome. Genome-editing systems have been utilized in a wide variety of plant species to characterize gene functions and improve agricultural traits. We describe the current applications of genome editing in plants, focusing on its potential for crop improvement in terms of adaptation, resilience, and end-use. In addition, we review novel breakthroughs that are extending the potential of genome-edited crops and the possibilities of their commercialization. Future prospects for integrating this revolutionary technology with conventional and new-age crop breeding strategies are also discussed.
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Affiliation(s)
- Yi Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Karen Massel
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, QLD, 4072, Australia
| | - Ian D Godwin
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, QLD, 4072, Australia
| | - Caixia Gao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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11
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Zhang Y, Massel K, Godwin ID, Gao C. Applications and potential of genome editing in crop improvement. Genome Biol 2018. [PMID: 30501614 DOI: 10.1186/s13059-018-1586] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023] Open
Abstract
Genome-editing tools provide advanced biotechnological techniques that enable the precise and efficient targeted modification of an organism's genome. Genome-editing systems have been utilized in a wide variety of plant species to characterize gene functions and improve agricultural traits. We describe the current applications of genome editing in plants, focusing on its potential for crop improvement in terms of adaptation, resilience, and end-use. In addition, we review novel breakthroughs that are extending the potential of genome-edited crops and the possibilities of their commercialization. Future prospects for integrating this revolutionary technology with conventional and new-age crop breeding strategies are also discussed.
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Affiliation(s)
- Yi Zhang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Science, Shandong Normal University, Jinan, 250014, China
| | - Karen Massel
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, QLD, 4072, Australia
| | - Ian D Godwin
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, QLD, 4072, Australia
| | - Caixia Gao
- The State Key Laboratory of Plant Cell and Chromosome Engineering, and Center for Genome Editing, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Vazquez-Vilar M, Orzaez D, Patron N. DNA assembly standards: Setting the low-level programming code for plant biotechnology. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 273:33-41. [PMID: 29907307 DOI: 10.1016/j.plantsci.2018.02.024] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 02/23/2018] [Accepted: 02/26/2018] [Indexed: 05/28/2023]
Abstract
Synthetic Biology is defined as the application of engineering principles to biology. It aims to increase the speed, ease and predictability with which desirable changes and novel traits can be conferred to living cells. The initial steps in this process aim to simplify the encoding of new instructions in DNA by establishing low-level programming languages for biology. Together with advances in the laboratory that allow multiple DNA molecules to be efficiently assembled together into a desired order in a single step, this approach has simplified the design and assembly of multigene constructs and has even facilitated the automated construction of synthetic chromosomes. These advances and technologies are now being applied to plants, for which there are a growing number of software and wetware tools for the design, construction and delivery of DNA molecules and for the engineering of endogenous genes. Here we review the efforts of the past decade that have established synthetic biology workflows and tools for plants and discuss the constraints and bottlenecks of this emerging field.
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Affiliation(s)
- Marta Vazquez-Vilar
- Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, Wageningen, 6708WE, The Netherlands
| | - Diego Orzaez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Spain.
| | - Nicola Patron
- Department of Engineering Biology, The Earlham Institute, Norwich Research Park, Norfolk, NR1 7UZ, UK.
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