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Reka D, Girish C. Plant-based vaccines against viral hepatitis: A panoptic review. World J Virol 2024; 13:97162. [PMID: 39323445 PMCID: PMC11401004 DOI: 10.5501/wjv.v13.i3.97162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 07/19/2024] [Accepted: 08/08/2024] [Indexed: 08/29/2024] Open
Abstract
The traditional vaccines against hepatitis have been instrumental in reducing the incidence of some types of viral hepatitis; however, the need for cost-effective, easily distributable, and needle-free vaccine alternatives has led to the exploration of plant-based vaccines. Plant-based techniques offer a promising avenue for producing viral hepatitis vaccines due to their low-cost cultivation, scalability, and the potential for oral administration. This review highlights the successful expression of hepatitis B surface antigens in plants and the subsequent formation of virus-like particles, which have shown immunogenicity in preclinical and clinical trials. The challenges such as achieving sufficient antigen expression levels, ensuring consistent dosing, and navigating regulatory frameworks, are addressed. The review considers the potential of plant-based vaccines to meet the demands of rapid vaccine deployment in response to outbreaks and their role in global immunization strategies, particularly in resource-limited settings. This review underscores the significant strides made in plant molecular farming and the potential of plant-based vaccines to complement existing immunization methods against viral hepatitis.
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Affiliation(s)
- Devanathan Reka
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605006, India
| | - Chandrashekaran Girish
- Department of Pharmacology, Jawaharlal Institute of Postgraduate Medical Education and Research, Puducherry 605006, India
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2
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Masani MYA, Norfaezah J, Bahariah B, Fizree MDPMAA, Sulaiman WNSW, Shaharuddin NA, Rasid OA, Parveez GKA. Towards DNA-free CRISPR/Cas9 genome editing for sustainable oil palm improvement. 3 Biotech 2024; 14:166. [PMID: 38817736 PMCID: PMC11133284 DOI: 10.1007/s13205-024-04010-w] [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: 01/04/2024] [Accepted: 05/18/2024] [Indexed: 06/01/2024] Open
Abstract
The CRISPR/Cas9 genome editing system has been in the spotlight compared to programmable nucleases such as ZFNs and TALENs due to its simplicity, versatility, and high efficiency. CRISPR/Cas9 has revolutionized plant genetic engineering and is broadly used to edit various plants' genomes, including those transformation-recalcitrant species such as oil palm. This review will comprehensively present the CRISPR-Cas9 system's brief history and underlying mechanisms. We then highlighted the establishment of the CRISPR/Cas9 system in plants with an emphasis on the strategies of highly efficient guide RNA design, the establishment of various CRISPR/Cas9 vector systems, approaches of multiplex editing, methods of transformation for stable and transient techniques, available methods for detecting and analyzing mutations, which have been applied and could be adopted for CRISPR/Cas9 genome editing in oil palm. In addition, we also provide insight into the strategy of DNA-free genome editing and its potential application in oil palm.
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Affiliation(s)
- Mat Yunus Abdul Masani
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Jamaludin Norfaezah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Bohari Bahariah
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | - Noor Azmi Shaharuddin
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, 43400 Serdang, Malaysia
| | - Omar Abdul Rasid
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ghulam Kadir Ahmad Parveez
- Malaysian Palm Oil Board (MPOB), 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
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Williams K, Subramani M, Lofton LW, Penney M, Todd A, Ozbay G. Tools and Techniques to Accelerate Crop Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:1520. [PMID: 38891328 PMCID: PMC11174677 DOI: 10.3390/plants13111520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/25/2024] [Accepted: 05/30/2024] [Indexed: 06/21/2024]
Abstract
As climate changes and a growing global population continue to escalate the need for greater production capabilities of food crops, technological advances in agricultural and crop research will remain a necessity. While great advances in crop improvement over the past century have contributed to massive increases in yield, classic breeding schemes lack the rate of genetic gain needed to meet future demands. In the past decade, new breeding techniques and tools have been developed to aid in crop improvement. One such advancement is the use of speed breeding. Speed breeding is known as the application of methods that significantly reduce the time between crop generations, thereby streamlining breeding and research efforts. These rapid-generation advancement tactics help to accelerate the pace of crop improvement efforts to sustain food security and meet the food, feed, and fiber demands of the world's growing population. Speed breeding may be achieved through a variety of techniques, including environmental optimization, genomic selection, CRISPR-Cas9 technology, and epigenomic tools. This review aims to discuss these prominent advances in crop breeding technologies and techniques that have the potential to greatly improve plant breeders' ability to rapidly produce vital cultivars.
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Affiliation(s)
- Krystal Williams
- Molecular Genetics and Epigenomics Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA;
| | - Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA;
| | - Lily W. Lofton
- Department of Plant Pathology, University of Georgia, Athens, GA 30602, USA;
- Toxicology & Mycotoxin Research Unit, US National Poultry Research Center, USDA-ARS, Athens, GA 30602, USA
| | - Miranda Penney
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA;
| | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA;
| | - Gulnihal Ozbay
- One Health Laboratory, Department of Agriculture and Natural Resources, College of Agriculture, Science, and Technology, Delaware State University, Dover, DE 19901, USA
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Bélanger JG, Copley TR, Hoyos-Villegas V, Charron JB, O'Donoughue L. A comprehensive review of in planta stable transformation strategies. PLANT METHODS 2024; 20:79. [PMID: 38822403 PMCID: PMC11140912 DOI: 10.1186/s13007-024-01200-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/01/2024] [Indexed: 06/03/2024]
Abstract
Plant transformation remains a major bottleneck to the improvement of plant science, both on fundamental and practical levels. The recalcitrant nature of most commercial and minor crops to genetic transformation slows scientific progress for a large range of crops that are essential for food security on a global scale. Over the years, novel stable transformation strategies loosely grouped under the term "in planta" have been proposed and validated in a large number of model (e.g. Arabidopsis and rice), major (e.g. wheat and soybean) and minor (e.g. chickpea and lablab bean) species. The in planta approach is revolutionary as it is considered genotype-independent, technically simple (i.e. devoid of or with minimal tissue culture steps), affordable, and easy to implement in a broad range of experimental settings. In this article, we reviewed and categorized over 300 research articles, patents, theses, and videos demonstrating the applicability of different in planta transformation strategies in 105 different genera across 139 plant species. To support this review process, we propose a classification system for the in planta techniques based on five categories and a new nomenclature for more than 30 different in planta techniques. In complement to this, we clarified some grey areas regarding the in planta conceptual framework and provided insights regarding the past, current, and future scientific impacts of these techniques. To support the diffusion of this concept across the community, this review article will serve as an introductory point for an online compendium about in planta transformation strategies that will be available to all scientists. By expanding our knowledge about in planta transformation, we can find innovative approaches to unlock the full potential of plants, support the growth of scientific knowledge, and stimulate an equitable development of plant research in all countries and institutions.
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Affiliation(s)
- Jérôme Gélinas Bélanger
- Centre de recherche sur les grains (CÉROM) Inc., 740 Chemin Trudeau, St-Mathieu-de-Beloeil, Québec, J3G 0E2, Canada.
- Department of Plant Science, McGill University, 21111 Lakeshore Road, St-Mathieu-de-Beloeil, Montréal, Québec, H9X 3V9, Canada.
| | - Tanya Rose Copley
- Centre de recherche sur les grains (CÉROM) Inc., 740 Chemin Trudeau, St-Mathieu-de-Beloeil, Québec, J3G 0E2, Canada
| | - Valerio Hoyos-Villegas
- Department of Plant Science, McGill University, 21111 Lakeshore Road, St-Mathieu-de-Beloeil, Montréal, Québec, H9X 3V9, Canada
| | - Jean-Benoit Charron
- Department of Plant Science, McGill University, 21111 Lakeshore Road, St-Mathieu-de-Beloeil, Montréal, Québec, H9X 3V9, Canada
| | - Louise O'Donoughue
- Centre de recherche sur les grains (CÉROM) Inc., 740 Chemin Trudeau, St-Mathieu-de-Beloeil, Québec, J3G 0E2, Canada.
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5
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Kumar S, Vishwakarma H, Ghosh G, Singh J, Padaria JC. In planta transformation in wheat: an improved protocol to develop wheat transformants. Mol Biol Rep 2024; 51:407. [PMID: 38460010 DOI: 10.1007/s11033-024-09333-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/07/2024] [Indexed: 03/11/2024]
Abstract
BACKGROUND Lack of efficient transformation protocol continues to be a major bottleneck for successful genome editing or transgenic development in wheat. An in planta transformation method was developed in Indian bread wheat in earlier study (Vasil et al. in Nat Biotechnol 10:667-674, 1992) which was labour-intensive and time-consuming. In the present study, in planta transformation method was improved to make it simple, efficient, less labour-intensive and time-saving. METHODS AND RESULTS PCR-based screening for generated transformants at T0 stage was introduced in this method. Shoot apical meristem of two days old wheat seedling was inoculated with the routine active culture of Agrobacterium tumefaciens harboring plasmid pCAMBIA1300-Ubi-GFP having gene GFP under the control of Zea mays ubiquitin promoter. PCR analysis at T0 stage confirmed 27 plants to be transgene positive. These 27 plants were only taken to the next generation (T1) and the rest were discarded. At T1 generation 6 plants were analyzed to be PCR positive. Out of them, 4 plants were confirmed to have stable integration of transgene (GFP). Fluorescent microscopy at T1 stage confirmed the 4 Southern hybridization positive plants to be expressing reporter gene GFP. CONCLUSIONS Screening at T0 stage, reduced the load of plants to be taken to T1 generation and their screening thereof at T1 with no overall loss in transformation efficiency. We successfully transformed wheat genotype HD2894 with 3.33% transformation efficiency using a simple, effective method which was less labour-intensive and less time-consuming. This method may be utilized to develop wheat transgenic as well as genome edited lines for desirable traits.
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Affiliation(s)
- Satish Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Harinder Vishwakarma
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Gourab Ghosh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Jaskirat Singh
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
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Luo W, Liu Y, Imai R. In Planta Genome Editing in Commercial Wheat Varieties: Use of TaQsd1 to Lengthen Seed Dormancy. Methods Mol Biol 2024; 2830:163-171. [PMID: 38977577 DOI: 10.1007/978-1-0716-3965-8_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Dependency on in vitro culture and regeneration limits the ability to use genome editing on elite wheat (Triticum aestivum L.) varieties. We recently developed an in planta particle bombardment (iPB) technique for gene editing in wheat that utilizes shoot apical meristems (SAMs) as a target tissue. Since the method does not require in vitro culture, it can therefore be used on recalcitrant varieties. In this chapter, we describe in detail the steps used in the iPB method. With this protocol, 3% to 5% of T0 plants grown from bombarded SAMs typically carry mutant alleles and approximately 1% to 2% of the T0 plants inherit mutant alleles in the next generation.
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Affiliation(s)
- Weifeng Luo
- Division of Crop Genome Editing, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Yuelin Liu
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, China
| | - Ryozo Imai
- Division of Crop Genome Editing, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan.
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Ahmar S, Hensel G, Gruszka D. CRISPR/Cas9-mediated genome editing techniques and new breeding strategies in cereals - current status, improvements, and perspectives. Biotechnol Adv 2023; 69:108248. [PMID: 37666372 DOI: 10.1016/j.biotechadv.2023.108248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/06/2023]
Abstract
Cereal crops, including triticeae species (barley, wheat, rye), as well as edible cereals (wheat, corn, rice, oat, rye, sorghum), are significant suppliers for human consumption, livestock feed, and breweries. Over the past half-century, modern varieties of cereal crops with increased yields have contributed to global food security. However, presently cultivated elite crop varieties were developed mainly for optimal environmental conditions. Thus, it has become evident that taking into account the ongoing climate changes, currently a priority should be given to developing new stress-tolerant cereal cultivars. It is necessary to enhance the accuracy of methods and time required to generate new cereal cultivars with the desired features to adapt to climate change and keep up with the world population expansion. The CRISPR/Cas9 system has been developed as a powerful and versatile genome editing tool to achieve desirable traits, such as developing high-yielding, stress-tolerant, and disease-resistant transgene-free lines in major cereals. Despite recent advances, the CRISPR/Cas9 application in cereals faces several challenges, including a significant amount of time required to develop transgene-free lines, laboriousness, and a limited number of genotypes that may be used for the transformation and in vitro regeneration. Additionally, developing elite lines through genome editing has been restricted in many countries, especially Europe and New Zealand, due to a lack of flexibility in GMO regulations. This review provides a comprehensive update to researchers interested in improving cereals using gene-editing technologies, such as CRISPR/Cas9. We will review some critical and recent studies on crop improvements and their contributing factors to superior cereals through gene-editing technologies.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Duesseldorf, Germany; Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, Olomouc, Czech Republic
| | - Damian Gruszka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia, Katowice, Poland.
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Animasaun DA, Lawrence JA. Antisense RNA (asRNA) technology: the concept and applications in crop improvement and sustainable agriculture. Mol Biol Rep 2023; 50:9545-9557. [PMID: 37755651 DOI: 10.1007/s11033-023-08814-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 09/11/2023] [Indexed: 09/28/2023]
Abstract
Antisense RNA (asRNA) technology is a method used to silence genes and inhibit their expression. Gene function relies on expression, which follows the central dogma of molecular biology. The use of asRNA can regulate gene expression by targeting specific mRNAs, which can result in changes in phenotype, disease resistance, and other traits associated with protein expression profiles. This technology uses short, single-stranded oligonucleotide strands that are complementary to the targeted mRNA. Manipulating and regulating protein expression during its translation can either knock out or knock down the expression of a gene of interest. Therefore, functional genomics can benefit from this technology since it allows for the regulation of protein expression. In this review, we discuss the concept, and applications of asRNA technology which include delaying ripening, prolonging shelf life, biofortification, and increasing biotic and abiotic resistance among others in crop improvement and sustainable agriculture.
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Affiliation(s)
- David Adedayo Animasaun
- Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, Kwara State, Nigeria.
- Plant Tissue Culture Lab, Central Research Laboratories, University of Ilorin, P.M.B.1515, Ilorin, Kwara State, Nigeria.
| | - Judith Amaka Lawrence
- Department of Plant Biology, Faculty of Life Sciences, University of Ilorin, P.M.B. 1515, Ilorin, Kwara State, Nigeria.
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Nishihara M, Muranaka T. Preface to the special issue "Current Status and Future Prospects for the Development of Crop Varieties and Breeding Materials Using Genome Editing Technology". PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:181-184. [PMID: 38293252 PMCID: PMC10824492 DOI: 10.5511/plantbiotechnology.23.0000p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Affiliation(s)
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan
- Institution for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka 565-0871, Japan
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10
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Kocsisova Z, Coneva V. Strategies for delivery of CRISPR/Cas-mediated genome editing to obtain edited plants directly without transgene integration. Front Genome Ed 2023; 5:1209586. [PMID: 37545761 PMCID: PMC10398581 DOI: 10.3389/fgeed.2023.1209586] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 06/28/2023] [Indexed: 08/08/2023] Open
Abstract
Increased understanding of plant genetics and the development of powerful and easier-to-use gene editing tools over the past century have revolutionized humankind's ability to deliver precise genotypes in crops. Plant transformation techniques are well developed for making transgenic varieties in certain crops and model organisms, yet reagent delivery and plant regeneration remain key bottlenecks to applying the technology of gene editing to most crops. Typical plant transformation protocols to produce transgenic, genetically modified (GM) varieties rely on transgenes, chemical selection, and tissue culture. Typical protocols to make gene edited (GE) varieties also use transgenes, even though these may be undesirable in the final crop product. In some crops, the transgenes are routinely segregated away during meiosis by performing crosses, and thus only a minor concern. In other crops, particularly those propagated vegetatively, complex hybrids, or crops with long generation times, such crosses are impractical or impossible. This review highlights diverse strategies to deliver CRISPR/Cas gene editing reagents to regenerable plant cells and to recover edited plants without unwanted integration of transgenes. Some examples include delivering DNA-free gene editing reagents such as ribonucleoproteins or mRNA, relying on reagent expression from non-integrated DNA, using novel delivery mechanisms such as viruses or nanoparticles, using unconventional selection methods to avoid integration of transgenes, and/or avoiding tissue culture altogether. These methods are advancing rapidly and already enabling crop scientists to make use of the precision of CRISPR gene editing tools.
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Khoo YW, Chong KP. Ganoderma boninense: general characteristics of pathogenicity and methods of control. FRONTIERS IN PLANT SCIENCE 2023; 14:1156869. [PMID: 37492765 PMCID: PMC10363743 DOI: 10.3389/fpls.2023.1156869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 06/23/2023] [Indexed: 07/27/2023]
Abstract
Ganoderma boninense (G. boninense) is a soil-borne fungus threatening oil palm at the present. It causes basal stem rot disease on oil palm. Within six months, this fungus can cause an oil palm plantation to suffer a significant 43% economic loss. The high persistence and nature of spread of G. boninense in soil make control of the disease challenging. Therefore, controlling the pathogen requires a thorough understanding of the mechanisms that underlie pathogenicity as well as its interactions with host plants. In this paper, we present the general characteristics, the pathogenic mechanisms, and the host's defensive system of G. boninense. We also review upcoming and most promising techniques for disease management that will have the least negative effects on the environment and natural resources.
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Affiliation(s)
- Ying Wei Khoo
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
| | - Khim Phin Chong
- Faculty of Science and Natural Resources, Universiti Malaysia Sabah, Kota Kinabalu, Sabah, Malaysia
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Sasaki K, Tanaka T. Overcoming Difficulties in Molecular Biological Analysis through a Combination of Genetic Engineering, Genome Editing, and Genome Analysis in Hexaploid Chrysanthemum morifolium. PLANTS (BASEL, SWITZERLAND) 2023; 12:2566. [PMID: 37447127 DOI: 10.3390/plants12132566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 06/11/2023] [Accepted: 06/29/2023] [Indexed: 07/15/2023]
Abstract
Chrysanthemum is one of the most commercially important ornamental plants globally, of which many new varieties are produced annually. Among these new varieties, many are the result of crossbreeding, while some are the result of mutation breeding. Recent advances in gene and genome sequencing technology have raised expectations about the use of biotechnology and genome breeding to efficiently breed new varieties. However, some features of chrysanthemum complicate molecular biological analysis. For example, chrysanthemum is a hexaploid hyperploid plant with a large genome, while its genome is heterogeneous because of the difficulty of obtaining pure lines due to self-incompatibility. Despite these difficulties, an increased number of reports on transcriptome analysis in chrysanthemum have been published as a result of recent technological advances in gene sequencing, which should deepen our understanding of the properties of these plants. In this review, we discuss recent studies using gene engineering, genome editing, and genome analysis, including transcriptome analysis, to analyze chrysanthemum, as well as the current status of and future prospects for chrysanthemum.
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Affiliation(s)
- Katsutomo Sasaki
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 2-1 Fujimoto, Tsukuba 305-0852, Ibaraki, Japan
| | - Tsuyoshi Tanaka
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8518, Ibaraki, Japan
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13
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Ye X, Shrawat A, Moeller L, Rode R, Rivlin A, Kelm D, Martinell BJ, Williams EJ, Paisley A, Duncan DR, Armstrong CL. Agrobacterium-mediated direct transformation of wheat mature embryos through organogenesis. FRONTIERS IN PLANT SCIENCE 2023; 14:1202235. [PMID: 37324676 PMCID: PMC10264787 DOI: 10.3389/fpls.2023.1202235] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/11/2023] [Indexed: 06/17/2023]
Abstract
Transgenic plant production in monocotyledonous species has primarily relied on embryogenic callus induction from both immature and mature embryos as the pathway for plant regeneration. We have efficiently regenerated fertile transgenic wheat plants through organogenesis after Agrobacterium-mediated direct transformation of mechanically isolated mature embryos from field-grown seed. Centrifugation of the mature embryos in the presence of Agrobacterium was found to be essential for efficient T-DNA delivery to the relevant regenerable cells. The inoculated mature embryos formed multiple buds/shoots on high-cytokinin medium, which directly regenerated into transgenic shoots on hormone-free medium containing glyphosate for selection. Rooted transgenic plantlets were obtained within 10-12 weeks after inoculation. Further optimization of this transformation protocol resulted in significant reduction of chimeric plants to below 5%, as indicated by leaf GUS staining and T1 transgene segregation analysis. Direct transformation of wheat mature embryos has substantial advantages over traditional immature embryo-based transformation systems, including long-term storability of the mature dry explants, scalability, and greatly improved flexibility and consistency in transformation experiments.
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14
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Luo W, Suzuki R, Imai R. Precise in planta genome editing via homology-directed repair in wheat. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:668-670. [PMID: 36529912 PMCID: PMC10037140 DOI: 10.1111/pbi.13984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/25/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Affiliation(s)
- Weifeng Luo
- Genome‐Edited Crop Development Group, Institute of Agrobiological SciencesNational Agriculture and Food Research Organization (NARO)TsukubaJapan
| | - Rintaro Suzuki
- Genome‐Edited Crop Development Group, Institute of Agrobiological SciencesNational Agriculture and Food Research Organization (NARO)TsukubaJapan
| | - Ryozo Imai
- Genome‐Edited Crop Development Group, Institute of Agrobiological SciencesNational Agriculture and Food Research Organization (NARO)TsukubaJapan
- Faculty of Life and Environmental SciencesUniversity of TsukubaTsukubaJapan
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15
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Pandey K, Karthik K, Singh SK, Vinod, Sreevathsa R, Srivastav M. Amenability of an Agrobacterium tumefaciens-mediated shoot apical meristem-targeted in planta transformation strategy in Mango ( Mangifera indica L.). GM CROPS & FOOD 2022; 13:342-354. [DOI: 10.1080/21645698.2022.2141014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Kuldeep Pandey
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kesiraju Karthik
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rohini Sreevathsa
- ICAR-National Institute for Plant Biotechnology, Lal Bahadur Shastri Building, Pusa Campus, New Delhi, India
| | - Manish Srivastav
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Wang Y, Zeng J, Su P, Zhao H, Li L, Xie X, Zhang Q, Wu Y, Wang R, Zhang Y, Yu B, Chen M, Wang Y, Yang G, He G, Chang J, Li Y. An established protocol for generating transgenic wheat for wheat functional genomics via particle bombardment. FRONTIERS IN PLANT SCIENCE 2022; 13:979540. [PMID: 36570946 PMCID: PMC9772560 DOI: 10.3389/fpls.2022.979540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 11/16/2022] [Indexed: 06/17/2023]
Abstract
Wheat is one of the most important food crops in the world and is considered one of the top targets in crop biotechnology. With the high-quality reference genomes of wheat and its relative species and the recent burst of genomic resources in Triticeae, demands to perform gene functional studies in wheat and genetic improvement have been rapidly increasing, requiring that production of transgenic wheat should become a routine technique. While established for more than 20 years, the particle bombardment-mediated wheat transformation has not become routine yet, with only a handful of labs being proficient in this technique. This could be due to, at least partly, the low transformation efficiency and the technical difficulties. Here, we describe the current version of this method through adaptation and optimization. We report the detailed protocol of producing transgenic wheat by the particle gun, including several critical steps, from the selection of appropriate explants (i.e., immature scutella), the preparation of DNA-coated gold particles, and several established strategies of tissue culture. More importantly, with over 20 years of experience in wheat transformation in our lab, we share the many technical details and recommendations and emphasize that the particle bombardment-mediated approach has fewer limitations in genotype dependency and vector construction when compared with the Agrobacterium-mediated methods. The particle bombardment-mediated method has been successful for over 30 wheat genotypes, from the tetraploid durum wheat to the hexaploid common wheat, from modern elite varieties to landraces. In conclusion, the particle bombardment-mediated wheat transformation has demonstrated its potential and wide applications, and the full set of protocol, experience, and successful reports in many wheat genotypes described here will further its impacts, making it a routine and robust technique in crop research labs worldwide.
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Affiliation(s)
- Yaqiong Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Jian Zeng
- Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern Region, Shaoguan University, Shaoguan, Guangdong, China
| | - Peipei Su
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Hongyan Zhao
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Li Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Xiaoxue Xie
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Qian Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Ya’nan Wu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Ruibin Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Yufan Zhang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Boju Yu
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Mingjie Chen
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Yuesheng Wang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Guangxiao Yang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Guangyuan He
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Junli Chang
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
| | - Yin Li
- The Genetic Engineering International Cooperation Base of Chinese Ministry of Science and Technology, The Key Laboratory of Molecular Biophysics of Chinese Ministry of Education, College of Life Science and Technology, Huazhong University of Science & Technology, Wuhan, China
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Ahmad M. Genomics and transcriptomics to protect rice ( Oryza sativa. L.) from abiotic stressors: -pathways to achieving zero hunger. FRONTIERS IN PLANT SCIENCE 2022; 13:1002596. [PMID: 36340401 PMCID: PMC9630331 DOI: 10.3389/fpls.2022.1002596] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
More over half of the world's population depends on rice as a major food crop. Rice (Oryza sativa L.) is vulnerable to abiotic challenges including drought, cold, and salinity since it grown in semi-aquatic, tropical, or subtropical settings. Abiotic stress resistance has bred into rice plants since the earliest rice cultivation techniques. Prior to the discovery of the genome, abiotic stress-related genes were identified using forward genetic methods, and abiotic stress-tolerant lines have developed using traditional breeding methods. Dynamic transcriptome expression represents the degree of gene expression in a specific cell, tissue, or organ of an individual organism at a specific point in its growth and development. Transcriptomics can reveal the expression at the entire genome level during stressful conditions from the entire transcriptional level, which can be helpful in understanding the intricate regulatory network relating to the stress tolerance and adaptability of plants. Rice (Oryza sativa L.) gene families found comparatively using the reference genome sequences of other plant species, allowing for genome-wide identification. Transcriptomics via gene expression profiling which have recently dominated by RNA-seq complements genomic techniques. The identification of numerous important qtl,s genes, promoter elements, transcription factors and miRNAs involved in rice response to abiotic stress was made possible by all of these genomic and transcriptomic techniques. The use of several genomes and transcriptome methodologies to comprehend rice (Oryza sativa, L.) ability to withstand abiotic stress have been discussed in this review.
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Affiliation(s)
- Mushtaq Ahmad
- Visiting Scientist Plant Sciences, University of Nebraska, Lincoln, NE, United States
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18
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Miller KJ, Thorpe C, Eggenberger AL, Lee K, Kang M, Liu F, Wang K, Jiang S. Identifying Factors that Determine Effectiveness of Delivery Agents in Biolistic Delivery Using a Library of Amine-Containing Molecules. ACS APPLIED BIO MATERIALS 2022; 5:4972-4980. [PMID: 36191156 DOI: 10.1021/acsabm.2c00689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biolistic transfection is a popular and versatile tool for plant transformation. A key step in the biolistic process is the binding of DNA to the heavy microprojectile using a delivery agent, usually a positively charged molecule containing amine groups. Currently, the choice of the commercial delivery agent is mostly limited to spermidine. In addition, the detailed delivery mechanism has not been reported. To help broaden the selection of the delivery agent and reveal the fundamental mechanisms that lead to high delivery performance, a library of amine-containing molecules was investigated. A double-barrel biolistic delivery device was utilized for testing hundreds of samples with much-improved consistency. The performance was evaluated on onion epidermis. The binding and release of DNA were measured via direct high-performance liquid chromatography analysis. This study shows that the overwhelming majority of the amine library performed at the same level as spermidine. To further interpret these results, correlations were performed with thousands of molecular descriptors generated by chemical modeling. It was discovered that the overall charge is most likely the key factor to a successful binding and delivery. Furthermore, even after increasing the amount of the DNA concentration 50-fold to stress the binding capacity of the molecules, the amines in the library continued to deliver at a near identical level while binding all the DNA. The increased DNA was also demonstrated with a Cas9 editing test that required a large amount of DNA to be delivered, and the result was consistent with the previously determined amine performance. This study greatly expands the delivery agent selection for biolistic delivery, allowing alternatives to a commercial reagent that are more shelf-stable and cheaper. The library also offers an approach to investigate more challenging delivery of protein and CRISPR-Cas via the biolistic process in the future.
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Affiliation(s)
- Kyle J Miller
- Department of Materials Science and Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Connor Thorpe
- Department of Materials Science and Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Alan L Eggenberger
- Department of Materials Science and Engineering, Iowa State University, Ames, Iowa 50011, United States
- Crop Bioengineering Center, Iowa State University, Ames, Iowa 50011, United States
| | - Keunsub Lee
- Crop Bioengineering Center, Iowa State University, Ames, Iowa 50011, United States
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Minjeong Kang
- Crop Bioengineering Center, Iowa State University, Ames, Iowa 50011, United States
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, United States
- Interdepartmental Plant Biology Major, Iowa State University, Ames, Iowa 50011, United States
| | - Fei Liu
- Department of Materials Science and Engineering, Iowa State University, Ames, Iowa 50011, United States
| | - Kan Wang
- Crop Bioengineering Center, Iowa State University, Ames, Iowa 50011, United States
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, United States
| | - Shan Jiang
- Department of Materials Science and Engineering, Iowa State University, Ames, Iowa 50011, United States
- Crop Bioengineering Center, Iowa State University, Ames, Iowa 50011, United States
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Selma S, Gianoglio S, Uranga M, Vázquez‐Vilar M, Espinosa‐Ruiz A, Drapal M, Fraser PD, Daròs J, Orzáez D. Potato virus X-delivered CRISPR activation programs lead to strong endogenous gene induction and transient metabolic reprogramming in Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 111:1550-1564. [PMID: 35822533 PMCID: PMC9541417 DOI: 10.1111/tpj.15906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/28/2022] [Accepted: 07/07/2022] [Indexed: 05/11/2023]
Abstract
Programmable transcriptional regulators based on CRISPR architecture are promising tools for the induction of plant gene expression. In plants, CRISPR gene activation is effective with respect to modulating development processes, such as the flowering time or customizing biochemical composition. The most widely used method for delivering CRISPR components into the plant is Agrobacterium tumefaciens-mediated genetic transformation, either transient or stable. However, as a result of their versatility and their ability to move, virus-derived systems have emerged as an interesting alternative for supplying the CRISPR components to the plant, in particular guide RNA (gRNA), which represents the variable component in CRISPR strategies. In the present study, we describe a Potato virus X-derived vector that, upon agroinfection in Nicotiana benthamiana, serves as a vehicle for delivery of gRNAs, producing highly specific virus-induced gene activation. The system works in combination with a N. benthamiana transgenic line carrying the remaining complementary CRISPR gene activation components, specifically the dCasEV2.1 cassette, which has been shown previously to mediate strong programmable transcriptional activation in plants. Using an easily scalable, non-invasive spraying method, we show that gRNA-mediated activation programs move locally and systemically, generating a strong activation response in different target genes. Furthermore, by activating three different endogenous MYB transcription factors, we demonstrate that this Potato virus X-based virus-induced gene reprogramming strategy results in program-specific metabolic fingerprints in N. benthamiana leaves characterized by distinctive phenylpropanoid-enriched metabolite profiles.
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Affiliation(s)
- Sara Selma
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Silvia Gianoglio
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Mireia Uranga
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Marta Vázquez‐Vilar
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Ana Espinosa‐Ruiz
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | | | | | - José‐Antonio Daròs
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
| | - Diego Orzáez
- Instituto Biología Molecular y celular de PlantasCSIC‐Universitat Politècnica de ValènciaValencia46022Spain
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20
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Wijerathna-Yapa A, Ramtekey V, Ranawaka B, Basnet BR. Applications of In Vitro Tissue Culture Technologies in Breeding and Genetic Improvement of Wheat. PLANTS (BASEL, SWITZERLAND) 2022; 11:2273. [PMID: 36079653 PMCID: PMC9459818 DOI: 10.3390/plants11172273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/13/2022] [Accepted: 08/29/2022] [Indexed: 12/20/2022]
Abstract
Sources of new genetic variability have been limited to existing germplasm in the past. Wheat has been studied extensively for various agronomic traits located throughout the genome. The large size of the chromosomes and the ability of its polyploid genome to tolerate the addition or loss of chromosomes facilitated rapid progress in the early study of wheat genetics using cytogenetic techniques. At the same time, its large genome size has limited the progress in genetic characterization studies focused on diploid species, with a small genome and genetic engineering procedures already developed. Today, the genetic transformation and gene editing procedures offer attractive alternatives to conventional techniques for breeding wheat because they allow one or more of the genes to be introduced or altered into an elite cultivar without affecting its genetic background. Recently, significant advances have been made in regenerating various plant tissues, providing the essential basis for regenerating transgenic plants. In addition, Agrobacterium-mediated, biolistic, and in planta particle bombardment (iPB) gene delivery procedures have been developed for wheat transformation and advanced transgenic wheat development. As a result, several useful genes are now available that have been transferred or would be helpful to be transferred to wheat in addition to the current traditional effort to improve trait values, such as resistance to abiotic and biotic factors, grain quality, and plant architecture. Furthermore, the in planta genome editing method will significantly contribute to the social implementation of genome-edited crops to innovate the breeding pipeline and leverage unique climate adaptations.
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Affiliation(s)
- Akila Wijerathna-Yapa
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD 4072, Australia
- School of Biological Sciences, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Vinita Ramtekey
- ICAR-Indian Institute of Seed Science, Kushmaur, Mau, Uttar Pradesh 275103, India
| | - Buddhini Ranawaka
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, St Lucia, QLD 4072, Australia
- Centre for Agriculture and the Bioeconomy, Institute for Future Environments, Queensland University of Technology (QUT), 2 George Street, Brisbane, QLD 4000, Australia
| | - Bhoja Raj Basnet
- Global Wheat Program, International Maize and Wheat Improvement Center (CIMMYT), El Batán 56237, Mexico
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21
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Li J, Xu Z, Zeng T, Zhou L, Li J, Hu H, Luo J, Wang C. Overexpression of TcCHS Increases Pyrethrin Content When Using a Genotype-Independent Transformation System in Pyrethrum ( Tanacetum cinerariifolium). PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11121575. [PMID: 35736726 PMCID: PMC9229838 DOI: 10.3390/plants11121575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 06/11/2022] [Accepted: 06/12/2022] [Indexed: 05/09/2023]
Abstract
Pyrethrum (Tanacetum cinerariifolium) is one of the most important industrial crops for the extraction of pyrethrins, which are natural insecticidal compounds. Progress in pyrethrum molecular breeding with the objective of increasing pyrethrin content has been slow for lack of a suitable gene transfer system. Regeneration recalcitrance is a crucial barrier to establishing a genetic transformation system in pyrethrum. Therefore, in this study, an Agrobacterium-mediated transformation system in pyrethrum was developed using shoot apical meristems from germinated seedlings. Factors affecting transformation efficiency were optimized. Optimal conditions included explants at the "no true leaf" stage with a half apical meristem, an Agrobacterium tumefaciens cell density of OD600 = 0.5, two days of cocultivation, and the incorporation of 1.5 mg L-1 6-BA and 30 mg L-1 kanamycin into the selection medium. Under the optimized conditions, two expression cassettes (proTcCHS-GUS and proRbcS-TcCHS) were successfully transformed into pyrethrum. Polymerase chain reaction (PCR), Southern blotting, reverse-transcription quantitative PCR (RT-qPCR), and histochemical staining confirmed the identity of proTcCHS-GUS transgenic plants. PCR and RT-qPCR analyses confirmed the identity of proRbcS-TcCHS transgenic plants. The transformation efficiency was 0.83% (5 transgenic lines/600 infected explants). The relative concentration of pyrethrins in proRbcS-TcCHS transformants (OX T0-1: 1.50% or OX T0-2: 1.24%) was higher than that in nontransformed plants (WT: 0.76%). Thus, the genetic transformation system overcame the low regeneration efficiency and integrated a foreign gene into the pyrethrum genome. The new system is a suitable and effective tool for creating high-yielding cultivars of pyrethrum.
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Affiliation(s)
- Jiawen Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
| | - Zhizhuo Xu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
| | - Tuo Zeng
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Li Zhou
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
| | - Jinjin Li
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
| | - Hao Hu
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
| | - Jing Luo
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
- Correspondence: (J.L.); (C.W.)
| | - Caiyun Wang
- Key Laboratory for Biology of Horticultural Plants, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China; (J.L.); (Z.X.); (T.Z.); (L.Z.); (J.L.); (H.H.)
- Correspondence: (J.L.); (C.W.)
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22
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Haroon M, Wang X, Afzal R, Zafar MM, Idrees F, Batool M, Khan AS, Imran M. Novel Plant Breeding Techniques Shake Hands with Cereals to Increase Production. PLANTS (BASEL, SWITZERLAND) 2022; 11:1052. [PMID: 35448780 PMCID: PMC9025237 DOI: 10.3390/plants11081052] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/07/2022] [Accepted: 04/10/2022] [Indexed: 06/01/2023]
Abstract
Cereals are the main source of human food on our planet. The ever-increasing food demand, continuously changing environment, and diseases of cereal crops have made adequate production a challenging task for feeding the ever-increasing population. Plant breeders are striving their hardest to increase production by manipulating conventional breeding methods based on the biology of plants, either self-pollinating or cross-pollinating. However, traditional approaches take a decade, space, and inputs in order to make crosses and release improved varieties. Recent advancements in genome editing tools (GETs) have increased the possibility of precise and rapid genome editing. New GETs such as CRISPR/Cas9, CRISPR/Cpf1, prime editing, base editing, dCas9 epigenetic modification, and several other transgene-free genome editing approaches are available to fill the lacuna of selection cycles and limited genetic diversity. Over the last few years, these technologies have led to revolutionary developments and researchers have quickly attained remarkable achievements. However, GETs are associated with various bottlenecks that prevent the scaling development of new varieties that can be dealt with by integrating the GETs with the improved conventional breeding methods such as speed breeding, which would take plant breeding to the next level. In this review, we have summarized all these traditional, molecular, and integrated approaches to speed up the breeding procedure of cereals.
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Affiliation(s)
- Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiukang Wang
- College of Life Sciences, Yan'an University, Yan'an 716000, China
| | - Rabail Afzal
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, Key Laboratory of Biological and Genetic Breeding of Cotton, Chinese Academy of Agricultural Science, Anyang 455000, China
| | - Fahad Idrees
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Maria Batool
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Abdul Saboor Khan
- Institute of Plant Sciences, University of Cologne, 50667 Cologne, Germany
| | - Muhammad Imran
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, South China Agriculture University, Guangzhou 510642, China
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23
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Kumagai Y, Liu Y, Hamada H, Luo W, Zhu J, Kuroki M, Nagira Y, Taoka N, Katoh E, Imai R. Introduction of a second "Green Revolution" mutation into wheat via in planta CRISPR/Cas9 delivery. PLANT PHYSIOLOGY 2022; 188:1838-1842. [PMID: 34908145 PMCID: PMC8968346 DOI: 10.1093/plphys/kiab570] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/11/2021] [Indexed: 05/24/2023]
Abstract
Direct delivery of CRISPR/Cas9 ribonucleoproteins into the shoot apical meristem via particle bombardment enabled introduction of a semidwarf1-orthologous mutation into an elite wheat variety.
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Affiliation(s)
- Yuya Kumagai
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan
| | - Yuelin Liu
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan
| | - Haruyasu Hamada
- Biotechnology Research Laboratories, Agri-Bio Research Center, Kaneka Corporation, Iwata, Shizuoka 438-0802, Japan
| | - Weifeng Luo
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan
| | - Jianghui Zhu
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan
| | - Misa Kuroki
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan
| | - Yozo Nagira
- Biotechnology Research Laboratories, Agri-Bio Research Center, Kaneka Corporation, Iwata, Shizuoka 438-0802, Japan
| | - Naoaki Taoka
- Biotechnology Research Laboratories, Agri-Bio Research Center, Kaneka Corporation, Iwata, Shizuoka 438-0802, Japan
| | - Etsuko Katoh
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Ryozo Imai
- Genome-Edited Crop Development Group, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki 305-8604, Japan
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24
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Silva TN, Thomas JB, Dahlberg J, Rhee SY, Mortimer JC. Progress and challenges in sorghum biotechnology, a multipurpose feedstock for the bioeconomy. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:646-664. [PMID: 34644381 PMCID: PMC8793871 DOI: 10.1093/jxb/erab450] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/10/2021] [Indexed: 05/09/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is the fifth most important cereal crop globally by harvested area and production. Its drought and heat tolerance allow high yields with minimal input. It is a promising biomass crop for the production of biofuels and bioproducts. In addition, as an annual diploid with a relatively small genome compared with other C4 grasses, and excellent germplasm diversity, sorghum is an excellent research species for other C4 crops such as maize. As a result, an increasing number of researchers are looking to test the transferability of findings from other organisms such as Arabidopsis thaliana and Brachypodium distachyon to sorghum, as well as to engineer new biomass sorghum varieties. Here, we provide an overview of sorghum as a multipurpose feedstock crop which can support the growing bioeconomy, and as a monocot research model system. We review what makes sorghum such a successful crop and identify some key traits for future improvement. We assess recent progress in sorghum transformation and highlight how transformation limitations still restrict its widespread adoption. Finally, we summarize available sorghum genetic, genomic, and bioinformatics resources. This review is intended for researchers new to sorghum research, as well as those wishing to include non-food and forage applications in their research.
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Affiliation(s)
- Tallyta N Silva
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jason B Thomas
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Jeff Dahlberg
- Joint BioEnergy Institute, Emeryville, CA, USA
- UC-ANR-KARE, 9240 S. Riverbend Ave, Parlier, CA, USA
| | - Seung Y Rhee
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
- Correspondence: or
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, SA, Australia
- Correspondence: or
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Laforest LC, Nadakuduti SS. Advances in Delivery Mechanisms of CRISPR Gene-Editing Reagents in Plants. Front Genome Ed 2022; 4:830178. [PMID: 35141701 PMCID: PMC8819002 DOI: 10.3389/fgeed.2022.830178] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/05/2022] [Indexed: 01/18/2023] Open
Abstract
Gene-editing by CRISPR/Cas systems has revolutionized plant biology by serving as a functional genomics tool. It has tremendously advanced plant breeding and crop improvement by accelerating the development of improved cultivars, creating genetic variability, and aiding in domestication of wild and orphan crops. Gene-editing is a rapidly evolving field. Several advancements include development of different Cas effectors with increased target range, efficacy, and enhanced capacity for precise DNA modifications with base editing and prime editing. The existing toolbox of various CRISPR reagents facilitate gene knockouts, targeted gene insertions, precise base substitutions, and multiplexing. However, the major challenge in plant genome-editing remains the efficient delivery of these reagents into plant cells. Plants have larger and more complex genome structures compared to other living systems due to the common occurrence of polyploidy and other genome re-arrangements. Further, rigid cell walls surrounding plant cells deter the entry of any foreign biomolecules. Unfortunately, genetic transformation to deliver gene-editing reagents has been established only in a limited number of plant species. Recently, there has been significant progress in CRISPR reagents delivery in plants. This review focuses on exploring these delivery mechanisms categorized into Agrobacterium-mediated delivery and breakthroughs, particle bombardment-based delivery of biomolecules and recent improvements, and protoplasts, a versatile system for gene-editing and regeneration in plants. The ultimate goal in plant gene-editing is to establish highly efficient and genotype-independent reagent delivery mechanisms for editing multiple targets simultaneously and achieve DNA-free gene-edited plants at scale.
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Affiliation(s)
- Larissa C. Laforest
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
| | - Satya Swathi Nadakuduti
- Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, United States
- Department of Environmental Horticulture, University of Florida, Gainesville, FL, United States
- *Correspondence: Satya Swathi Nadakuduti,
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Son S, Park SR. Challenges Facing CRISPR/Cas9-Based Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:902413. [PMID: 35677236 PMCID: PMC9169250 DOI: 10.3389/fpls.2022.902413] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/29/2022] [Indexed: 05/18/2023]
Abstract
The development of plant varieties with desired traits is imperative to ensure future food security. The revolution of genome editing technologies based on the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has ushered in a new era in plant breeding. Cas9 and the single-guide RNA (sgRNA) form an effective targeting complex on a locus or loci of interest, enabling genome editing in all plants with high accuracy and efficiency. Therefore, CRISPR/Cas9 can save both time and labor relative to what is typically associated with traditional breeding methods. However, despite improvements in gene editing, several challenges remain that limit the application of CRISPR/Cas9-based genome editing in plants. Here, we focus on four issues relevant to plant genome editing: (1) plant organelle genome editing; (2) transgene-free genome editing; (3) virus-induced genome editing; and (4) editing of recalcitrant elite crop inbred lines. This review provides an up-to-date summary on the state of CRISPR/Cas9-mediated genome editing in plants that will push this technique forward.
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Bellido AM, Souza Canadá ED, Permingeat HR, Echenique V. Genetic Transformation of Apomictic Grasses: Progress and Constraints. FRONTIERS IN PLANT SCIENCE 2021; 12:768393. [PMID: 34804102 PMCID: PMC8602796 DOI: 10.3389/fpls.2021.768393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 10/05/2021] [Indexed: 05/17/2023]
Abstract
The available methods for plant transformation and expansion beyond its limits remain especially critical for crop improvement. For grass species, this is even more critical, mainly due to drawbacks in in vitro regeneration. Despite the existence of many protocols in grasses to achieve genetic transformation through Agrobacterium or biolistic gene delivery, their efficiencies are genotype-dependent and still very low due to the recalcitrance of these species to in vitro regeneration. Many plant transformation facilities for cereals and other important crops may be found around the world in universities and enterprises, but this is not the case for apomictic species, many of which are C4 grasses. Moreover, apomixis (asexual reproduction by seeds) represents an additional constraint for breeding. However, the transformation of an apomictic clone is an attractive strategy, as the transgene is immediately fixed in a highly adapted genetic background, capable of large-scale clonal propagation. With the exception of some species like Brachiaria brizantha which is planted in approximately 100 M ha in Brazil, apomixis is almost non-present in economically important crops. However, as it is sometimes present in their wild relatives, the main goal is to transfer this trait to crops to fix heterosis. Until now this has been a difficult task, mainly because many aspects of apomixis are unknown. Over the last few years, many candidate genes have been identified and attempts have been made to characterize them functionally in Arabidopsis and rice. However, functional analysis in true apomictic species lags far behind, mainly due to the complexity of its genomes, of the trait itself, and the lack of efficient genetic transformation protocols. In this study, we review the current status of the in vitro culture and genetic transformation methods focusing on apomictic grasses, and the prospects for the application of new tools assayed in other related species, with two aims: to pave the way for discovering the molecular pathways involved in apomixis and to develop new capacities for breeding purposes because many of these grasses are important forage or biofuel resources.
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Affiliation(s)
- Andrés M. Bellido
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
| | | | | | - Viviana Echenique
- Departamento de Agronomía, Centro de Recursos Naturales Renovables de la Zona Semiárida (CERZOS – CCT – CONICET Bahía Blanca), Universidad Nacional del Sur (UNS), Bahía Blanca, Argentina
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28
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Hisano H, Abe F, Hoffie RE, Kumlehn J. Targeted genome modifications in cereal crops. BREEDING SCIENCE 2021; 71:405-416. [PMID: 34912167 PMCID: PMC8661484 DOI: 10.1270/jsbbs.21019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/13/2021] [Indexed: 05/15/2023]
Abstract
The recent advent of customizable endonucleases has led to remarkable advances in genetic engineering, as these molecular scissors allow for the targeted introduction of mutations or even precisely predefined genetic modifications into virtually any genomic target site of choice. Thanks to its unprecedented precision, efficiency, and functional versatility, this technology, commonly referred to as genome editing, has become an effective force not only in basic research devoted to the elucidation of gene function, but also for knowledge-based improvement of crop traits. Among the different platforms currently available for site-directed genome modifications, RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) endonucleases have proven to be the most powerful. This review provides an application-oriented overview of the development of customizable endonucleases, current approaches to cereal crop breeding, and future opportunities in this field.
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Affiliation(s)
- Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama 710-0046, Japan
| | - Fumitaka Abe
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Robert E. Hoffie
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Stadt Seeland/OT Gatersleben, Germany
| | - Jochen Kumlehn
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Stadt Seeland/OT Gatersleben, Germany
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29
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Nagahara S, Higashiyama T, Mizuta Y. Detection of a biolistic delivery of fluorescent markers and CRISPR/Cas9 to the pollen tube. PLANT REPRODUCTION 2021; 34:191-205. [PMID: 34146158 PMCID: PMC8360903 DOI: 10.1007/s00497-021-00418-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/05/2021] [Indexed: 05/02/2023]
Abstract
Biolistic delivery into pollen. In recent years, genome editing techniques, such as the CRISPR/Cas9 system, have been highlighted as a new approach to plant breeding. Agrobacterium-mediated transformation has been widely utilized to generate transgenic plants by introducing plasmid DNA containing CRISPR/Cas9 into plant cells. However, this method has general limitations, such as the limited host range of Agrobacterium and difficulties in tissue culture, including callus induction and regeneration. To avoid these issues, we developed a method to genetically modify germ cells without the need for Agrobacterium-mediated transfection and tissue culture using tobacco as a model. In this study, plasmid DNA containing sequences of Cas9, guide RNA, and fluorescent reporter was introduced into pollen using a biolistic delivery system. Based on the transient expression of fluorescent reporters, the Arabidopsis UBQ10 promoter was found to be the most suitable promoter for driving the expression of the delivered gene in pollen tubes. We also evaluated the delivery efficiency in male germ cells in the pollen by expression of the introduced fluorescent marker. Mutations were detected in the target gene in the genomic DNA extracted from CRISPR/Cas9-introduced pollen tubes, but were not detected in the negative control. Bombarded pollen germinated pollen tubes and delivered their contents into the ovules in vivo. Although it is necessary to improve biolistic delivery efficiency and establish a method for the screening of genome-modified seeds, our findings provide important insights for the detection and production of genome-modified seeds by pollen biolistic delivery.
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Affiliation(s)
- Shiori Nagahara
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Tetsuya Higashiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
- Division of Biological Sciences, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bukyo-ku, Tokyo, 113-0033, Japan
| | - Yoko Mizuta
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
- Institute for Advanced Research (IAR), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan.
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30
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Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
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Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
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31
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Sukegawa S, Saika H, Toki S. Plant genome editing: ever more precise and wide reaching. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1208-1218. [PMID: 33730414 DOI: 10.1111/tpj.15233] [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: 01/18/2021] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Genome-editing technologies consisting of targeted mutagenesis and gene targeting enable us to modify genes of interest rapidly and precisely. The discovery in 2012 of CRISPR/Cas9 systems and their development as sequence-specific nucleases has brought about a paradigm shift in biology. Initially, CRISPR/Cas9 was applied in targeted mutagenesis to knock out a target gene. Thereafter, advances in genome-editing technologies using CRISPR/Cas9 developed rapidly, with base editing systems for transition substitution using a combination of Cas9 nickase and either cytidine or adenosine deaminase being reported in 2016 and 2017, respectively, and later in 2021 bringing reports of transversion substitution using Cas9 nickase, cytidine deaminase and uracil DNA glycosylase. Moreover, technologies for gene targeting and prime editing systems using DNA or RNA as donors have also been developed in recent years. Besides these precise genome-editing strategies, reports of successful chromosome engineering using CRISPR/Cas9 have been published recently. The application of genome editing to crop breeding has advanced in parallel with the development of these technologies. Genome-editing enzymes can be introduced into plant cells, and there are now many examples of crop breeding using genome-editing technologies. At present, it is no exaggeration to say that we are now in a position to be able to modify a gene precisely and rearrange genomes and chromosomes in a predicted way. In this review, we introduce and discuss recent highlights in the field of precise gene editing, chromosome engineering and genome engineering technology in plants.
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Affiliation(s)
- Satoru Sukegawa
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Hiroaki Saika
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Ibaraki, Japan
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Kanagawa, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Kanagawa, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
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32
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Ahmar S, Mahmood T, Fiaz S, Mora-Poblete F, Shafique MS, Chattha MS, Jung KH. Advantage of Nanotechnology-Based Genome Editing System and Its Application in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2021; 12:663849. [PMID: 34122485 PMCID: PMC8194497 DOI: 10.3389/fpls.2021.663849] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/26/2021] [Indexed: 05/05/2023]
Abstract
Agriculture is an important source of human food. However, current agricultural practices need modernizing and strengthening to fulfill the increasing food requirements of the growing worldwide population. Genome editing (GE) technology has been used to produce plants with improved yields and nutritional value as well as with higher resilience to herbicides, insects, and diseases. Several GE tools have been developed recently, including clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases, a customizable and successful method. The main steps of the GE process involve introducing transgenes or CRISPR into plants via specific gene delivery systems. However, GE tools have certain limitations, including time-consuming and complicated protocols, potential tissue damage, DNA incorporation in the host genome, and low transformation efficiency. To overcome these issues, nanotechnology has emerged as a groundbreaking and modern technique. Nanoparticle-mediated gene delivery is superior to conventional biomolecular approaches because it enhances the transformation efficiency for both temporal (transient) and permanent (stable) genetic modifications in various plant species. However, with the discoveries of various advanced technologies, certain challenges in developing a short-term breeding strategy in plants remain. Thus, in this review, nanobased delivery systems and plant genetic engineering challenges are discussed in detail. Moreover, we have suggested an effective method to hasten crop improvement programs by combining current technologies, such as speed breeding and CRISPR/Cas, with nanotechnology. The overall aim of this review is to provide a detailed overview of nanotechnology-based CRISPR techniques for plant transformation and suggest applications for possible crop enhancement.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, Universidad de Talca, Talca, Chile
| | - Tahir Mahmood
- Chinese Academy of Agricultural Sciences, Beijing, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | | | | | | | - Ki-Hung Jung
- Graduate School of Biotechnology & Crop Biotech Institute, Kyung Hee University, Yongin, South Korea
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33
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Liu L, Lindsay PL, Jackson D. Next Generation Cereal Crop Yield Enhancement: From Knowledge of Inflorescence Development to Practical Engineering by Genome Editing. Int J Mol Sci 2021; 22:5167. [PMID: 34068350 PMCID: PMC8153303 DOI: 10.3390/ijms22105167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
Artificial domestication and improvement of the majority of crops began approximately 10,000 years ago, in different parts of the world, to achieve high productivity, good quality, and widespread adaptability. It was initiated from a phenotype-based selection by local farmers and developed to current biotechnology-based breeding to feed over 7 billion people. For most cereal crops, yield relates to grain production, which could be enhanced by increasing grain number and weight. Grain number is typically determined during inflorescence development. Many mutants and genes for inflorescence development have already been characterized in cereal crops. Therefore, optimization of such genes could fine-tune yield-related traits, such as grain number. With the rapidly advancing genome-editing technologies and understanding of yield-related traits, knowledge-driven breeding by design is becoming a reality. This review introduces knowledge about inflorescence yield-related traits in cereal crops, focusing on rice, maize, and wheat. Next, emerging genome-editing technologies and recent studies that apply this technology to engineer crop yield improvement by targeting inflorescence development are reviewed. These approaches promise to usher in a new era of breeding practice.
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Affiliation(s)
| | | | - David Jackson
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; (L.L.); (P.L.L.)
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34
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Liu Q, Yang F, Zhang J, Liu H, Rahman S, Islam S, Ma W, She M. Application of CRISPR/Cas9 in Crop Quality Improvement. Int J Mol Sci 2021; 22:4206. [PMID: 33921600 PMCID: PMC8073294 DOI: 10.3390/ijms22084206] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/06/2023] Open
Abstract
The various crop species are major agricultural products and play an indispensable role in sustaining human life. Over a long period, breeders strove to increase crop yield and improve quality through traditional breeding strategies. Today, many breeders have achieved remarkable results using modern molecular technologies. Recently, a new gene-editing system, named the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, has also succeeded in improving crop quality. It has become the most popular tool for crop improvement due to its versatility. It has accelerated crop breeding progress by virtue of its precision in specific gene editing. This review summarizes the current application of CRISPR/Cas9 technology in crop quality improvement. It includes the modulation in appearance, palatability, nutritional components and other preferred traits of various crops. In addition, the challenge in its future application is also discussed.
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Affiliation(s)
- Qier Liu
- Institute of Agricultural Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China;
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Fan Yang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Jingjuan Zhang
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Hang Liu
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shanjida Rahman
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Shahidul Islam
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Wujun Ma
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
| | - Maoyun She
- State Agricultural Biotechnology Centre, College of Science, Health, Engineering and Education, Murdoch University, Perth, WA 6150, Australia; (F.Y.); (J.Z.); (H.L.); (S.R.); (S.I.)
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35
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An improved biolistic delivery and analysis method for evaluation of DNA and CRISPR-Cas delivery efficacy in plant tissue. Sci Rep 2021; 11:7695. [PMID: 33833247 PMCID: PMC8032657 DOI: 10.1038/s41598-021-86549-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 03/05/2021] [Indexed: 12/03/2022] Open
Abstract
Biolistic delivery is widely used for genetic transformation but inconsistency between bombardment samples for transient gene expression analysis often hinders quantitative analyses. We developed a methodology to improve the consistency of biolistic delivery results by using a double-barrel device and a cell counting software. The double-barrel device enables a strategy of incorporating an internal control into each sample, which significantly decreases variance of the results. The cell counting software further reduces errors and increases throughput. The utility of this new platform is demonstrated by optimizing conditions for delivering DNA using the commercial transfection reagent TransIT-2020. In addition, the same approach is applied to test the efficacy of multiple gRNAs for CRISPR-Cas9-mediated gene editing. The novel combination of the bombardment device and analysis method allows simultaneous comparison and optimization of parameters in the biolistic delivery. The platform developed here can be broadly applied to any target samples using biolistics, including animal cells and tissues.
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36
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Imai R, Hamada H, Liu Y, Linghu Q, Kumagai Y, Nagira Y, Miki R, Taoka N. In planta particle bombardment (iPB): A new method for plant transformation and genome editing. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:171-176. [PMID: 32821224 PMCID: PMC7434670 DOI: 10.5511/plantbiotechnology.20.0206a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Transformation is a key step in modern breeding technology that involves genome editing. The requirement for in vitro tissue culture and regeneration hampers application of this technology to commercially important varieties of many crop species. To overcome this problem, we developed a simple and reproducible in planta transformation method in wheat (Tritticum aestivum L.). Our in planta particle bombardment (iPB) method utilizes the shoot apical meristem (SAM) as a target tissue. The SAM contains a subepidermal cell layer termed L2, from which germ cells later develop during floral organogenesis. The iPB method can also be used for genome editing through transient CRISPR/Cas9 expression or direct delivery of the CRISPR/Cas9 ribonucleoprotein. In this review, we describe the iPB technology and provide an overview of its current and future applications in plant transformation and genome editing.
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Affiliation(s)
- Ryozo Imai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tukuba, Ibaraki 305-8634, Japan
- E-mail: Tel & Fax: +81-29-838-8378
| | - Haruyasu Hamada
- Pharma & Supplemental Nutrition Solutions Vehicle, Biotechnology Research Laboratories, KANEKA CORPORATION, Takasago, Hyogo 676-8688, Japan
| | - Yuelin Liu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tukuba, Ibaraki 305-8634, Japan
| | - Qianyan Linghu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tukuba, Ibaraki 305-8634, Japan
| | - Yuya Kumagai
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tukuba, Ibaraki 305-8634, Japan
| | - Yozo Nagira
- Pharma & Supplemental Nutrition Solutions Vehicle, Biotechnology Research Laboratories, KANEKA CORPORATION, Takasago, Hyogo 676-8688, Japan
| | - Ryuji Miki
- Pharma & Supplemental Nutrition Solutions Vehicle, Biotechnology Research Laboratories, KANEKA CORPORATION, Takasago, Hyogo 676-8688, Japan
| | - Naoaki Taoka
- Pharma & Supplemental Nutrition Solutions Vehicle, Biotechnology Research Laboratories, KANEKA CORPORATION, Takasago, Hyogo 676-8688, Japan
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Tabei Y, Muranaka T. Preface to the special issue "Technology in tissue culture toward horizon of plant biotechnology". PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:117-120. [PMID: 32821217 PMCID: PMC7434682 DOI: 10.5511/plantbiotechnology.20.0000p] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Affiliation(s)
- Yutaka Tabei
- Strategic Planning Headquarters, National Agriculture and Food Research Organization, 3-1-1 Kannondai, Tsukuba, Ibaraki 305-8517, Japan
| | - Toshiya Muranaka
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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38
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Takamizo T, Sato H. Protocol for Agrobacterium-mediated transformation of tall fescue and future perspective on the application of genome editing. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2020; 37:157-161. [PMID: 32821222 PMCID: PMC7434684 DOI: 10.5511/plantbiotechnology.20.0309a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/09/2020] [Indexed: 06/11/2023]
Abstract
Tall fescue (Festuca arundinacea Schreb.) is a major cool-season perennial grass grown for forage and turf. We have obtained transgenic tall fescue by Agrobacterium-mediated transformation to improve agronomically important traits. In our protocol, we use embryogenic calli derived from not only mature seeds but also shoot tips. Although tall fescue cultivars consist of various genotypes with different genetic variation, we can produce transgenic plants at any time with calli induced from shoot tips of in vitro-maintained responsive genotypes. When the hygromycin phosphotransferase gene is used as a selectable marker, transformants are selected by incubation with 100 mg l-1 hygromycin in both selection and regeneration media. Since tall fescue is an anemophilous species, the cultivation of transgenic plants poses the risk of transgenic pollen flow. Recently, it has been reported that genome-edited plants without the integration of foreign DNA fragments can be produced by an Agrobacterium-mediated transient gene expression system. We hope that our protocol will contribute to production of transgene-free genome-edited tall fescue.
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Affiliation(s)
- Tadashi Takamizo
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, Tochigi 329-2793, Japan
| | - Hiroko Sato
- Hokkaido Agricultural Research Center, National Agriculture and Food Research Organization, Sapporo, Hokkaido 062-8555, Japan
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39
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Ellison EE, Nagalakshmi U, Gamo ME, Huang PJ, Dinesh-Kumar S, Voytas DF. Multiplexed heritable gene editing using RNA viruses and mobile single guide RNAs. NATURE PLANTS 2020; 6:620-624. [PMID: 32483329 DOI: 10.1038/s41477-020-0670-y] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 04/22/2020] [Indexed: 05/20/2023]
Abstract
An in planta gene editing approach was developed wherein Cas9 transgenic plants are infected with an RNA virus that expresses single guide RNAs (sgRNAs). The sgRNAs are augmented with sequences that promote cell-to-cell mobility. Mutant progeny are recovered in the next generation at frequencies ranging from 65 to 100%; up to 30% of progeny derived from plants infected with a virus expressing three sgRNAs have mutations in all three targeted loci.
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Affiliation(s)
- Evan E Ellison
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
- Plant and Microbial Biology Graduate Program, University of Minnesota, St. Paul, MN, USA
| | - Ugrappa Nagalakshmi
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
| | - Pin-Jui Huang
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Savithramma Dinesh-Kumar
- Department of Plant Biology and The Genome Center, College of Biological Sciences, University of California, Davis, Davis, CA, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA.
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA.
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA.
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40
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Wada N, Ueta R, Osakabe Y, Osakabe K. Precision genome editing in plants: state-of-the-art in CRISPR/Cas9-based genome engineering. BMC PLANT BIOLOGY 2020; 20:234. [PMID: 32450802 PMCID: PMC7249668 DOI: 10.1186/s12870-020-02385-5] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 04/05/2020] [Indexed: 05/19/2023]
Abstract
Traditionally, generation of new plants with improved or desirable features has relied on laborious and time-consuming breeding techniques. Genome-editing technologies have led to a new era of genome engineering, enabling an effective, precise, and rapid engineering of the plant genomes. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (CRISPR/Cas9) has emerged as a new genome-editing tool, extensively applied in various organisms, including plants. The use of CRISPR/Cas9 allows generating transgene-free genome-edited plants ("null segregants") in a short period of time. In this review, we provide a critical overview of the recent advances in CRISPR/Cas9 derived technologies for inducing mutations at target sites in the genome and controlling the expression of target genes. We highlight the major breakthroughs in applying CRISPR/Cas9 to plant engineering, and challenges toward the production of null segregants. We also provide an update on the efforts of engineering Cas9 proteins, newly discovered Cas9 variants, and novel CRISPR/Cas systems for use in plants. The application of CRISPR/Cas9 and related technologies in plant engineering will not only facilitate molecular breeding of crop plants but also accelerate progress in basic research.
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Affiliation(s)
- Naoki Wada
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Risa Ueta
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Yuriko Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan
| | - Keishi Osakabe
- Graduate School of Technology, Industrial and Social Sciences, Tokushima University, Tokushima, Japan.
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41
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Biolistic DNA Delivery in Turfgrass Embryonic Callus Initiated from Mature Seeds. Methods Mol Biol 2020. [PMID: 32277458 DOI: 10.1007/978-1-0716-0356-7_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
We describe a protocol for the establishment and preparation of creeping bentgrass (Agrostis stolonifera L.) cultivar "Penn A-4" embryonic calli, biolistic transformation, selection, and regeneration of transgenic plants. The embryonic callus is initiated from mature seeds, maintained by visual selection under the dissecting microscope and subjected to bombardment with plasmid DNA containing a bialaphos-resistance (bar) gene. PCR, Southern, and Northern blot analyses are used to confirm the transgene integration and expression.
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42
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Zlobin NE, Lebedeva MV, Taranov VV. CRISPR/Cas9 genome editing through in planta transformation. Crit Rev Biotechnol 2020; 40:153-168. [PMID: 31903793 DOI: 10.1080/07388551.2019.1709795] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this review, the application of CRISPR/Cas9 plant genome editing using alternative transformation methods is discussed. Genome editing by the CRISPR/Cas9 system is usually implemented via the generation of transgenic plants carrying Cas9 and sgRNA genes in the genome. Transgenic plants are usually developed by in vitro regeneration from single transformed cells, which requires using different in vitro culture-based methods. Despite their common application, these methods have some disadvantages and limitations. Thus, some methods of plant transformation that do not depend on in vitro regeneration have been developed. These methods are known as "in planta" transformation. The main focus of this review is the so-called floral dip in planta transformation method, although other approaches are also described. The main features of in planta transformation in the context of CRISPR/Cas9 genome editing are discussed. Furthermore, multiple ways to increase the effectiveness of this approach and to broaden its use in different plant species are considered.
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Affiliation(s)
- Nikolay E Zlobin
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russian
| | - Marina V Lebedeva
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russian
| | - Vasiliy V Taranov
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russian
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43
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Abstract
The following protocol describes the genetic transformation of wheat using the BioRad PDS/1000-He particle delivery system. Immature embryos are isolated 12-16 days post-anthesis, the embryonic axis is removed, and the immature scutella are precultured for 1-2 days prior to particle bombardment. Gold particles are coated with plasmid DNA containing the gene(s) of interest plus a selectable marker gene, in this instance bar (bialaphos resistance), and are fired into the cells to deliver the DNA. Subsequent tissue culture and regeneration steps allow recovery of plantlets, assisted by the inclusion of PPT (phosphinothricin tripeptide), the active ingredient of glufosinate-ammonium containing herbicides, to help select transformants. This updated method introduces selection earlier in the regeneration process which provides a shortened protocol while maintaining high transformation efficiencies.
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Affiliation(s)
| | - Angela Doherty
- Plant Sciences Department, Rothamsted Research, Hertfordshire, UK
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44
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Maher MF, Nasti RA, Vollbrecht M, Starker CG, Clark MD, Voytas DF. Plant gene editing through de novo induction of meristems. Nat Biotechnol 2020; 38:84-89. [PMID: 31844292 PMCID: PMC6954279 DOI: 10.1038/s41587-019-0337-2] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 10/30/2019] [Indexed: 11/12/2022]
Abstract
Plant gene editing is typically performed by delivering reagents such as Cas9 and single guide RNAs to explants in culture. Edited cells are then induced to differentiate into whole plants by exposure to various hormones. The creation of edited plants through tissue culture is often inefficient, time-consuming, works for only limited species and genotypes, and causes unintended changes to the genome and epigenome. Here we report two methods to generate gene-edited dicotyledonous plants through de novo meristem induction. Developmental regulators and gene-editing reagents are delivered to somatic cells of whole plants. This induces meristems that produce shoots with targeted DNA modifications, and gene edits are transmitted to the next generation. The de novo induction of gene-edited meristems sidesteps the need for tissue culture and promises to overcome a bottleneck in plant gene editing.
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Affiliation(s)
- Michael F Maher
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
| | - Ryan A Nasti
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
| | - Macy Vollbrecht
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
| | - Colby G Starker
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA
| | - Matthew D Clark
- Department of Horticultural Sciences, University of Minnesota, St. Paul, MN, USA
| | - Daniel F Voytas
- Department of Plant and Microbial Biology, University of Minnesota, St. Paul, MN, USA.
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, USA.
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, USA.
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, USA.
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45
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Koeppel I, Hertig C, Hoffie R, Kumlehn J. Cas Endonuclease Technology-A Quantum Leap in the Advancement of Barley and Wheat Genetic Engineering. Int J Mol Sci 2019; 20:ijms20112647. [PMID: 31146387 PMCID: PMC6600890 DOI: 10.3390/ijms20112647] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/24/2019] [Accepted: 05/24/2019] [Indexed: 12/21/2022] Open
Abstract
Domestication and breeding have created productive crops that are adapted to the climatic conditions of their growing regions. Initially, this process solely relied on the frequent occurrence of spontaneous mutations and the recombination of resultant gene variants. Later, treatments with ionizing radiation or mutagenic chemicals facilitated dramatically increased mutation rates, which remarkably extended the genetic diversity of crop plants. However, a major drawback of conventionally induced mutagenesis is that genetic alterations occur simultaneously across the whole genome and at very high numbers per individual plant. By contrast, the newly emerging Cas endonuclease technology allows for the induction of mutations at user-defined positions in the plant genome. In fundamental and breeding-oriented research, this opens up unprecedented opportunities for the elucidation of gene functions and the targeted improvement of plant performance. This review covers historical aspects of the development of customizable endonucleases, information on the mechanisms of targeted genome modification, as well as hitherto reported applications of Cas endonuclease technology in barley and wheat that are the agronomically most important members of the temperate cereals. Finally, current trends in the further development of this technology and some ensuing future opportunities for research and biotechnological application are presented.
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Affiliation(s)
- Iris Koeppel
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Christian Hertig
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Robert Hoffie
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
| | - Jochen Kumlehn
- Plant Reproductive Biology, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.
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46
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Huang F, Liu T, Tang J, Duan W, Hou X. BcMAF2 activates BcTEM1 and represses flowering in Pak-choi (Brassica rapa ssp. chinensis). PLANT MOLECULAR BIOLOGY 2019; 100:19-32. [PMID: 31001712 DOI: 10.1007/s11103-019-00867-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 01/07/2019] [Indexed: 05/08/2023]
Abstract
BcMAF2 plays a key role in flowering regulation by controlling BcTEM1, BcSOC1 and BCSPL15 in Pak-choi. Flowering is a key event in the life cycle of plants. Flowering time shows an extensive variation from different Pak-choi (Brassica rapa ssp. chinensis) cultivars. However, the regulation mechanism of flowering in Pak-choi remains rarely known. In this study, a systematic identification and functional analysis of a Pak-choi MADS Affecting Flowering (MAF) gene, BcMAF2, was carried out. BcMAF2 encoded a protein containing a conserved MADS-box domain, which was localized in the nucleus. QPCR analysis indicated that the expression of BcMAF2 was higher in the leaves and flowers. Overexpression of BcMAF2 in Arabidopsis showed that BcMAF2 repressed flowering, which was further confirmed by silencing endogenous BcMAF2 in Pak-choi. In addition, Tempranillo 1 (TEM1) expression was up-regulated and MAF2 expression was down-regulated in the BcMAF2-overexpressing Arabidopsis. The expression of BcMAF2 and BcTEM1 was down-regulated in BcMAF2-silencing Pak-choi plants. The yeast one-hybrid, dual luciferase and qPCR results revealed that BcMAF2 protein could directly bind to BcTEM1 promoter and activate its expression, which was not reported in Arabidopsis. Meanwhile, a self-inhibition was found in BcMAF2. Taken together, this work suggested that BcMAF2 could repress flowering by directly activating BcTEM1.
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Affiliation(s)
- Feiyi Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jun Tang
- Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Weike Duan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, China.
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47
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Tarafdar A, Vishwakarma H, Gothandapani S, Bhati M, Biswas K, Prakash A, Chaturvedi U, Solanke AU, Padaria JC. A quick, easy and cost-effective in planta method to develop direct transformants in wheat. 3 Biotech 2019; 9:180. [PMID: 31058046 PMCID: PMC6470228 DOI: 10.1007/s13205-019-1708-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 04/08/2019] [Indexed: 10/27/2022] Open
Abstract
Agrobacterium mediated in planta method was used to transform Indian elite wheat genotype HD2894 with herbicide-tolerant CP4-EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) gene. The apical meristems of germinated seeds were targeted for introgression of transgene. The obtained T1 plants were screened by spraying 1% glyphosate and only positive transformants survived. The presence of transgene was also confirmed by PCR and Southern hybridization. Using this method, 3.07% transformation rate was observed. To identify transgenic lines carrying stably integrated CP4-EPSPS gene, the transgenic populations were screened in T3 generation using 1% glyphosate and lines with 100% survival were considered as homozygous. No significant morpho-physiological variations were observed within the transgenic lines as compared to non-transgenic plants. The present study resulted in herbicide-tolerant transgenic wheat and provides a valuable tool for development of wheat genetic transformation.
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Affiliation(s)
- Avijit Tarafdar
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Harinder Vishwakarma
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - S. Gothandapani
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Meenal Bhati
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Koushik Biswas
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Arul Prakash
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Uttara Chaturvedi
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Amolkumar U. Solanke
- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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48
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Chen K, Wang Y, Zhang R, Zhang H, Gao C. CRISPR/Cas Genome Editing and Precision Plant Breeding in Agriculture. ANNUAL REVIEW OF PLANT BIOLOGY 2019; 70:667-697. [PMID: 30835493 DOI: 10.1146/annurev-arplant-050718-100049] [Citation(s) in RCA: 630] [Impact Index Per Article: 126.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Enhanced agricultural production through innovative breeding technology is urgently needed to increase access to nutritious foods worldwide. Recent advances in CRISPR/Cas genome editing enable efficient targeted modification in most crops, thus promising to accelerate crop improvement. Here, we review advances in CRISPR/Cas9 and its variants and examine their applications in plant genome editing and related manipulations. We highlight base-editing tools that enable targeted nucleotide substitutions and describe the various delivery systems, particularly DNA-free methods, that have linked genome editing with crop breeding. We summarize the applications of genome editing for trait improvement, development of techniques for fine-tuning gene regulation, strategies for breeding virus resistance, and the use of high-throughput mutant libraries. We outline future perspectives for genome editing in plant synthetic biology and domestication, advances in delivery systems, editing specificity, homology-directed repair, and gene drives. Finally, we discuss the challenges and opportunities for precision plant breeding and its bright future in agriculture.
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Affiliation(s)
- Kunling Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Yanpeng Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Rui Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Huawei Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Genome Editing, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China 100101;
- University of Chinese Academy of Sciences, Beijing, China 100864
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49
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Genetic Modification for Wheat Improvement: From Transgenesis to Genome Editing. BIOMED RESEARCH INTERNATIONAL 2019; 2019:6216304. [PMID: 30956982 PMCID: PMC6431451 DOI: 10.1155/2019/6216304] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 02/08/2019] [Accepted: 02/21/2019] [Indexed: 12/12/2022]
Abstract
To feed the growing human population, global wheat yields should increase to approximately 5 tonnes per ha from the current 3.3 tonnes by 2050. To reach this goal, existing breeding practices must be complemented with new techniques built upon recent gains from wheat genome sequencing, and the accumulated knowledge of genetic determinants underlying the agricultural traits responsible for crop yield and quality. In this review we primarily focus on the tools and techniques available for accessing gene functions which lead to clear phenotypes in wheat. We provide a view of the development of wheat transformation techniques from a historical perspective, and summarize how techniques have been adapted to obtain gain-of-function phenotypes by gene overexpression, loss-of-function phenotypes by expressing antisense RNAs (RNA interference or RNAi), and most recently the manipulation of gene structure and expression using site-specific nucleases, such as CRISPR/Cas9, for genome editing. The review summarizes recent successes in the application of wheat genetic manipulation to increase yield, improve nutritional and health-promoting qualities in wheat, and enhance the crop's resistance to various biotic and abiotic stresses.
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50
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Wang J, Huang F, You X, Hou X. Identification and Functional Characterization of a Cold-Related Protein, BcHHP5, in Pak-Choi ( Brassica rapa ssp. chinensis). Int J Mol Sci 2018; 20:E93. [PMID: 30587842 PMCID: PMC6337265 DOI: 10.3390/ijms20010093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 12/05/2018] [Accepted: 12/19/2018] [Indexed: 01/21/2023] Open
Abstract
In plants, heptahelical proteins (HHPs) have been shown to respond to a variety of abiotic stresses, including cold stress. Up to the present, the regulation mechanism of HHP5 under low temperature stress remains unclear. In this study, BcHHP5 was isolated from Pak-choi (Brassica rapa ssp. chinensis cv. Suzhouqing). Sequence analysis and phylogenetic analysis indicated that BcHHP5 in Pak-choi is similar to AtHHP5 in Arabidopsis thaliana. Structure analysis showed that the structure of the BcHHP5 protein is relatively stable and highly conservative. Subcellular localization indicated that BcHHP5 was localized on the cell membrane and nuclear membrane. Furthermore, real-time quantitative polymerase chain reaction (RT-qPCR) analysis showed that BcHHP5 was induced to express by cold and other abiotic stresses. In Pak-choi, BcHHP5-silenced assay, inhibiting the action of endogenous BcHHP5, indicated that BcHHP5-silenced might have a negative effect on cold tolerance, which was further confirmed. All of these results indicate that BcHHP5 might play a role in abiotic response. This work can serve as a reference for the functional analysis of other cold-related proteins from Pak-choi in the future.
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Affiliation(s)
- Jin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Feiyi Huang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiong You
- College of Sciences, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture/Engineering Research Center of Germplasm Enhancement and Utilization of Horticultural Crops, Ministry of Education, Nanjing Agricultural University, Nanjing 210095, China.
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