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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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Chen C, Hu Y, Ikeuchi M, Jiao Y, Prasad K, Su YH, Xiao J, Xu L, Yang W, Zhao Z, Zhou W, Zhou Y, Gao J, Wang JW. Plant regeneration in the new era: from molecular mechanisms to biotechnology applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2581-2. [PMID: 38833085 DOI: 10.1007/s11427-024-2581-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 03/26/2024] [Indexed: 06/06/2024]
Abstract
Plants or tissues can be regenerated through various pathways. Like animal regeneration, cell totipotency and pluripotency are the molecular basis of plant regeneration. Detailed systematic studies on Arabidopsis thaliana gradually unravel the fundamental mechanisms and principles underlying plant regeneration. Specifically, plant hormones, cell division, epigenetic remodeling, and transcription factors play crucial roles in reprogramming somatic cells and reestablishing meristematic cells. Recent research on basal non-vascular plants and monocot crops has revealed that plant regeneration differs among species, with various plant species using distinct mechanisms and displaying significant differences in regenerative capacity. Conducting multi-omics studies at the single-cell level, tracking plant regeneration processes in real-time, and deciphering the natural variation in regenerative capacity will ultimately help understand the essence of plant regeneration, improve crop regeneration efficiency, and contribute to future crop design.
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Affiliation(s)
- Chunli Chen
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
| | - Yuxin Hu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences (CAS), China National Botanical Garden, Beijing, 100093, China.
| | - Momoko Ikeuchi
- Division of Biological Sciences, Graduate School of Science and Technology, Nara Institute of Science and Technology, Nara, 630-0192, Japan.
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China.
| | - Kalika Prasad
- Indian Institute of Science Education and Research, Pune, 411008, India.
- , Thiruvananthapuram, 695551, India.
| | - Ying Hua Su
- State Key Laboratory of Wheat Improvement, College of Life Sciences, Shandong Agricultural University, Tai'an, 271018, China.
- Sino-German Joint Research Center on Agricultural Biology, Shandong Agricultural University, Tai'an, 271018, China.
| | - Jun Xiao
- Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology (IGDB), CAS, Beijing, 100101, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), IGDB, CAS, Beijing, 100101, China.
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
| | - Weibing Yang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- CEPAMS, SIPPE, CAS, Shanghai, 200032, China.
| | - Zhong Zhao
- Hefei National Laboratory for Physical Sciences at the Microscale, CEMPS, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wenkun Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
| | - Yun Zhou
- Department of Botany and Plant Pathology and Center for Plant Biology, Purdue University, West Lafayette, 47907, USA.
| | - Jian Gao
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China
| | - Jia-Wei Wang
- National Key Laboratory of Plant Molecular Genetics, CEMPS, Institute of Plant Physiology and Ecology (SIPPE), CAS, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Plant Carbon Capture, CAS, Shanghai, 200032, China.
- New Cornerstone Science Laboratory, Shanghai, 200032, China.
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3
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Lee SY, Kang B, Venkatesh J, Lee JH, Lee S, Kim JM, Back S, Kwon JK, Kang BC. Development of virus-induced genome editing methods in Solanaceous crops. HORTICULTURE RESEARCH 2024; 11:uhad233. [PMID: 38222822 PMCID: PMC10782499 DOI: 10.1093/hr/uhad233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/01/2023] [Indexed: 01/16/2024]
Abstract
Genome editing (GE) using CRISPR/Cas systems has revolutionized plant mutagenesis. However, conventional transgene-mediated GE methods have limitations due to the time-consuming generation of stable transgenic lines expressing the Cas9/single guide RNA (sgRNA) module through tissue cultures. Virus-induced genome editing (VIGE) systems have been successfully employed in model plants, such as Arabidopsis thaliana and Nicotiana spp. In this study, we developed two VIGE methods for Solanaceous plants. First, we used the tobacco rattle virus (TRV) vector to deliver sgRNAs into a transgenic tomato (Solanum lycopersicum) line of cultivar Micro-Tom expressing Cas9. Second, we devised a transgene-free GE method based on a potato virus X (PVX) vector to deliver Cas9 and sgRNAs. We designed and cloned sgRNAs targeting Phytoene desaturase in the VIGE vectors and determined optimal conditions for VIGE. We evaluated VIGE efficiency through deep sequencing of the target gene after viral vector inoculation, detecting 40.3% and 36.5% mutation rates for TRV- and PVX-mediated GE, respectively. To improve editing efficiency, we applied a 37°C heat treatment, which increased the editing efficiency by 33% to 46% and 56% to 76% for TRV- and PVX-mediated VIGE, respectively. To obtain edited plants, we subjected inoculated cotyledons to tissue culture, yielding successful editing events. We also demonstrated that PVX-mediated GE can be applied to other Solanaceous crops, such as potato (Solanum tuberosum) and eggplant (Solanum melongena). These simple and highly efficient VIGE methods have great potential for generating genome-edited plants in Solanaceous crops.
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Affiliation(s)
- Seo-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bomi Kang
- Interdisciplinary Program in Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jelli Venkatesh
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Joung-Ho Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seyoung Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Min Kim
- Interdisciplinary Program in Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Seungki Back
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Byoung-Cheorl Kang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program in Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
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Odahara M, Ara MT, Nakagawa R, Horii Y, Ishio S, Ogita S, Numata K. A multiple shoot induction system for peptide-mediated gene delivery into plastids in Arabidopsis thaliana, Nicotiana benthamiana, and Fragaria× ananassa. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:263-271. [PMID: 38434117 PMCID: PMC10905367 DOI: 10.5511/plantbiotechnology.23.0501a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/01/2023] [Indexed: 03/05/2024]
Abstract
The plastid is a promising target for the production of valuable biomolecules via genetic engineering. We recently developed a plastid-specific gene delivery system for leaves or seedlings using KH-AtOEP34, a functional peptide composed of the polycationic DNA-binding peptide KH and the Arabidopsis thaliana plastid-targeting peptide OEP34. Here, we established a liquid culture system for inducing multiple shoots in the model plants A. thaliana and Nicotiana benthamiana and the crop plant strawberry (Fragaria×ananassa) and tested the use of these plant materials for peptide-mediated gene delivery to plastids. Our liquid culture system efficiently induced multiple shoots that were enriched in meristems. Using these meristems, we performed KH-AtOEP34-mediated gene delivery to plastids and tested the delivery and integration of a cassette composed of the spectinomycin resistance gene aadA, the GFP reporter gene, and sequences homologous to plastid DNA. Genotyping PCR revealed the integration of the cassette DNA into plastid DNA several days after delivery in all three plants. Confocal laser scanning microscopy and immunoblotting confirmed the presence of plasmid-derived GFP in the plastids of meristems, indicating that the plasmid DNA was successfully integrated into plastid DNA and that the cassette was expressed. These results suggest the meristems developed in our liquid culture system are applicable to peptide-mediated delivery of exogeneous DNA into plastids. The multiple shoots generated in our liquid novel culture system represent promising materials for in planta peptide-mediated plastid transformation in combination with spectinomycin selection.
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Affiliation(s)
- Masaki Odahara
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Most Tanziman Ara
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Remi Nakagawa
- Resources Group, Tsukuba Research Institute, Sumitomo Forestry Co., Ltd., Tsukuba, Ibaraki 300-2646, Japan
| | - Yoko Horii
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Shougo Ishio
- Resources Group, Tsukuba Research Institute, Sumitomo Forestry Co., Ltd., Tsukuba, Ibaraki 300-2646, Japan
| | - Shinjiro Ogita
- Department of Local Resources, Faculty of Bioresource Sciences, Prefectural University of Hiroshima, Shobara, Hiroshima 727-0023, Japan
| | - Keiji Numata
- Biomacromolecule Research Team, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
- Department of Material Chemistry, Kyoto University, Kyoto, Kyoto 615-8510, Japan
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Tamizi AA, Md-Yusof AA, Mohd-Zim NA, Nazaruddin NH, Sekeli R, Zainuddin Z, Samsulrizal NH. Agrobacterium-mediated in planta transformation of cut coleoptile: a new, simplified, and tissue culture-independent method to deliver the CRISPR/Cas9 system in rice. Mol Biol Rep 2023; 50:9353-9366. [PMID: 37819494 DOI: 10.1007/s11033-023-08842-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/25/2023] [Indexed: 10/13/2023]
Abstract
BACKGROUND Agrobacterium-mediated transformation and particle bombardment are the two common approaches for genome editing in plant species using CRISPR/Cas9 system. Both methods require careful manipulations of undifferentiated cells and tissue culture to regenerate the potentially edited plants. However, tissue culture techniques are laborious and time-consuming. METHODS AND RESULTS In this study, we have developed a simplified, tissue culture-independent protocol to deliver the CRISPR/Cas9 system through in planta transformation in Malaysian rice (Oryza sativa L. subsp. indica cv. MR 219). Sprouting seeds with cut coleoptile were used as the target for the infiltration by Agrobacterium tumefaciens and we achieved 9% transformation efficiency. In brief, the dehusked seeds were surface-sterilised and imbibed, and the coleoptile was cut to expose the apical meristem. Subsequently, the cut coleoptile was inoculated with A. tumefaciens strain EHA105 harbouring CRISPR/Cas9 expression vector. The co-cultivation was conducted for five to six days in a dark room (25 ± 2 °C) followed by rooting, acclimatisation, and growing phases. Two-month-old plant leaves were then subjected to a hygromycin selection, and hygromycin-resistant plants were identified as putative transformants. Further validation through the polymerase chain reaction verified the integration of the Cas9 gene in four putative T0 lines. During the fruiting stage, it was confirmed that the Cas9 gene was still present in three randomly selected tillers from two 4-month-old transformed plants. CONCLUSION This protocol provides a rapid method for editing the rice genome, bypassing the need for tissue culture. This article is the first to report the delivery of the CRISPR/Cas9 system for in planta transformation in rice.
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Affiliation(s)
- Amin-Asyraf Tamizi
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400, Serdang, Selangor, Malaysia
| | - Anis Afuza Md-Yusof
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia
| | - Nurul Asyikin Mohd-Zim
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia
- FGV R&D Sdn. Bhd, FGV Innovation Centre, PT 23417 Lengkuk Teknologi, 71760, Bandar Enstek, Negeri Sembilan, Malaysia
| | - Nazrul Hisham Nazaruddin
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400, Serdang, Selangor, Malaysia
| | - Rogayah Sekeli
- Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400, Serdang, Selangor, Malaysia.
| | - Zarina Zainuddin
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia
- Plant Productivity and Sustainable Resource Unit, Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia
| | - Nurul Hidayah Samsulrizal
- Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia.
- Plant Productivity and Sustainable Resource Unit, Department of Plant Science, Kulliyyah of Science, International Islamic University Malaysia (IIUM), 25200, Kuantan, Pahang, Malaysia.
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Mann CWG, Sawyer A, Gardiner DM, Mitter N, Carroll BJ, Eamens AL. RNA-Based Control of Fungal Pathogens in Plants. Int J Mol Sci 2023; 24:12391. [PMID: 37569766 PMCID: PMC10418863 DOI: 10.3390/ijms241512391] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Our duty to conserve global natural ecosystems is increasingly in conflict with our need to feed an expanding population. The use of conventional pesticides not only damages the environment and vulnerable biodiversity but can also still fail to prevent crop losses of 20-40% due to pests and pathogens. There is a growing call for more ecologically sustainable pathogen control measures. RNA-based biopesticides offer an eco-friendly alternative to the use of conventional fungicides for crop protection. The genetic modification (GM) of crops remains controversial in many countries, though expression of transgenes inducing pathogen-specific RNA interference (RNAi) has been proven effective against many agronomically important fungal pathogens. The topical application of pathogen-specific RNAi-inducing sprays is a more responsive, GM-free approach to conventional RNAi transgene-based crop protection. The specific targeting of essential pathogen genes, the development of RNAi-nanoparticle carrier spray formulations, and the possible structural modifications to the RNA molecules themselves are crucial to the success of this novel technology. Here, we outline the current understanding of gene silencing pathways in plants and fungi and summarize the pioneering and recent work exploring RNA-based biopesticides for crop protection against fungal pathogens, with a focus on spray-induced gene silencing (SIGS). Further, we discuss factors that could affect the success of RNA-based control strategies, including RNA uptake, stability, amplification, and movement within and between the plant host and pathogen, as well as the cost and design of RNA pesticides.
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Affiliation(s)
- Christopher W. G. Mann
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Anne Sawyer
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Donald M. Gardiner
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Neena Mitter
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia; (D.M.G.); (N.M.)
| | - Bernard J. Carroll
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia; (C.W.G.M.); (A.S.); (B.J.C.)
| | - Andrew L. Eamens
- School of Health, University of the Sunshine Coast, Maroochydore, QLD 4558, Australia
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Nishiguchi M, Futamura N, Endo M, Mikami M, Toki S, Katahata SI, Ohmiya Y, Konagaya KI, Nanasato Y, Taniguchi T, Maruyama TE. CRISPR/Cas9-mediated disruption of CjACOS5 confers no-pollen formation on sugi trees (Cryptomeria japonica D. Don). Sci Rep 2023; 13:11779. [PMID: 37479866 PMCID: PMC10361980 DOI: 10.1038/s41598-023-38339-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 07/06/2023] [Indexed: 07/23/2023] Open
Abstract
Sugi (Cryptomeria japonica D. Don) is an economically important coniferous tree in Japan. However, abundant sugi pollen grains are dispersed and transported by the wind each spring and cause a severe pollen allergy syndrome (Japanese cedar pollinosis). The use of pollen-free sugi that cannot produce pollen has been thought as a countermeasure to Japanese cedar pollinosis. The sugi CjACOS5 gene is an ortholog of Arabidopsis ACOS5 and rice OsACOS12, which encode an acyl-CoA synthetase that is involved in the synthesis of sporopollenin in pollen walls. To generate pollen-free sugi, we mutated CjACOS5 using the CRISPR/Cas9 system. As a result of sugi transformation mediated by Agrobacterium tumefaciens harboring the CjACOS5-targeted CRISPR/Cas9 vector, 1 bp-deleted homo biallelic mutant lines were obtained. Chimeric mutant lines harboring both mutant and wild-type CjACOS5 genes were also generated. The homo biallelic mutant lines had no-pollen in male strobili, whereas chimeric mutant lines had male strobili with or without pollen grains. Our results suggest that CjACOS5 is essential for the production of pollen in sugi and that its disruption is useful for the generation of pollen-free sugi. In addition to conventional transgenic technology, genome editing technology, including CRISPR/Cas9, can confer new traits on sugi.
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Affiliation(s)
- Mitsuru Nishiguchi
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan.
| | - Norihiro Futamura
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
| | - Masafumi Mikami
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), 1-2 Owashi, Tsukuba, Ibaraki, 305-8634, Japan
- Graduate School of Nanobioscience, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama, Kanagawa, 236-0027, Japan
- Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga, 520-2194, Japan
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Shin-Ichiro Katahata
- Faculty of Applied Biological Sciences, Gifu University, Yanagido 1-1, Gifu, 501-1193, Japan
| | - Yasunori Ohmiya
- Extension and International Cooperation Department, Forest Tree Breeding Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Ken-Ichi Konagaya
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Toru Taniguchi
- Forest Bio-Research Center, Forestry and Forest Products Research Institute (FFPRI), 3809-1 Ishi, Juo, Hitachi, Ibaraki, 319-1301, Japan
| | - Tsuyoshi Emilio Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute (FFPRI), 1 Matsunosato, Tsukuba, Ibaraki, 305-8687, Japan
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8
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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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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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10
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Yanagawa Y, Suenaga Y, Iijima Y, Endo M, Sanada N, Katoh E, Toki S, Okino A, Mitsuhara I. Genome editing by introduction of Cas9/sgRNA into plant cells using temperature-controlled atmospheric pressure plasma. PLoS One 2023; 18:e0281767. [PMID: 36795787 PMCID: PMC9934431 DOI: 10.1371/journal.pone.0281767] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 01/31/2023] [Indexed: 02/17/2023] Open
Abstract
Previously, we developed a technique to introduce a superfolder green fluorescent protein (sGFP) fusion protein directly into plant cells using atmospheric-pressure plasma. In this study, we attempted genome editing using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein 9) system using this protein introduction technique. As an experimental system to evaluate genome editing, we utilized transgenic reporter plants carrying the reporter genes L-(I-SceI)-UC and sGFP-waxy-HPT. The L-(I-SceI)-UC system allowed the detection of successful genome editing by measuring the chemiluminescent signal observed upon re-functionalization of the luciferase (LUC) gene following genome editing. Similarly, the sGFP-waxy-HPT system conferred hygromycin resistance caused by hygromycin phosphotransferase (HPT) during genome editing. CRISPR/Cas9 ribonucleoproteins targeting these reporter genes were directly introduced into rice calli or tobacco leaf pieces after treatment with N2 and/or CO2 plasma. Cultivation of the treated rice calli on a suitable medium plate produced the luminescence signal, which was not observed in the negative control. Four types of genome-edited sequences were obtained upon sequencing the reporter genes of genome-edited candidate calli. sGFP-waxy-HPT-carrying tobacco cells exhibited hygromycin resistance during genome editing. After repeated cultivation of the treated tobacco leaf pieces on a regeneration medium plate, the calli were observed with leaf pieces. A green callus that was hygromycin-resistant was harvested, and a genome-edited sequence in the tobacco reporter gene was confirmed. As direct introduction of the Cas9/sgRNA (single guide RNA) complex using plasma enables genome editing in plants without any DNA introduction, this method is expected to be optimized for many plant species and may be widely applied for plant breeding in the future.
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Affiliation(s)
- Yuki Yanagawa
- Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, Japan
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa, Japan
- * E-mail: , (YY); (IM)
| | - Yuma Suenaga
- Laboratory for Future Interdisciplinary Research of Science and Technology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Yusuke Iijima
- Laboratory for Future Interdisciplinary Research of Science and Technology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Masaki Endo
- Institute of Agrobiological Sciences, 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
| | - Naoko Sanada
- Advanced Analysis Center, NARO, Tsukuba, Ibaraki, Japan
| | - Etsuko Katoh
- Advanced Analysis Center, NARO, Tsukuba, Ibaraki, Japan
- Faculty of Food and Nutritional Science, Toyo University, Ora-gun, Gunma, Japan
| | - Seiichi Toki
- Institute of Agrobiological Sciences, 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
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, Japan
| | - Akitoshi Okino
- Laboratory for Future Interdisciplinary Research of Science and Technology, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Kanagawa, Japan
| | - Ichiro Mitsuhara
- Institute of Agrobiological Sciences, NARO, Tsukuba, Ibaraki, Japan
- * E-mail: , (YY); (IM)
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Touzdjian Pinheiro Kohlrausch Távora F, de Assis dos Santos Diniz F, de Moraes Rêgo-Machado C, Chagas Freitas N, Barbosa Monteiro Arraes F, Chumbinho de Andrade E, Furtado LL, Osiro KO, Lima de Sousa N, Cardoso TB, Márcia Mertz Henning L, Abrão de Oliveira Molinari P, Feingold SE, Hunter WB, Fátima Grossi de Sá M, Kobayashi AK, Lima Nepomuceno A, Santiago TR, Correa Molinari HB. CRISPR/Cas- and Topical RNAi-Based Technologies for Crop Management and Improvement: Reviewing the Risk Assessment and Challenges Towards a More Sustainable Agriculture. Front Bioeng Biotechnol 2022; 10:913728. [PMID: 35837551 PMCID: PMC9274005 DOI: 10.3389/fbioe.2022.913728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated gene (Cas) system and RNA interference (RNAi)-based non-transgenic approaches are powerful technologies capable of revolutionizing plant research and breeding. In recent years, the use of these modern technologies has been explored in various sectors of agriculture, introducing or improving important agronomic traits in plant crops, such as increased yield, nutritional quality, abiotic- and, mostly, biotic-stress resistance. However, the limitations of each technique, public perception, and regulatory aspects are hindering its wide adoption for the development of new crop varieties or products. In an attempt to reverse these mishaps, scientists have been researching alternatives to increase the specificity, uptake, and stability of the CRISPR and RNAi system components in the target organism, as well as to reduce the chance of toxicity in nontarget organisms to minimize environmental risk, health problems, and regulatory issues. In this review, we discuss several aspects related to risk assessment, toxicity, and advances in the use of CRISPR/Cas and topical RNAi-based technologies in crop management and breeding. The present study also highlights the advantages and possible drawbacks of each technology, provides a brief overview of how to circumvent the off-target occurrence, the strategies to increase on-target specificity, the harm/benefits of association with nanotechnology, the public perception of the available techniques, worldwide regulatory frameworks regarding topical RNAi and CRISPR technologies, and, lastly, presents successful case studies of biotechnological solutions derived from both technologies, raising potential challenges to reach the market and being social and environmentally safe.
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Affiliation(s)
| | | | | | | | | | | | | | - Karen Ofuji Osiro
- Department of Phytopathology, University of Brasília, Brasília, Brazil
- Embrapa Agroenergy, Brasília, Brazil
| | | | | | | | | | | | - Wayne B. Hunter
- USDA-ARS, U.S. Horticultural Research Laboratory, Fort Pierce, FL, United States
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12
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Viswan A, Yamagishi A, Hoshi M, Furuhata Y, Kato Y, Makimoto N, Takeshita T, Kobayashi T, Iwata F, Kimura M, Yoshizumi T, Nakamura C. Microneedle Array-Assisted, Direct Delivery of Genome-Editing Proteins Into Plant Tissue. FRONTIERS IN PLANT SCIENCE 2022; 13:878059. [PMID: 35812975 PMCID: PMC9263851 DOI: 10.3389/fpls.2022.878059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Genome editing in plants employing recombinant DNA often results in the incorporation of foreign DNA into the host genome. The direct delivery of genome-editing proteins into plant tissues is desired to prevent undesirable genetic alterations. However, in most currently available methods, the point of entry of the genome-editing proteins cannot be controlled and time-consuming processes are required to select the successfully transferred samples. To overcome these limitations, we considered a novel microneedle array (MNA)-based delivery system, in which the needles are horizontally aligned from the substrate surface, giving it a comb-like configuration. We aimed to deliver genome-editing proteins directly into the inner layers of leaf tissues; palisade, the spongy and subepidermal L2 layers of the shoot apical meristem (SAM) which include cells that can differentiate into germlines. The array with needles 2 μm wide and 60 μm long was effective in inserting into Arabidopsis thaliana leaves and Glycine max (L.) Merr. (soybeans) SAM without the needles buckling or breaking. The setup was initially tested for the delivery of Cre recombinase into the leaves of the reporter plant A. thaliana by quantifying the GUS (β-glucuronidase) expression that occurred by the recombination of the loxP sites. We observed GUS expression at every insertion. Additionally, direct delivery of Cas9 ribonucleoprotein (RNP) targeting the PDS11/18 gene in soybean SAM showed an 11 bp deletion in the Cas9 RNP target site. Therefore, this method effectively delivered genome-editing proteins into plant tissues with precise control over the point of entry.
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Affiliation(s)
- Anchu Viswan
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Ayana Yamagishi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Masamichi Hoshi
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yuichi Furuhata
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Yoshio Kato
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Natsumi Makimoto
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Toshihiro Takeshita
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Takeshi Kobayashi
- Sensing System Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Futoshi Iwata
- Graduate School of Medical Photonics, Shizuoka University, Hamamatsu, Japan
| | - Mitsuhiro Kimura
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Japan
| | - Takeshi Yoshizumi
- Faculty of Agriculture, Takasaki University of Health and Welfare, Takasaki, Japan
| | - Chikashi Nakamura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
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13
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CRISPR/Cas9 Technique for Temperature, Drought, and Salinity Stress Responses. Curr Issues Mol Biol 2022; 44:2664-2682. [PMID: 35735623 PMCID: PMC9221872 DOI: 10.3390/cimb44060182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Global warming and climate change have severely affected plant growth and food production. Therefore, minimizing these effects is required for sustainable crop yields. Understanding the molecular mechanisms in response to abiotic stresses and improving agricultural traits to make crops tolerant to abiotic stresses have been going on unceasingly. To generate desirable varieties of crops, traditional and molecular breeding techniques have been tried, but both approaches are time-consuming. Clustered regularly interspaced short palindromic repeat/Cas9 (CRISPR/Cas9) and transcription activator-like effector nucleases (TALENs) are genome-editing technologies that have recently attracted the attention of plant breeders for genetic modification. These technologies are powerful tools in the basic and applied sciences for understanding gene function, as well as in the field of crop breeding. In this review, we focus on the application of genome-editing systems in plants to understand gene function in response to abiotic stresses and to improve tolerance to abiotic stresses, such as temperature, drought, and salinity stresses.
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14
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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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15
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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: 13] [Impact Index Per Article: 6.5] [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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16
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Tanaka Y, Nanasato Y, Omura K, Endoh K, Kawano T, Iwasaki T. Direct protein delivery into intact plant cells using polyhistidine peptides. Biosci Biotechnol Biochem 2021; 85:1405-1414. [PMID: 33791772 DOI: 10.1093/bbb/zbab055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/23/2021] [Indexed: 02/06/2023]
Abstract
Polyhistidine peptides (PHPs), sequences comprising only histidine residues (>His8), are effective cell-penetrating peptides for plant cells. Using PHP-fusion proteins, we aimed to deliver proteins into cultured plant cells from Nicotiana tabacum, Oryza sativa, and Cryptomeria japonica. Co-cultivation of cultured cells with fusion proteins combining maltose-binding protein (MBP), red fluorescent protein (RFP), and various PHPs (MBP-RFP-His8-His20) in one polypeptide showed the cellular uptake of fusion proteins in all plant cell lines. Maximum intracellular fluorescence was shown in MBP-RFP-His20. Further, adenylate cyclase (CyaA), a synthase of cyclic adenosine monophosphate (cAMP) activated by cytosolic calmodulin, was used as a reporter for protein delivery in living cells. A fusion protein combining MBP, RFP, CyaA, and His20 (MBP-RFP-CyaA-His20) was delivered into plant cells and increased intracellular fluorescence and cAMP production in all cell lines. The present study demonstrates that PHPs are effective carriers of proteins into the intracellular space of various cultured plant cells.
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Affiliation(s)
- Yoshino Tanaka
- Department of Agriculture, Graduate School of Sustainability Science, Tottori University, Tottori, Japan
| | - Yoshihiko Nanasato
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Kousei Omura
- Department of Agriculture, Graduate School of Sustainability Science, Tottori University, Tottori, Japan
| | - Keita Endoh
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Ibaraki, Japan
| | - Tsuyoshi Kawano
- Department of Agriculture, Graduate School of Sustainability Science, Tottori University, Tottori, Japan
| | - Takashi Iwasaki
- Department of Agriculture, Graduate School of Sustainability Science, Tottori University, Tottori, Japan
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17
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Pickerill ES, Bernstein DA. CRISPR mediated genome editing, a tool to dissect RNA modification processes. Methods Enzymol 2021; 658:435-452. [PMID: 34517958 DOI: 10.1016/bs.mie.2021.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Though over 100 distinct RNA modifications have been identified, the roles for many of these modifications in vivo remain unknown. Genome editing is one tool investigators are using to better understand the roles these modifications play and the consequences of their absence. In this chapter, we describe how CRISPR mediated genome editing can be used to interrogate the process of RNA modification in C. albicans. Furthermore, we discuss how the protocols described can be altered to meet experimental demands. The underlying theory on which these protocols are based are applicable to a variety of model systems. The protocols described utilize the widely used S. pyogenes Cas9, but the field of genome editing is quickly evolving. We discuss the recent developments of more flexible CRISPR systems that can target a greater number of sites in the genome. These and other advancements make CRISPR mediated genome editing a practical methodology to investigate RNA modification.
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Affiliation(s)
- Ethan S Pickerill
- Department of Biology, Ball State University, Muncie, IN, United States
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18
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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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19
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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: 33] [Impact Index Per Article: 11.0] [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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Nuccio ML, Claeys H, Heyndrickx KS. CRISPR-Cas technology in corn: a new key to unlock genetic knowledge and create novel products. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:11. [PMID: 37309473 PMCID: PMC10236071 DOI: 10.1007/s11032-021-01200-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/04/2021] [Indexed: 06/14/2023]
Abstract
Since its inception in 2012, CRISPR-Cas technologies have taken the life science community by storm. Maize genetics research is no exception. Investigators around the world have adapted CRISPR tools to advance maize genetics research in many ways. The principle application has been targeted mutagenesis to confirm candidate genes identified using map-based methods. Researchers are also developing tools to more effectively apply CRISPR-Cas technologies to maize because successful application of CRISPR-Cas relies on target gene identification, guide RNA development, vector design and construction, CRISPR-Cas reagent delivery to maize tissues, and plant characterization, each contributing unique challenges to CRISPR-Cas efficacy. Recent advances continue to chip away at major barriers that prevent more widespread use of CRISPR-Cas technologies in maize, including germplasm-independent delivery of CRISPR-Cas reagents and production of high-resolution genomic data in relevant germplasm to facilitate CRISPR-Cas experimental design. This has led to the development of novel breeding tools to advance maize genetics and demonstrations of how CRISPR-Cas technologies might be used to enhance maize germplasm. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01200-9.
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Liu Y, Luo W, Linghu Q, Abe F, Hisano H, Sato K, Kamiya Y, Kawaura K, Onishi K, Endo M, Toki S, Hamada H, Nagira Y, Taoka N, Imai R. In planta Genome Editing in Commercial Wheat Varieties. FRONTIERS IN PLANT SCIENCE 2021; 12:648841. [PMID: 33790930 PMCID: PMC8006942 DOI: 10.3389/fpls.2021.648841] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Accepted: 02/19/2021] [Indexed: 05/03/2023]
Abstract
Limitations for the application of genome editing technologies on elite wheat (Triticum aestivum L.) varieties are mainly due to the dependency on in vitro culture and regeneration capabilities. Recently, we developed an in planta particle bombardment (iPB) method which has increased process efficiency since no culture steps are required to create stably genome-edited wheat plants. Here, we report the application of the iPB method to commercially relevant Japanese elite wheat varieties. The biolistic delivery of gold particles coated with plasmids expressing CRISPR/Cas9 components designed to target TaQsd1 were bombarded into the embryos of imbibed seeds with their shoot apical meristem (SAM) exposed. Mutations in the target gene were subsequently analyzed within flag leaf tissue by using cleaved amplified polymorphic sequence (CAPS) analysis. A total of 9/358 (2.51%) of the bombarded plants (cv. "Haruyokoi," spring type) carried mutant alleles in the tissue. Due to the chimeric nature of the T0 plants, only six of them were inherited to the next (T1) generation. Genotypic analysis of the T2 plants revealed a single triple-recessive homozygous mutant of the TaQsd1 gene. Compared to wild type, the homozygous mutant exhibited a 7 days delay in the time required for 50% seed germination. The iPB method was also applied to two elite winter cultivars, "Yumechikara" and "Kitanokaori," which resulted in successful genome editing at slightly lower efficiencies as compared to "Haruyokoi." Taken together, this report demonstrates that the in planta genome editing method through SAM bombardment can be applicable to elite wheat varieties that are otherwise reluctant to callus culture.
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Affiliation(s)
- Yuelin Liu
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Weifeng Luo
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Qianyan Linghu
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Fumitaka Abe
- Division of Basic Research, Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Hiroshi Hisano
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Yoko Kamiya
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kanako Kawaura
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Kazumitsu Onishi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Japan
| | - Masaki Endo
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Seiichi Toki
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Haruyasu Hamada
- Biotechnology Research Laboratories, Pharma and Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago, Japan
| | - Yozo Nagira
- Biotechnology Research Laboratories, Pharma and Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago, Japan
| | - Naoaki Taoka
- Biotechnology Research Laboratories, Pharma and Supplemental Nutrition Solutions Vehicle, Kaneka Corporation, Takasago, Japan
| | - Ryozo Imai
- Division of Applied Genetics, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
- *Correspondence: Ryozo Imai,
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Chen G, Zhou Y, Kishchenko O, Stepanenko A, Jatayev S, Zhang D, Borisjuk N. Gene editing to facilitate hybrid crop production. Biotechnol Adv 2020; 46:107676. [PMID: 33285253 DOI: 10.1016/j.biotechadv.2020.107676] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 11/23/2020] [Accepted: 11/28/2020] [Indexed: 11/18/2022]
Abstract
Capturing heterosis (hybrid vigor) is a promising way to increase productivity in many crops; hybrid crops often have superior yields, disease resistance, and stress tolerance compared with their parental inbred lines. The full utilization of heterosis faces a number of technical problems related to the specifics of crop reproductive biology, such as difficulties with generating and maintaining male-sterile lines and the low efficiency of natural cross-pollination for some genetic combinations. Innovative technologies, such as development of artificial in vitro systems for hybrid production and apomixis-based systems for maintenance of the resulting heterotic progeny, may substantially facilitate the production of hybrids. Genome editing using specifically targeted nucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (CRISPR/Cas9) systems, which recognize targets by RNA:DNA complementarity, has recently become an integral part of research and development in life science. In this review, we summarize the progress of genome editing technologies for facilitating the generation of mutant male sterile lines, applications of haploids for hybrid production, and the use of apomixis for the clonal propagation of elite hybrid lines.
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Affiliation(s)
- Guimin Chen
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China
| | - Yuzhen Zhou
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.
| | - Olena Kishchenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China; Institute of Cell Biology & Genetic Engineering, National Academy of Science of Ukraine, Kyiv, Ukraine.
| | - Anton Stepanenko
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China; Institute of Cell Biology & Genetic Engineering, National Academy of Science of Ukraine, Kyiv, Ukraine.
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic & Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China; School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA, Australia.
| | - Nikolai Borisjuk
- Jiangsu Key Laboratory for Eco-Agricultural Biotechnology around Hongze Lake, School of Life Sciences, Huaiyin Normal University, Huai'an, China; Jiangsu Collaborative Innovation Centre of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Huai'an, China.
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