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Zhou Q, Li S, Zhao M, Liu Y, He N, Zhou X, Zhou D, Qian Z. Subchronic feeding study of glyphosate-tolerant maize GG2 with the gr79-epsps and gat genes in Wistar Han RCC rats. Regul Toxicol Pharmacol 2023; 145:105520. [PMID: 37884076 DOI: 10.1016/j.yrtph.2023.105520] [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: 07/29/2023] [Revised: 10/07/2023] [Accepted: 10/18/2023] [Indexed: 10/28/2023]
Abstract
The genetically modified (GM) maize GG2 contains gr79-epsps and gat genes, conferring glyphosate tolerance. The present study aimed to investigate potential effects of maize GG2 in a 90-day subchronic feeding study on Wistar Han RCC rats. Maize grains from GG2 or non-GM maize were incorporated into diets at concentrations of 25% and 50% and administered to Wistar Han RCC rats (n = 10/sex/group) for 90 days. The basal-diet group of rats (n = 10/sex/group) were fed with common commercialized rodent diet. Compared with rats fed with the corresponding non-GM maize and the basal-diet, no biologically relevant differences were observed in rats fed with the maize GG2, according to the results of body weight/gain, feed consumption/utilization, clinical signs, mortality, ophthalmology, clinical pathology (hematology, prothrombin time, urinalysis, serum chemistry), organ weights, and gross and microscopic pathology. Under the conditions of this study, these results indicated that maize GG2 is as safe as the non-GM maize in this 90-day feeding study.
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Affiliation(s)
- Qinghong Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Shufei Li
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Miao Zhao
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Yinghua Liu
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Ning He
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Xiaoli Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Dianming Zhou
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China
| | - Zhiyong Qian
- Department of Toxicology, Tianjin Centers for Disease Control and Prevention, Tianjin, 300011, China.
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2
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Singh C, Kumar R, Sehgal H, Bhati S, Singhal T, Gayacharan, Nimmy MS, Yadav R, Gupta SK, Abdallah NA, Hamwieh A, Kumar R. Unclasping potentials of genomics and gene editing in chickpea to fight climate change and global hunger threat. Front Genet 2023; 14:1085024. [PMID: 37144131 PMCID: PMC10153629 DOI: 10.3389/fgene.2023.1085024] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 03/24/2023] [Indexed: 09/09/2023] Open
Abstract
Genomics and genome editing promise enormous opportunities for crop improvement and elementary research. Precise modification in the specific targeted location of a genome has profited over the unplanned insertional events which are generally accomplished employing unadventurous means of genetic modifications. The advent of new genome editing procedures viz; zinc finger nucleases (ZFNs), homing endonucleases, transcription activator like effector nucleases (TALENs), Base Editors (BEs), and Primer Editors (PEs) enable molecular scientists to modulate gene expressions or create novel genes with high precision and efficiency. However, all these techniques are exorbitant and tedious since their prerequisites are difficult processes that necessitate protein engineering. Contrary to first generation genome modifying methods, CRISPR/Cas9 is simple to construct, and clones can hypothetically target several locations in the genome with different guide RNAs. Following the model of the application in crop with the help of the CRISPR/Cas9 module, various customized Cas9 cassettes have been cast off to advance mark discrimination and diminish random cuts. The present study discusses the progression in genome editing apparatuses, and their applications in chickpea crop development, scientific limitations, and future perspectives for biofortifying cytokinin dehydrogenase, nitrate reductase, superoxide dismutase to induce drought resistance, heat tolerance and higher yield in chickpea to encounter global climate change, hunger and nutritional threats.
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Affiliation(s)
- Charul Singh
- USBT, Guru Govind Singh Indraprastha University, Delhi, India
| | - Ramesh Kumar
- Department of Biochemistry, University of Allahabad Prayagraj, Prayagraj, India
| | - Hansa Sehgal
- Department of Biological Sciences, Birla Institute of Technology and Sciences, Pilani, India
| | - Sharmista Bhati
- School of Biotechnology, Gautam Buddha University, Greater Noida, India
| | - Tripti Singhal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gayacharan
- Division of Germplasm Evaluation, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - M. S. Nimmy
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | | | | | | | - Aladdin Hamwieh
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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3
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Sharma P, Pandey A, Malviya R, Dey S, Karmakar S, Gayen D. Genome editing for improving nutritional quality, post-harvest shelf life and stress tolerance of fruits, vegetables, and ornamentals. Front Genome Ed 2023; 5:1094965. [PMID: 36911238 PMCID: PMC9998953 DOI: 10.3389/fgeed.2023.1094965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 02/03/2023] [Indexed: 03/14/2023] Open
Abstract
Agricultural production relies on horticultural crops, including vegetables, fruits, and ornamental plants, which sustain human life. With an alarming increase in human population and the consequential need for more food, it has become necessary for increased production to maintain food security. Conventional breeding has subsidized the development of improved verities but to enhance crop production, new breeding techniques need to be acquired. CRISPR-Cas9 system is a unique and powerful genome manipulation tool that can change the DNA in a precise way. Based on the bacterial adaptive immune system, this technique uses an endonuclease that creates double-stranded breaks (DSBs) at the target loci under the guidance of a single guide RNA. These DSBs can be repaired by a cellular repair mechanism that installs small insertion and deletion (indels) at the cut sites. When equated to alternate editing tools like ZFN, TALENs, and meganucleases, CRISPR- The cas-based editing tool has quickly gained fast-forward for its simplicity, ease to use, and low off-target effect. In numerous horticultural and industrial crops, the CRISPR technology has been successfully used to enhance stress tolerance, self-life, nutritional improvements, flavor, and metabolites. The CRISPR-based tool is the most appropriate one with the prospective goal of generating non-transgenic yields and avoiding the regulatory hurdles to release the modified crops into the market. Although several challenges for editing horticultural, industrial, and ornamental crops remain, this new novel nuclease, with its crop-specific application, makes it a dynamic tool for crop improvement.
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Affiliation(s)
- Punam Sharma
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Anuradha Pandey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Rinku Malviya
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | - Sharmistha Dey
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
| | | | - Dipak Gayen
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, India
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4
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Shcherban AB. Plant genome modification: from induced mutagenesis to genome editing. Vavilovskii Zhurnal Genet Selektsii 2022; 26:684-696. [DOI: 10.18699/vjgb-22-83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/20/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Affiliation(s)
- A. B. Shcherban
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RAS
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5
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Villalobos-López MA, Arroyo-Becerra A, Quintero-Jiménez A, Iturriaga G. Biotechnological Advances to Improve Abiotic Stress Tolerance in Crops. Int J Mol Sci 2022; 23:12053. [PMID: 36233352 PMCID: PMC9570234 DOI: 10.3390/ijms231912053] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/02/2022] [Accepted: 10/06/2022] [Indexed: 11/16/2022] Open
Abstract
The major challenges that agriculture is facing in the twenty-first century are increasing droughts, water scarcity, flooding, poorer soils, and extreme temperatures due to climate change. However, most crops are not tolerant to extreme climatic environments. The aim in the near future, in a world with hunger and an increasing population, is to breed and/or engineer crops to tolerate abiotic stress with a higher yield. Some crop varieties display a certain degree of tolerance, which has been exploited by plant breeders to develop varieties that thrive under stress conditions. Moreover, a long list of genes involved in abiotic stress tolerance have been identified and characterized by molecular techniques and overexpressed individually in plant transformation experiments. Nevertheless, stress tolerance phenotypes are polygenetic traits, which current genomic tools are dissecting to exploit their use by accelerating genetic introgression using molecular markers or site-directed mutagenesis such as CRISPR-Cas9. In this review, we describe plant mechanisms to sense and tolerate adverse climate conditions and examine and discuss classic and new molecular tools to select and improve abiotic stress tolerance in major crops.
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Affiliation(s)
- Miguel Angel Villalobos-López
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Analilia Arroyo-Becerra
- Laboratorio de Genómica Funcional y Biotecnología de Plantas, Centro de Investigación en Biotecnología Aplicada, Instituto Politécnico Nacional, Ex-Hacienda San Juan Molino Carretera Estatal Km 1.5, Santa Inés-Tecuexcomac-Tepetitla 90700, Tlaxcala, Mexico
| | - Anareli Quintero-Jiménez
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
| | - Gabriel Iturriaga
- División de Estudios de Posgrado e Investigación, Tecnológico Nacional de México/I.T. Roque, Km. 8 Carretera Celaya-Juventino Rosas, Roque, Celaya 38110, Guanajato, Mexico
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Dhugga KS. Gene Editing to Accelerate Crop Breeding. FRONTIERS IN PLANT SCIENCE 2022; 13:889995. [PMID: 35712601 PMCID: PMC9196881 DOI: 10.3389/fpls.2022.889995] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/09/2022] [Indexed: 06/07/2023]
Abstract
Recent advances in biotechnology have helped increase tissue transformation efficiency and the frequency and specificity of gene editing to an extent that introducing allelic variants directly in elite varieties has become possible. In comparison to the conventional approach of crossing an elite recipient line with an exotic donor parent to introduce the trait of interest followed by repeated backcrossing, direct introduction of major-effect allelic variants into elite varieties saves time and resources, and eliminates yield drag resulting from the residual donor genes at the end of backcrossing.
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Affiliation(s)
- Kanwarpal S. Dhugga
- International Center for Maize and Wheat Improvement (CIMMYT), El Batan, Mexico
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7
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Van Vu T, Das S, Hensel G, Kim JY. Genome editing and beyond: what does it mean for the future of plant breeding? PLANTA 2022; 255:130. [PMID: 35587292 PMCID: PMC9120101 DOI: 10.1007/s00425-022-03906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
MAIN CONCLUSION Genome editing offers revolutionized solutions for plant breeding to sustain food production to feed the world by 2050. Therefore, genome-edited products are increasingly recognized via more relaxed legislation and community adoption. The world population and food production are disproportionally growing in a manner that would have never matched each other under the current agricultural practices. The emerging crisis is more evident with the subtle changes in climate and the running-off of natural genetic resources that could be easily used in breeding in conventional ways. Under these circumstances, affordable CRISPR-Cas-based gene-editing technologies have brought hope and charged the old plant breeding machine with the most energetic and powerful fuel to address the challenges involved in feeding the world. What makes CRISPR-Cas the most powerful gene-editing technology? What are the differences between it and the other genetic engineering/breeding techniques? Would its products be labeled as "conventional" or "GMO"? There are so many questions to be answered, or that cannot be answered within the limitations of our current understanding. Therefore, we would like to discuss and answer some of the mentioned questions regarding recent progress in technology development. We hope this review will offer another view on the role of CRISPR-Cas technology in future of plant breeding for food production and beyond.
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Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
- National Key Laboratory for Plant Cell Biotechnology, Agricultural Genetics Institute, km 02, Pham Van Dong Road, Co Nhue 1, Bac Tu Liem, Hanoi, 11917, Vietnam
| | - Swati Das
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Goetz Hensel
- Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich-Heine-University, Universitätsstraße 1, 40225, Düsseldorf, Germany.
- Centre of Region Haná for Biotechnological and Agricultural Research, Czech Advanced Technology and Research Institute, Palacký University Olomouc, 78371, Olomouc, Czech Republic.
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea.
- Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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8
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Tripathi L, Dhugga KS, Ntui VO, Runo S, Syombua ED, Muiruri S, Wen Z, Tripathi JN. Genome Editing for Sustainable Agriculture in Africa. Front Genome Ed 2022; 4:876697. [PMID: 35647578 PMCID: PMC9133388 DOI: 10.3389/fgeed.2022.876697] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/21/2022] [Indexed: 12/25/2022] Open
Abstract
Sustainable intensification of agriculture in Africa is essential for accomplishing food and nutritional security and addressing the rising concerns of climate change. There is an urgent need to close the yield gap in staple crops and enhance food production to feed the growing population. In order to meet the increasing demand for food, more efficient approaches to produce food are needed. All the tools available in the toolbox, including modern biotechnology and traditional, need to be applied for crop improvement. The full potential of new breeding tools such as genome editing needs to be exploited in addition to conventional technologies. Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas)-based genome editing has rapidly become the most prevalent genetic engineering approach for developing improved crop varieties because of its simplicity, efficiency, specificity, and easy to use. Genome editing improves crop variety by modifying its endogenous genome free of any foreign gene. Hence, genome-edited crops with no foreign gene integration are not regulated as genetically modified organisms (GMOs) in several countries. Researchers are using CRISPR/Cas-based genome editing for improving African staple crops for biotic and abiotic stress resistance and improved nutritional quality. Many products, such as disease-resistant banana, maize resistant to lethal necrosis, and sorghum resistant to the parasitic plant Striga and enhanced quality, are under development for African farmers. There is a need for creating an enabling environment in Africa with science-based regulatory guidelines for the release and adoption of the products developed using CRISPR/Cas9-mediated genome editing. Some progress has been made in this regard. Nigeria and Kenya have recently published the national biosafety guidelines for the regulation of gene editing. This article summarizes recent advances in developments of tools, potential applications of genome editing for improving staple crops, and regulatory policies in Africa.
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Affiliation(s)
- Leena Tripathi
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Valentine O. Ntui
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | | | - Easter D. Syombua
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
| | - Samwel Muiruri
- International Institute of Tropical Agriculture (IITA), Nairobi, Kenya
- Kenyatta University, Nairobi, Kenya
| | - Zhengyu Wen
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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9
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Chen H, Neubauer M, Wang JP. Enhancing HR Frequency for Precise Genome Editing in Plants. FRONTIERS IN PLANT SCIENCE 2022; 13:883421. [PMID: 35592579 PMCID: PMC9113527 DOI: 10.3389/fpls.2022.883421] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/29/2022] [Indexed: 06/15/2023]
Abstract
Gene-editing tools, such as Zinc-fingers, TALENs, and CRISPR-Cas, have fostered a new frontier in the genetic improvement of plants across the tree of life. In eukaryotes, genome editing occurs primarily through two DNA repair pathways: non-homologous end joining (NHEJ) and homologous recombination (HR). NHEJ is the primary mechanism in higher plants, but it is unpredictable and often results in undesired mutations, frameshift insertions, and deletions. Homology-directed repair (HDR), which proceeds through HR, is typically the preferred editing method by genetic engineers. HR-mediated gene editing can enable error-free editing by incorporating a sequence provided by a donor template. However, the low frequency of native HR in plants is a barrier to attaining efficient plant genome engineering. This review summarizes various strategies implemented to increase the frequency of HDR in plant cells. Such strategies include methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants. Through the use and further refinement of these methods, HR-based gene editing may one day be commonplace in plants, as it is in other systems.
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Affiliation(s)
- Hao Chen
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
- College of Forestry, Shandong Agricultural University, Tai’an, China
| | - Matthew Neubauer
- Department of Plant and Microbial Biology, Program in Genetics, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Department of Forestry and Environmental Resources, Forest Biotechnology Group, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Wei T, Wen X, Niu C, An S, Wang D, Xi Z, Wang NN. Design of Acetohydroxyacid Synthase Herbicide-Resistant Germplasm through MB-QSAR and CRISPR/Cas9-Mediated Base-Editing Approaches. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:2817-2824. [PMID: 35192362 DOI: 10.1021/acs.jafc.1c07180] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The development of herbicide-resistant germplasm is significant in solving the increasingly severe weed problem in crop fields. In this study, we, for the first time, rationally designed a predictable and effective approach to create herbicide-resistant germplasm by combining mutation-dependent biomacromolecular quantitative structure-activity relationship (MB-QSAR) and CRISPR/Cas9-mediated base-editing strategies. Our results showed that the homozygous P197F-G654D-G655S or P197F-G654N-G655S Arabidopsis plants exhibited high resistance to multiple acetohydroxyacid synthase-inhibiting herbicides, including chlorsulfuron, bispyribac-sodium, and flucarbazone-sodium. Additionally, the plants with the homozygous P197S mutant displayed increased susceptibility to bispyribac-sodium than the wild-type but more resistance to flumetsulam than other mutants. Besides, we found that the herbicide resistance levels of the gene-edited plants have a good correlation with MB-QSAR prediction.
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Affiliation(s)
- Tao Wei
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
- National Engineering Research Center of Pesticide (Tianjin), State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Xin Wen
- National Engineering Research Center of Pesticide (Tianjin), State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Congwei Niu
- National Engineering Research Center of Pesticide (Tianjin), State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Sijing An
- National Engineering Research Center of Pesticide (Tianjin), State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Dawei Wang
- National Engineering Research Center of Pesticide (Tianjin), State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Zhen Xi
- National Engineering Research Center of Pesticide (Tianjin), State Key Laboratory of Elemento-Organic Chemistry, and Department of Chemical Biology, College of Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, Nankai University, Tianjin 300071, China
| | - Ning Ning Wang
- Tianjin Key Laboratory of Protein Sciences, Department of Plant Biology and Ecology, College of Life Sciences, Nankai University, Tianjin 300071, China
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Sang Y, Mejuto JC, Xiao J, Simal-Gandara J. Assessment of Glyphosate Impact on the Agrofood Ecosystem. PLANTS (BASEL, SWITZERLAND) 2021; 10:405. [PMID: 33672572 PMCID: PMC7924050 DOI: 10.3390/plants10020405] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/16/2021] [Accepted: 02/17/2021] [Indexed: 02/07/2023]
Abstract
Agro-industries should adopt effective strategies to use agrochemicals such as glyphosate herbicides cautiously in order to protect public health. This entails careful testing and risk assessment of available choices, and also educating farmers and users with mitigation strategies in ecosystem protection and sustainable development. The key to success in this endeavour is using scientific research on biological pest control, organic farming and regulatory control, etc., for new developments in food production and safety, and for environmental protection. Education and research is of paramount importance for food and nutrition security in the shadow of climate change, and their consequences in food production and consumption safety and sustainability. This review, therefore, diagnoses on the use of glyphosate and the associated development of glyphosate-resistant weeds. It also deals with the risk assessment on human health of glyphosate formulations through environment and dietary exposures based on the impact of glyphosate and its metabolite AMPA-(aminomethyl)phosphonic acid-on water and food. All this to setup further conclusions and recommendations on the regulated use of glyphosate and how to mitigate the adverse effects.
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Affiliation(s)
- Yaxin Sang
- College of Food Science and Technology, Hebei Agricultural University, Baoding 071001, China;
| | - Juan-Carlos Mejuto
- Department of Physical Chemistry, Faculty of Science, University of Vigo—Ourense Campus, E32004 Ourense, Spain;
| | - Jianbo Xiao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macau, China
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
| | - Jesus Simal-Gandara
- Nutrition and Bromatology Group, Department of Analytical and Food Chemistry, Faculty of Food Science and Technology, University of Vigo—Ourense Campus, E32004 Ourense, Spain
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Naegeli H, Bresson J, Dalmay T, Dewhurst IC, Epstein MM, Firbank LG, Guerche P, Hejatko J, Moreno FJ, Mullins E, Nogué F, Sánchez Serrano JJ, Savoini G, Veromann E, Veronesi F, Casacuberta J, Gennaro A, Paraskevopoulos K, Raffaello T, Rostoks N. Applicability of the EFSA Opinion on site-directed nucleases type 3 for the safety assessment of plants developed using site-directed nucleases type 1 and 2 and oligonucleotide-directed mutagenesis. EFSA J 2020; 18:e06299. [PMID: 33281977 PMCID: PMC7684970 DOI: 10.2903/j.efsa.2020.6299] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The European Commission requested the EFSA Panel on Genetically Modified Organisms (GMO) to assess whether section 4 (hazard identification) and the conclusions of EFSA's Scientific opinion on the risk assessment of plants developed using zinc finger nuclease type 3 technique (ZFN-3) and other site-directed nucleases (SDN) with similar function are valid for plants developed via SDN-1, SDN-2 and oligonucleotide-directed mutagenesis (ODM). In delivering this Opinion, the GMO Panel compared the hazards associated with plants produced via SDN-1, SDN-2 and ODM with those associated with plants obtained via both SDN-3 and conventional breeding. Unlike for SDN-3 methods, the application of SDN-1, SDN-2 and ODM approaches aims to modify genomic sequences in a way which can result in plants not containing any transgene, intragene or cisgene. Consequently, the GMO Panel concludes that those considerations which are specifically related to the presence of a transgene, intragene or cisgene included in section 4 and the conclusions of the Opinion on SDN-3 are not relevant to plants obtained via SDN-1, SDN-2 or ODM as defined in this Opinion. Overall, the GMO Panel did not identify new hazards specifically linked to the genomic modification produced via SDN-1, SDN-2 or ODM as compared with both SDN-3 and conventional breeding. Furthermore, the GMO Panel considers that the existing Guidance for risk assessment of food and feed from genetically modified plants and the Guidance on the environmental risk assessment of genetically modified plants are sufficient but are only partially applicable to plants generated via SDN-1, SDN-2 or ODM. Indeed, those guidance documents' requirements that are linked to the presence of exogenous DNA are not relevant for the risk assessment of plants developed via SDN-1, SDN-2 or ODM approaches if the genome of the final product does not contain exogenous DNA.
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13
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Guo Y, Cheng L, Long W, Gao J, Zhang J, Chen S, Pu H, Hu M. Synergistic mutations of two rapeseed AHAS genes confer high resistance to sulfonylurea herbicides for weed control. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2811-2824. [PMID: 32556395 DOI: 10.1007/s00122-020-03633-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/05/2020] [Indexed: 06/11/2023]
Abstract
A double mutant 5N of rapeseed was obtained with a synergistic effect of high resistance to sulfonylurea herbicide. Excellent weed control was observed in Ning R201 created by 5N resources. Sulfonylurea herbicides, which inhibit acetohydroxyacid synthase (AHAS), have become the most widely used herbicides worldwide. However, weed control in rapeseed crop production remains challenging in China due to the shortage of available herbicide-resistant cultivars. In this study, we developed a rapeseed line (PN19) with sulfonylurea herbicide resistance through seed mutagenesis. Molecular analysis revealed a Trp-574-Leu mutation in BnAHAS1-2R of PN19 according to the sequence of Arabidopsis thaliana, and an allele-specific cleaved amplified polymorphic sequence marker was developed to target the point mutation. A double mutant (5N) with very high sulfonylurea resistance was then created through pyramiding two mutant genes of PN19 and M342 by molecular marker-assisted selection. Herbicide resistance identification, toxicology testing, and an in vitro enzyme activity assay of AHAS in 5N indicated that each mutant was four and eight times more resistant to sulfonylurea than M342 and PN19, respectively. Protein structure analysis of AHAS1 demonstrated that the leucine of mutant Trp-574-Leu destroyed the original π-plane stacking effect of the local region for tribenuron-methyl binding, leading to herbicide tolerance. Isobole graph analysis showed a significant synergistic effect of the combination of two mutant genes in 5N for improved tolerance to sulfonylurea herbicides. Finally, we bred rapeseed variety Ning R201 using 5N herbicide resistance resources, and observed excellent weed control performance. Together, these results demonstrate the practical value of 5N application for optimizing and simplifying rapeseed cultivation in China.
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Affiliation(s)
- Yue Guo
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Li Cheng
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
| | - Weihua Long
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jianqin Gao
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jiefu Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Song Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Huiming Pu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China.
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
| | - Maolong Hu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing Sub-center, National Center of Oil Crops Improvement, Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture, Nanjing, 210014, China.
- Institute of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu, China.
- Provincial Key Laboratory of Agrobiology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China.
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14
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Abstract
Genome editing methods have commonly relied on the initial introduction of double-stranded DNA breaks (DSBs), resulting in stochastic insertions, deletions, and translocations at the target genomic locus. To achieve gene correction, these methods typically require the introduction of exogenous DNA repair templates and low-efficiency homologous recombination processes. In this review, we describe alternative, mechanistically motivated strategies to perform chemistry on the genome of unmodified cells without introducing DSBs. One such strategy, base editing, uses chemical and biological insights to directly and permanently convert one target base pair to another. Despite its recent introduction, base editing has already enabled a number of new capabilities and applications in the genome editing community. We summarize these advances here and discuss the new possibilities that this method has unveiled, concluding with a brief analysis of future prospects for genome and transcriptome editing without double-stranded DNA cleavage.
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Affiliation(s)
- Alexis C. Komor
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093
| | | | - David R. Liu
- Broad Institute of MIT and Harvard, Cambridge, MA, 021413
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, 02138
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, 02138
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15
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Tiricz H, Nagy B, Ferenc G, Török K, Nagy I, Dudits D, Ayaydin F. Relaxed chromatin induced by histone deacetylase inhibitors improves the oligonucleotide-directed gene editing in plant cells. JOURNAL OF PLANT RESEARCH 2018; 131:179-189. [PMID: 28836127 DOI: 10.1007/s10265-017-0975-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 07/26/2017] [Indexed: 06/07/2023]
Abstract
Improving efficiency of oligonucleotide-directed mutagenesis (ODM) is a prerequisite for wide application of this gene-editing approach in plant science and breeding. Here we have tested histone deacetylase inhibitor treatments for induction of relaxed chromatin and for increasing the efficiency of ODM in cultured maize cells. For phenotypic assay we produced transgenic maize cell lines expressing the non-functional Green Fluorescent Protein (mGFP) gene carrying a TAG stop codon. These transgenic cells were bombarded with corrective oligonucleotide as editing reagent to recover GFP expression. Repair of green fluorescent protein function was monitored by confocal fluorescence microscopy and flow cytometry was used for quantification of correction events. Sequencing PCR fragments of the GFP gene from corrected cells indicated a nucleotide exchange in the stop codon (TAG) from T to G nucleotide that resulted in the restoration of GFP function. We show that pretreatment of maize cells with sodium butyrate (5-10 mM) and nicotinamide (1-5 mM) as known inhibitors of histone deacetylases can cause elevated chromatin sensitivity to DNase I that was visualized in agarose gels and confirmed by the reduced presence of intact PCR template for the inserted exogenous mGFP gene. Maize cells with more relaxed chromatin could serve as an improved recipient for targeted nucleotide exchange as indicated by an average of 2.67- to 3.62-fold increase in GFP-positive cells. Our results stimulate further studies on the role of the condition of the recipient cells in ODM and testing the application of chromatin modifying agents in other, programmable nuclease-based genome-editing techniques in higher plants.
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Affiliation(s)
- Hilda Tiricz
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Bettina Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Györgyi Ferenc
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - Katalin Török
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
| | - István Nagy
- Institute of Biochemistry, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- SeqOmics Biotechnology Ltd., Mórahalom, Hungary
| | - Dénes Dudits
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary.
| | - Ferhan Ayaydin
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
- Laboratory of Cellular Imaging, Biological Research Centre, Hungarian Academy of Sciences, Szeged, Hungary
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16
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Liang C, Sun B, Meng Z, Meng Z, Wang Y, Sun G, Zhu T, Lu W, Zhang W, Malik W, Lin M, Zhang R, Guo S. Co-expression of GR79 EPSPS and GAT yields herbicide-resistant cotton with low glyphosate residues. PLANT BIOTECHNOLOGY JOURNAL 2017; 15:1622-1629. [PMID: 28418615 PMCID: PMC5698046 DOI: 10.1111/pbi.12744] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 04/11/2017] [Accepted: 04/11/2017] [Indexed: 05/22/2023]
Abstract
Glyphosate-resistant (GR) crops have been adopted on a massive scale by North and South American farmers. Currently, about 80% of the 120 million hectares of the global genetically modified (GM) crops are GR crop varieties. However, the adoption of GR plants in China has not occurred at the same pace, owing to several factors including, among other things, labour markets and the residual effects of glyphosate in transgenic plants. Here, we report the co-expression of codon-optimized forms of GR79 EPSPS and N-acetyltransferase (GAT) genes in cotton. We found five times more resistance to glyphosate with 10-fold reduction in glyphosate residues in two pGR79 EPSPS-pGAT co-expression cotton lines, GGCO2 and GGCO5. The GGCO2 line was used in a hybridization programme to develop new GR cottons. Field trials at five locations during three growing seasons showed that pGR79-pGAT transgenic cotton lines have the same agronomic performance as conventional varieties, but were USD 390-495 cheaper to produce per hectare because of the high cost of conventional weed management practices. Our strategy to pyramid these genes clearly worked and thus offers attractive promise for the engineering and breeding of highly resistant low-glyphosate-residue cotton varieties.
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Affiliation(s)
- Chengzhen Liang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Bao Sun
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Zhigang Meng
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Zhaohong Meng
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Yuan Wang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Guoqing Sun
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Tao Zhu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Wei Lu
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Wei Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Waqas Malik
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
- Department of Plant Breeding and GeneticsBahauddin Zakariya UniversityMultanPakistan
| | - Min Lin
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Rui Zhang
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
| | - Sandui Guo
- Biotechnology Research InstituteChinese Academy of Agricultural SciencesBeijingChina
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17
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Jiang WZ, Weeks DP. A gene-within-a-gene Cas9/sgRNA hybrid construct enables gene editing and gene replacement strategies in Chlamydomonas reinhardtii. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.04.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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18
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Limera C, Sabbadini S, Sweet JB, Mezzetti B. New Biotechnological Tools for the Genetic Improvement of Major Woody Fruit Species. FRONTIERS IN PLANT SCIENCE 2017; 8:1418. [PMID: 28861099 PMCID: PMC5559511 DOI: 10.3389/fpls.2017.01418] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 07/31/2017] [Indexed: 05/09/2023]
Abstract
The improvement of woody fruit species by traditional plant breeding techniques has several limitations mainly caused by their high degree of heterozygosity, the length of their juvenile phase and auto-incompatibility. The development of new biotechnological tools (NBTs), such as RNA interference (RNAi), trans-grafting, cisgenesis/intragenesis, and genome editing tools, like zinc-finger and CRISPR/Cas9, has introduced the possibility of more precise and faster genetic modifications of plants. This aspect is of particular importance for the introduction or modification of specific traits in woody fruit species while maintaining unchanged general characteristics of a selected cultivar. Moreover, some of these new tools give the possibility to obtain transgene-free modified fruit tree genomes, which should increase consumer's acceptance. Over the decades biotechnological tools have undergone rapid development and there is a continuous addition of new and valuable techniques for plant breeders. This makes it possible to create desirable woody fruit varieties in a fast and more efficient way to meet the demand for sustainable agricultural productivity. Although, NBTs have a common goal i.e., precise, fast, and efficient crop improvement, individually they are markedly different in approach and characteristics from each other. In this review we describe in detail their mechanisms and applications for the improvement of fruit trees and consider the relationship between these biotechnological tools and the EU biosafety regulations applied to the plants and products obtained through these techniques.
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Affiliation(s)
- Cecilia Limera
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Silvia Sabbadini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
| | - Jeremy B. Sweet
- J. T. Environmental Consultants LtdCambridge, United Kingdom
| | - Bruno Mezzetti
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle MarcheAncona, Italy
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19
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Ran Y, Liang Z, Gao C. Current and future editing reagent delivery systems for plant genome editing. SCIENCE CHINA-LIFE SCIENCES 2017; 60:490-505. [PMID: 28527114 DOI: 10.1007/s11427-017-9022-1] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/22/2017] [Indexed: 01/01/2023]
Abstract
Many genome editing tools have been developed and new ones are anticipated; some have been extensively applied in plant genetics, biotechnology and breeding, especially the CRISPR/Cas9 system. These technologies have opened up a new era for crop improvement due to their precise editing of user-specified sequences related to agronomic traits. In this review, we will focus on an update of recent developments in the methodologies of editing reagent delivery, and consider the pros and cons of current delivery systems. Finally, we will reflect on possible future directions.
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Affiliation(s)
- Yidong Ran
- Genovo Biotechnology Co., Ltd., Tianjin, 301700, China.
| | - Zhen Liang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
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20
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Pacher M, Puchta H. From classical mutagenesis to nuclease-based breeding - directing natural DNA repair for a natural end-product. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 90:819-833. [PMID: 28027431 DOI: 10.1111/tpj.13469] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 12/22/2016] [Accepted: 12/22/2016] [Indexed: 05/18/2023]
Abstract
Production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damage in an error-prone way. In the case of radiation, multiple double-strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site-directed nucleases (SDNs) - also referred to as sequence-specific nucleases - like the CRISPR/Cas system has enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at pre-defined sites in plant genomes. As these changes are not necessarily associated with the permanent integration of foreign DNA, the obtained organisms per se cannot be regarded as genetically modified as there is no way to distinguish them from natural variants. This applies to changes induced by DSBs as well as single-strand breaks, and involves repair by non-homologous end-joining and homologous recombination. The recent development of SDN-based 'DNA-free' approaches makes mutagenesis strategies in classical breeding indistinguishable from SDN-derived targeted genome modifications, even in regard to current regulatory rules. With the advent of new SDN technologies, much faster and more precise genome editing becomes available at reasonable cost, and potentially without requiring time-consuming deregulation of newly created phenotypes. This review will focus on classical mutagenesis breeding and the application of newly developed SDNs in order to emphasize similarities in the context of the regulatory situation for genetically modified crop plants.
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Affiliation(s)
- Michael Pacher
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, PO 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, PO 6980, 76049, Karlsruhe, Germany
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21
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Dutta D, Fauer C, Hickey K, Salifu M, Stabenfeldt SE. Tunable delayed controlled release profile from layered polymeric microparticles. J Mater Chem B 2017; 5:4487-4498. [PMID: 28652916 DOI: 10.1039/c7tb00138j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Composite microparticles (MPs) with layered architecture, engineered from poly(L-lactic acid) (PLLA) and poly(D,L-lactic-co-glycolic acid) (PLGA), are promising devices for achieving the delayed release of proteins. Here, we build on a water-in-oil-in-oil-in-water emulsion method of fabricating layered MPs with an emphasis on modulating the delay period of the protein release profile. Particle hardening parameters (i.e. polymer precipitation rate and total hardening time) following water-in-oil-in-oil-in-water emulsions are known to affect MP structure such as the core/shell material and cargo localization. We demonstrate that layered MPs fabricated with two different solvent evaporation parameters not only alter polymer and protein distribution within the hardened MPs, but also affect their protein release profiles. Secondly, we hypothesize that ethanol (EtOH), a semi-polar solvent miscible in both the solvent (dichloromethane; DCM) and non-solvent aqueous phases, likely alters DCM and water flux from the dispersed oil phase. The results reveal that EtOH affects protein distribution within MPs, and may also influence MP structural properties such as porosity and polymer distribution. To our knowledge, we are the first to demonstrate EtOH as a means for modulating critical release parameters from protein-loaded, layered PLGA/PLLA MPs. Throughout all the groups in the study, we achieved differential delay periods (between 0 - 30 days after an initial burst release) and total protein release periods (~30 - >58 days) as a function of solvent evaporation parameters and EtOH content. The layered MPs proposed in the study potentially have wide-reaching applications in tissue engineering for delayed and sequential protein release.
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Affiliation(s)
- D Dutta
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - C Fauer
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - K Hickey
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - M Salifu
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
| | - S E Stabenfeldt
- School of Biological and Health Systems Engineering, Arizona State University, Tempe, AZ, USA
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22
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Hilscher J, Bürstmayr H, Stoger E. Targeted modification of plant genomes for precision crop breeding. Biotechnol J 2017; 12. [PMID: 27726285 DOI: 10.1002/biot.201600173] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 08/22/2016] [Accepted: 09/09/2016] [Indexed: 02/03/2023]
Abstract
The development of gene targeting and gene editing techniques based on programmable site-directed nucleases (SDNs) has increased the precision of genome modification and made the outcomes more predictable and controllable. These approaches have achieved rapid advances in plant biotechnology, particularly the development of improved crop varieties. Here, we review the range of alterations which have already been implemented in plant genomes, and summarize the reported efficiencies of precise genome modification. Many crop varieties are being developed using SDN technologies and although their regulatory status in the USA is clear there is still a decision pending in the EU. DNA-free genome editing strategies are briefly discussed because they also present a unique regulatory challenge. The potential applications of genome editing in plant breeding and crop improvement are highlighted by drawing examples from the recent literature.
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Affiliation(s)
- Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Hermann Bürstmayr
- Institute for Biotechnology in Plant Production (IFA Tulln), University of Natural Resources and Life Sciences, Tulln, Austria
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
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23
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Bialk P, Sansbury B, Rivera-Torres N, Bloh K, Man D, Kmiec EB. Analyses of point mutation repair and allelic heterogeneity generated by CRISPR/Cas9 and single-stranded DNA oligonucleotides. Sci Rep 2016; 6:32681. [PMID: 27609304 PMCID: PMC5016854 DOI: 10.1038/srep32681] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 08/10/2016] [Indexed: 11/25/2022] Open
Abstract
The repair of a point mutation can be facilitated by combined activity of a single-stranded oligonucleotide and a CRISPR/Cas9 system. While the mechanism of action of combinatorial gene editing remains to be elucidated, the regulatory circuitry of nucleotide exchange executed by oligonucleotides alone has been largely defined. The presence of the appropriate CRISPR/Cas9 system leads to an enhancement in the frequency of gene editing directed by single-stranded DNA oligonucleotides. While CRISPR/Cas9 executes double-stranded DNA cleavage efficiently, closure of the broken chromosomes is dynamic, as varying degrees of heterogeneity of the cleavage products appear to accompany the emergence of the corrected base pair. We provide a detailed analysis of allelic variance at and surrounding the target site. In one particular case, we report sequence alteration directed by a distinct member of the same gene family. Our data suggests that single-stranded DNA molecules may influence DNA junction heterogeneity created by CRISPR/Cas9.
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Affiliation(s)
- Pawel Bialk
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America
| | - Brett Sansbury
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America.,Department of Medical Laboratory Science, College of Health Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Natalia Rivera-Torres
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America.,Department of Medical Laboratory Science, College of Health Sciences, University of Delaware, Newark, Delaware, United States of America
| | - Kevin Bloh
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America.,Nemours Center for Childhood Cancer Research, Alfred I. duPont Hospital for Children, Wilmington, Delaware, United States of America
| | - Dula Man
- Department of Chemistry, Delaware State University, Dover, Delaware, United States of America
| | - Eric B Kmiec
- Gene Editing Institute, Helen F. Graham Cancer Center and Research Institute, Newark, Delaware, United States of America.,Department of Medical Laboratory Science, College of Health Sciences, University of Delaware, Newark, Delaware, United States of America
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24
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Steinert J, Schiml S, Puchta H. Homology-based double-strand break-induced genome engineering in plants. PLANT CELL REPORTS 2016; 35:1429-38. [PMID: 27084537 DOI: 10.1007/s00299-016-1981-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 03/31/2016] [Indexed: 05/19/2023]
Abstract
This review summarises the recent progress in DSB-induced gene targeting by homologous recombination in plants. We are getting closer to efficiently inserting genes or precisely exchanging single amino acids. Although the basic features of double-strand break (DSB)-induced genome engineering were established more than 20 years ago, only in recent years has the technique come into the focus of plant biologists. Today, most scientists apply the recently discovered CRISPR/Cas system for inducing site-specific DSBs in genes of interest to obtain mutations by non-homologous end joining (NHEJ), which is the prevailing and often imprecise mechanism of DSB repair in somatic plant cells. However, predefined changes like the site-specific insertion of foreign genes or an exchange of single amino acids can be achieved by DSB-induced homologous recombination (HR). Although DSB induction drastically enhances the efficiency of HR, the efficiency is still about two orders of magnitude lower than that of NHEJ. Therefore, significant effort have been put forth to improve DSB-induced HR based technologies. This review summarises the previous studies as well as discusses the most recent developments in using the CRISPR/Cas system to improve these processes for plants.
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Affiliation(s)
- Jeannette Steinert
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Simon Schiml
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute II, Karlsruhe Institute of Technology, POB 6980, 76049, Karlsruhe, Germany.
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25
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Cardi T, Neal Stewart C. Progress of targeted genome modification approaches in higher plants. PLANT CELL REPORTS 2016; 35:1401-16. [PMID: 27025856 DOI: 10.1007/s00299-016-1975-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/21/2016] [Indexed: 05/07/2023]
Abstract
Transgene integration in plants is based on illegitimate recombination between non-homologous sequences. The low control of integration site and number of (trans/cis)gene copies might have negative consequences on the expression of transferred genes and their insertion within endogenous coding sequences. The first experiments conducted to use precise homologous recombination for gene integration commenced soon after the first demonstration that transgenic plants could be produced. Modern transgene targeting categories used in plant biology are: (a) homologous recombination-dependent gene targeting; (b) recombinase-mediated site-specific gene integration; (c) oligonucleotide-directed mutagenesis; (d) nuclease-mediated site-specific genome modifications. New tools enable precise gene replacement or stacking with exogenous sequences and targeted mutagenesis of endogeneous sequences. The possibility to engineer chimeric designer nucleases, which are able to target virtually any genomic site, and use them for inducing double-strand breaks in host DNA create new opportunities for both applied plant breeding and functional genomics. CRISPR is the most recent technology available for precise genome editing. Its rapid adoption in biological research is based on its inherent simplicity and efficacy. Its utilization, however, depends on available sequence information, especially for genome-wide analysis. We will review the approaches used for genome modification, specifically those for affecting gene integration and modification in higher plants. For each approach, the advantages and limitations will be noted. We also will speculate on how their actual commercial development and implementation in plant breeding will be affected by governmental regulations.
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Affiliation(s)
- Teodoro Cardi
- Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Centro di Ricerca per l'Orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano, Italy.
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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26
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Biotech Approaches to Overcome the Limitations of Using Transgenic Plants in Organic Farming. SUSTAINABILITY 2016. [DOI: 10.3390/su8050497] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Schaart JG, van de Wiel CCM, Lotz LAP, Smulders MJM. Opportunities for Products of New Plant Breeding Techniques. TRENDS IN PLANT SCIENCE 2016; 21:438-449. [PMID: 26654659 DOI: 10.1016/j.tplants.2015.11.006] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/30/2015] [Accepted: 11/06/2015] [Indexed: 05/21/2023]
Abstract
Various new plant breeding techniques (NPBT) have a similar aim, namely to produce improved crop varieties that are difficult to obtain through traditional breeding methods. Here, we review the opportunities for products created using NPBTs. We categorize products of these NPBTs into three product classes with a different degree of genetic modification. For each product class, recent examples are described to illustrate the potential for breeding new crops with improved traits. Finally, we touch upon the future applications of these methods, such as cisgenic potato genotypes in which specific combinations of Phytophthora infestans resistance genes have been stacked for use in durable cultivation, or the creation of new disease resistances by knocking out or removing S-genes using genome-editing techniques.
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Affiliation(s)
- Jan G Schaart
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands.
| | | | - Lambertus A P Lotz
- Wageningen UR Agrosystems Research, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
| | - Marinus J M Smulders
- Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB Wageningen, The Netherlands
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Wolt JD, Wang K, Yang B. The Regulatory Status of Genome-edited Crops. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:510-8. [PMID: 26251102 PMCID: PMC5042095 DOI: 10.1111/pbi.12444] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/24/2015] [Accepted: 07/03/2015] [Indexed: 05/18/2023]
Abstract
Genome editing with engineered nucleases (GEEN) represents a highly specific and efficient tool for crop improvement with the potential to rapidly generate useful novel phenotypes/traits. Genome editing techniques initiate specifically targeted double strand breaks facilitating DNA-repair pathways that lead to base additions or deletions by non-homologous end joining as well as targeted gene replacements or transgene insertions involving homology-directed repair mechanisms. Many of these techniques and the ancillary processes they employ generate phenotypic variation that is indistinguishable from that obtained through natural means or conventional mutagenesis; and therefore, they do not readily fit current definitions of genetically engineered or genetically modified used within most regulatory regimes. Addressing ambiguities regarding the regulatory status of genome editing techniques is critical to their application for development of economically useful crop traits. Continued regulatory focus on the process used, rather than the nature of the novel phenotype developed, results in confusion on the part of regulators, product developers, and the public alike and creates uncertainty as of the use of genome engineering tools for crop improvement.
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Affiliation(s)
- Jeffrey D Wolt
- Department of Agronomy, Iowa State University, Ames, IA, USA
- Biosafety Institute for Genetically Modified Agricultural Products, Iowa State University, Ames, IA, USA
- Crop Bioengineering Consortium, Iowa State University, Ames, IA, USA
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, USA
- Crop Bioengineering Consortium, Iowa State University, Ames, IA, USA
| | - Bing Yang
- Crop Bioengineering Consortium, Iowa State University, Ames, IA, USA
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, IA, USA
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Sauer NJ, Mozoruk J, Miller RB, Warburg ZJ, Walker KA, Beetham PR, Schöpke CR, Gocal GFW. Oligonucleotide-directed mutagenesis for precision gene editing. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:496-502. [PMID: 26503400 PMCID: PMC5057361 DOI: 10.1111/pbi.12496] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 09/18/2015] [Accepted: 09/23/2015] [Indexed: 05/23/2023]
Abstract
Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed.
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Rivera-Torres N, Kmiec EB. Genetic spell-checking: gene editing using single-stranded DNA oligonucleotides. PLANT BIOTECHNOLOGY JOURNAL 2016; 14:463-470. [PMID: 26402400 DOI: 10.1111/pbi.12473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/07/2015] [Accepted: 08/12/2015] [Indexed: 06/05/2023]
Abstract
Single-stranded oligonucleotides (ssODNs) can be used to direct the exchange of a single nucleotide or the repair of a single base within the coding region of a gene in a process that is known, generically, as gene editing. These molecules are composed of either all DNA residues or a mixture of RNA and DNA bases and utilize inherent metabolic functions to execute the genetic alteration within the context of a chromosome. The mechanism of action of gene editing is now being elucidated as well as an understanding of its regulatory circuitry, work that has been particularly important in establishing a foundation for designing effective gene editing strategies in plants. Double-strand DNA breakage and the activation of the DNA damage response pathway play key roles in determining the frequency with which gene editing activity takes place. Cellular regulators respond to such damage and their action impacts the success or failure of a particular nucleotide exchange reaction. A consequence of such activation is the natural slowing of replication fork progression, which naturally creates a more open chromatin configuration, thereby increasing access of the oligonucleotide to the DNA template. Herein, how critical reaction parameters influence the effectiveness of gene editing is discussed. Functional interrelationships between DNA damage, the activation of DNA response pathways and the stalling of replication forks are presented in detail as potential targets for increasing the frequency of gene editing by ssODNs in plants and plant cells.
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Affiliation(s)
- Natalia Rivera-Torres
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
| | - Eric B Kmiec
- Gene Editing Institute, Center for Translational Cancer Research, Helen F. Graham Cancer Center & Research Institute, Christiana Care Health System, Newark, DE, USA
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Lombardo L, Coppola G, Zelasco S. New Technologies for Insect-Resistant and Herbicide-Tolerant Plants. Trends Biotechnol 2016; 34:49-57. [DOI: 10.1016/j.tibtech.2015.10.006] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 10/21/2015] [Accepted: 10/22/2015] [Indexed: 12/17/2022]
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Sun Y, Li J, Xia L. Precise Genome Modification via Sequence-Specific Nucleases-Mediated Gene Targeting for Crop Improvement. FRONTIERS IN PLANT SCIENCE 2016; 7:1928. [PMID: 28066481 PMCID: PMC5167731 DOI: 10.3389/fpls.2016.01928] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 12/05/2016] [Indexed: 05/17/2023]
Abstract
Genome editing technologies enable precise modifications of DNA sequences in vivo and offer a great promise for harnessing plant genes in crop improvement. The precise manipulation of plant genomes relies on the induction of DNA double-strand breaks by sequence-specific nucleases (SSNs) to initiate DNA repair reactions that are based on either non-homologous end joining (NHEJ) or homology-directed repair (HDR). While complete knock-outs and loss-of-function mutations generated by NHEJ are very valuable in defining gene functions, their applications in crop improvement are somewhat limited because many agriculturally important traits are conferred by random point mutations or indels at specific loci in either the genes' encoding or promoter regions. Therefore, genome modification through SSNs-mediated HDR for gene targeting (GT) that enables either gene replacement or knock-in will provide an unprecedented ability to facilitate plant breeding by allowing introduction of precise point mutations and new gene functions, or integration of foreign genes at specific and desired "safe" harbor in a predefined manner. The emergence of three programmable SSNs, such as zinc finger nucleases, transcriptional activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) systems has revolutionized genome modification in plants in a more controlled manner. However, while targeted mutagenesis is becoming routine in plants, the potential of GT technology has not been well realized for traits improvement in crops, mainly due to the fact that NHEJ predominates DNA repair process in somatic cells and competes with the HDR pathway, and thus HDR-mediated GT is a relative rare event in plants. Here, we review recent research findings mainly focusing on development and applications of precise GT in plants using three SSNs systems described above, and the potential mechanisms underlying HDR events in plant cells. We then address the challenges and propose future perspectives in order to facilitate the implementation of precise genome modification through SSNs-mediated GT for crop improvement in a global context.
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Wang M, Liu Y, Zhang C, Liu J, Liu X, Wang L, Wang W, Chen H, Wei C, Ye X, Li X, Tu J. Gene editing by co-transformation of TALEN and chimeric RNA/DNA oligonucleotides on the rice OsEPSPS gene and the inheritance of mutations. PLoS One 2015; 10:e0122755. [PMID: 25856577 PMCID: PMC4391873 DOI: 10.1371/journal.pone.0122755] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 02/12/2015] [Indexed: 01/08/2023] Open
Abstract
Although several site-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas, have emerged as powerful tools for targeted gene editing in many organisms, to date, gene targeting (GT) in plants remains a formidable challenge. In the present study, we attempted to substitute a single base in situ on the rice OsEPSPS gene by co-transformation of TALEN with chimeric RNA/DNA oligonucleotides (COs), including different strand composition such as RNA/DNA (C1) or DNA/RNA (C2) but contained the same target base to be substituted. In contrast to zero GT event obtained by the co-transformation of TALEN with homologous recombination plasmid (HRP), we obtained one mutant showing target base substitution although accompanied by undesired deletion of 12 bases downstream the target site from the co-transformation of TALEN and C1. In addition to this typical event, we also obtained 16 mutants with different length of base deletions around the target site among 105 calli lines derived from transformation of TALEN alone (4/19) as well as co-transformation of TELAN with either HRP (5/30) or C1 (2/25) or C2 (5/31). Further analysis demonstrated that the homozygous gene-edited mutants without foreign gene insertion could be obtained in one generation. The induced mutations in transgenic generation were also capable to pass to the next generation stably. However, the genotypes of mutants did not segregate normally in T1 population, probably due to lethal mutations. Phenotypic assessments in T1 generation showed that the heterozygous plants with either one or three bases deletion on target sequence, called d1 and d3, were more sensitive to glyphosate and the heterozygous d1 plants had significantly lower seed-setting rate than wild-type.
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Affiliation(s)
- Mugui Wang
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Yujun Liu
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Cuicui Zhang
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jianping Liu
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xin Liu
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Liangchao Wang
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Wenyi Wang
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Hao Chen
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Chuchu Wei
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xiufen Ye
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Xinyuan Li
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
| | - Jumin Tu
- Institute of Crop Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang Province, China
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RNA-Seq transcriptome analysis of maize inbred carrying nicosulfuron-tolerant and nicosulfuron-susceptible alleles. Int J Mol Sci 2015; 16:5975-89. [PMID: 25782159 PMCID: PMC4394515 DOI: 10.3390/ijms16035975] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 01/28/2023] Open
Abstract
Postemergence applications of nicosulfuron can cause great damage to certain maize inbred lines and hybrids. Variation among different responses to nicosulfuron may be attributed to differential rates of herbicide metabolism. We employed RNA-Seq analysis to compare transcriptome responses between nicosulfuron-treated and untreated in both tolerant and susceptible maize plants. A total of 71.8 million paired end Illumina RNA-Seq reads were generated, representing the transcription of around 40,441 unique reads. About 345,171 gene ontology (GO) term assignments were conducted for the annotation in terms of biological process, cellular component and molecular function categories, and 6413 sequences with 108 enzyme commission numbers were assigned to 134 predicted Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways. Digital gene expression profile (DGE) analysis using Solexa sequencing was performed within the susceptible and tolerant maize between the nicosulfuron-treated and untreated conditions, 13 genes were selected as the candidates most likely involved in herbicide metabolism, and quantitative RT-PCR validated the RNA-Seq results for eight genes. This transcriptome data may provide opportunities for the study of sulfonylurea herbicides susceptibility emergence of Zea mays.
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Herbicides: History, Classification and Genetic Manipulation of Plants for Herbicide Resistance. SUSTAINABLE AGRICULTURE REVIEWS 2015. [DOI: 10.1007/978-3-319-09132-7_3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Small Fragment Homologous Replacement (SFHR): sequence-specific modification of genomic DNA in eukaryotic cells by small DNA fragments. Methods Mol Biol 2014; 1114:85-101. [PMID: 24557898 DOI: 10.1007/978-1-62703-761-7_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The sequence-specific correction of a mutated gene (e.g., point mutation) by the Small Fragment Homologous Replacement (SFHR) method is a highly attractive approach for gene therapy. Small DNA fragments (SDFs) were used in SFHR to modify endogenous genomic DNA in both human and murine cells. The advantage of this gene targeting approach is to maintain the physiologic expression pattern of targeted genes without altering the regulatory sequences (e.g., promoter, enhancer), but the application of this technique requires the knowledge of the sequence to be targeted. In our recent study, an optimized SFHR protocol was used to replace the eGFP mutant sequence in SV-40-transformed mouse embryonic fibroblast (MEF-SV40), with the wild-type eGFP sequence. Nevertheless in the past, SFHR has been used to correct several mutant genes, each related to a specific genetic disease (e.g., spinal muscular atrophy, cystic fibrosis, severe combined immune deficiency). Several parameters can be modified to optimize the gene modification efficiency, as described in our recent study. In this chapter we describe the main guidelines that should be followed in SFHR application, in order to increase technique efficiency.
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Que Q, Elumalai S, Li X, Zhong H, Nalapalli S, Schweiner M, Fei X, Nuccio M, Kelliher T, Gu W, Chen Z, Chilton MDM. Maize transformation technology development for commercial event generation. FRONTIERS IN PLANT SCIENCE 2014; 5:379. [PMID: 25140170 PMCID: PMC4122164 DOI: 10.3389/fpls.2014.00379] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2014] [Accepted: 07/17/2014] [Indexed: 05/22/2023]
Abstract
Maize is an important food and feed crop in many countries. It is also one of the most important target crops for the application of biotechnology. Currently, there are more biotech traits available on the market in maize than in any other crop. Generation of transgenic events is a crucial step in the development of biotech traits. For commercial applications, a high throughput transformation system producing a large number of high quality events in an elite genetic background is highly desirable. There has been tremendous progress in Agrobacterium-mediated maize transformation since the publication of the Ishida et al. (1996) paper and the technology has been widely adopted for transgenic event production by many labs around the world. We will review general efforts in establishing efficient maize transformation technologies useful for transgenic event production in trait research and development. The review will also discuss transformation systems used for generating commercial maize trait events currently on the market. As the number of traits is increasing steadily and two or more modes of action are used to control key pests, new tools are needed to efficiently transform vectors containing multiple trait genes. We will review general guidelines for assembling binary vectors for commercial transformation. Approaches to increase transformation efficiency and gene expression of large gene stack vectors will be discussed. Finally, recent studies of targeted genome modification and transgene insertion using different site-directed nuclease technologies will be reviewed.
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Affiliation(s)
- Qiudeng Que
- Syngenta Biotechnology, Inc.Research Triangle Park, NC, USA
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Hartung F, Schiemann J. Precise plant breeding using new genome editing techniques: opportunities, safety and regulation in the EU. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 78:742-52. [PMID: 24330272 DOI: 10.1111/tpj.12413] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 12/04/2013] [Accepted: 12/09/2013] [Indexed: 05/04/2023]
Abstract
Several new plant breeding techniques (NPBTs) have been developed during the last decade, and make it possible to precisely perform genome modifications in plants. The major problem, other than technical aspects, is the vagueness of regulation concerning these new techniques. Since the definition of eight NPBTs by a European expert group in 2007, there has been an ongoing debate on whether the resulting plants and their products are covered by GMO legislation. Obviously, cover by GMO legislation would severely hamper the use of NPBT, because genetically modified plants must pass a costly and time-consuming GMO approval procedure in the EU. In this review, we compare some of the NPBTs defined by the EU expert group with classical breeding techniques and conventional transgenic plants. The list of NPBTs may be shortened (or extended) during the international discussion process initiated by the Organization for Economic Co-operation and Development. From the scientific point of view, it may be argued that plants developed by NPBTs are often indistinguishable from classically bred plants and are not expected to possess higher risks for health and the environment. In light of the debate on the future regulation of NPBTs and the accumulated evidence on the biosafety of genetically modified plants that have been commercialized and risk-assessed worldwide, it may be suggested that plants modified by crop genetic improvement technologies, including genetic modification, NPBTs or other future techniques, should be evaluated according to the new trait and the resulting end product rather than the technique used to create the new plant variety.
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Affiliation(s)
- Frank Hartung
- Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Erwin Baur Straße 27, D-06484, Quedlinburg, Germany
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Bertoni C. Emerging gene editing strategies for Duchenne muscular dystrophy targeting stem cells. Front Physiol 2014; 5:148. [PMID: 24795643 PMCID: PMC4001063 DOI: 10.3389/fphys.2014.00148] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/28/2014] [Indexed: 01/06/2023] Open
Abstract
The progressive loss of muscle mass characteristic of many muscular dystrophies impairs the efficacy of most of the gene and molecular therapies currently being pursued for the treatment of those disorders. It is becoming increasingly evident that a therapeutic application, to be effective, needs to target not only mature myofibers, but also muscle progenitors cells or muscle stem cells able to form new muscle tissue and to restore myofibers lost as the result of the diseases or during normal homeostasis so as to guarantee effective and lost lasting effects. Correction of the genetic defect using oligodeoxynucleotides (ODNs) or engineered nucleases holds great potential for the treatment of many of the musculoskeletal disorders. The encouraging results obtained by studying in vitro systems and model organisms have set the groundwork for what is likely to become an emerging field in the area of molecular and regenerative medicine. Furthermore, the ability to isolate and expand from patients various types of muscle progenitor cells capable of committing to the myogenic lineage provides the opportunity to establish cell lines that can be used for transplantation following ex vivo manipulation and expansion. The purpose of this article is to provide a perspective on approaches aimed at correcting the genetic defect using gene editing strategies and currently under development for the treatment of Duchenne muscular dystrophy (DMD), the most sever of the neuromuscular disorders. Emphasis will be placed on describing the potential of using the patient own stem cell as source of transplantation and the challenges that gene editing technologies face in the field of regenerative biology.
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Affiliation(s)
- Carmen Bertoni
- Department of Neurology, David Geffen School of Medicine, University of California Los Angeles CA, USA
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40
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Kondo K, Nakamura K. [Scientific review on novel genome editing techniques]. Food Hygiene and Safety Science (Shokuhin Eiseigaku Zasshi) 2014; 55:231-46. [PMID: 25743586 DOI: 10.3358/shokueishi.55.231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Whitford R, Fleury D, Reif JC, Garcia M, Okada T, Korzun V, Langridge P. Hybrid breeding in wheat: technologies to improve hybrid wheat seed production. JOURNAL OF EXPERIMENTAL BOTANY 2013; 64:5411-28. [PMID: 24179097 DOI: 10.1093/jxb/ert333] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Global food security demands the development and delivery of new technologies to increase and secure cereal production on finite arable land without increasing water and fertilizer use. There are several options for boosting wheat yields, but most offer only small yield increases. Wheat is an inbred plant, and hybrids hold the potential to deliver a major lift in yield and will open a wide range of new breeding opportunities. A series of technological advances are needed as a base for hybrid wheat programmes. These start with major changes in floral development and architecture to separate the sexes and force outcrossing. Male sterility provides the best method to block self-fertilization, and modifying the flower structure will enhance pollen access. The recent explosion in genomic resources and technologies provides new opportunities to overcome these limitations. This review outlines the problems with existing hybrid wheat breeding systems and explores molecular-based technologies that could improve the hybrid production system to reduce hybrid seed production costs, a prerequisite for a commercial hybrid wheat system.
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Affiliation(s)
- Ryan Whitford
- Australian Centre for Plant Functional Genomics, School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, South Australia 5064, Australia
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Da Ines O, White CI. Gene Site-Specific Insertion in Plants. SITE-DIRECTED INSERTION OF TRANSGENES 2013. [DOI: 10.1007/978-94-007-4531-5_11] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Abstract
The first crops obtained through new plant breeding techniques are close to commercialization. Regulatory issues will determine the adoption of the techniques by breeders.
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Breyer D, Herman P, Brandenburger A, Gheysen G, Remaut E, Soumillion P, Van Doorsselaere J, Custers R, Pauwels K, Sneyers M, Reheul D. Genetic modification through oligonucleotide-mediated mutagenesis. A GMO regulatory challenge? ACTA ACUST UNITED AC 2009; 8:57-64. [PMID: 19833073 DOI: 10.1051/ebr/2009007] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In the European Union, the definition of a GMO is technology-based. This means that a novel organism will be regulated under the GMO regulatory framework only if it has been developed with the use of defined techniques. This approach is now challenged with the emergence of new techniques. In this paper, we describe regulatory and safety issues associated with the use of oligonucleotide-mediated mutagenesis to develop novel organisms. We present scientific arguments for not having organisms developed through this technique fall within the scope of the EU regulation on GMOs. We conclude that any political decision on this issue should be taken on the basis of a broad reflection at EU level, while avoiding discrepancies at international level.
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Affiliation(s)
- Didier Breyer
- Scientific Institute of Public Health, Division of Biosafety and Biotechnology, Brussels, Belgium.
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45
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Laplante J, Rajcan I, Tardif FJ. Multiple allelic forms of acetohydroxyacid synthase are responsible for herbicide resistance in Setaria viridis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:577-585. [PMID: 19495723 DOI: 10.1007/s00122-009-1067-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2008] [Accepted: 05/09/2009] [Indexed: 05/25/2023]
Abstract
In weed species, resistance to herbicides inhibiting acetohydroxyacid synthase (AHAS) is often conferred by genetic mutations at one of six codons in the AHAS gene. These mutations provide plants with various levels of resistance to different chemical classes of AHAS inhibitors. Five green foxtail [Setaria viridis (L.) Beauv.] populations were reported in Ontario with potential resistance to the AHAS-inhibiting herbicide imazethapyr. The objectives of this study were to confirm resistance, establish the resistance spectrum for each of the five populations, and determine its genetic basis. Dose response curves were generated for whole plant growth and enzyme activity, and the AHAS gene was sequenced. Resistance was confirmed by determining the resistance factor to imazethapyr in the five resistant green foxtail populations for whole plant dose response experiments (21- to 182-fold) and enzyme assays (15- to 260-fold). All five imazethapyr-resistant populations showed cross-resistance to nicosulfuron and flucarbazone while only three populations had cross-resistance to pyrithiobac. Sequence analyses revealed single base-pair mutations in the resistant populations of green foxtail. These mutations were coded for Thr, Asn, or Ile substitution at Ser(653). In addition, a new mutation was found in one population that coded for an Asp substitution at Gly(654). There is an agreement between the spectra of resistance observed and the type of resistance known to be conferred by these substitutions. Moreover, it indicates that, under similar selection pressure (imazethapyr), a variety of mutations can be selected for different populations, making the resistance pattern difficult to predict from herbicide exposure history.
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Affiliation(s)
- Julie Laplante
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Jander G, Barth C. Tandem gene arrays: a challenge for functional genomics. TRENDS IN PLANT SCIENCE 2007; 12:203-10. [PMID: 17416543 DOI: 10.1016/j.tplants.2007.03.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2006] [Revised: 02/20/2007] [Accepted: 03/27/2007] [Indexed: 05/14/2023]
Abstract
In sequenced plant genomes, 15% or more of the identified genes are members of tandem-arrayed gene families. Because mutating only one gene in a duplicated pair often produces no measurable phenotype, this poses a particular challenge for functional analysis. To generate phenotypic knockouts, it is necessary to create deletions that affect multiple genes, select for rare meiotic recombination between tightly linked loci, or perform sequential mutant screens in the same plant line. Successfully implemented strategies include PCR-based screening for fast neutron-induced deletions, selection for recombination between herbicide resistance markers, and localized transposon mutagenesis. Here, we review the relative merits of current genetic approaches and discuss the prospect of site-directed mutagenesis for generating elusive knockouts of tandem-arrayed gene families.
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Affiliation(s)
- Georg Jander
- Boyce Thompson Institute for Plant Research, Tower Road, Cornell University, Ithaca, NY 14853, USA.
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Dong C, Beetham P, Vincent K, Sharp P. Oligonucleotide-directed gene repair in wheat using a transient plasmid gene repair assay system. PLANT CELL REPORTS 2006; 25:457-65. [PMID: 16404599 DOI: 10.1007/s00299-005-0098-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2005] [Revised: 11/10/2005] [Accepted: 11/20/2005] [Indexed: 05/06/2023]
Abstract
Oligonucleotide-directed gene repair is a potential technique for agricultural trait modification in economically important crops. However, large variation in the repair frequencies among the scientific reports indicates that there are many factors influencing the repair process. We report here a transient assay system using GFP as a reporter for testing the efficiency of plasmid DNA repair in cultured wheat cells. This assay showed that osmotic medium supplemented with 2,4-D increased the oligo-targeting frequency, and that the repair of a point mutation was more efficient than repair of a single base deletion mutation in cultured scutellum cells of immature wheat embryos. This study provides the first evidence that oligonucleotide-directed mutagenesis is applicable to regenerable cultured wheat scutellum cells.
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Affiliation(s)
- Chongmei Dong
- Plant Breeding Institute, University of Sydney, PMB 11, Camden, NSW, 2570, Australia.
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Yin WX, Wu XS, Liu G, Li ZH, Watt RM, Huang JD, Liu DP, Liang CC. Targeted correction of a chromosomal point mutation by modified single-stranded oligonucleotides in a GFP recovery system. Biochem Biophys Res Commun 2005; 334:1032-41. [PMID: 16039616 DOI: 10.1016/j.bbrc.2005.06.193] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Accepted: 06/29/2005] [Indexed: 11/29/2022]
Abstract
Synthetic oligonucleotides had been employed in DNA repair and promised great potentials in gene therapy. To test the ability of single-stranded oligonucleotide (SSO)-mediated gene repair within a chromosomal site in human cells, a HeLa cell line stably integrated with mutant enhanced green fluorescence protein gene (mEGFP) in the genome was established. Transfection with specific SSOs successfully repaired the mEGFP gene and resulted in the expression of functional fluorescence proteins, which could be detected by fluorescence microscopy and FACS assay. Western blot showed that EGFP was only present in the cells transfected with correction SSOs rather than the control SSOs. Furthermore, DNA sequencing confirmed that phenotype change resulted from the designated nucleotide correction at the target site. Using this reporter system, we determined the optimal structure of SSO by investigating the effect of length, modifications, and polarities of SSOs as well as the positions of the mismatch-forming nucleotide on the efficiency of SSO-mediated gene repair. Interestingly, we found that SSOs with mismatch-forming nucleotide positioned at different positions have varying potencies that homology at the 5'-end of SSOs was more crucial for the SSO's activity. These results provided guidance for designing effective SSOs as tools for treating monogenic inherited diseases.
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Affiliation(s)
- Wen-Xuan Yin
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), Beijing 100005, PR China
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Iida S, Terada R. Modification of endogenous natural genes by gene targeting in rice and other higher plants. PLANT MOLECULAR BIOLOGY 2005; 59:205-19. [PMID: 16217613 DOI: 10.1007/s11103-005-2162-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2004] [Accepted: 02/11/2005] [Indexed: 05/04/2023]
Abstract
The capability to modify a genomic sequence into a designed sequence is a powerful tool for biologists and breeders to elucidate the function of an individual gene and its cis-acting elements of multigene families in the genome. Gene targeting refers to the alteration of a specific DNA sequence in an endogenous gene at its original locus in the genome. In higher plants, however, the overwhelming occurrence of the random integration of transgenes by non-homologous end-joining is the main obstacle to develop efficient gene targeting. Two approaches have been undertaken to modify a genomic sequence in higher plants- chimeric RNA/DNA oligonucleotide-directed gene targeting to generate a site-specific base conversion, and homologous recombination-dependent gene targeting to produce either a base change or a gene replacement in a sequence-specific manner. The successful and reproducible targeting of an endogenous gene by homologous recombination, independently of gene-specific selection by employing a strong positive-negative selection, has been demonstrated for the first time in rice, an important staple food and a model plant for other cereal species. This review addresses the current status of targeting of an endogenous natural gene in rice and other higher plants and discusses possible models for Agrobacterium- mediated gene targeting by homologous recombination using a strong positive-negative selection.
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Affiliation(s)
- Shigeru Iida
- Division of Molecular Genetics, National Institutes of Natural Sciences, National Institute for Basic Biology, Myodaiji, Okazaki 444-8585, Japan.
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Miki B, McHugh S. Selectable marker genes in transgenic plants: applications, alternatives and biosafety. J Biotechnol 2004; 107:193-232. [PMID: 14736458 DOI: 10.1016/j.jbiotec.2003.10.011] [Citation(s) in RCA: 216] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Approximately fifty marker genes used for transgenic and transplastomic plant research or crop development have been assessed for efficiency, biosafety, scientific applications and commercialization. Selectable marker genes can be divided into several categories depending on whether they confer positive or negative selection and whether selection is conditional or non-conditional on the presence of external substrates. Positive selectable marker genes are defined as those that promote the growth of transformed tissue whereas negative selectable marker genes result in the death of the transformed tissue. The positive selectable marker genes that are conditional on the use of toxic agents, such as antibiotics, herbicides or drugs were the first to be developed and exploited. More recent developments include positive selectable marker genes that are conditional on non-toxic agents that may be substrates for growth or that induce growth and differentiation of the transformed tissues. Newer strategies include positive selectable marker genes which are not conditional on external substrates but which alter the physiological processes that govern plant development. A valuable companion to the selectable marker genes are the reporter genes, which do not provide a cell with a selective advantage, but which can be used to monitor transgenic events and manually separate transgenic material from non-transformed material. They fall into two categories depending on whether they are conditional or non-conditional on the presence of external substrates. Some reporter genes can be adapted to function as selectable marker genes through the development of novel substrates. Despite the large number of marker genes that exist for plants, only a few marker genes are used for most plant research and crop development. As the production of transgenic plants is labor intensive, expensive and difficult for most species, practical issues govern the choice of selectable marker genes that are used. Many of the genes have specific limitations or have not been sufficiently tested to merit their widespread use. For research, a variety of selection systems are essential as no single selectable marker gene was found to be sufficient for all circumstances. Although, no adverse biosafety effects have been reported for the marker genes that have been adopted for widespread use, biosafety concerns should help direct which markers will be chosen for future crop development. Common sense dictates that marker genes conferring resistance to significant therapeutic antibiotics should not be used. An area of research that is growing rapidly but is still in its infancy is the development of strategies for eliminating selectable marker genes to generate marker-free plants. Among the several technologies described, two have emerged with significant potential. The simplest is the co-transformation of genes of interest with selectable marker genes followed by the segregation of the separate genes through conventional genetics. The more complicated strategy is the use of site-specific recombinases, under the control of inducible promoters, to excise the marker genes and excision machinery from the transgenic plant after selection has been achieved. In this review each of the genes and processes will be examined to assess the alternatives that exist for producing transgenic plants.
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Affiliation(s)
- Brian Miki
- Research Branch, Agriculture and Agri-Food Canada, Room 2091, KW Neatby Bldg., CEF, 960 Carling Avenue, Ottawa, Ont., Canada K1A 0C6.
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