1
|
Chi J, Ding L, Wang X, Chen X, Peng C, Xu J. A platform for precise quantification of gene editing products based on microfluidic chip-based digital PCR. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:4783-4793. [PMID: 38961688 DOI: 10.1039/d4ay00863d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The new generation of gene editing technologies, primarily based on CRISPR/Cas9 and its derivatives, allows for more precise editing of organisms. However, when the editing efficiency is low, only a small fraction of gene fragments is edited, leaving behind minimal traces and making it difficult to detect and evaluate the editing effects. Although a series of technologies and methods have been developed, they lack the ability for precise quantification and quantitative analysis of these products. Digital polymerase chain reaction (dPCR) offers advantages such as high precision and sensitivity, making it suitable for absolute quantification of nucleic acid samples. In the present study, we developed a novel platform for precise quantification of gene editing products based on microfluidic chip-based dPCR. The results indicated that our assay accurately identified different types of edited samples within a variety of different types, including more complex genomic crops such as tetraploid rapeseed and soybean (highly repetitive sequence). The sensitivity of this detection platform was as low as 8.14 copies per μL, with a detection limit of 0.1%. These results demonstrated the superior performance of the platform, including high sensitivity, low detection limit, and wide applicability, enabling precise quantification and assessment of gene editing efficiency. In conclusion, microfluidic chip-based dPCR was used as a powerful tool for precise quantification and assessment of gene editing products.
Collapse
Affiliation(s)
- Jingzheng Chi
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Lin Ding
- College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China.
| |
Collapse
|
2
|
Paleologo M, Lanubile A, Camardo Leggieri M, Graffigna G, Gomarasca P, Barello S. Public perception of new plant breeding techniques and the psychosocial determinants of acceptance: A systematic review. PUBLIC UNDERSTANDING OF SCIENCE (BRISTOL, ENGLAND) 2024:9636625241254981. [PMID: 38863424 DOI: 10.1177/09636625241254981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2024]
Abstract
Advancements in New Plant Breeding Techniques have emerged as promising tools for enhancing crop productivity, quality, and resilience in the face of global challenges, such as climate change and food security. However, the successful implementation of these techniques relies also on public acceptance of this innovation. Understanding what shapes public perception and acceptance of New Plant Breeding Techniques is crucial for effective science communication, policymaking, and the sustainable adoption of these innovations. The objective of this systematic review was to synthesize existing research on the public perception of New Plant Breeding Techniques applied to food crops and explore the psychosocial determinants that influence acceptance. Twenty papers published between 2015 and 2023 were included on various New Plant Breeding Techniques and their reception by the general public. Determinants affecting the acceptance of food crops derived from New Plant Breeding Techniques were categorized into six areas: sociodemographic factors, perceived benefits and risks, attitudes toward science, communication strategies, personal values, and product characteristics.
Collapse
|
3
|
Puchta H. Regulation of gene-edited plants in Europe: from the valley of tears into the shining sun? ABIOTECH 2024; 5:231-238. [PMID: 38974871 PMCID: PMC11224193 DOI: 10.1007/s42994-023-00130-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/04/2023] [Indexed: 07/09/2024]
Abstract
Some 20 years ago, the EU introduced complex regulatory rules for the growth of transgenic crops, which resulted in a de facto ban to grow these plants in fields within most European countries. With the rise of novel genome editing technologies, it has become possible to improve crops genetically in a directed way without the need for incorporation of foreign genes. Unfortunately, in 2018, the European Court of Justice ruled that such gene-edited plants are to be regulated like transgenic plants. Since then, European scientists and breeders have challenged this decision and requested a revision of this outdated law. Finally, after 5 years, the European Commission has now published a proposal on how, in the future, to regulate crops produced by new breeding technologies. The proposal tries to find a balance between the different interest groups in Europe. On one side, genetically modified plants, which cannot be discerned from their natural counterparts, will exclusively be used for food and feed and are-besides a registration step-not to be regulated at all. On the other side, plants expressing herbicide resistance are to be excluded from this regulation, a concession to the strong environmental associations and NGOs in Europe. Moreover, edited crops are to be excluded from organic farming to protect the business interests of the strong organic sector in Europe. Nevertheless, if this law passes European parliament and council, unchanged, it will present a big step forward toward establishing a more sustainable European agricultural system. Thus, it might soon be possible to develop and grow crops that are more adapted to global warming and whose cultivation will require lower amounts of pesticides. However, there is still a long way to go until the law is passed. Too often, the storm of arguments raised by the opponents, based on irrational fears of mutations and a naive understanding of nature, has fallen on fruitful ground in Europe.
Collapse
Affiliation(s)
- Holger Puchta
- Department of Molecular Biology, Joseph Gottlieb Kölreuter Institute for Plant Sciences, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, 76131 Karlsruhe, Germany
| |
Collapse
|
4
|
Su Z, Wang X, Chen X, Ding L, Zeng X, Xu J, Peng C. Novel CRISPR/SpRY system for rapid detection of CRISPR/Cas-mediated gene editing in rice. Anal Chim Acta 2024; 1303:342519. [PMID: 38609262 DOI: 10.1016/j.aca.2024.342519] [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: 03/06/2024] [Revised: 03/21/2024] [Accepted: 03/21/2024] [Indexed: 04/14/2024]
Abstract
The gene editing technology represented by clustered rule-interspersed short palindromic repeats (CRISPR)/Cas9 has developed as a common tool in the field of biotechnology. Many gene-edited products in plant varieties have recently been commercialized. However, the rapid on-site visual detection of gene-edited products without instrumentation remains challenging. This study aimed to develop a novel and efficient method, termed the CRISPR/SpRY detection platform, for the rapid screening of CRISPR/Cas9-induced mutants based on CRISPR/SpRY-mediated in vitro cleavage using rice (Oryza sativa L.) samples genetically edited at the TGW locus as an example. We designed the workflow of the CRISPR/SpRY detection platform and conducted a feasibility assessment. Subsequently, we optimized the reaction system of CRISPR/SpRY, and developed a one-pot CRISPR/SpRY assay by integrating recombinase polymerase amplification (RPA). The sensitivity of the method was further verified using recombinant plasmids. The proposed method successfully identified various types of mutations, including insertions, deletions (indels), and nucleotide substitutions, with excellent sensitivity. Finally, the applicability of this method was validated using different rice samples. The entire process was completed in less than an hour, with a limit of detection as low as 1%. Compared with previous methods, our approach is simple to operate, instrumentation-free, cost-effective, and time-efficient. The primary significance lies in the liberation of our developed system from the limitations imposed using protospacer adjacent motif sequences. This expands the scope and versatility of the CRISPR-based detection platform, making it a promising and groundbreaking platform for detecting mutations induced by gene editing.
Collapse
Affiliation(s)
- Zhixun Su
- College of Food Science and Technology, Ningbo University, Ningbo, 315800, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaofu Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoyun Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Lin Ding
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoqun Zeng
- College of Food Science and Technology, Ningbo University, Ningbo, 315800, China
| | - Junfeng Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cheng Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Key Laboratory of Traceability for Agricultural Genetically Modified Organisms, Ministry of Agriculture and Rural Affairs, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
5
|
Pallarz S, Fiedler S, Wahler D, Lämke J, Grohmann L. Reproducibility of next-generation-sequencing-based analysis of a CRISPR/Cas9 genome edited oil seed rape. FOOD CHEMISTRY. MOLECULAR SCIENCES 2023; 7:100182. [PMID: 37822547 PMCID: PMC10562171 DOI: 10.1016/j.fochms.2023.100182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 10/13/2023]
Abstract
Next-generation-sequencing (NGS) becomes increasingly important for laboratories tasked with the detection of genetically modified organisms (GMOs) in food, feed and seeds. Its implementation into standardized workflows demands reliable intra- and inter-laboratory reproducibility. Here, we analyze the reproducibility of short- and long-read targeted NGS and long-read whole genome sequencing (WGS) data between three independent laboratories. Replicate samples were submitted for sequencing and comparatively analyzed. The targeted-NGS-samples consisted of oil seed rape (OSR) sampled from a commodity shipment spiked with a genome edited (GE) OSR and the WGS-samples consisted of leaf material from the GMOs' parental line. All laboratories delivered highly reproducible high-quality targeted NGS data with little variation. The detection of GMO-related sequences works well regardless of the facility, while the mapping to the complex genome is superior using long read data. Long read WGS is currently not suitable for routine use in enforcement laboratories, due to a large inter-laboratory variation.
Collapse
Affiliation(s)
- Steffen Pallarz
- Department Genetic Engineering and Other Biotechnological Processes, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Stefan Fiedler
- Department Method Standardisation, Reference Laboratories, Resistance To Antibiotics, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Daniela Wahler
- Department Genetic Engineering and Other Biotechnological Processes, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Jörn Lämke
- Department Method Standardisation, Reference Laboratories, Resistance To Antibiotics, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| | - Lutz Grohmann
- Department Genetic Engineering and Other Biotechnological Processes, Federal Office of Consumer Protection and Food Safety (BVL), P.O. Box 110260, 10832 Berlin, Germany
| |
Collapse
|
6
|
Zanatta CB, Hoepers AM, Nodari RO, Agapito-Tenfen SZ. Specificity Testing for NGT PCR-Based Detection Methods in the Context of the EU GMO Regulations. Foods 2023; 12:4298. [PMID: 38231759 DOI: 10.3390/foods12234298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/07/2023] [Accepted: 11/20/2023] [Indexed: 01/19/2024] Open
Abstract
The term new genomic techniques (NGTs) is an umbrella term used to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework used to detect GMOs in Europe is an established single harmonized procedure that is mandatory for the authorization of GM food and feed, thus generating a reliable, transparent, and effective labeling scheme for GMO products. However, NGT products can challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, the current detection methods might fail to meet the minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems' specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. In addition, it also empirically tested the PCR system evaluated during the in silico analysis. Two mutant genotypes produced by CRISPR-Cas9 in Arabidopsis thaliana were used as a case study. Overall, our results demonstrate that the single PCR system developed for identifying a nucleotide insertion in the grf1-3 genotype has multiple matches in the databases, which do not enable the discrimination of this mutated event. Empirical assays further support this demonstration. In contrast, the second mutated genotype, grf8-61, which contains a -3 bp deletion, did not yield any matches in the sequence variant database. However, the primer sequences were not efficient during the empirical assay. Our approach represents a first step in decision making for analytical methods for NGT detection, identification, and quantification in light of the European labeling regulations.
Collapse
Affiliation(s)
- Caroline Bedin Zanatta
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Aline Martins Hoepers
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | - Rubens Onofre Nodari
- Department of Crop Science, Federal University of Santa Catarina, Florianópolis 88034000, Brazil
| | | |
Collapse
|
7
|
Wu K, Xu C, Li T, Ma H, Gong J, Li X, Sun X, Hu X. Application of Nanotechnology in Plant Genetic Engineering. Int J Mol Sci 2023; 24:14836. [PMID: 37834283 PMCID: PMC10573821 DOI: 10.3390/ijms241914836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/20/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
The ever-increasing food requirement with globally growing population demands advanced agricultural practices to improve grain yield, to gain crop resilience under unpredictable extreme weather, and to reduce production loss caused by insects and pathogens. To fulfill such requests, genome engineering technology has been applied to various plant species. To date, several generations of genome engineering methods have been developed. Among these methods, the new mainstream technology is clustered regularly interspaced short palindromic repeats (CRISPR) with nucleases. One of the most important processes in genome engineering is to deliver gene cassettes into plant cells. Conventionally used systems have several shortcomings, such as being labor- and time-consuming procedures, potential tissue damage, and low transformation efficiency. Taking advantage of nanotechnology, the nanoparticle-mediated gene delivery method presents technical superiority over conventional approaches due to its high efficiency and adaptability in different plant species. In this review, we summarize the evolution of plant biomolecular delivery methods and discussed their characteristics as well as limitations. We focused on the cutting-edge nanotechnology-based delivery system, and reviewed different types of nanoparticles, preparation of nanomaterials, mechanism of nanoparticle transport, and advanced application in plant genome engineering. On the basis of established methods, we concluded that the combination of genome editing, nanoparticle-mediated gene transformation and de novo regeneration technologies can accelerate crop improvement efficiently in the future.
Collapse
Affiliation(s)
- Kexin Wu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Changbin Xu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Tong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Haijie Ma
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Jinli Gong
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Xiaolong Li
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Xuepeng Sun
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| | - Xiaoli Hu
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
- Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vegetable, Ministry of Agriculture and Rural Affairs, Hangzhou 311300, China
| |
Collapse
|
8
|
Karunarathne S, Walker E, Sharma D, Li C, Han Y. Genetic resources and precise gene editing for targeted improvement of barley abiotic stress tolerance. J Zhejiang Univ Sci B 2023; 24:1069-1092. [PMID: 38057266 PMCID: PMC10710907 DOI: 10.1631/jzus.b2200552] [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: 10/31/2022] [Accepted: 01/17/2023] [Indexed: 07/11/2023]
Abstract
Abiotic stresses, predominately drought, heat, salinity, cold, and waterlogging, adversely affect cereal crops. They limit barley production worldwide and cause huge economic losses. In barley, functional genes under various stresses have been identified over the years and genetic improvement to stress tolerance has taken a new turn with the introduction of modern gene-editing platforms. In particular, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) is a robust and versatile tool for precise mutation creation and trait improvement. In this review, we highlight the stress-affected regions and the corresponding economic losses among the main barley producers. We collate about 150 key genes associated with stress tolerance and combine them into a single physical map for potential breeding practices. We also overview the applications of precise base editing, prime editing, and multiplexing technologies for targeted trait modification, and discuss current challenges including high-throughput mutant genotyping and genotype dependency in genetic transformation to promote commercial breeding. The listed genes counteract key stresses such as drought, salinity, and nutrient deficiency, and the potential application of the respective gene-editing technologies will provide insight into barley improvement for climate resilience.
Collapse
Affiliation(s)
- Sakura Karunarathne
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia
| | - Esther Walker
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Darshan Sharma
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia
| | - Chengdao Li
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| | - Yong Han
- Western Crop Genetics Alliance, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, WA 6150, Australia.
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia.
| |
Collapse
|
9
|
Eckerstorfer MF, Dolezel M, Engelhard M, Giovannelli V, Grabowski M, Heissenberger A, Lener M, Reichenbecher W, Simon S, Staiano G, Wüst Saucy AG, Zünd J, Lüthi C. Recommendations for the Assessment of Potential Environmental Effects of Genome-Editing Applications in Plants in the EU. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091764. [PMID: 37176822 PMCID: PMC10180588 DOI: 10.3390/plants12091764] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/11/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023]
Abstract
The current initiative of the European Commission (EC) concerning plants produced using certain new genomic techniques, in particular, targeted mutagenesis and cisgenesis, underlines that a high level of protection for human and animal health and the environment needs to be maintained when using such applications. The current EU biosafety regulation framework ensures a high level of protection with a mandatory environmental risk assessment (ERA) of genetically modified (GM) products prior to the authorization of individual GMOs for environmental release or marketing. However, the guidance available from the European Food Safety Authority (EFSA) for conducting such an ERA is not specific enough regarding the techniques under discussion and needs to be further developed to support the policy goals towards ERA, i.e., a case-by-case assessment approach proportionate to the respective risks, currently put forward by the EC. This review identifies important elements for the case-by-case approach for the ERA that need to be taken into account in the framework for a risk-oriented regulatory approach. We also discuss that the comparison of genome-edited plants with plants developed using conventional breeding methods should be conducted at the level of a scientific case-by-case assessment of individual applications rather than at a general, technology-based level. Our considerations aim to support the development of further specific guidance for the ERA of genome-edited plants.
Collapse
Affiliation(s)
- Michael F Eckerstorfer
- Umweltbundesamt-Environment Agency Austria (EAA), Landuse and Biosafety Unit, Spittelauer Lände 5, 1090 Vienna, Austria
| | - Marion Dolezel
- Umweltbundesamt-Environment Agency Austria (EAA), Landuse and Biosafety Unit, Spittelauer Lände 5, 1090 Vienna, Austria
| | - Margret Engelhard
- Federal Agency for Nature Conservation, Division of Assessment of GMOs/Enforcement of Genetic Engineering Act, Konstantinstr. 110, 53179 Bonn, Germany
| | - Valeria Giovannelli
- ISPRA (Italian Institute for Environmental Protection and Research), Department for Environmental Monitoring and Protection and for Biodiversity Conservation, Via Vitaliano Brancati, 48, 00144 Rome, Italy
| | - Marcin Grabowski
- Ministry of Climate and Environment, Department Nature Conservation, GMO Unit, Wawelska 52/54, 00-922 Warsaw, Poland
| | - Andreas Heissenberger
- Umweltbundesamt-Environment Agency Austria (EAA), Landuse and Biosafety Unit, Spittelauer Lände 5, 1090 Vienna, Austria
| | - Matteo Lener
- ISPRA (Italian Institute for Environmental Protection and Research), Department for Environmental Monitoring and Protection and for Biodiversity Conservation, Via Vitaliano Brancati, 48, 00144 Rome, Italy
| | - Wolfram Reichenbecher
- Federal Agency for Nature Conservation, Division of Assessment of GMOs/Enforcement of Genetic Engineering Act, Konstantinstr. 110, 53179 Bonn, Germany
| | - Samson Simon
- Federal Agency for Nature Conservation, Division of Assessment of GMOs/Enforcement of Genetic Engineering Act, Konstantinstr. 110, 53179 Bonn, Germany
| | - Giovanni Staiano
- ISPRA (Italian Institute for Environmental Protection and Research), Department for Environmental Monitoring and Protection and for Biodiversity Conservation, Via Vitaliano Brancati, 48, 00144 Rome, Italy
| | - Anne Gabrielle Wüst Saucy
- Federal Office for the Environment (FOEN), Biotechnology Section, Soil and Biotechnology Division, 3003 Bern, Switzerland
| | - Jan Zünd
- Federal Office for the Environment (FOEN), Biotechnology Section, Soil and Biotechnology Division, 3003 Bern, Switzerland
| | - Christoph Lüthi
- Federal Office for the Environment (FOEN), Biotechnology Section, Soil and Biotechnology Division, 3003 Bern, Switzerland
| |
Collapse
|
10
|
Marone D, Mastrangelo AM, Borrelli GM. From Transgenesis to Genome Editing in Crop Improvement: Applications, Marketing, and Legal Issues. Int J Mol Sci 2023; 24:ijms24087122. [PMID: 37108285 PMCID: PMC10138802 DOI: 10.3390/ijms24087122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/30/2023] [Accepted: 04/06/2023] [Indexed: 04/29/2023] Open
Abstract
The biotechnological approaches of transgenesis and the more recent eco-friendly new breeding techniques (NBTs), in particular, genome editing, offer useful strategies for genetic improvement of crops, and therefore, recently, they have been receiving increasingly more attention. The number of traits improved through transgenesis and genome editing technologies is growing, ranging from resistance to herbicides and insects to traits capable of coping with human population growth and climate change, such as nutritional quality or resistance to climatic stress and diseases. Research on both technologies has reached an advanced stage of development and, for many biotech crops, phenotypic evaluations in the open field are already underway. In addition, many approvals regarding main crops have been granted. Over time, there has been an increase in the areas cultivated with crops that have been improved through both approaches, but their use in various countries has been limited by legislative restrictions according to the different regulations applied which affect their cultivation, marketing, and use in human and animal nutrition. In the absence of specific legislation, there is an on-going public debate with favorable and unfavorable positions. This review offers an updated and in-depth discussion on these issues.
Collapse
Affiliation(s)
- Daniela Marone
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy
| | - Anna Maria Mastrangelo
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy
| | - Grazia Maria Borrelli
- Council for Agricultural Research and Economics, Research Centre for Cereal and Industrial Crops, 71122 Foggia, Italy
| |
Collapse
|
11
|
Targeted High-Throughput Sequencing Enables the Detection of Single Nucleotide Variations in CRISPR/Cas9 Gene-Edited Organisms. Foods 2023; 12:foods12030455. [PMID: 36765984 PMCID: PMC9914749 DOI: 10.3390/foods12030455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/09/2023] [Accepted: 01/16/2023] [Indexed: 01/20/2023] Open
Abstract
Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) organisms and their derived food/feed products commercialized on the European Union market fall within the scope of European Union Directive 2001/18/EC. Consequently, their control in the food/feed chain by GMO enforcement laboratories is required by the competent authorities to guarantee food/feed safety and traceability (2003/1829/EC; 2003/1830/EC). However, their detection is potentially challenging at both the analytical and interpretation levels since this requires methodological approaches that can target and detect a specific single nucleotide variation (SNV) introduced into a GE organism. In this study, we propose a targeted high-throughput sequencing approach, including (i) a prior PCR-based enrichment step to amplify regions of interest, (ii) a sequencing step, and (iii) a data analysis methodology to identify SNVs of interest. To investigate if the performance of this targeted high-throughput sequencing approach is compatible with the performance criteria used in the GMO detection field, several samples containing different percentages of a GE rice line carrying a single adenosine insertion in OsMADS26 were prepared and analyzed. The SNV of interest in samples containing the GE rice line could successfully be detected, both at high and low percentages. No impact related to food processing or to the presence of other crop species was observed. The present proof-of-concept study has allowed us to deliver the first experimental-based evidence indicating that the proposed targeted high-throughput sequencing approach may constitute, in the future, a specific and sensitive tool to support the safety and traceability of the food/feed chain regarding GE plants carrying SNVs.
Collapse
|
12
|
Sprink T, Wilhelm R, Hartung F. Genome editing around the globe: An update on policies and perceptions. PLANT PHYSIOLOGY 2022; 190:1579-1587. [PMID: 35976141 PMCID: PMC9614466 DOI: 10.1093/plphys/kiac359] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 07/05/2022] [Indexed: 05/11/2023]
Abstract
A decade ago, the CRISPR/Cas system has been adapted for genome editing. Since then, hundreds of organisms have been altered using genome editing and discussions were raised on the regulatory status of genome edited organisms esp. crops. To date, many countries have made decisions on the regulatory status of products of genome editing, by exempting some kinds of edits from the classical GMO regulation. However, the guidance differs between countries even in the same region. Several countries are still debating the issue or are in the progress of updating guidance and regulatory systems to cover products of genome editing. The current global situation of different regulatory systems is putting a harmonized framework on genome-edited crops in the far future. In this update, we summarize the current developments in the field of regulation concerning edited crops and present a short insight into perception of genome editing in the society.
Collapse
Affiliation(s)
| | - Ralf Wilhelm
- Julius Kuehn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Saxony-Anhalt, Germany
| | - Frank Hartung
- Julius Kuehn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Saxony-Anhalt, Germany
| |
Collapse
|
13
|
de Lange J, Nalley LL, Yang W, Shew A, de Steur H. The future of CRISPR gene editing according to plant scientists. iScience 2022; 25:105012. [PMID: 36093047 PMCID: PMC9460836 DOI: 10.1016/j.isci.2022.105012] [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: 05/10/2022] [Revised: 06/29/2022] [Accepted: 08/19/2022] [Indexed: 11/18/2022] Open
Abstract
This study surveyed 669 plant scientists globally to elicit how (which outcomes of gene editing), where (which continent) and what (which crops) are most likely to benefit from CRISPR research and if there is a consensus about specific barriers to commercial adoption in agriculture. Further, we disaggregated public and private plant scientists to see if there was heterogeneity in their views of the future of CRISPR research. Our findings suggest that maize and soybeans are anticipated to benefit the most from CRISPR technology with fungus and virus resistance the most common vehicle for its implementation. Across the board, plant scientists viewed consumer perception/knowledge gap to be the most impeding barrier of CRISPR adoption. Although CRISPR has been hailed as a technology that can help alleviate food insecurity and improve agricultural sustainability, our study has shown that plant scientists believe there are some large concerns about the consumer perceptions of CRISPR.
Collapse
Affiliation(s)
- Job de Lange
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Lawton Lanier Nalley
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Wei Yang
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Aaron Shew
- Department of Agricultural Economics, University of Arkansas, Fayetteville, AR 72701, USA
| | - Hans de Steur
- Department of Agricultural Economics, University of Gent, Gent, Belgium
| |
Collapse
|
14
|
Ramsay T, Robinson B, Coche I, Hackett K, Emerson C. Ethical aspects of GMO regulation in the EU: Regulating new plant breeding techniques as GM has negative effects on sustainability, diversity and inclusion: Regulating new plant breeding techniques as GM has negative effects on sustainability, diversity and inclusion. EMBO Rep 2022; 23:e55583. [PMID: 35900903 PMCID: PMC9442288 DOI: 10.15252/embr.202255583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 07/13/2022] [Indexed: 07/30/2023] Open
Abstract
Plant breeding plays a crucial role for the EU to live up to its values and promises of sustainability, innovation and diversity and inclusion. The current regulations, however, make it de facto impossible to use new breeding technologies.
Collapse
|
15
|
Spök A, Sprink T, Allan AC, Yamaguchi T, Dayé C. Towards social acceptability of genome-edited plants in industrialised countries? Emerging evidence from Europe, United States, Canada, Australia, New Zealand, and Japan. Front Genome Ed 2022; 4:899331. [PMID: 36120531 PMCID: PMC9473316 DOI: 10.3389/fgeed.2022.899331] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 07/15/2022] [Indexed: 11/24/2022] Open
Abstract
The agricultural biotechnology world has been divided into two blocks; countries adopting GM crops for commercial cultivation (adopters) and others without any or without relevant cultivation of such crops (non-adopters). Meanwhile, an increasing number of adopter countries have exempted certain genome-edited (GE) crops from legal GMO pre-market approval and labelling requirements. Among them are major exporters of agricultural commodities such as United States, Canada, and Australia. Due to the relaxed legislation more GE plants are expected to enter the market soon. Many countries in the non-adopter group, however, depend on import of large volumes of agricultural commodities from adopter countries. Unlike first generation GM, certain GE crops cannot be identified as unambiguously originating from genome editing using available techniques. Consequently, pressure is mounting on non-adopter jurisdictions to reconsider their policies and legislations. Against this backdrop, the paper explores recent developments relevant for social acceptability in selected non-adopters, Japan, New Zealand, the EU, Norway, and Switzerland in contrast to United States, Canada, and Australia. While Japan is already opening-up and Norway and Switzerland are discussing revisions of their policies, the EU and New Zealand are struggling with challenges resulting from high court decisions. In an attempt to take a closer look into the inner dynamics of these developments, the concept of social acceptability proposed by Wüstenhagen et al. (Energy Policy, 2007, 35(5), 2683-2691) is employed. This aids the understanding of developments in the jurisdictions considered and identifies specific or cross-cutting challenges.
Collapse
Affiliation(s)
- Armin Spök
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| | - Thorben Sprink
- Institute for Biosafety in Plant Biotechnology, Julius Kühn-Institut, Federal Research Center for Cultivated Plants, Quedlinburg, Germany
| | - Andrew C. Allan
- New Cultivar Innovation, Plant & Food Research, Auckland, New Zealand
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Tomiko Yamaguchi
- College of Liberal Arts, International Christian University, Tokyo, Japan
| | - Christian Dayé
- Science, Technology and Society Unit, Graz University of Technology, Graz, Austria
| |
Collapse
|
16
|
Qin S, Fan Y, Hu S, Wang Y, Wang Z, Cao Y, Liu Q, Tan S, Dai Z, Zhou W. iPReditor-CMG: Improving a predictive RNA editor for crop mitochondrial genomes using genomic sequence features and an optimal support vector machine. PHYTOCHEMISTRY 2022; 200:113222. [PMID: 35561852 DOI: 10.1016/j.phytochem.2022.113222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
In crops, RNA editing is one of the most important post-transcriptional processes in which specific cytidines (C) in virtually all mitochondrial protein-coding genes are converted to uridines (U). Despite extensive recent research in RNA editing, exploring all of the C-to-U editing events efficiently on the genomic scale remains challengeable. Developing accurate prediction methods for the detection of RNA editing sites would dramatically reduce experimental determination. Therefore, we propose a novel method, iPReditor-CMG (improved predictive RNA editor for crop mitochondrial genomes), to predict crop mitochondrial editing sites using genome sequence and an optimised support vector machine (SVM). We first selected three mitochondrial genomes with known RNA editing sites from Arabidopsis thaliana, Brassica napus and Oryza sativa, released by NCBI, as the training and test sets. The genes and their transcripts from self-sequenced tobacco mitochondrial ATPase were selected as the validation set. The iPReditor-CMG first coded the genome sequences as numerical vectors and then performed an efficient feature selection on the high-dimensional feature space, where the SVM was employed in feature selection and following modelling. The average independent prediction accuracy of intraspecific editing sites across three species was 0.85, and up to 0.91 in A. thaliana, which outperformed the reference models. For the interspecific independent prediction, the prediction accuracy between dicotyledons was 0.78 and the accuracy between dicotyledons and monocotyledons was 0.56, which implies that there might be similarity in the C-to-U editing mechanism in close relatives. Finally, the best model was identified with an independent test accuracy of 0.91 and an AUC of 0.88, which suggested that five unreported feature sequences, i.e. TGACA, ACAAC, GTAGA, CCGTT and TAACA, are closely associated with the editing phenomenon. Multiple tests supported that the iPReditor-CMG could be effectively applied to predict editing sites in crop mitochondria, which may further contribute to understanding the mechanisms of site editing and post-transcriptional events in crop mitochondria.
Collapse
Affiliation(s)
- Sidong Qin
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China
| | - Yanjun Fan
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China; Shanxi Province Jincheng City Landscaping Service Center, Shanxi, 048000, China
| | - Shengnan Hu
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China
| | - Yongqiang Wang
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China
| | - Ziqi Wang
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China
| | - Yixiang Cao
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China
| | - Qiyuan Liu
- Key Laboratory of Crop Physiology, Ecology and Genetic Breeding, Ministry of Education, College of Agronomy, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Siqiao Tan
- College of Information and Intelligence, Hunan Agricultural University, Changsha, 410128, China
| | - Zhijun Dai
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China
| | - Wei Zhou
- Hunan Provincial Engineering and Technology Research Center for Agricultural Big Data Analysis and Decision-Making, Hunan Agricultural University, Changsha, 410128, China; Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, Hunan Agricultural University, Changsha, 410128, China.
| |
Collapse
|
17
|
Fraiture MA, Guiderdoni E, Meunier AC, Papazova N, Roosens NH. ddPCR strategy to detect a gene-edited plant carrying a single variation point: Technical feasibility and interpretation issues. Food Control 2022. [DOI: 10.1016/j.foodcont.2022.108904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
The socio-economic factors affecting the emergence and impacts of new genomic techniques in agriculture: A scoping review. Trends Food Sci Technol 2022. [DOI: 10.1016/j.tifs.2022.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
19
|
Thomson MJ, Biswas S, Tsakirpaloglou N, Septiningsih EM. Functional Allele Validation by Gene Editing to Leverage the Wealth of Genetic Resources for Crop Improvement. Int J Mol Sci 2022; 23:ijms23126565. [PMID: 35743007 PMCID: PMC9223900 DOI: 10.3390/ijms23126565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/09/2022] [Accepted: 06/10/2022] [Indexed: 02/05/2023] Open
Abstract
Advances in molecular technologies over the past few decades, such as high-throughput DNA marker genotyping, have provided more powerful plant breeding approaches, including marker-assisted selection and genomic selection. At the same time, massive investments in plant genetics and genomics, led by whole genome sequencing, have led to greater knowledge of genes and genetic pathways across plant genomes. However, there remains a gap between approaches focused on forward genetics, which start with a phenotype to map a mutant locus or QTL with the goal of cloning the causal gene, and approaches using reverse genetics, which start with large-scale sequence data and work back to the gene function. The recent establishment of efficient CRISPR-Cas-based gene editing promises to bridge this gap and provide a rapid method to functionally validate genes and alleles identified through studies of natural variation. CRISPR-Cas techniques can be used to knock out single or multiple genes, precisely modify genes through base and prime editing, and replace alleles. Moreover, technologies such as protoplast isolation, in planta transformation, and the use of developmental regulatory genes promise to enable high-throughput gene editing to accelerate crop improvement.
Collapse
|
20
|
Kumar J, Kumar A, Sen Gupta D, Kumar S, DePauw RM. Reverse genetic approaches for breeding nutrient-rich and climate-resilient cereal and food legume crops. Heredity (Edinb) 2022; 128:473-496. [PMID: 35249099 PMCID: PMC9178024 DOI: 10.1038/s41437-022-00513-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/10/2022] [Accepted: 02/10/2022] [Indexed: 12/21/2022] Open
Abstract
In the last decade, advancements in genomics tools and techniques have led to the discovery of many genes. Most of these genes still need to be characterized for their associated function and therefore, such genes remain underutilized for breeding the next generation of improved crop varieties. The recent developments in different reverse genetic approaches have made it possible to identify the function of genes controlling nutritional, biochemical, and metabolic traits imparting drought, heat, cold, salinity tolerance as well as diseases and insect-pests. This article focuses on reviewing the current status and prospects of using reverse genetic approaches to breed nutrient-rich and climate resilient cereal and food legume crops.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India.
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, 250 004, India
| | - Ron M DePauw
- Advancing Wheat Technologies, 118 Strathcona Rd SW, Calgary, AB, T3H 1P3, Canada
| |
Collapse
|
21
|
Advances in Electrochemical Techniques for the Detection and Analysis of Genetically Modified Organisms: An Analysis Based on Bibliometrics. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10050194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Since the first successful transgenic plants obtained in 1983, dozens of plants have been tested. On the one hand, genetically modified plants solve the problems of agricultural production. However, due to exogenous genes of transgenic plants, such as its seeds or pollen drift, diffusion between populations will likely lead to superweeds or affect the original traits. The detection technology of transgenic plants and their products have received considerable attention. Electrochemical sensing technology is a fast, low-cost, and portable analysis technology. This review interprets the application of electrochemical technology in the analysis and detection of transgenic products through bibliometrics. A total of 83 research articles were analyzed, spanning 2001 to 2021. We described the different stages in the development history of the subject and the contributions of countries and institutions to the topic. Although there were more annual publications in some years, there was no explosive growth in any period. The lack of breakthroughs in this technology is a significant factor in the lack of experts from other fields cross-examining the subject. Through keyword co-occurrence analysis, different research directions on this topic were discussed. The use of nanomaterials with excellent electrical conductivity allows for more sensitive detection of GM crops by electrochemical sensors. Furthermore, co-citation analysis was used to interpret the most popular reports on the topic. In the end, we predict the future development of this topic according to the analysis results.
Collapse
|
22
|
Van Vu T, Das S, Hensel G, Kim JY. Genome editing and beyond: what does it mean for the future of plant breeding? PLANTA 2022; 255:130. [PMID: 35587292 PMCID: PMC9120101 DOI: 10.1007/s00425-022-03906-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/26/2022] [Indexed: 05/04/2023]
Abstract
Genome editing offers revolutionized solutions for plant breeding to sustain food production to feed the world by 2050. Therefore, genome-edited products are increasingly recognized via more relaxed legislation and community adoption. The world population and food production are disproportionally growing in a manner that would have never matched each other under the current agricultural practices. The emerging crisis is more evident with the subtle changes in climate and the running-off of natural genetic resources that could be easily used in breeding in conventional ways. Under these circumstances, affordable CRISPR-Cas-based gene-editing technologies have brought hope and charged the old plant breeding machine with the most energetic and powerful fuel to address the challenges involved in feeding the world. What makes CRISPR-Cas the most powerful gene-editing technology? What are the differences between it and the other genetic engineering/breeding techniques? Would its products be labeled as "conventional" or "GMO"? There are so many questions to be answered, or that cannot be answered within the limitations of our current understanding. Therefore, we would like to discuss and answer some of the mentioned questions regarding recent progress in technology development. We hope this review will offer another view on the role of CRISPR-Cas technology in future of plant breeding for food production and beyond.
Collapse
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.
| |
Collapse
|
23
|
Exploring Consumers’ Attitudes towards Food Products Derived by New Plant Breeding Techniques. SUSTAINABILITY 2022. [DOI: 10.3390/su14105995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
New plant breeding techniques (NPBTs) are seen as promising and innovative tools to achieve food security and food safety. Biotechnological innovations have great potential to address sustainable food development, and they are expected in the near future to play a critical role in feeding a growing population without exerting added pressure on the environment. There is, however, a considerable debate as to how these new techniques should be regulated and whether some or all of them should fall within the scope of EU legislation on genetically modified organisms (GMOs), despite the product obtained being free from genes foreign to the species. In the EU, the adoption of these methods does not rely only on the scientific community but requires social acceptance and a political process that leads to an improved regulatory framework. In this paper, we present the results of an online survey carried out in Italy with 700 randomly selected participants on consumer attitudes towards food obtained by NPBTs. By applying the decision tree machine learning algorithm J48 to our dataset, we identified significant attributes to predict the main drivers of purchasing such products. A classification model accuracy assessment has also been developed to evaluate the overall performance of the classifier. The result of the model highlighted the role of consumers’ self-perceived knowledge and their trust in the European approval process for NPBT, as well as the need for a detailed label. Our findings may support decision makers and underpin the development of NPBT products in the market.
Collapse
|
24
|
Assessment of the Real-Time PCR Method Claiming to be Specific for Detection and Quantification of the First Commercialised Genome-Edited Plant. FOOD ANAL METHOD 2022. [DOI: 10.1007/s12161-022-02237-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Abstract
A real-time PCR method was recently published with a claim to be specific for the detection and identification of some genome-edited oilseed rape (OSR) lines commercialised in North America. The method was designed to detect a single base mutation in the AHAS1C gene, which confers herbicide tolerance. The authors claim that the method is event-specific for the genome-edited OSR line 5715 and fulfils all requirements for GMO analytical methods according to EU regulations. We have thoroughly assessed the method in relation to the minimum performance requirements (MPR) established by the European Network of GMO Laboratories (ENGL). The method was found to be sufficiently sensitive and robust when tested with pure genomic DNA of the OSR line 40 K. However, our results show that the method is not event-specific and detects also OSR lines carrying the same point mutation caused by somaclonal variation. Moreover, impaired robustness was observed using non-modified genomic DNA at the amount specified in the original protocol. Significant non-specific PCR amplifications with PCR products as non-target template DNA and with genomic DNA from numerous OSR varieties as well as from wild radish were found by three ISO/IEC 17025 accredited reference laboratories in tests using different master mixes and PCR cycler models. The assessment shows that the method does not meet the MPR for qualitative PCR methods and therefore is not fit-for-purpose for official controls of genetically modified products in the EU. Suggestions are provided for conditions under which analytical methods for genome-edited organisms should be validated.
Collapse
|
25
|
Tay Fernandez CG, Nestor BJ, Danilevicz MF, Marsh JI, Petereit J, Bayer PE, Batley J, Edwards D. Expanding Gene-Editing Potential in Crop Improvement with Pangenomes. Int J Mol Sci 2022; 23:ijms23042276. [PMID: 35216392 PMCID: PMC8879065 DOI: 10.3390/ijms23042276] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 02/14/2022] [Accepted: 02/15/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.
Collapse
|
26
|
Joo KA, Muszynski MG, Kantar MB, Wang ML, He X, Del Valle Echevarria AR. Utilizing CRISPR-Cas in Tropical Crop Improvement: A Decision Process for Fitting Genome Engineering to Your Species. Front Genet 2021; 12:786140. [PMID: 34868276 PMCID: PMC8633396 DOI: 10.3389/fgene.2021.786140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 10/29/2021] [Indexed: 11/13/2022] Open
Abstract
Adopting modern gene-editing technologies for trait improvement in agriculture requires important workflow developments, yet these developments are not often discussed. Using tropical crop systems as a case study, we describe a workflow broken down into discrete processes with specific steps and decision points that allow for the practical application of the CRISPR-Cas gene editing platform in a crop of interest. While we present the steps of developing genome-edited plants as sequential, in practice parts can be done in parallel, which are discussed in this perspective. The main processes include 1) understanding the genetic basis of the trait along with having the crop’s genome sequence, 2) testing and optimization of the editing reagents, development of efficient 3) tissue culture and 4) transformation methods, and 5) screening methods to identify edited events with commercial potential. Our goal in this perspective is to help any lab that wishes to implement this powerful, easy-to-use tool in their pipeline, thus aiming to democratize the technology.
Collapse
Affiliation(s)
- Kathleen A Joo
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael G Muszynski
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Michael B Kantar
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States
| | - Ming-Li Wang
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Xiaoling He
- Hawaii Agriculture Research Center, Waipahu, HI, United States
| | - Angel R Del Valle Echevarria
- Department of Tropical Plant and Soil Sciences, University of Hawaii at Manoa, Honolulu, HI, United States.,Hawaii Agriculture Research Center, Waipahu, HI, United States
| |
Collapse
|
27
|
Yassitepe JEDCT, da Silva VCH, Hernandes-Lopes J, Dante RA, Gerhardt IR, Fernandes FR, da Silva PA, Vieira LR, Bonatti V, Arruda P. Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties. FRONTIERS IN PLANT SCIENCE 2021; 12:766702. [PMID: 34721493 PMCID: PMC8553389 DOI: 10.3389/fpls.2021.766702] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 09/15/2021] [Indexed: 05/17/2023]
Abstract
Over the past decades, advances in plant biotechnology have allowed the development of genetically modified maize varieties that have significantly impacted agricultural management and improved the grain yield worldwide. To date, genetically modified varieties represent 30% of the world's maize cultivated area and incorporate traits such as herbicide, insect and disease resistance, abiotic stress tolerance, high yield, and improved nutritional quality. Maize transformation, which is a prerequisite for genetically modified maize development, is no longer a major bottleneck. Protocols using morphogenic regulators have evolved significantly towards increasing transformation frequency and genotype independence. Emerging technologies using either stable or transient expression and tissue culture-independent methods, such as direct genome editing using RNA-guided endonuclease system as an in vivo desired-target mutator, simultaneous double haploid production and editing/haploid-inducer-mediated genome editing, and pollen transformation, are expected to lead significant progress in maize biotechnology. This review summarises the significant advances in maize transformation protocols, technologies, and applications and discusses the current status, including a pipeline for trait development and regulatory issues related to current and future genetically modified and genetically edited maize varieties.
Collapse
Affiliation(s)
- Juliana Erika de Carvalho Teixeira Yassitepe
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Viviane Cristina Heinzen da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - José Hernandes-Lopes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Ricardo Augusto Dante
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Isabel Rodrigues Gerhardt
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Fernanda Rausch Fernandes
- Embrapa Informática Agropecuária, Campinas, Brazil
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Priscila Alves da Silva
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Leticia Rios Vieira
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Vanessa Bonatti
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
| | - Paulo Arruda
- Genomics for Climate Change Research Center (GCCRC), Universidade Estadual de Campinas, Campinas, Brazil
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, Brazil
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil
| |
Collapse
|
28
|
Entine J, Felipe MSS, Groenewald JH, Kershen DL, Lema M, McHughen A, Nepomuceno AL, Ohsawa R, Ordonio RL, Parrott WA, Quemada H, Ramage C, Slamet-Loedin I, Smyth SJ, Wray-Cahen D. Regulatory approaches for genome edited agricultural plants in select countries and jurisdictions around the world. Transgenic Res 2021; 30:551-584. [PMID: 33970411 PMCID: PMC8316157 DOI: 10.1007/s11248-021-00257-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 04/21/2021] [Indexed: 12/28/2022]
Abstract
Genome editing in agriculture and food is leading to new, improved crops and other products. Depending on the regulatory approach taken in each country or region, commercialization of these crops and products may or may not require approval from the respective regulatory authorities. This paper describes the regulatory landscape governing genome edited agriculture and food products in a selection of countries and regions.
Collapse
Affiliation(s)
- Jon Entine
- Genetic Literacy Project, Cincinnati, OH, USA
| | - Maria Sueli S Felipe
- Genomic Sciences and Biotechnology Program, Catholic University of Brasília, Brasília, DF, Brazil
| | | | | | - Martin Lema
- Departamento de Ciencia Y Tecnología and Maestría en Ciencia, Tecnología y Sociedad, Universidad Nacional de Quilmes, Bernal Buenos Aires, Argentina
| | - Alan McHughen
- Botany and Plant Sciences, University of California, Riverside, CA, USA.
| | | | - Ryo Ohsawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Reynante L Ordonio
- Crop Biotechnology Center, Philippine Rice Research Institute, Maligaya, Science City of Munoz, Philippines
| | - Wayne A Parrott
- Department of Crop and Soil Sciences and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Hector Quemada
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Carl Ramage
- Office of the Deputy Vice-Chancellor (Research and Industry Engagement), Rautaki Solutions Pty Ltd, La Trobe University, Melbourne, VIC, Australia
| | - Inez Slamet-Loedin
- Fellow of The World Academy of Sciences, Cluster Lead-Trait and Genome Engineering, International Rice Research Institute, Manila, Philippines
| | - Stuart J Smyth
- Department of Agricultural and Resource Economics, University of Saskatchewan, Saskatoon, SK, Canada
| | - Diane Wray-Cahen
- United States Department of Agriculture, Foreign Agricultural Service, Washington, DC, USA
| |
Collapse
|
29
|
Matres JM, Hilscher J, Datta A, Armario-Nájera V, Baysal C, He W, Huang X, Zhu C, Valizadeh-Kamran R, Trijatmiko KR, Capell T, Christou P, Stoger E, Slamet-Loedin IH. Genome editing in cereal crops: an overview. Transgenic Res 2021; 30:461-498. [PMID: 34263445 PMCID: PMC8316241 DOI: 10.1007/s11248-021-00259-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 05/15/2021] [Indexed: 02/06/2023]
Abstract
Genome-editing technologies offer unprecedented opportunities for crop improvement with superior precision and speed. This review presents an analysis of the current state of genome editing in the major cereal crops- rice, maize, wheat and barley. Genome editing has been used to achieve important agronomic and quality traits in cereals. These include adaptive traits to mitigate the effects of climate change, tolerance to biotic stresses, higher yields, more optimal plant architecture, improved grain quality and nutritional content, and safer products. Not all traits can be achieved through genome editing, and several technical and regulatory challenges need to be overcome for the technology to realize its full potential. Genome editing, however, has already revolutionized cereal crop improvement and is poised to shape future agricultural practices in conjunction with other breeding innovations.
Collapse
Affiliation(s)
- Jerlie Mhay Matres
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Julia Hilscher
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Akash Datta
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Victoria Armario-Nájera
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Can Baysal
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Wenshu He
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Xin Huang
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Changfu Zhu
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Rana Valizadeh-Kamran
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
- Department of Biotechnology, Azarbaijan Shahid Madani University, Tabriz, Iran
| | - Kurniawan R Trijatmiko
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines
| | - Teresa Capell
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Department of Plant Production and Forestry Science, School of Agrifood and Forestry Science and Engineering (ETSEA), University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva Stoger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - Inez H Slamet-Loedin
- Genetic Design and Validation Unit, International Rice Research Institute, Los Banos, Philippines.
| |
Collapse
|
30
|
Biosafety of Genome Editing Applications in Plant Breeding: Considerations for a Focused Case-Specific Risk Assessment in the EU. BIOTECH 2021; 10:biotech10030010. [PMID: 35822764 PMCID: PMC9245463 DOI: 10.3390/biotech10030010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 11/23/2022] Open
Abstract
An intensely debated question is whether or how a mandatory environmental risk assessment (ERA) should be conducted for plants obtained through novel genomic techniques, including genome editing (GE). Some countries have already exempted certain types of GE applications from their regulations addressing genetically modified organisms (GMOs). In the European Union, the European Court of Justice confirmed in 2018 that plants developed by novel genomic techniques for directed mutagenesis are regulated as GMOs. Thus, they have to undergo an ERA prior to deliberate release or being placed on the market. Recently, the European Food Safety Authority (EFSA) published two opinions on the relevance of the current EU ERA framework for GM plants obtained through novel genomic techniques (NGTs). Regarding GE plants, the opinions confirmed that the existing ERA framework is suitable in general and that the current ERA requirements need to be applied in a case specific manner. Since EFSA did not provide further guidance, this review addresses a couple of issues relevant for the case-specific assessment of GE plants. We discuss the suitability of general denominators of risk/safety and address characteristics of GE plants which require particular assessment approaches. We suggest integrating the following two sets of considerations into the ERA: considerations related to the traits developed by GE and considerations addressing the assessment of method-related unintended effects, e.g., due to off-target modifications. In conclusion, we recommend that further specific guidance for the ERA and monitoring should be developed to facilitate a focused assessment approach for GE plants.
Collapse
|
31
|
Mushtaq M, Ahmad Dar A, Skalicky M, Tyagi A, Bhagat N, Basu U, Bhat BA, Zaid A, Ali S, Dar TUH, Rai GK, Wani SH, Habib-Ur-Rahman M, Hejnak V, Vachova P, Brestic M, Çığ A, Çığ F, Erman M, EL Sabagh A. CRISPR-Based Genome Editing Tools: Insights into Technological Breakthroughs and Future Challenges. Genes (Basel) 2021; 12:797. [PMID: 34073848 PMCID: PMC8225059 DOI: 10.3390/genes12060797] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/11/2022] Open
Abstract
Genome-editing (GE) is having a tremendous influence around the globe in the life science community. Among its versatile uses, the desired modifications of genes, and more importantly the transgene (DNA)-free approach to develop genetically modified organism (GMO), are of special interest. The recent and rapid developments in genome-editing technology have given rise to hopes to achieve global food security in a sustainable manner. We here discuss recent developments in CRISPR-based genome-editing tools for crop improvement concerning adaptation, opportunities, and challenges. Some of the notable advances highlighted here include the development of transgene (DNA)-free genome plants, the availability of compatible nucleases, and the development of safe and effective CRISPR delivery vehicles for plant genome editing, multi-gene targeting and complex genome editing, base editing and prime editing to achieve more complex genetic engineering. Additionally, new avenues that facilitate fine-tuning plant gene regulation have also been addressed. In spite of the tremendous potential of CRISPR and other gene editing tools, major challenges remain. Some of the challenges are related to the practical advances required for the efficient delivery of CRISPR reagents and for precision genome editing, while others come from government policies and public acceptance. This review will therefore be helpful to gain insights into technological advances, its applications, and future challenges for crop improvement.
Collapse
Affiliation(s)
- Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Aejaz Ahmad Dar
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Milan Skalicky
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Anshika Tyagi
- ICAR-National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Nancy Bhagat
- School of Biotechnology, University of Jammu, Jammu 180006, India;
| | - Umer Basu
- Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India;
| | | | - Abbu Zaid
- Plant Physiology and Biochemistry Section, Department of Botany Aligarh Muslim University, Aigarh 202002, India;
| | - Sajad Ali
- Centre of Research for Development, University of Kashmir, Srinagar 190006, India;
| | | | - Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu 180009, India; (M.M.); (A.A.D.)
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu 192101, India
| | - Muhammad Habib-Ur-Rahman
- Department of Crop Science, Institute of Crop Science and Resource Conservation (INRES), University Bonn, 53115 Bonn, Germany;
| | - Vaclav Hejnak
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Pavla Vachova
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
| | - Marian Brestic
- Department of Botany and Plant Physiology, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, Kamycka 129, 165 00 Prague, Czech Republic; (M.S.); (V.H.); (P.V.); (M.B.)
- Department of Plant Physiology, Slovak University of Agriculture, Nitra, Tr. A. Hlinku 2, 949 01 Nitra, Slovakia
| | - Arzu Çığ
- Department of Horticulture, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey;
| | - Fatih Çığ
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Murat Erman
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
| | - Ayman EL Sabagh
- Department of Field Crops, Faculty of Agriculture, Siirt University, Siirt 56100, Turkey; (F.Ç.); (M.E.)
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| |
Collapse
|
32
|
Yang C, Ge J, Fu X, Luo K, Xu C. Dual Reproductive Cell-Specific Promoter-Mediated Split-Cre/LoxP System Suitable for Exogenous Gene Deletion in Hybrid Progeny of Transgenic Arabidopsis. Int J Mol Sci 2021; 22:5080. [PMID: 34064885 PMCID: PMC8151399 DOI: 10.3390/ijms22105080] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 01/02/2023] Open
Abstract
Genetically modified (GM) crops possess some superior characteristics, such as high yield and insect resistance, but their biosafety has aroused broad public concern. Some genetic engineering technologies have recently been proposed to remove exogenous genes from GM crops. Few approaches have been applied to maintain advantageous traits, but excising exogenous genes in seeds or fruits from these hybrid crops has led to the generation of harvested food without exogenous genes. In a previous study, split-Cre mediated by split intein could recombine its structure and restore recombination activity in hybrid plants. In the current study, the recombination efficiency of split-Cre under the control of ovule-specific or pollen-specific promoters was validated by hybridization of transgenic Arabidopsis containing the improved expression vectors. In these vectors, all exogenous genes were flanked by two loxP sites, including promoters, resistance genes, reporter genes, and split-Cre genes linked to the reporter genes via LP4/2A. A gene deletion system was designed in which NCre was driven by proDD45, and CCre was driven by proACA9 and proDLL. Transgenic lines containing NCre were used as paternal lines to hybridize with transgenic lines containing CCre. Because this hybridization method results in no co-expression of the NCre and CCre genes controlled by reproduction-specific promoters in the F1 progeny, the desirable characteristics could be retained. After self-crossing in F1 progeny, the expression level and protein activity of reporter genes were detected, and confirmed that recombination of split-Cre had occurred and the exogenous genes were partially deleted. The gene deletion efficiency represented by the quantitative measurements of GUS enzyme activity was over 59%, with the highest efficiency of 73% among variable hybrid combinations. Thus, in the present study a novel dual reproductive cell-specific promoter-mediated gene deletion system was developed that has the potential to take advantage of the merits of GM crops while alleviating biosafety concerns.
Collapse
Affiliation(s)
| | | | | | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (J.G.); (X.F.)
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Key Laboratory of Eco-Environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing 400715, China; (C.Y.); (J.G.); (X.F.)
| |
Collapse
|
33
|
Um T, Park T, Shim JS, Kim YS, Lee GS, Choi IY, Kim JK, Seo JS, Park SC. Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops. Int J Mol Sci 2021; 22:ijms22073743. [PMID: 33916772 PMCID: PMC8038395 DOI: 10.3390/ijms22073743] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/27/2021] [Accepted: 03/31/2021] [Indexed: 12/20/2022] Open
Abstract
Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology.
Collapse
Affiliation(s)
- Taeyoung Um
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (T.U.); (Y.S.K.)
| | - Taehyeon Park
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (T.P.); (J.-K.K.)
| | - Jae Sung Shim
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Korea;
| | - Youn Shic Kim
- Agriculture and Life Sciences Research Institute, Kangwon National University, Chuncheon 24341, Korea; (T.U.); (Y.S.K.)
| | - Gang-Seob Lee
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
| | - Ik-Young Choi
- Department of Agricultural and Life Industry, Kangwon National University, Chuncheon 24341, Korea;
| | - Ju-Kon Kim
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (T.P.); (J.-K.K.)
| | - Jun Sung Seo
- Crop Biotechnology Institute, GreenBio Science and Technology, Seoul National University, Pyeongchang 25354, Korea; (T.P.); (J.-K.K.)
- Correspondence: (J.S.S.); (S.C.P.); Tel.: +82-33-339-5826 (J.S.S.); +82-63-238-4584 (S.C.P.)
| | - Soo Chul Park
- Department of Agricultural Biotechnology, National Academy of Agricultural Science, Rural Development Administration, Jeonju 54874, Korea;
- Correspondence: (J.S.S.); (S.C.P.); Tel.: +82-33-339-5826 (J.S.S.); +82-63-238-4584 (S.C.P.)
| |
Collapse
|
34
|
|
35
|
Hussain A, Ding X, Alariqi M, Manghwar H, Hui F, Li Y, Cheng J, Wu C, Cao J, Jin S. Herbicide Resistance: Another Hot Agronomic Trait for Plant Genome Editing. PLANTS (BASEL, SWITZERLAND) 2021; 10:621. [PMID: 33805182 PMCID: PMC8064318 DOI: 10.3390/plants10040621] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/16/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022]
Abstract
Weeds have continually interrupted crop plants since their domestication, leading to a greater yield loss compared to diseases and pests that necessitated the practice of weed control measures. The control of weeds is crucial to ensuring the availability of sufficient food for a rapidly increasing human population. Chemical weed control (herbicides) along with integrated weed management (IWM) practices can be the most effective and reliable method of weed management programs. The application of herbicides for weed control practices calls for the urgency to develop herbicide-resistant (HR) crops. Recently, genome editing tools, especially CRISPR-Cas9, have brought innovation in genome editing technology that opens up new possibilities to provide sustainable farming in modern agricultural industry. To date, several non-genetically modified (GM) HR crops have been developed through genome editing that can present a leading role to combat weed problems along with increasing crop productivity to meet increasing food demand around the world. Here, we present the chemical method of weed control, approaches for herbicide resistance development, and possible advantages and limitations of genome editing in herbicide resistance. We also discuss how genome editing would be effective in combating intensive weed problems and what would be the impact of genome-edited HR crops in agriculture.
Collapse
Affiliation(s)
- Amjad Hussain
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Xiao Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Muna Alariqi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Hakim Manghwar
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China;
| | - Fengjiao Hui
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| | - Yapei Li
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Junqi Cheng
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Chenglin Wu
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Jinlin Cao
- Tobacco Research Institute of Hubei Province, Wuhan 430030, China; (A.H.); (Y.L.); (J.C.); (C.W.)
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; (X.D.); (M.A.); (F.H.)
| |
Collapse
|
36
|
Genome-Edited Plants: Opportunities and Challenges for an Anticipatory Detection and Identification Framework. Foods 2021; 10:foods10020430. [PMID: 33669278 PMCID: PMC7920036 DOI: 10.3390/foods10020430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/28/2022] Open
Abstract
It is difficult to trace and identify genome-edited food and feed products if relevant information is not made available to competent authorities. This results in major challenges, as genetically modified organism (GMO) regulatory frameworks for food and feed that apply to countries such as the member states of the European Union (EU) require enforcement based on detection. An international anticipatory detection and identification framework for voluntary collaboration and collation of disclosed information on genome-edited plants could be a valuable tool to address these challenges caused by data gaps. Scrutinizing different information sources and establishing a level of information that is sufficient to unambiguously conclude on the application of genome editing in the plant breeding process can support the identification of genome-edited products by complementing the results of analytical detection. International coordination to set up an appropriate state-of-the-art database is recommended to overcome the difficulty caused by the non-harmonized bio-safety regulation requirements of genome-edited food and feed products in various countries. This approach helps to avoid trade disruptions and to facilitate GMO/non-GMO labeling schemes. Implementation of the legal requirements for genome-edited food and feed products in the EU and elsewhere would substantially benefit from such an anticipatory framework.
Collapse
|
37
|
Zhou X, Ge S, Sun Y, Ran M, Liu Y, Mao Y, Cao X. Highly sensitive SERS assay of genetically modified organisms in maize via a nanoflower substrate coupled with hybridization chain reaction amplification. NEW J CHEM 2021. [DOI: 10.1039/d1nj03913j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel biosensor based on a high-density “hot spot” SERS substrate coupled with HCR amplification strategy was developed for the ultrasensitive detection of genetically modified organisms in maize.
Collapse
Affiliation(s)
- Xinyu Zhou
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, P. R. China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, P. R. China
| | - Shengjie Ge
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, P. R. China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, P. R. China
| | - Yue Sun
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, P. R. China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, P. R. China
| | - Menglin Ran
- The First Clinical College, Dalian Medical University, Dalian, P. R. China
| | - Yifan Liu
- The First Clinical College, Dalian Medical University, Dalian, P. R. China
| | - Yu Mao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, P. R. China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, P. R. China
| | - Xiaowei Cao
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, 225001, P. R. China
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, P. R. China
- Jiangsu Key Laboratory of Experimental & Translational Noncoding RNA Research, Medical College, Yangzhou University, Yangzhou, P. R. China
| |
Collapse
|
38
|
Burgio G, Teboul L. Anticipating and Identifying Collateral Damage in Genome Editing. Trends Genet 2020; 36:905-914. [PMID: 33039248 PMCID: PMC7658041 DOI: 10.1016/j.tig.2020.09.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023]
Abstract
Genome editing has powerful applications in research, healthcare, and agriculture. However, the range of possible molecular events resulting from genome editing has been underestimated and the technology remains unpredictable on, and away from, the target locus. This has considerable impact in providing a safe approach for therapeutic genome editing, agriculture, and other applications. This opinion article discusses how to anticipate and detect those editing events by a combination of assays to capture all possible genomic changes. It also discusses strategies for preventing unwanted effects, critical to appraise the benefit or risk associated with the use of the technology. Anticipating and verifying the result of genome editing are essential for the success for all applications.
Collapse
Affiliation(s)
- Gaëtan Burgio
- Department of Immunology and Infectious Disease, The John Curtin School of Medical Research, the Australian National University, Canberra, ACT 2603, Australia.
| | - Lydia Teboul
- The Mary Lyon Centre, Medical Research Council Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK.
| |
Collapse
|
39
|
Dalla Costa L, Piazza S, Pompili V, Salvagnin U, Cestaro A, Moffa L, Vittani L, Moser C, Malnoy M. Strategies to produce T-DNA free CRISPRed fruit trees via Agrobacterium tumefaciens stable gene transfer. Sci Rep 2020; 10:20155. [PMID: 33214661 PMCID: PMC7678832 DOI: 10.1038/s41598-020-77110-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 11/02/2020] [Indexed: 12/31/2022] Open
Abstract
Genome editing via CRISPR/Cas9 is a powerful technology, which has been widely applied to improve traits in cereals, vegetables and even fruit trees. For the delivery of CRISPR/Cas9 components into dicotyledonous plants, Agrobacterium tumefaciens mediated gene transfer is still the prevalent method, although editing is often accompanied by the integration of the bacterial T-DNA into the host genome. We assessed two approaches in order to achieve T-DNA excision from the plant genome, minimizing the extent of foreign DNA left behind. The first is based on the Flp/FRT system and the second on Cas9 and synthetic cleavage target sites (CTS) close to T-DNA borders, which are recognized by the sgRNA. Several grapevine and apple lines, transformed with a panel of CRISPR/SpCas9 binary vectors, were regenerated and characterized for T-DNA copy number and for the rate of targeted editing. As detected by an optimized NGS-based sequencing method, trimming at T-DNA borders occurred in 100% of the lines, impairing in most cases the excision. Another observation was the leakage activity of Cas9 which produced pierced and therefore non-functional CTS. Deletions of genomic DNA and presence of filler DNA were also noticed at the junctions between T-DNA and genomic DNA. This study proved that many factors must be considered for designing efficient binary vectors capable of minimizing the presence of exogenous DNA in CRISPRed fruit trees.
Collapse
Affiliation(s)
- Lorenza Dalla Costa
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy.
| | - Stefano Piazza
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Valerio Pompili
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Umberto Salvagnin
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Loredana Moffa
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Lorenzo Vittani
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Claudio Moser
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| | - Mickael Malnoy
- Research and Innovation Centre, Fondazione Edmund Mach, via E. Mach 1, 38098, San Michele all'Adige, Italy
| |
Collapse
|
40
|
Legal and practical challenges to authorization of gene edited plants in the EU. N Biotechnol 2020; 60:183-188. [PMID: 33115638 DOI: 10.1016/j.nbt.2020.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 10/16/2020] [Accepted: 10/17/2020] [Indexed: 11/23/2022]
Abstract
According to a predominant interpretation of the C-528/16 judgment of the Court of Justice of the European Union, mutants resulting from gene editing, even those featuring only single nucleotide variants, should be subject to the authorization procedures designed for organisms developed through genetic modification (i.e. insertion of large DNA fragments). In this article, we illustrate practical problems with the authorization of products of gene editing in the EU. On the basis of these problems, we analyze the influence of the current interpretation of EU legislation and judgment on the practical ability to authorize and detect such products on the EU market. We show that the predominant interpretation of the judgment leads to legally unacceptable consequences, in particular to the violation of the principle of proportionality with regard to individuals who wish to develop and market products of gene editing. As a result of our considerations, we show that the C-528/16 judgment did not need to be interpreted in the dominant way.
Collapse
|
41
|
Menz J, Modrzejewski D, Hartung F, Wilhelm R, Sprink T. Genome Edited Crops Touch the Market: A View on the Global Development and Regulatory Environment. FRONTIERS IN PLANT SCIENCE 2020; 11:586027. [PMID: 33163013 PMCID: PMC7581933 DOI: 10.3389/fpls.2020.586027] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/16/2020] [Indexed: 05/18/2023]
Abstract
Products of genome editing as the most promising "New Plant Breeding Technology" (NPBT) have made the transition from the lab to the market in a short time. Globally, research activities employing genome editing are constantly expanding and more and more plants with market-oriented traits are being developed, and companies have already released the first genome edited crops to the market. Few countries, most of which are located in the Americas, have adapted legislations to these technologies or released guidelines supporting the use of genome editing. Other countries are debating the path to come either because there is no clarity on the legal classification or due consensus is hampered by a renewed GMO debate. In recent years (2017-2020), eight countries have introduced guidelines clarifying the legal status of genome edited products and many of those are actively committed to international harmonization of their policies. In this publication we give an overview on the current and potentially future international regulatory environment and an update on plants derived by genome editing with market-oriented traits.
Collapse
Affiliation(s)
| | | | | | - Ralf Wilhelm
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Germany
| | - Thorben Sprink
- Julius Kühn Institute (JKI) – Federal Research Centre for Cultivated Plants, Institute for Biosafety in Plant Biotechnology, Quedlinburg, Germany
| |
Collapse
|
42
|
Chhalliyil P, Ilves H, Kazakov SA, Howard SJ, Johnston BH, Fagan J. A Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plant. Foods 2020; 9:foods9091245. [PMID: 32906573 PMCID: PMC7556030 DOI: 10.3390/foods9091245] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 11/30/2022] Open
Abstract
Discussion regarding the regulatory status of genome-edited crops has focused on precision of editing and on doubts regarding the feasibility of analytical monitoring compliant with existing GMO regulations. Effective detection methods are important, both for regulatory enforcement and traceability in case of biosafety, environmental or socio-economic impacts. Here, we approach the analysis question for the first time in the laboratory and report the successful development of a quantitative PCR detection method for the first commercialized genome-edited crop, a canola with a single base pair edit conferring herbicide tolerance. The method is highly sensitive and specific (quantification limit, 0.05%), compatible with the standards of practice, equipment and expertise typical in GMO laboratories, and readily integrable into their analytical workflows, including use of the matrix approach. The method, validated by an independent laboratory, meets all legal requirements for GMO analytical methods in jurisdictions such as the EU, is consistent with ISO17025 accreditation standards and has been placed in the public domain. Having developed a qPCR method for the most challenging class of genome edits, single-nucleotide variants, this research suggests that qPCR-based method development may be applicable to virtually any genome-edited organism. This advance resolves doubts regarding the feasibility of extending the regulatory approach currently employed for recombinant DNA-based GMOs to genome-edited organisms.
Collapse
Affiliation(s)
- Pradheep Chhalliyil
- Health Research Institute, 505 Dimick Drive, P.O. Box 370, Fairfield, IA 52556, USA;
| | - Heini Ilves
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - Sergei A. Kazakov
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - Stephanie J. Howard
- The Sustainability Council of New Zealand, P.O. Box 24304, Wellington 6142, New Zealand;
| | - Brian H. Johnston
- Somagenics, Inc., 2161 Delaware Ave, Suite E, Santa Cruz, CA 95060, USA; (H.I.); (S.A.K.); (B.H.J.)
| | - John Fagan
- Health Research Institute, 505 Dimick Drive, P.O. Box 370, Fairfield, IA 52556, USA;
- Correspondence: ; Tel.: +1-641-451-5454
| |
Collapse
|
43
|
Biswas S, Li R, Hong J, Zhao X, Yuan Z, Zhang D, Shi J. Effective identification of CRISPR/Cas9-induced and naturally occurred mutations in rice using a multiplex ligation-dependent probe amplification-based method. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:2323-2334. [PMID: 32405769 DOI: 10.1007/s00122-020-03600-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/01/2020] [Indexed: 05/11/2023]
Abstract
A multiplex ligation-dependent probe amplification (MLPA)-based method was developed and successfully utilized to efficiently detect both CRISPR/Cas9-induced and naturally occurred mutations in rice. The site-specific nuclease-based CRISPR/Cas9 system has emerged as one of the most efficient genome editing tools to modify multiple genomic targets simultaneously in various organisms, including plants for both fundamental and applied researches. Screening for both on-target and off-target mutations in CRISPR/Cas9-generated mutants at the early stages is an indispensable step for functional analysis and subsequent application. Various methods have been developed to detect CRISPR/Cas9-induced mutations in plants. Still, very few have focused on the detection of both on- and off-targets simultaneously, let alone the detection of natural mutations. Here, we report a multiplex capable method that allows to detect CRISPR/Cas9 induced on- and off-target mutations as well as naturally occurred mutation based on a multiplex ligation-dependent probe amplification (MLPA) method. We demonstrated that unlike other methods, the modified target-specific MLPA method can accurately identify any INDELs generated naturally or by the CRISPR/Cas9 system and that it can detect natural variation and zygosity of the CRISPR/Cas9-generated mutants in rice as well. Furthermore, its high sensitivity allowed to define INDELs down to 1 bp and substitutions to a single nucleotide. Therefore, this sensitive, reliable, and cheap method would further accelerate functional analysis and marker-assisted breeding in plants, including rice.
Collapse
Affiliation(s)
- Sukumar Biswas
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Rong Li
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiangxiang Zhao
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Zheng Yuan
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection, Huaian, 223300, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Shanghai Jiao Tong University-University of Adelaide Joint Centre for Agriculture and Health, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| |
Collapse
|
44
|
Kersten B, Leite Montalvão AP, Hoenicka H, Vettori C, Paffetti D, Fladung M. Sequencing of two transgenic early-flowering poplar lines confirmed vector-free single-locus T-DNA integration. Transgenic Res 2020; 29:321-337. [PMID: 32356192 PMCID: PMC7283205 DOI: 10.1007/s11248-020-00203-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 04/18/2020] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing (NGS) approaches are attractive alternatives to the PCR-based characterisation of genetically modified plants for safety assessment and labelling since NGS is highly sensitive to the detection of T-DNA inserts as well as vector backbone sequences in transgenic plants. In this study, two independent transgenic male Populus tremula lines, T193-2 and T195-1, both carrying the FLOWERING LOCUS T gene from Arabidopsis thaliana under control of a heat-inducible promoter (pHSP::AtFT) and the non-transgenic control clone W52, were further characterised by NGS and third-generation sequencing. The results support previous findings that the T-DNA was hemizygously inserted in one genomic locus of each line. However, the T-DNA insertions consist of conglomerations of one or two T-DNA copies together with a small T-DNA fragment without AtFT parts. Based on NGS data, no additional T-DNA splinters or vector backbone sequences could be identified in the genome of the two transgenic lines. Seedlings derived from crosses between the pHSP::AtFT transgenic male parents and female wild type plants are therefore expected to be T-DNA splinter or vector backbone free. Thus, PCR analyses amplifying a partial T-DNA fragment with AtFT-specific primers are sufficient to determine whether the seedlings are transgenic or not. An analysis of 72 second generation-seedlings clearly showed that about 50% of them still reveal the presence of the T-DNA, confirming data already published. To prove if unanticipated genomic changes were induced by T-DNA integration, extended future studies using long-range sequencing technologies are required once a suitable chromosome-level P. tremula reference genome sequence is available.
Collapse
Affiliation(s)
- Birgit Kersten
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
| | | | - Hans Hoenicka
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany
| | - Cristina Vettori
- Institute of Bioscience and Bioresources (IBBR), National Research Council (CNR), Via Madonna del Piano 10, 50019, Sesto Fiorentino, FI, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry, Agricultural Genetics Section, University of Florence, P. le delle Cascine 18, 50144, Florence, Italy
| | - Matthias Fladung
- Thünen Institute of Forest Genetics, 22927, Grosshansdorf, Germany.
| |
Collapse
|
45
|
Bak A, Emerson JB. Cauliflower mosaic virus (CaMV) Biology, Management, and Relevance to GM Plant Detection for Sustainable Organic Agriculture. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.00021] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
|
46
|
Van Vu T, Sung YW, Kim J, Doan DTH, Tran MT, Kim JY. Challenges and Perspectives in Homology-Directed Gene Targeting in Monocot Plants. RICE (NEW YORK, N.Y.) 2019; 12:95. [PMID: 31858277 PMCID: PMC6923311 DOI: 10.1186/s12284-019-0355-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 12/04/2019] [Indexed: 05/18/2023]
Abstract
Continuing crop domestication/redomestication and modification is a key determinant of the adaptation and fulfillment of the food requirements of an exploding global population under increasingly challenging conditions such as climate change and the reduction in arable lands. Monocotyledonous crops are not only responsible for approximately 70% of total global crop production, indicating their important roles in human life, but also the first crops to be challenged with the abovementioned hurdles; hence, monocot crops should be the first to be engineered and/or de novo domesticated/redomesticated. A long time has passed since the first green revolution; the world is again facing the challenge of feeding a predicted 9.7 billion people in 2050, since the decline in world hunger was reversed in 2015. One of the major lessons learned from the first green revolution is the importance of novel and advanced trait-carrying crop varieties that are ideally adapted to new agricultural practices. New plant breeding techniques (NPBTs), such as genome editing, could help us succeed in this mission to create novel and advanced crops. Considering the importance of NPBTs in crop genetic improvement, we attempt to summarize and discuss the latest progress with major approaches, such as site-directed mutagenesis using molecular scissors, base editors and especially homology-directed gene targeting (HGT), a very challenging but potentially highly precise genome modification approach in plants. We therefore suggest potential approaches for the improvement of practical HGT, focusing on monocots, and discuss a potential approach for the regulation of genome-edited products.
Collapse
Affiliation(s)
- Tien Van Vu
- Division of Applied Life Science (BK21 Plus 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
| | - Yeon Woo Sung
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jihae Kim
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Duong Thi Hai Doan
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Mil Thi Tran
- Division of Applied Life Science (BK21 Plus program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 660-701, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Plus 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.
| |
Collapse
|
47
|
Socioeconomic Impact of Genome Editing on Agricultural Value Chains: The Case of Fungal-Resistant and Coeliac-Safe Wheat. SUSTAINABILITY 2019. [DOI: 10.3390/su11226421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome editing (GE) is gaining increasing importance in plant breeding, since it provides opportunities to develop improved crops with high precision and speed. However, little is known about the socioeconomic impact of genome editing on agricultural value chains. This qualitative study analyzes how genome-edited crops could affect agriculture value chains. Based on the hypothetical case of producing and processing fungal-resistant and coeliac-safe wheat in Germany, we conducted semi-structured, in-depth interviews with associations and companies operating in the value chains of wheat. A value chain analysis and qualitative content analysis were combined to assess the costs and benefits of the crops studied along the value chains of wheat. The results show that the use of fungal-resistant and coeliac-safe wheat can provide benefits at each step of the value chains. Fungal-resistant wheat benefits actors by reducing the problems and costs resulting from fungal-diseases and mycotoxins. Coeliac-safe wheat benefits actors by producing high value-added products, which can be safely consumed by patients suffering from coeliac disease. However, the results also show that low acceptance of GE by society and food retailers poses a significant barrier for the use of genome-edited crops in agricultural value chains.
Collapse
|
48
|
Mueller S. On DNA Signatures, Their Dual-Use Potential for GMO Counterfeiting, and a Cyber-Based Security Solution. Front Bioeng Biotechnol 2019; 7:189. [PMID: 31440503 PMCID: PMC6693310 DOI: 10.3389/fbioe.2019.00189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 07/18/2019] [Indexed: 12/13/2022] Open
Abstract
This study investigates the role and functionality of special nucleotide sequences ("DNA signatures") to detect the presence of an organism and to distinguish it from all others. After highlighting vulnerabilities of the prevalent DNA signature paradigm for the identification of agricultural genetically modified (GM) organisms it will be argued that these so-called signatures really are no signatures at all - when compared to the notion of traditional (handwritten) signatures and their generalizations in the modern (digital) world. It is suggested that a recent contamination event of an unauthorized GM Bacillus subtilis strain (Paracchini et al., 2017) in Europe could have been-or the same way could be - the consequence of exploiting gaps of prevailing DNA signatures. Moreover, a recent study (Mueller, 2019) proposes that such DNA signatures may intentionally be exploited to support the counterfeiting or even weaponization of GM organisms (GMOs). These concerns mandate a re-conceptualization of how DNA signatures need to be realized. After identifying central issues of the new vulnerabilities and overlying them with practical challenges that bio-cyber hackers would be facing, recommendations are made how DNA signatures may be enhanced. To overcome the core problem of signature transferability in bioengineered mediums, it is necessary that the identifier needs to remain secret during the entire verification process. On the other hand, however, the goal of DNA signatures is to enable public verifiability, leading to a paradoxical dilemma. It is shown that this can be addressed with ideas that underlie special cryptographic signatures, in particular those of "zero-knowledge" and "invisibility." This means more than mere signature hiding, but relies on a knowledge-based proof and differentiation of a secret (here, as assigned to specific clones) which can be realized without explicit demonstration of that secret. A re-conceptualization of these principles can be used in form of a combined (digital and physical) method to establish confidentiality and prevent un-impersonation of the manufacturer. As a result, this helps mitigate the circulation of possibly hazardous GMO counterfeits and also addresses the situation whereby attackers try to blame producers for deliberately implanting illicit adulterations hidden within authorized GMOs.
Collapse
|
49
|
Jansing J, Schiermeyer A, Schillberg S, Fischer R, Bortesi L. Genome Editing in Agriculture: Technical and Practical Considerations. Int J Mol Sci 2019; 20:E2888. [PMID: 31200517 PMCID: PMC6627516 DOI: 10.3390/ijms20122888] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/29/2019] [Accepted: 06/06/2019] [Indexed: 01/31/2023] Open
Abstract
The advent of precise genome-editing tools has revolutionized the way we create new plant varieties. Three groups of tools are now available, classified according to their mechanism of action: Programmable sequence-specific nucleases, base-editing enzymes, and oligonucleotides. The corresponding techniques not only lead to different outcomes, but also have implications for the public acceptance and regulatory approval of genome-edited plants. Despite the high efficiency and precision of the tools, there are still major bottlenecks in the generation of new and improved varieties, including the efficient delivery of the genome-editing reagents, the selection of desired events, and the regeneration of intact plants. In this review, we evaluate current delivery and regeneration methods, discuss their suitability for important crop species, and consider the practical aspects of applying the different genome-editing techniques in agriculture.
Collapse
Affiliation(s)
- Julia Jansing
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
| | - Andreas Schiermeyer
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Stefan Schillberg
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074 Aachen, Germany.
| | - Rainer Fischer
- Indiana Biosciences Research Institute (IBRI), 1345 W. 16th St. Suite 300, Indianapolis, IN 46202, USA.
| | - Luisa Bortesi
- Aachen-Maastricht Institute for Biobased Materials (AMIBM), Maastricht University, Brightlands Chemelot Campus, Urmonderbaan 22, 6167 RD Geleen, The Netherlands.
| |
Collapse
|
50
|
Wasmer M. Roads Forward for European GMO Policy-Uncertainties in Wake of ECJ Judgment Have to be Mitigated by Regulatory Reform. Front Bioeng Biotechnol 2019; 7:132. [PMID: 31231643 PMCID: PMC6561310 DOI: 10.3389/fbioe.2019.00132] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 05/15/2019] [Indexed: 11/25/2022] Open
Abstract
This article gives an overview of legal and procedural uncertainties regarding genome edited organisms and possible ways forward for European GMO policy. After a recent judgment by the European Court of Justice (ECJ judgment of 25 July 2018, C-528/16), organisms obtained by techniques of genome editing are GMOs and subject to the same obligations as transgenic organisms. Uncertainties emerge if genome edited organisms cannot be distinguished from organisms bred by conventional techniques, such as crossing or random mutagenesis. In this case, identical organisms can be subject to either GMO law or exempt from regulation because of the use of a technique that cannot be identified. Regulatory agencies might not be able to enforce GMO law for such cases in the long term. As other jurisdictions do not regulate such organisms as GMOs, accidental imports might occur and undermine European GMO regulation. In the near future, the EU Commission as well as European and national regulatory agencies will decide on how to apply the updated interpretation of the law. In order to mitigate current legal and procedural uncertainties, a first step forward lies in updating all guidance documents to specifically address genome editing specifically address genome editing, including a solution for providing a unique identifier. In part, the authorization procedure for GMO release can be tailored to different types of organisms by making use of existing flexibilities in GMO law. However, only an amendment to the regulations that govern the process of authorization for GMO release can substantially lower the burden for innovators. In a second step, any way forward has to aim at amending, supplementing or replacing the European GMO Directive (2001/18/EC). The policy options presented in this article presuppose political readiness for reform. This may not be realistic in the current political situation. However, if the problems of current GMO law are just ignored, European competitiveness and research in green biotechnology will suffer.
Collapse
Affiliation(s)
- Martin Wasmer
- Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, Hanover, Germany
| |
Collapse
|