THIRD WORLD NETWORK BIOSAFETY INFORMATION SERVICE
Dear Friends and Colleagues
International Detection and Identification Framework for Gene-Edited Plants
Current developments in modern plant biotechnology present a number of challenges related to detection and identification of GMOs. More and more frequently, such GMOs do not contain standard screening elements, i.e., specific genetic elements of non-plant origin that are commonly present in transgenic GMOs. It is difficult to trace and identify genome-edited food and feed products if relevant information is not made available to competent authorities. Two recently published articles, highlighted below, explore the issue in more depth.
Genome editing allows the targeted modification of nucleotide sequences in organisms, including plants, and often produces single nucleotide variants (SNVs), which are the most challenging class of genome edits to detect. However, analyses of existing and upcoming methods show that SNVs can be reliably detected, providing the technical possibility of tracking genome-edited plants. The test method for these products must meet advanced requirements regarding specificity, which can be increased by digital polymerase chain reaction (PCR) systems. Sequencing methods may also be used to detect DNA modifications caused by genome editing. (Item 1)
The prerequisite for integrating new methods into the current testing process is the availability of established detection methods and adequate reference material. In order to allow easy access for enforcement laboratories to all relevant information, it is recommended to establish an international anticipatory detection and identification framework for voluntary collaboration and collation of disclosed information on genome-edited plants. This approach would highly depend on the cooperation of competent authorities, governmental agencies, researchers and companies. The key element of such a network is the voluntary disclosure of information by the developers and authorities involved in pre-submission consultations; publicly available data, e.g., from the scientific literature and patents, are also valuable information sources. By exploiting a variety of different information sources in a systematic manner, and by establishing which level of information is sufficient to conclude on the identity of a particular genome-edited product, it is reasonable to expect that identification of genome-edited food or feed products is possible. (Item 2)
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Item 1
DETECTION METHODS FIT-FOR-PURPOSE IN ENFORCEMENT CONTROL OF GENETICALLY MODIFIED PLANTS PRODUCED WITH NOVEL GENOMIC TECHNIQUES (NGTS)
By Ribarits, A.; Narendja, F.; Stepanek, W.; Hochegger, R.
Agronomy 11 (1), 61 (2021)
Online: 30 Dec 2020
https://doi.org/10.3390/agronomy11010061
https://www.mdpi.com/2073-4395/11/1/61/htm
Abstract
The comprehensive EU regulatory framework regarding GMOs aims at preventing damage to human and animal health and the environment, and foresees labelling and traceability. Genome-edited plants and products fall under these EU GMO regulations, which have to be implemented in enforcement control activities. GMO detection methods currently used by enforcement laboratories are based on real-time PCR, where specificity and sensitivity are important performance parameters. Genome editing allows the targeted modification of nucleotide sequences in organisms, including plants, and often produces single nucleotide variants (SNVs), which are the most challenging class of genome edits to detect. The test method must therefore meet advanced requirements regarding specificity, which can be increased by modifying a PCR method. Digital PCR systems achieve a very high sensitivity and have advantages in quantitative measurement. Sequencing methods may also be used to detect DNA modifications caused by genome editing. Whereas most PCR methods can be carried out in an enforcement laboratory with existing technical equipment and staff, the processing of the sequencing data requires additional resources and the appropriate bioinformatic expertise.
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Conclusions
To date, the detection of GMOs is typically based on qPCR, a method widely used in official enforcement laboratories to target DNA. The analyses of existing and upcoming methods showed that SNVs are reliably detected, providing the technical possibility of tracking genome-edited plants. These PCR methods can usually be carried out with the available technical equipment and by existing staff in a GMO control laboratory. However, an analytical method for the detection of a genome-edited product should be found fit for the intended purpose by the EURL before it is applied for official control purposes by enforcement laboratories.
The prerequisite for integrating the new methods into the current testing process is the availability of established detection methods and adequate reference material. In order to allow easy access for enforcement laboratories to all relevant information, it is recommended to establish an international NGT method database. Furthermore, in order to enable method development and to examine the characteristics of applications by genome editing, action is needed to finance research activities on both the international and European levels. In addition, guidelines for the validation of detection methods must be developed to fulfill the regulatory requirements and to ensure transferability of the methods across laboratories. Such activity should include sequencing as promising alternative methodology in the near future.
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Item 2
GENOME-EDITED PLANTS: OPPORTUNITIES AND CHALLENGES FOR AN ANTICIPATORY DETECTION AND
IDENTIFICATION FRAMEWORK
By Ribarits, A.; Eckerstorfer, M.; Simon, S.; Stepanek, W.
Foods 10(2), 430 (2021)
Online: 16 Feb 2021
https://doi.org/10.3390/foods10020430
https://www.mdpi.com/2304-8158/10/2/430
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.
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Outlook
The approaches used currently for detection and identification of classic GMOs and GM food and feed products may guide the development of similar approaches for genome-edited products. However, concerning the identification of genome-edited plants, specific considerations are necessary. The availability of information concerning the introduced genetic modification(s) is a required starting point to develop detection methods, and, moreover, to establish the connection between an analytical detection result and a specific product. In addition, unique and product-specific modifications allow establishment of the identity of a genome-edited product.
The detectable presence of characteristic modifications may indicate the identity of a genome-edited product with a sufficiently high level of probability. For instance, if it is known that genome-edited powdery mildew-resistant bread wheat is on the global market, the simultaneous detection of the characteristic known mutations in the three MLO gene homoeoalleles in a wheat sample would be a strong indication that this sample contains genome-edited wheat.
To unequivocally establish a direct link between a detected sequence and a specific product, diverse sources of information may feed into a process to identify a genome-edited product. This approach would highly depend on the cooperation of competent authorities, governmental agencies, researchers and companies. The key element of such a network is the voluntary disclosure of information by the developers and authorities involved in pre-submission consultations; publicly available data, e.g., from the scientific literature and patents, are also valuable information sources. It is advisable to establish a mechanism for checking the quality of the collected information.
According to Jordan et al., a cooperative governance network including developers and authorities could support the information exchange required to facilitate the international trade of genome-edited products. A number of such cooperative networks have been successfully established for the governance of food products, e.g., coffee or fish products. They have performed well in comparable situations by defining broadly acceptable criteria for products and processes, and establishing institutional capacity when government-based regulations are neither established nor sufficient.
An anticipatory framework may act as a trusted source that provides for a platform of information exchange with defined mechanisms for submission and exchange, quality checks and provisions for the disclosure of information. The suggested framework should take advantage of various relevant best practice examples: stewardship programs, cooperative governance networks, information exchange, information disclosure practices (patents, USDA-APHIS AIR) and appropriate database design. International cooperation and support is required based on an adequate structure. For this, the necessary resources need to be made available to ensure long-term operability.
The use of this detection and identification framework depends on the regulatory landscape. Concretely, if products of genome-editing are regulated, the respective statutory authorities need to decide on the level of information that is required for identification. Detection methods and criteria defined by the authorities also allow the implementation of voluntary labeling schemes. Development and validation of appropriate detection and identification methods should be undertaken by developers (for products that are notified) and by governmental institutions that are provided with the necessary resources (for non-authorized products or when regulations do not require an analytical method).
Given the rapid advances in development, fast implementation of an international anticipatory detection and identification framework for collaboration and the collation of voluntarily disclosed information is advisable. By exploiting a variety of different information sources in a systematic manner, and by establishing which level of information is sufficient to conclude on the identity of a particular genome-edited product, it is reasonable to expect that identification of genome-edited food or feed products is possible.