Genome-Edited Plants: Opportunities and Challenges for an Anticipatory Detection and Identification Framework

The authors of the study discuss the problem of the traceability of genome-edited plants that contain only small changes in their genome, such as point mutations, small insertions or deletions. The study explains which information is necessary to detect genome-edited plants and to identify products. It also presents sources of information that may contain relevant data on genome-edited plants.

Detection and identification of genome-edited products
A validated detection method, i.e. one that is tested and checked by reference laboratories, is a prerequisite for the identification of genome-edited plants or their products. Evidence can be provided by using a specific analysis method, such as a PCR analysis, to find a specific genetic alteration in the DNA sequence. For precise identification, it must be possible to assign genome-edited plants to a specific product and a specific developer, typically by means of case-specific evidence. The necessary information on specific changes in the DNA can either be provided directly by the developer, or taken from databases, or from patent applications. For the development of a specific detection method, reference material is required with which the method can be tested. If the alterations in the DNA are known and reference material is available, they can be detected, as shown, for example, in the Chhalliyil et al., 2020 study. Such detection methods can detect both single point mutations and several combined changes in the DNA sequence.

Unlike traditional GMOs developed using ‘old’ genetic engineering techniques, genome-edited plants do not contain any genetic markers that can be easily found by using analytical methods. In ‘old’ genetic engineering, DNA sequences built into the plant genome can easily be detected together with the transgenic DNA, e.g. certain promoter sequences. In contrast, genome-edited plants often contain only small changes in the DNA sequence that can only be detected with the help of case-specific analysis methods. The changed traits of genome-edited plants are diverse and different to previous GMOs.

Available data sources for genome-edited plants
The developers hold the information on the specific alterations in the DNA sequence in genome-edited plants. In some non-EU countries, such as the USA, Argentina, Brazil or Australia, genome-edited plants with small changes in their genome (induced by SDN-1 applications) are not subject to regulation. Therefore, the developers do not have to provide the responsible authorities with any information on the exact genetic modifications. Nonetheless, there are a few publicly accessible non-EU databases (such as the American Department of Agriculture (USDA-APHIS) or the Canadian Department of Health Canada, Novel Food Information), which can be used to obtain information. However, the exact details of the changes in the DNA sequence are often not published.

Scientific publications are an important source of information on changes in genome-edited plants and often contain the exact DNA sequences needed to develop specific detection methods. This information should be systematically collected and linked to other information available from other sources. There are already databases that have implemented such concepts, e.g. the Plant Genome Editing Database (PGED) or CrisprGE. Both databases collect information on target genes and the exact changes in the DNA sequence so that these can be used to develop specific detection methods.

Information on the exact DNA changes in genome-edited plants can also be found in patent applications and thus used to develop detection methods. Patents can also contain other relevant information, e.g. technical data. However, not all patents contain such information. There are two publicly accessible patent databases (Espacenet and EPOQUE) which can be used to search for relevant patents.

Existing databases that can be used to collect information

Biosafety Clearing House (BCH)

The BCH is an international platform that provides information on genetically modified organisms (GMOs). It was set up under the Cartagena Protocol on Biosafety. The BCH database can be used as a source of information for GMOs. There are already several entries relating to genome-edited plants, such as the Cibus herbicide-tolerant oilseed rape and a maize variety with a different type of growth developed by the University of Ghent.

EUginius (EUropean GMO INItiative for a Unified database System)

The EUginius database is an initiative set up by the Federal Office for Consumer Protection and Food Safety together with Wageningen University that contains information on classic GMOs and genome-edited plants. As yet, only methods to detect classic GMOs have been entered into the database, but not for genome edited plants. The Chhalliyil et al., 2020 verification procedure for the Cibus oilseed rape is so far unavailable. EUginius also contains, where available, information on the changes made by genome editing.

Both databases could be expanded and used as international registers for genome-edited plants.

Two concrete examples
The authors use two specific examples to show how searches for relevant information on genome-edited plants can be conducted. The first example is the above-mentioned Cibus oilseed rape, for which information was collected from various sources in order to develop a detection method (Chhalliyil et al., 2020). Data were evaluated from the EUginius database and the BCH together with information from Health Canada, Novel Food Information. This method makes the detection of the specific DNA changes possible. However, information is still required from the developer in order to clearly identify whether the genome-edited oilseed rape is really the one developed by Cibus.

The second example is a wheat variety engineered to be resistant to powdery mildew with TALENs technology (Wang, et al 2014). 6 copies of the MLO gene were changed simultaneously in this wheat variety. Information about the exact DNA changes is included in the scientific study. Further information is also contained in the associated patent. This means that sufficient data are available to develop a specific detection method (PCR methods) and to detect the specific combination of changes in the DNA. If this wheat were to come onto the global market, the detection of these combined DNA changes would be a very strong indication that it is the genome-edited wheat.

Finally, the authors of the study present a suggestion on how to solve the problem of detecting and identifying genome-edited plants. It largely depends on the cooperation of companies, scientists, authorities and politics in order to collect and make available the information required for the development of a detection method. An international database in which such information is collected could support the international trade of genome-edited products.

Ribarits A, Eckerstorfer M, Simon S, Stepanek W (2021) Genome-Edited Plants: Opportunities and Challenges for an Anticipatory Detection and Identification Framework. Foods 10 (2):430
Chhalliyil P, Ilves H, Kazakov SA, Howard SJ, Johnston BH, Fagan J (2020) A Real-Time Quantitative PCR Method Specific for Detection and Quantification of the First Commercialized Genome-Edited Plant. Foods 9 (9). doi:10.3390/foods9091245
Wang Y, Cheng X, Shan Q, Zhang Y, Liu J, Gao C, Qiu JL (2014) Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew. Nat Biotechnol 32 (9):947-951. doi:10.1038/nbt.2969