Successful detection methods for new genomic techniques

It’s becoming increasingly clear from studies that detection and identification of new GMO (new genomic techniques, NGT) plants will be possible, as long as such research continues to be supported. That means, as the first article below says, “Refusing to regulate new genetic engineering processes on the pretext that their detection is too difficult, if not impossible, as the agricultural industry and some of the scientific and political circles linked to it constantly assert, is therefore no longer defensible in good conscience.”

1. Successful detection methods for new genomic techniques – Swiss Alliance for Agriculture Without Genetic Engineering
2. Feasibility study on "Detection and identification methods for genome-edited plants and plant products" completed: Reports have been published – German Federal Office for Agriculture and Food
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1. Successful detection methods for new genomic techniques
Swiss Alliance for Agriculture Without Genetic Engineering, undated
https://stopogm.ch/themes/nouvelles-techniques-de-modification-genetiques/835-1-succes-dans-les-methodes-de-detection-des-nouvelles-technologies-genetiques/

Since January 2021, researchers at the Leibniz Institute for Plant Genetics and Crop Research (IPK) and Christian-Albrecht University Kiel have been investigating approaches for the detection and identification of plants whose genomes have been modified by new genomic techniques (NGT), and testing their practical use. Over the course of the three-year project, the researchers succeeded in developing analytical methods for detecting previously known mutations in NGT lines. In addition, clues to an analytical approach that could - in some cases - be used to identify NGT lines as such, i.e. to distinguish them from a conventional line with the same mutation, were confirmed during the research project, the researchers write. The experiments were carried out in a closed system, without dissemination.

The project began with barley and oilseed rape lines, into whose genetic make-up researchers from the participating institutes selectively introduced small modifications (mutations) using CRISPR/Cas genetic scissors. Approaches based on polymerase chain reaction (PCR) and next-generation sequencing (NGS) were tested for mutation detection. For identification, the researchers followed the approach of using other mutations in the gene pool of NGT lines that are in close proximity to the induced mutation and not present in the comparison lines.

For the barley and oilseed rape lines studied, two analytical methods were established, which reliably detected the introduced mutations, even in seed mixtures containing quantities of only 0.9% and 0.1%. The accredited reference laboratories involved in the project optimised the methods and successfully tested them for specificity, selectivity and applicability.

Detection and identification procedures required for official controls

Plants whose genetic make-up has been modified using new genomic techniques (NGTs) are currently subject to genetically modified organism (GMO) regulations in the EU and Switzerland. For market control purposes, and as a prerequisite for the release of GMOs, reliable detection and identification methods are needed for official control, so that genome-edited products can be distinguished from conventional crop products - i.e. unequivocally identified. The GMO detection methods available to date, which can detect known foreign DNA sequences, can only be applied to a limited extent to NGT plants, which do not contain such DNA sequences.

However, the study shows that the genetic change to be looked for must be precisely documented and known. To ensure this, companies wishing to market NTG plants should be obliged to make information on the genetic sequence and reference material available to the supervisory authorities, writes the Gene Technology Information Service. Under the current legal situation, they are only obliged to do so if they apply for authorisation for their plant in the EU or Switzerland. This is why it is currently difficult for the authorities to develop testing, detection and identification methods for four NGT plants that are already marketed outside Europe.

The current study, commissioned by the German Federal Office for Agriculture and Food, shows that the detection and identification of NGT plants will be possible in the future, provided that the corresponding research projects are launched and promoted. Refusing to regulate new genetic engineering processes on the pretext that their detection is too difficult, if not impossible, as the agricultural industry and some of the scientific and political circles linked to it constantly assert, is therefore no longer defensible in good conscience.

Further information

* Feasibility study on “Detection and identification methods for plants and plant products produced by genome editing” completed: German Federal Institute for Agriculture and Food

* Detection methods developed for genome-edited rapeseed and barley, Informationsdienst Gentechnik, 01.08.2024

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2. Feasibility study on "Detection and identification methods for genome-edited plants and plant products" completed: Reports have been published
BLE (German Federal Office for Agriculture and Food), undated
https://www.ble.de/SharedDocs/Meldungen/DE/2024/240702_genomeditierte_Pflanzen.html

Researchers from the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) in Gatersleben and the Christian-Albrechts-Universität zu Kiel have joined forces to experimentally search for approaches for the detection and identification of genome-edited plants and test them for practical applicability. The project, aimed at supporting decision-making, has been funded by the Federal Ministry of Food and Agriculture (BMEL) since January 2021 and supported by the BLE as project sponsor, and ended on 30 November 2023.

Overall, the researchers were able to develop analytical methods to detect the previously known mutations in the genome-edited lines. They also confirmed indications of an analytical approach that could - in certain cases - be used to identify genome-edited lines as such, i.e. to distinguish them from a conventional line with the same mutation.

The starting point for the project was barley and rapeseed lines into whose genetic material the research institutions had introduced small changes (mutations) using the CRISPR/Cas gene scissors. The genetic material of the plant lines was comprehensively sequenced as the basis for the development of the analysis methods. This showed that only the target areas targeted with the gene scissors had the expected mutations. In contrast, areas similar to the target area (off-targets) did not contain any mutations. In contrast to the genome-edited barley line, the genetic material of the genome-edited rapeseed lines still carried fragments of the transgene used during the production process to introduce the gene scissors. No evidence of other structural changes that the use of the gene scissors could have left in the genome was found in either case. The experiments were carried out in a closed system without release.

Approaches based on polymerase chain reaction (PCR) and next generation sequencing (NGS), i.e. a technology for the high-throughput analysis of DNA, were tested for the detection of mutations. Two analysis methods were established for the barley and rapeseed lines analysed, which allowed reliable detection of the mutations introduced, even in seed mixtures containing only 0.9% and 0.1%. Accredited reference laboratories involved in the project optimised the methods and successfully tested them for specificity, selectivity and applicability. Procedures and results were recorded in so-called Standard Operating Procedure (SOP) drafts. In addition, the project partners developed the prototype of a bioinformatic analysis pipeline for NGS data (amplicon deep sequencing).

In order to identify these mutations, the researchers took the approach of using other mutations in the genome of the genome-edited lines that are close to the induced mutation and are not present in reference lines.

No such mutations were found in the analysed barley line. For oilseed rape, sequencing revealed a neighbouring mutation, so that an identification approach based on the detection of this combined with the detection of the induced mutation could be tested and found to be suitable in principle. However, in the present case, the distance between the two mutations would be too great to rule out the independent occurrence of the two mutations under agricultural cultivation conditions.

Background

Plants whose genetic material has been specifically modified (‘genome-edited’) using new genomic techniques fall under the regulations for genetically modified organisms (GMOs) in the EU. For market control and as a prerequisite for the placing on the market of GMOs, court-proof detection and identification procedures are required for official control that allow genome-edited products to be distinguished from conventional breeding products - i.e. clearly identified - and, if necessary, even minor admixtures to be detected with sufficient certainty.Previously available and established methods for the detection of GMOs, with which known foreign DNA sequences are detected, can only be transferred to genome-edited plants that do not contain such DNA sequences to a limited extent.

Further information

The final reports of the project partners are available here:
www.ble.de/ptble-DETECT
www.ble.de/ptble-RapsNMT

Feasibility study on detection and identification methods for genome-edited plants and plant products - Joint final report


Read these articles on the GMWatch site and access linked sources 
https://gmwatch.org/en/106-news/latest-news/20457

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