Next-generation framework for the detection of genetically modified organisms in the food and feed supply

• Forschungsstelle: BLW
• Projektnummer: 19.18

Schlüsselwörter (Deutsch)

Genetisch veränderte Organismen, Nutzpflanzen, Genombearbeitung, nächste Generation von Sequenzierung, genetische Nachweisverfahren

Schlüsselwörter (Englisch)

Genetically modified organisms, crops, genome editing, next generation sequencing, genetic detection assays

Schlüsselwörter (Französisch)

Organismes génétiquement modifiés, cultures, édition du génome, prochaine génération de séquençage, essais de détection génétique

Schlüsselwörter (Italienisch)

Organismi geneticamente modificati, coltivazioni, editing del genoma, sequenziamento di nuova generazione, metodi di rilevamento genetico

Kurzbeschreibung (Englisch)

Genetically modified (GM) crops of the past decade contained simple, well characterized modifications. Newer GM technologies (like CRISPR) lead to more precise and more complex modifications. This creates a need for validated tools that allow the precise identification of genome editing in imported crops. This research proposal aims to produce fundamental knowledge on the feasibility, specificity and sensitivity to detect a large number of genetic modifications in different organisms. The proposal is structured into four steps that cover various aspects of the detection of GMO:
1: Development of a reliable and expandable multiplex assay based on next generation sequencing (NGS) to screen all currently catalogued genetic modifications in crops imported into Switzerland.
2: Validation of NGS-based assays with various seed material relevant for Switzerland, establishment of benchmarks for sensitivity and specificity, development of bioinformatics pipelines.
3: Generation of a statistical framework to detect on-target and off-target CRISPR based genome editing in major crops.
4: Proof-of-concept NGS for the establishment of benchmarks for the detection of previously unknown genetic modifications in major crops.

Kurzbeschreibung (Französisch)

Les cultures génétiquement modifiées (GM) de la dernière décennie contenaient des modifications simples et bien caractérisées. Les nouvelles technologies GM (comme CRISPR) conduisent à des modifications plus précises et plus complexes. Il est donc nécessaire de disposer d'outils validés qui permettent l'identification précise de l'édition du génome dans les cultures importées. Cette proposition de recherche vise à produire des connaissances fondamentales sur la faisabilité, la spécificité et la sensibilité pour détecter un grand nombre de modifications génétiques dans différents organismes. La proposition est structurée en quatre étapes qui couvrent divers aspects de la détection des OGM :
1 : Développement d'un test multiplex fiable et extensible basé sur le séquençage de nouvelle génération (NGS) pour examiner toutes les modifications génétiques actuellement cataloguées dans les cultures importées en Suisse.
2 : Validation d'essais basés sur les NGS à l'aide de diverses semences pertinentes pour la Suisse, établissement de points de référence pour la sensibilité et la spécificité, développement de pipelines bioinformatiques.
3 : Génération d'un cadre statistique pour détecter la vérification du génome sur cible et hors cible basée sur le CRISPR dans les principales cultures.
4 : Preuve du concept de NGS pour l'établissement de repères pour la détection de modifications génétiques précédemment inconnues dans les principales cultures.

Projektziele (Englisch)

The overarching aim of this research proposal is to produce fundamental knowledge on the feasibility,specificity and sensitivity to detect a large number of individual genetic modifications in different organisms. Particularly relevant will be to systematically evaluate the potential to develop an effective screening for the new generation of genetic modifications based on CRISPR/Cas9 technology. A focus will also be placed on the ability of next-generation sequencing assays to detect unknown or poorly documented genetic modifications that may enter the market.

Abstract (Englisch)

Advances in genetic engineering make it possible to improve or introduce desired traits in crops at an accelerating pace. In Switzerland, the import of genetically modified (GM) crops are tightly regulated. A core mandate of federal authorities is to ensure effective monitoring. GM crops of the past decade contained simple, well characterized modifications that can be efficiently recognized by currently implemented screenings. Newer GM technologies (i.e. CRISPR variants) are used to create more precise and more complex modifications. This creates an urgent need for validated tools that allow the precise identification of genome editing in imported crops. In this research project, we accomplished the following aims. We first designed and validated a next-generation multiplex sequencing assay targeting GM loci monitored in Switzerland and the EU. The assay was capable to identify the species from which the material originated, show reasonable sensitivity despite multiplexing hundreds of loci simultaneously. In the next set of aims, we developed a mathematical model that lays the foundation to detect cis-genesis gene editing events in plant or animal specimen. We then wrote software to apply the mathematical model to genome sequencing data and, finally, we analyze rice genome sequencing datasets to assess the sensitivity and performance of the software. In summary, we built foundations how future challenges of GM monitoring can be addressed.