Strategies to detect unauthorized GMO in the food and feed chain

To guarantee the traceability on the market and the freedom of choice for consumers, genetically modified organisms (GMO) legislations have been established in many countries, including in Europe (EU). However, the implementation of these legislations by the enforcement laboratories is becoming complex due mainly to the increasing number and diversity of GMO. To cope with the problematic of EU unauthorized GMO, this PhD aims to improve and strengthen the existing GMO detection system using high-tech approaches. First, as a study case, an overview of genetically modified (GM) rice, developed around the world was carried out to collect information related inter alia on elements found in their transgenic cassette. Second, according to this information, key targets, frequently found in GMO (p35S and tNOS) or exclusively observed in EU unauthorized GMO (t35S pCAMBIA), were selected to develop a strategy allowing to detect and characterize a broad range of GMO. This strategy, fully integrated in the GMO routine analysis, consists to characterize sequences surrounding detected key transgenic elements using a DNA walking approach. By this way, the acquisition of sequences from the junction between the transgenic cassette and the plant genome as well as the associations of elements typically found in transgenic constructs allow to confirm the presence of GMO in food/feed matrices. Due to its good performance thoroughly assessed via several unprocessed and processed food/feed matrices, this strategy represents a key tool, easily implementable by the enforcement laboratories. With the aim to even more simplify the workflow and increase the throughput of this strategy, the sequencing step was performed using the Next Generation Sequencing (NGS) technology instead of the Sanger technology. In parallel, the detection of GMO in alimentary matrices using exclusively the NGS technology, through a whole genome sequencing (WGS) approach, was also investigated. As this last approach does not theoretically require any prior information about the targeted sequences, GMO composed only of unknown transgenic elements could be detected.
i
ii ABSTRACT
This work has thus allowed to provide additional strategies to the current GMO detection system in order to characterize a larger spectrum of GMO, both authorized or not.