Advances in identifying GM plants: toward the routine detection of ‘hidden’ and ‘new’ GMOs

International audience; The growing knowledge in genetics, epigenomics, epitranscriptomics, and the 3D - or even 4D - genome structure provides an increasing number of detection targets that can be used to identify species or genetic lines, whether modified or not. Biotic and abiotic stresses also induce numerous unintentional genetic, epigenetic, and epitranscriptomic modifications. Those changes are transmissible and can be ordered in regions and classified. The detection target is characterised by the mutagenesis technique used. For instance, the detection of transgenic GMO or SDN3 modification of New Breeding Techniques (NBTs) will target their insertion's junction fragments into the genome. Each insertion induces epigenetic, and probably epitranscriptomic, changes which can also be targeted. In addition, one group of markers is linked to the trait(s) introduced or modified by the breeder whose sequence could be used in quantification and "screening". The other target will be a subset of the elements of a matrix approach (as described in the previous chapter). General selection markers, such as those used for plant breeding, together with mutagenesis techniques specific markers, could differentiate genetically modified organisms (GMOs) of any origin. They can be used to quantify and certify, through a global approach to the organism, that the trait modification is artefactual and not "natural." The growing mastery of single-cell sequencing techniques should soon make it possible to differentiate the modifications due, for example, to each step of a Crispr-Cas transformation of cells in culture. This chapter will focus mainly on detection targets based on nucleic acids, DNA, RNA, modified or unmodified, for their routine use in private and enforcement detection laboratories to comply with food labelling and European traceability rules. The chapter use the wording “hidden” GMOs and “new” GMOs as defined by the French NGOs and farmers’ union at the origin of the 2018 European Court of Justice ruling.