TWN Info Service on Biosafety
17 December 2025
Third World Network
www.twn.my
Dear Friends and Colleagues
Detection of genome-edited organisms with subtle mutations is possible
A new peer-reviewed study demonstrates the development of a detection method for a non-commercialised genome-edited rice line that has been engineered to have just a single nucleotide insertion.
GMOs commercialised to date often share some of the same foreign (transgenic) genetic material, making detection generally straightforward. In contrast, many genome-edited organisms have not been developed to carry transgenic material, but instead may only be designed to carry small genetic changes such as single base pair edits, deletions or insertions.
As such, detection methods for genome-edited organisms need to be tailored to the on-target changes being made, as well as other potential genetic markers, such as unintended off-target effects, or the genetic background of the particular edited cultivar.
The study details the development of identification targets within the genome, including the ‘on-target’ insertion, as well as a cultivar-specific ‘genetic fingerprint’, developed by sequencing the cultivar and detecting unique genetic signatures that are distinct from other rice varieties.
When combining these two approaches, the method was able to detect the presence of the genome-edited rice, even at very low levels of 0.9-0.1%. This would be sensitive enough to detect cases of unintended contamination.
This is a vital proof-of-concept study that shows that genome-edited organisms can be detected in the food chain. Detection would be a vital step in maintaining transparency in the food system to track and monitor genome-edited organisms, operationalise consumer choice and to facilitate labelling of genome-edited products.
With best wishes,
Third World Network
————————————————————————————————–
Genetic fingerprints derived from genome database mining allow accurate identification of genome-edited rice in the food chain via targeted high-throughput sequencing
Alice Fraiture et al., (2025), Food Research International, v221
https://doi.org/10.1016/j.foodres.2025.117218
Abstract
Genome-edited (GE) organisms are currently classified as GMOs according to European legislation, requiring traceability and labelling in the food and feed supply chain. However, unambiguous identification of a specific GE organism with one or more induced single nucleotide variations (SNVs) dispersed across the genome remains challenging. This study explored whole-genome sequencing-based characterization, public genome databases, and machine learning tools to select key genetic elements and create a unique fingerprint for distinguishing a specific GE line. As a case study, a GE Nipponbare rice line containing a single CRISPR-Cas-induced SNV was used. To experimentally assess the detection of this fingerprint, a targeted high-throughput sequencing approach, including multiplex PCR-based enrichment of key genetic elements, was developed and successfully tested. This promising proof-of-concept demonstrates the potential of combining a unique genetic fingerprint with targeted high-throughput sequencing to facilitate the accurate detection of GE organisms, thereby supporting food traceability and regulatory compliance for the development of new GE lines, as well as protecting associated intellectual property.