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This research explores new detection strategies for genome-edited plants, particularly focusing on non-genomic methods.

February 28, 2026Open Access

Beyond DNA: Non-Genomic Detection Strategies and Epigenetic Editing in Genome-Edited Plant

Key Points

This research explores new detection strategies for genome-edited plants, particularly focusing on non-genomic methods.
Systematic literature review following PRISMA methodology
Assessment of detection methods based on metabolome, proteome, microRNA, methylation, and glycosylation
Comparison of GM plants with non-GM counterparts using '-omic' approaches
NGT-induced alterations are hard to distinguish from natural variants
DNA-based methods predominantly detect GM plants
Limited evidence of stable heritability in NGT-induced epimutations
New untargeted detection methods for genetic engineering are necessary

Abstract

As a result of the increase in innovative genome editing techniques aimed at introducing agronomically relevant traits, the detection of genetically modified (GM) crops has become challenging. While DNA-based detection methods have traditionally been used to identify and trace GM organisms under regulatory frameworks, new genomic techniques (NGTs), such as CRISPR/Cas9, are capable of inducing mutations that are difficult to distinguish from those occurring naturally. For this purpose, a systematic literature review was performed following the PRISMA methodology covering all detection methods based on metabolome, proteome, microRNA, methylation and glycosylation profiling of GM plants. In addition, considering that not only DNA can be edited but also the epigenome, the possibility of the existence of NGT-edited plants at the epigenetic level was explored. The search retrieved an increasing number of publications over the years using “-omic” approaches to compare GM plants with their non-GM conventional counterparts. The most abundant techniques were metabolomics and proteomics, and a few articles were also identified on miRNA and methylation profiles, but none on glycosylation. However, none of these techniques showed consistent results in detecting common markers caused by the genetic engineering process. Research articles in which mutations are induced in the epigenome by NGTs were scarce, especially when considering the study of their heritability. On the other hand, its potential application and stable transmission across generations was observed. Overall, the results underline the need to develop new detection methods that allow untargeted identification of plants modified by different Genetic Engineering techniques. • NGT alterations are currently indistinguishable from natural variants, complicating GMO identification • DNA-based methods remain as the main techniques for detecting GM- and NGT-edited plant • Updates on legislation will require new detection techniques for edited plant • Untargeted approaches are needed to detect markers of the genetic engineering process. • Limited studies suggest NGT-induced epimutations may be stable and heritable

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