The term new genomic techniques (NGTs) is an umbrella term used to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework used to detect GMOs in Europe is an established single harmonized procedure that is mandatory for the authorization of GM food and feed, thus generating a reliable, transparent, and effective labeling scheme for GMO products. However, NGT products can challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, the current detection methods might fail to meet the minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems’ specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. In addition, it also empirically tested the PCR system evaluated during the in silico analysis. Two mutant genotypes produced by CRISPR-Cas9 in Arabidopsis thaliana were used as a case study. Overall, our results demonstrate that the single PCR system developed for identifying a nucleotide insertion in the grf1-3 genotype has multiple matches in the databases, which do not enable the discrimination of this mutated event. Empirical assays further support this demonstration. In contrast, the second mutated genotype, grf8-61, which contains a -3 bp deletion, did not yield any matches in the sequence variant database. However, the primer sequences were not efficient during the empirical assay. Our approach represents a first step in decision making for analytical methods for NGT detection, identification, and quantification in light of the European labeling regulations.

RESUMO A industrialização da agricultura e da pecuária, além de gerar um ambiente propício à disseminação de agentes infecciosos, é responsável pelo uso generalizado de diversas substâncias tóxicas que afetam a saúde humana, animal e ambiental. O objetivo deste estudo foi promover a reflexão sobre o uso de agrotóxicos e medicamentos veterinários como elementos de debate na construção da Saúde Única. Para isso, foi realizada uma revisão exploratória literária de artigos, livros e documentos oficiais disponíveis em plataformas de banco de dados. A discussão inclui as problemáticas do uso de substâncias tóxicas em plantas e animais. Aborda, também, como os resíduos oriundos de sua utilização impactam a qualidade de alimentos, ar, solo, água com consequências à saúde humana. Embora essa discussão seja escassa na temática de Saúde Única, é fundamental que, além da participação da sociedade civil organizada, gestores públicos assegurem, por meio de políticas públicas, maior segurança e controle na utilização de substâncias tóxicas na agricultura e na pecuária.

PCR methods are widely applied for the detection of genetically modified organisms (GMOs) in Europe, facilitating compliance with stringent regulatory requirements and enabling the accurate identification and quantification of genetically modified traits in various crops and foodstuffs. This manuscript investigates the suitability of real-time PCR methods for detecting organisms generated through new genomic techniques (NGTs), specifically focusing on a case study using Arabidopsis thaliana as a model gene-edited plant. Given the complexities of European regulations regarding genetically modified organisms (GMOs) and the classification of gene-edited plants, there is a pressing need for robust detection methods. Our study highlights the development and validation of a novel single-plex real-time PCR method targeting a specific single nucleotide polymorphism (SNP) in the grf1-3 gene modified using CRISPR-Cas9 technology. We emphasize the effectiveness of locked nucleic acid (LNA)-modified primers in improving specificity. The results demonstrate that while the grf1-3 LNA method successfully detected and quantified gene-edited Arabidopsis DNA, achieving absolute specificity remains a challenge. This study also addresses the significance of the cross-laboratory method for validation, demonstrating that the method developed for an SNP-modified allele can be performed in accordance with the precision and trueness criteria established by the European Network of GMO Laboratories (ENGL). Furthermore, we call for continued collaboration among regulatory agencies, academia, and industry stakeholders to refine detection strategies. This proactive approach is essential not only for regulatory compliance but also for maintaining public trust in the safe integration of gene-edited organisms into food products.

The objective of this work was to compare the purple garlic cultivated in the Planalto Catarinense region with the one in Midwestern/ Southeastern region of Brazil, concerning colorimetric and chemical aspects, as well as genetic patterns. The color of the bulbils was determined through colorimetric analysis, the volatile compounds were characterized by solid phase micro-extraction and gas chromatography, and the genetic diversity was analyzed using microsatellite markers. Garlic bulbs grown in the Planalto Catarinense region have a more intense purplish color. The samples from the Midwestern/Southeastern region present a significantly lower concentration of volatile compounds. There is no consistent genetic difference between samples from the Planalto Catarinense and Midwestern/Southeastern regions. The purple garlic from each cultivation region has singularities, mainly due to the farmers’ management method and edaphoclimatic factors. The uniqueness presented through the colorimetric and chemical analyses fulfills the basic requirements that are necessary for the Geographical Indication of these products.

The term new genomic techniques (NGTs), is an umbrella term to describe a variety of techniques that can alter the genetic material of an organism and that have emerged or have been developed since 2001, when the existing genetically modified organism (GMO) legislation was adopted. The analytical framework to detect GMOs in Europe is a established single harmonized procedure which is mandatory for authorization of GM food and feed, thus generating reliable, transparent and effective labelling scheme for GMO products. However, NGT products challenge the implementation and enforcement of the current regulatory system in the EU, relating in particular to the detection of NGT products that contain no foreign genetic material. Consequently, current detection methods will fail to meet minimum performance requirements. Although existing detection methods may be able to detect and quantify even small alterations in the genome, this does not necessarily confirm the distinction between products resulting from NGTs subject to the GMO legislation and other products. Therefore, this study provides a stepwise approach for the in silico prediction of PCR systems specificity by testing a bioinformatics pipeline for amplicon and primer set searches in current genomic databases. We have tested our methodology in two mutant genotypes produced by CRISPR/Cas9 in Arabidopsis thaliana. Overall, our results demonstrated that the single PCR system developed for the identification of a nucleotide insertion in the grf1-3 genotype has sufficient hits in the databases that would not allow discrimination of this mutanted event. Differently, the second mutated genotype grf8-61 which contains a -3bp deletion, found no matches in the sequence variant database. Our approach is the first step in decision making on PCR system and modification of them for empirical testings.