Development of event-specific qPCR detection methods for genetically modified alfalfa events J101, J163 and KK179

Quantitative real-time PCR analysis of four genetically modified soybean events using plasmid and genomic DNA calibrators

A calibration curve is required for reliable and accurate quantitative real-time PCR analysis of genetically modified (GM) organisms, necessitating the use of reference materials as calibrators. In this study, two types of DNA calibrators-plasmid DNA (pDNA) and genomic DNA (gDNA)-were used to quantify four GM soybean events (SYHT0H2, MON87751, DAS-44406-6, and DAS-81419-2). The PCR efficiency and linearity for the calibrators adhered to the CODEX guidelines. The conversion factor (Cf) was calculated as the ratio of copies of GM events to those of endogenous genes using the pDNA calibration curve. To assess the accuracy and repeatability of these assays, quantification at GM levels of 3% and 1% was performed. Based on our results, we believe that the pDNA calibrator assessed in this study can be used as a reference material for GMO quantitative analysis and can replace gDNA, especially considering the ease of management and advantages of mass production.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-023-01392-0.

The Digital MIQE Guidelines Update: Minimum Information for Publication of Quantitative Digital PCR Experiments for 2020

Digital PCR (dPCR) has developed considerably since the publication of the Minimum Information for Publication of Digital PCR Experiments (dMIQE) guidelines in 2013, with advances in instrumentation, software, applications, and our understanding of its technological potential. Yet these developments also have associated challenges; data analysis steps, including threshold setting, can be difficult and preanalytical steps required to purify, concentrate, and modify nucleic acids can lead to measurement error. To assist independent corroboration of conclusions, comprehensive disclosure of all relevant experimental details is required. To support the community and reflect the growing use of dPCR, we present an update to dMIQE, dMIQE2020, including a simplified dMIQE table format to assist researchers in providing key experimental information and understanding of the associated experimental process. Adoption of dMIQE2020 by the scientific community will assist in standardizing experimental protocols, maximize efficient utilization of resources, and further enhance the impact of this powerful technology.

Targeted MinION sequencing of transgenes

The presence of genetically modified organisms (GMO) is commonly assessed using real-time PCR methods targeting the most common transgenic elements found in GMOs. Once the presence of GM material has been established using these screening methods, GMOs are further identified using a battery of real-time PCR methods, each being specific of one GM event and usually targeting the junction of the plant genome and of the transgenic DNA insert. If, using these specific methods, no GMO could be identified, the presence of an unauthorized GMO is suspected. In this context, the aim of this work was to develop a fast and simple method to obtain the sequence of the transgene and of its junction with plant DNA, with the presence of a screening sequence as only prior knowledge. An unauthorized GM petunia, recently found on the French market, was used as template during the development of this new molecular tool. The innovative proposed protocol is based on the circularization of fragmented DNA followed by the amplification of the transgene and of its flanking regions using long-range inverse PCR. Sequencing was performed using the Oxford Nanopore MinION technology and a bioinformatic pipeline was developed.