Development, optimization, and single laboratory validation of an event-specific real-time PCR method for the detection and quantification of Golden Rice 2 using a novel taxon-specific assay

Development and collaborative validation of an event-specific quantitative real-time PCR method for detection of genetically modified CC-2 maize

As one of the developed genetically modified (GM) maize varieties in China, CC-2 has demonstrated promising commercial prospects during demonstration planting. The establishment of detection methods is a technical prerequisite for effective supervision and regulation of CC-2 maize. In this study, we have developed an event-specific quantification method that targets the junction region between the exogenous gene and the 5' flanking genomic DNA (gDNA) of CC-2. The accuracy and precision of this method were evaluated across high, medium, and low levels of CC-2 maize content, revealing biases within ±25% and satisfactory precision data. Additionally, we determined the limits of quantification of the method to be 0.05% (equivalent to 20 copies) of the CC-2 maize. A collaborative trial further confirmed that our event-specific method for detecting CC-2 produces reliable, comparable, and reproducible results when applied to five different samples provided by various sources. Furthermore, we calculated the expanded uncertainty associated with determining the content level of CC-2 in these samples.

A universal quantification of transgenic soybean event DAS-68416-4 using duplex digital PCR

BACKGROUND

As labeling thresholds and low level presence thresholds of genetically modified (GM) components are implemented in more and more countries and regions, the demands for accurate quantification are increasing rapidly. At the same time, digital polymerase chain reaction (PCR) showed considerable benefits compared with former real-time fluorescence PCR in GM component quantification.

RESULTS

A universal quantification method using duplex digital PCR was established for detection of transgenic soybean event DAS-68416-4. The absolute limits of quantification (LOQs) of DAS-68416-4 event-specific gene and lectin reference gene were 0.61 copies μL-1 and 4.6 copies μL-1 respectively in droplet digital PCR, while 0.522 copies μL-1 and 5.192 copies μL-1 in chip digital PCR. The relative LOQs of DAS-68416-4 percentage content was 0.1% in both two digital PCR systems.

CONCLUSION

Gene copy ratio is the universal means of expression internationally used in transgenic component contents. Digital polymerase chain reaction (PCR) executes absolute quantification on specific genes, thus is considered to be suitable for detection of transgenic component contents. It was proved in this research on transgenic soybean event DAS-68416-4. Results indicated perfect satisfaction for transgenic component quantification needs in various technical performances of duplex digital PCR including repeatability, quantitative linear relationship and relative limits of quantification. © 2020 Society of Chemical Industry.

Sensitive detection of Piper nigrum L. adulterants by a novel screening approach based on qPCR

The spice made from the fruits of Piper nigrum L. (Piperaceae) has high economic value since the beginnings of international trade. Because its price has been increasing, adulterations with papaya seeds, cayenne pepper and maize flour were reported. These have been screened by methodologies dedicated to the detection of single adulterants lacking sensitivity and specificity. Herein we propose a specific, highly-sensitive, high-throughput and affordable qPCR-based methodology for the detection of P. nigrum contaminants (Carica papaya, Zea mays and Capsicum annuum) using plant DNA barcodes trnL and psbA-trnH. The method enables the specific detection of contaminants in a short time with low limits of detection (LOD₆ values of 1, 2 and 10 Haploid Genome Equivalents). A market survey (29 samples) revealed 41% of samples contaminated, though about ¾ at very low levels indicating accidental contamination. The proposed tool will contribute to the improvement of quality of this much traded spice.

Identification of single target taxon-specific reference assays for the most commonly genetically transformed crops using digital droplet PCR

Knowledge of the number of DNA sequences targeted by the taxon-specific reference assays is essential for correct GM quantification and is key to the harmonisation of measurement results. In the present study droplet digital PCR (ddPCR) was used to determine the number of DNA target copies of taxon-specific assays validated for real-time PCR for the four main genetically modified (GM) crops. The transferability of experimental conditions from real-time PCR to ddPCR was also explored, as well as the effect of DNA digestion. The results of this study indicate that for each crop at least one taxon-specific assay can be identified as having a single DNA target. A short list of taxon-specific reference assays is proposed as best candidates for the relative quantification of GM events for soybean, maize, cotton and oilseed rape. The investigated assays could be in most cases transferred to ddPCR without further optimisation. The use of DNA digestion did not improve ddPCR characteristics such as rain and resolution at the conditions tested.

Towards Plant Species Identification in Complex Samples: A Bioinformatics Pipeline for the Identification of Novel Nuclear Barcode Candidates

Monitoring of the food chain to fight fraud and protect consumer health relies on the availability of methods to correctly identify the species present in samples, for which DNA barcoding is a promising candidate. The nuclear genome is a rich potential source of barcode targets, but has been relatively unexploited until now. Here, we show the development and use of a bioinformatics pipeline that processes available genome sequences to automatically screen large numbers of input candidates, identifies novel nuclear barcode targets and designs associated primer pairs, according to a specific set of requirements. We applied this pipeline to identify novel barcodes for plant species, a kingdom for which the currently available solutions are known to be insufficient. We tested one of the identified primer pairs and show its capability to correctly identify the plant species in simple and complex samples, validating the output of our approach.

International ring trial for the validation of an event-specific Golden Rice 2 quantitative real-time polymerase chain reaction method

This article describes the international validation of the quantitative real-time polymerase chain reaction (PCR) detection method for Golden Rice 2. The method consists of a taxon-specific assay amplifying a fragment of rice Phospholipase D α2 gene, and an event-specific assay designed on the 3' junction between transgenic insert and plant DNA. We validated the two assays independently, with absolute quantification, and in combination, with relative quantification, on DNA samples prepared in haploid genome equivalents. We assessed trueness, precision, efficiency, and linearity of the two assays, and the results demonstrate that both the assays independently assessed and the entire method fulfill European and international requirements for methods for genetically modified organism (GMO) testing, within the dynamic range tested. The homogeneity of the results of the collaborative trial between Europe and Asia is a good indicator of the robustness of the method.