Development and strategy of reference materials for the DNA-based detection of genetically modified organisms

GMOIT: a tool for effective screening of genetically modified crops

BACKGROUND

Advancement in agricultural biotechnology has resulted in increasing numbers of commercial varieties of genetically modified (GM) crops worldwide. Though several databases on GM crops are available, these databases generally focus on collecting and providing information on transgenic crops rather than on screening strategies. To overcome this, we constructed a novel tool named, Genetically Modified Organisms Identification Tool (GMOIT), designed to integrate basic and genetic information on genetic modification events and detection methods.

RESULTS

At present, data for each element from 118 independent genetic modification events in soybean, maize, canola, and rice were included in the database. Particularly, GMOIT allows users to customize assay ranges and thus obtain the corresponding optimized screening strategies using common elements or specific locations as the detection targets with high flexibility. Using the 118 genetic modification events currently included in GMOIT as the range and algorithm selection results, a "6 + 4" protocol (six exogenous elements and four endogenous reference genes as the detection targets) covering 108 events for the four crops was established. Plasmids pGMOIT-1 and pGMOIT-2 were constructed as positive controls or calibrators in qualitative and quantitative transgene detection.

CONCLUSIONS

Our study provides a simple, practical tool for selecting, detecting, and screening strategies for a sustainable and efficient application of genetic modification.

Development and Validation of a New Robust Detection Method for Low-Content DNA Using ΔΔCq-Based Real-Time PCR with Optimized Standard Plasmids as a Control Sample

Real-time polymerase chain reaction (PCR) is the gold standard for DNA detection in many fields, including food analysis. However, robust detection using a real-time PCR for low-content DNA samples remains challenging. In this study, we developed a robust real-time PCR method for low-content DNA using genetically modified (GM) maize at concentrations near the limit of detection (LOD) as a model. We evaluated the LOD of real-time PCR targeting two common GM maize sequences (P35S and TNOS) using GM maize event MON863 containing a copy of P35S and TNOS. The interlaboratory study revealed that the LOD differed among laboratories partly because DNA input amounts were variable depending on measurements of DNA concentrations. To minimize this variability for low-content DNA samples, we developed ΔΔCq-based real-time PCR. In this study, ΔCq and ΔΔCq are as follows: ΔCq = Cq (P35S or TNOS) – Cq (SSIIb; maize endogenous gene), ΔΔCq = ΔCq (analytical sample) – ΔCq (control sample at concentrations near the LOD). The presence of GM maize was determined based on ΔΔCq values. In addition, we used optimized standard plasmids containing SSIIb, P35S, and TNOS with ΔCq equal to the MON863 genomic DNA (gDNA) at concentrations near the LOD as a control sample. A validation study indicated that at least 0.2% MON863 gDNA could be robustly detected. Using several GM maize certified reference materials, we have demonstrated that this method was practical for detecting low-content GM crops and thus for validating GM food labeling. With appropriate standards, this method would be applicable in many fields, not just food.

Digital PCR-Based Characterization of a g10evo-epsps Gene-Specific Matrix Reference Material for Its Food and Feed Detection

g10evo-epsps is a novel glyphosate herbicide-resistant gene that has been transferred to various crops such as soybean, corn, cotton, and rice. Here, we developed a gene-specific digital Polymerase Chain Reaction (dPCR) detection method for absolute quantitative analysis of g10evo-epsps, and characterized g10evo-epsps certified reference materials (CRM) using ZUTS-33 soybean powder as the candidate material. Stability tests of matrix CRMs demonstrate that these CRMs can be stored stably for 6 months and transported for 10 days at room temperature and withstand summer high temperatures (below 60 °C). CRM characterization is based on the copy number ratio of g10evo-epsps to lectin. Eight qualified laboratories independently validated the CRM using dPCR method, with a measurement of 0.98 (copy/copy) and an extended uncertainty of 0.08 (copy/copy). The g10evo-epsps matrix CRM described here may be used for qualitative and quantitative testing, method evaluation, laboratory quality control, and other related fields.

Collaborative Ring Trial of the Applicability of a Reference Plasmid DNA Calibrant in the Quantitative Analysis of GM Maize Event MON810

Certified reference materials (CRMs) is one of the critical requirements in a quantitative analytical method, such as in the quantification of genetically modified (GM) contents in food/feed products. Plasmid-DNA-based CRMs are becoming essential in GM content quantification. Herein, we report the construction of one plasmid DNA calibrant, pMON810, for the quantification of the GM maize event MON810 which is commercially planted and used for food/feeds worldwide, and the collaborative ring trial was used to validate its applicability. pMON10 was proven to have high specificity for the MON810 event. The limit of detection (LOD) and limit of quantification (LOQ) of real-time PCR assays of MON810 event and maize endogenous gene using pMON810 as calibrant was 2 copies/μL and 5 copies/μL, respectively. A total of eight laboratories participated in the ring trial and returned valid test results. Each sample was performed with three repeats and three parallels in each repeat. Statistical analysis of the ring trial results showed that pMON810 as a calibrant had high PCR efficiency (ranging from 0.885 to 1.008) and good linearity (ranging from 0.9933 to 0.9997) in MON810 and endogenous gene real-time PCR assays. The bias between the test values and true values ranged from 4.60 to 20.00% in the quantification of five blind samples. These results indicate that pMON810 is suitable for use as a calibrant for the quantification of MON810 events in routine lab analysis or to evaluate detection methods for MON810, as well as being used as a substitute for the matrix-based CRM of MON810.

Design and storage stability of reference materials for microfluidic quantitative PCR-based equine gene doping tests

One method of gene doping in horseracing is administering of exogenous genetic materials, known as transgenes. Several polymerase chain reaction (PCR)-based methods have been developed for detecting transgenes with high sensitivity and specificity. However, novel designs for reference materials (RMs) and/or positive template controls (PTCs) are necessary for simultaneous analysis of multiple transgene targets. In this study, we designed and developed a novel RM for simultaneously detecting multiple targets via microfluidic quantitative PCR (MFQPCR). Twelve equine genes were selected as targets in this study. A sequence region including primers and probes for quantitative PCR was designed, and a 10 bp sequence was inserted to allow the RM to be distinguished from the original transgene sequences. The sequences of individual detection sites were then connected for 12 genes and cloned into a single plasmid vector. We performed fragment size analysis to distinguish between the PCR products of the original transgene sequence and those of the RM, enabling identification of RM contamination. PTCs diluted to 10,000, 1,000, 100, and 10 copies/µl with horse genomic DNA from RM were stably stored at 4°C for 1 year. As digital PCR enabled absolute quantification, the designed substances can serve as an RM. These findings indicate that the RM design and storage conditions were suitable for gene doping tests using MFQPCR.

Development of dual-emission cluster of Ag atoms for genetically modified organisms detection

A DNA-silver nanocluster with two distinct emissions is devised, in which this unique modality has been exploited to develop a novel nanosensor for transgenic DNA detection. TEM and fluorescence analysis revealed the formation of Ag nanoclusters with a size of around 2 nm, which exhibit dual-emissions at 550 nm (green) and 630 nm (red). Moreover, in the presence of the target sequence (CaMV 35S promoter) from the transgenic plant, the nanoclusters showed an enhancement in the green emission and a reduction in the red emission. This property provided a ratiometric-sensing platform which lacks unavoidable noises. The ratio of green to red fluorescence emission (G/R) of the nanoclusters exhibited a linear relation with the target concentration in the range 10 to 1000 nM. However, the control DNA did not affect this ratio, which clearly confirmed the selective response of the designed nanosensor. This sensing platform had a detection limit of 1.5 nM and identified the DNA of transgenic soybeans within a short time. The mechanistic evaluation of the nanoclusters further revealed the role of protonated cytosine bases in the dual emission behavior. Finally, unique features of the designed nanosensor may improve the current approaches for the development and manufacturing of GMO detection tools.

Development of Genomic DNA Certified Reference Materials for Genetically Modified Rice Kefeng 6

The application of certified reference materials (CRMs) to genetically modified organism (GMO) detection is essential for guaranteeing the accuracy, comparability, and traceability of quantitative results over time and among laboratories. Clean leaves from GM rice Kefeng 6 were used as raw materials to develop a batch of genomic DNA (gDNA) CRMs. The optimized KF6/PLD duplex digital PCR was used for collaborative characterization of Kefeng 6 gDNA CRMs by eight qualified laboratories; this batch of gDNA CRMs was certified for two property values, namely, copy number ratio and copy number concentration, which were 1.03 ± 0.04 and (1.60 ± 0.11) × 10⁵ copies/μL, respectively. The gDNA CRMs displayed good between-vial homogeneity when the minimum sample intake of 2 μL was taken into account. Stability studies indicated that the gDNA CRMs should be transported below 25 °C, and cold chain transport was recommended. Shelf life was assessed to be at least 12 months, and when using gDNA CRMs, freeze-thaw should not exceed 10 cycles. Compared to the available gDNA CRMs in the market, this batch of gDNA CRMs has accurate property values with combined uncertainties, providing user-friendly calibrators for GM rice Kefeng 6 inspection and monitoring. The development and characterization of Kefeng 6 gDNA CRMs contribute to the establishment of a copy number-based reference system for GMO detection.

Development of a certified genomic DNA reference material for detection and quantification of genetically modified rice KMD

Qualitative and quantitative detection of genetically modified products is inseparable from the application of reference materials (RMs). In this study, a batch of genomic DNA (gDNA) certified reference materials (CRMs) was developed using genetically modified rice Kemingdao (KMD) homozygotes as the raw material. The gDNA CRMs in this batch showed good homogeneity; the minimum sample intake was determined to be 2 μL. The stability study showed that transportation by cold chain is preferable, no significant degradation trend was observed during a 12-month period when storing the gDNA CRMs at 4 °C and - 20 °C, and the number of freeze-thaw cycles cannot exceed 10. The property values of the copy number ratio of transgene and endogenous gene and the copy number concentration for gDNA CRMs were determined by a collaborative characterization of eight laboratories using the duplex KMD/PLD droplet digital PCR (ddPCR) assays. The uncertainty components of characterization, potential between-unit heterogeneity, and potential degradation during long-term storage were combined to estimate the expanded uncertainty of the certified value with a coverage factor k of 2.0. The certified value of copy number ratio for KMD gDNA CRM is 0.99 ± 0.05, and that of copy number concentration is (1.76 ± 0.10) × 10⁵ copies/μL. Compared to the gDNA CRMs in availability, this batch of KMD gDNA CRMs is assigned accurate property values and can be directly used for qualitative and quantitative detection of GMOs as well as evaluation of the parameters of analytical methods with no need of further DNA concentration measurement. Graphical abstract.