Detection of eight GMO maize events by qualitative, multiplex PCR and fluorescence capillary gel electrophoresis

Specific legislation in the EU and several other countries requires that foods containing genetically modified organisms (GMOs) should be approved and labelled. This has necessitated the development of methods for detection of such materials. For screening purposes these methods should preferably enable detection of several different GMOs. Here we present a simple, robust, qualitative, nineplex PCR method for event-specific detection of maize T25, GA21, TC1507, MON863, MON810, NK603, construct specific detection of BT176, BT11 and detection of the endogenous hmga maize reference gene. PCR is carried out with primers labelled with fluorescent groups and the amplicons are detected using fluorescence capillary electrophoresis. Using mixtures of DNA from different certified reference materials, the detection limit was determined to approximately 0.1% for each GMO. Good agreement was observed in 85 of 88 determinations when eleven food and feed samples were analysed using the multiplex PCR assay and compared to results from quantitative real-time 5′-nuclease PCR. Discrepancies were only observed for one GMO at or close to the detection limit. The presented method is therefore suitable for screening purposes for food and feed containing the most common maize GMOs.     

Determination of eight genetically modified maize events by quantitative, multiplex PCR and fluorescence capillary gel electrophoresis

Specific legislation in the EU requires that foods containing more than 0.9% of genetically modified organisms (GMOs) should be labelled. This has necessitated the development of methods for detection and quantification of such materials. Here we present a robust, quantitative, 9-plex PCR method for event-specific detection of maize TC1507, MON863, MON810, T25, NK603, GA21, construct specific detection of BT11, BT176 and detection of the endogenous hmga maize reference gene. The method is suitable for quantification in the 0–2% range with a detection limit of approximately 0.1%. PCR is carried out in two stages. In the first stage, bipartite primers containing a universal 5′-sequence and a GMO specific 3′-sequence are used. In the second PCR stage only a universal primer is used. Trypsin digestion between the first and second PCR stages enhances signal strength and reproducibility. Probes hybridising to the PCR amplicons are then labelled by primer extension and detected by fluorescence capillary electrophoresis. Good agreement was observed in 76 of 80 determinations when 10 food and feed samples were analysed using the multiplex PCR assay and compared to results from quantitative real-time 5′-nuclease PCR. The presented method is therefore suitable for quantification purposes for food and feed containing the most common maize GMOs.     

Quantitative,multiplex ligation-dependent probe amplification for the determination of eight genetically modified maize events

Specific legislation in the EU requires that foods containing more than 0.9% of genetically modified organisms (GMOs) should be labelled. To this end, we have developed a robust, quantitative, sensitive, nine-plex ligation-dependent probe amplification method, GMO-MLPA, for event-specific detection of maize TC1507, MON810, NK603, MON863, BT176, T25, GA21, construct-specific detection of BT11, and detection of the endogenous hmga maize reference gene. Ligated probes are amplified by PCR. Amplicons are detected using capillary electrophoresis. Specific GMO signals are normalised relative to the signal from the endogenous hmga gene and quantified by comparing with known standard curves. The method is suitable for quantification in the 0–2% range. Agreement was obtained in 149 of 160 determinations when 11 known mixtures of GMO and 9 food and feed samples were analysed using the GMO-MLPA method and compared to results from quantitative real-time 5′-nuclease PCR. The presented method is, therefore, suitable for quantification purposes for food and feed containing the most common maize GMOs.     

A simple procedure for quantification of genetically modified organisms using hybrid amplicon standards

Determination of the genetically modified organism (GMO) content in foods and feeds by means of real-time polymerase chain reaction (PCR) requires appropriate calibration standards. For this purpose, commercial certified reference materials calibrants (CRMCs) are commonly used. However, quantitative results depend on the actual GMO content of the standards, which may vary from lot to lot. Furthermore, commercial CRMCs are available in the range of 0%-5% only, thus limiting the quantification working range. More recently, recombinant plasmid standards have been used as an alternative to commercial CRMCs. Their production, however, necessitates cloning and microbiology facilities. Here we describe an easy and cost-effective procedure for construction of hybrid amplicon standards containing both transgene and reference gene targets in a tandem orientation on the same molecule. These standards can be rapidly produced in abundant amounts without any equipment for cloning and culturing of recombinant strains. This approach has proved accurate and precise and exhibits major advantages over genomic DNA or plasmids. In this paper we present a validation study for quantitative analysis of Roundup Ready soybean and the 35S-CaMV promoter in genetically modified maize and soybean.     

Screening of genetically modified organisms and specific detection of Bt176 maize in flours and starches by PCR-enzyme linked immunosorbent assay

Polymerase chain reaction (PCR)-enzyme linked immunosorbent assays (ELISAs) targeting either the 35S promoter or the Bt176 specific junction sequence were developed to screen for the presence of genetically modified organisms (GMOs) and specifically detect Bt176 maize in flours and starches. Two additional PCR-ELISA assays were developed to validate the results: one, based on the detection of the maize alcohol dehydrogenase 1 promoter specifically detected the presence of maize, and the other, based on the detection of a conserved sequence of plants ( 26S ribosomal RNA gene), validated the extracted DNA amplification. The PCR-ELISA assays developed here were highly specific and found to be as sensitive as the reference Southern hybridisation assay. The PCR-ELISA tests were at least 6 times more sensitive than gel electrophoresis and allowed 0.1% GMOs to be detected in Bt176, Bt11, Mon810 maize and Roundup Ready soybean. The PCR-ELISA tests are a method of choice for GMO screening and identifying Bt176 maize in flours and native starches. They may offer a cheaper alternative to the expensive real-time PCR assays and may be useful in laboratory GMO monitoring.     

Detection of GM Canola MS11, DP-073496-4, and MON88302 events using multiplex PCR coupled with capillary electrophoresis

As of 2020, 11 GM canola events have been authorized as food for humans in Korea. However, there are no simultaneous multiplex detection methods for 3 GM canola events (DP-073496-4, MON88302, and MS11). Thus, we established the multiplex polymerase chain reaction (PCR) method coupled with capillary electrophoresis to detect 3 GM canola events. To verify the specificity of event-specific primers, various GM crops of 3 GM soybean events, 6 GM maize events, 2 GM cotton events and 11 GM canola events were prepared. The limit of detection of the developed multiplex PCR was approximately 0.0125% for 3 GM canola events. Certified GM canola and stacked events were analyzed to validate the developed multiplex PCR. This study focuses on establishing multiplex PCR coupled with capillary electrophoresis for newly approved GM canola events and contributes to efficient monitoring GM canola samples in Korea.     

Collaborative Study of a T-nos Real-Time PCR Method for Screening of Genetically Modified Organisms in Food Products

In the EU the presence of genetically modified organisms (GMO) in food is controlled by the Member States official laboratories within their national inspection and monitoring programs. The most frequently used approach to detect the presence of GMO material in different food matrices is the PCR-based screening for the CaMV 35S promoter and the nos terminator (T-nos) DNA sequence from Agrobacterium tumefaciens. A real-time PCR method for detection of T-nos and its validation in a collaborative trial study is described in this paper. The PCR system amplifies a 84 bp fragment and showed to be sensitive to detect at least 5 copies of the T-nos DNA sequence. The assay was adapted for use in real-time PCR instruments using plastic reaction vials and glass capillaries, respectively. A total of 24 laboratories participated in the study and each laboratory received 18 DNA blind samples prepared from GMO certified reference materials (0.1 % and 0.5 % NK601 maize) and from a non-GM maize flour. All samples containing NK603 maize DNA were correctly classified as T-nos positive by the participating laboratories. For the blank samples (0 % GMO) only three false-positive results were reported. A detailed evaluation of the results of the collaborative trial study is described.     

Development of two screening duplex PCR assays for genetically modified organism quantification using multiplex real-time PCR master mixes

Since 2001, the traceability and labelling of genetically modified organism (GMO) food and feed derived products are obligatory in the European Union. Genetically modified organisms (GMO) are commonly detected via PCR tests. These tests typically involve several steps: (1) screening (2) construct specific (3) event specific and (4) reference gene. Screening tests are based on sequences frequently used for GM development, allowing for the detection of a large number of GMOs. To improve GMO detection efficiency, using specific multiplex master mixes, we developed two real-time PCR screening duplex PCR assays for the detection of P35S/Tnos and Pnos/T35S sequences. By combining these tests, we were able to reduce the time and cost of analysis. For the Pnos/T35S duplex, good sensitivity was obtained using one of the mixes compared to the others. Both duplexes had 100% specificity when tested on DNA from GM maize, rapeseed and soybean. When the duplexes were tested on DNA containing various amounts of GM maize and soybean, the corresponding targets were detected. The detection limit of our methods was found to be between 2 and 8 haploid genome copies for both P35S/Tnos and Pnos/T35S tests. In summary, with high efficiency and good linearity, the proposed two screening duplexes allow for more efficient GMO detection.     

Collaborative Study of a T-nos Real-Time PCR Method for Screening of Genetically Modified Organisms in Food Products

In the EU the presence of genetically modified organisms (GMO) in food is controlled by the Member States official laboratories within their national inspection and monitoring programs. The most frequently used approach to detect the presence of GMO material in different food matrices is the PCR-based screening for the CaMV 35S promoter and the nos terminator (T-nos) DNA sequence from Agrobacterium tumefaciens. A real-time PCR method for detection of T-nos and its validation in a collaborative trial study is described in this paper. The PCR system amplifies a 84 bp fragment and showed to be sensitive to detect at least 5 copies of the T-nos DNA sequence. The assay was adapted for use in real-time PCR instruments using plastic reaction vials and glass capillaries, respectively. A total of 24 laboratories participated in the study and each laboratory received 18 DNA blind samples prepared from GMO certified reference materials (0.1 % and 0.5 % NK601 maize) and from a non-GM maize flour. All samples containing NK603 maize DNA were correctly classified as T-nos positive by the participating laboratories. For the blank samples (0 % GMO) only three false-positive results were reported. A detailed evaluation of the results of the collaborative trial study is described. Received: March 19, 2007     

一种转基因马铃薯PCR鉴别方法的建立

为建立一种鉴别转基因马铃薯的PCR方法,设计转基因马铃薯常用调控元件的特异性引物,以4种转基因马铃薯标准品系EH92-527-1、AV43-6-G7、AM04-1020、PH05-026-0048为模板进行单基因PCR和多重PCR扩增工艺方法研究。经琼脂糖凝胶电泳结果分析后,从中筛选出一组引物特异性较强,且无交叉污染或非特异性扩增现象的引物组合对。对9种已知转基因马铃薯样品进行多重PCR验证,均得到条带清晰且区分明显的目的条带。成功建立了能够快速、准确鉴别转基因马铃薯中多种调控元件的多重PCR与单基因PCR相结合的检测方法。     

Validation of the performance of a GMO multiplex screening assay based on microarray detection

A new screening method for the detection and identification of GMO, based on the use of multiplex PCR followed by microarray, has been developed and is presented. The technology is based on the identification of quite ubiquitous GMO genetic target elements first amplified by PCR, followed by direct hybridisation of the amplicons on a predefined microarray (DualChip^® GMO, Eppendorf, Germany). The validation was performed within the framework of a European project (Co-Extra, contract no 007158) and in collaboration with 12 laboratories specialised in GMO detection. The present study reports the strategy and the results of an ISO complying validation of the method carried out through an inter-laboratory study. Sets of blind samples were provided consisting of DNA reference materials covering all the elements detectable by specific probes present on the array. The GMO concentrations varied from 1% down to 0.045%. In addition, a mixture of two GMO events (0.1% RRS diluted in 100% TOPAS19/2) was incorporated in the study to test the robustness of the assay in extreme conditions. Data were processed according to ISO 5725 standard. The method was evaluated with predefined performance criteria with respect to the EC CRL method acceptance criteria. The overall method performance met the acceptance criteria; in particular, the results showed that the method is suitable for the detection of the different target elements at 0.1% concentration of GMO with a 95% accuracy rate. This collaborative trial showed that the method can be considered as fit for the purpose of screening with respect to its intra- and inter-laboratory accuracy. The results demonstrated the validity of combining multiplex PCR with array detection as provided by the DualChip^® GMO (Eppendorf, Germany) for the screening of GMO. The results showed that the technology is robust, practical and suitable as a screening tool.     

Development of a modular system for detection of genetically modified organisms in food based on ligation-dependent probe amplification

The application of a method based on ligation-dependent probe amplification to the simultaneous detection of different genetically modified organisms in food is described. The ligation reaction of target-specific probes with characteristic lengths and universal primer binding sites is followed by PCR amplification using fluorescein-labeled primers. The separation and the detection of DNA fragments are achieved by capillary electrophoresis via laser-induced fluorescence. The approach allows the simultaneous detection of several targets corresponding to different levels of specificity in a one-tube assay. Synthetic oligonucleotides were designed to detect (1) reference genes in the genome from maize, soya and rapeseed, (2) the CaMV 35S-promotor as screening element, (3) the construct-specific 35S-pat junction, and (4) the event-specific regions of the transgenic maize line MON 810 and of Roundup Ready soya. Specificity and sensitivity (GMO content 0.1%) of the approach were shown for all targets. This novel analytical strategy represents a flexible, modular system for the surveillance of GMO-derived products that can be readily complemented by further target sequences of interest.     

Quantitative detection of the 35S promoter and the NOS terminator using quantitative competitive PCR

 DNA-based analytical methods are often used to verify the presence of genetically modified organisms (GMOs) in food. In Switzerland, a preliminary study, organized by a subcommission of the Swiss Food Manual, of different polymerase chain reaction (PCR) systems for the detection of GMOs showed that the application of qualitative PCR systems can lead to interlaboratory differences of at least a factor of 10. These differences can be diminished using internal standards (competitors). The quantitative competitive (QC) PCR for the detection of the 35S promoter or the NOS terminator in food samples is presented. The GMO content of food samples can be determined using QC-PCR. Received: 2 July 1998 / Revised version: 15 October 1998     

Tracing transgenic maize as affected by breadmaking process and raw material for the production of a traditional maize bread, broa

Broa is a maize bread highly consumed and appreciated, especially in the north and central zones of Portugal. In the manufacturing of broa, maize flour and maize semolina might be used, besides other cereals such as wheat and rye. Considering the needs for genetically modified organism (GMO) traceability in highly processed foods, the aim of this work was to assess DNA degradation, DNA amplification and GMO quantification along breadmaking process of broa. DNA degradation was noticed by its decrease of integrity after dough baking and in all parts of bread sampling. The PCR amplification results of extracted DNA from the three distinct maize breads (broa 1, 2 and 3) showed that sequences for maize invertase gene and for events MON810 and TC1507 were easily detected with strong products. Real-time PCR revealed that quantification of GMO was feasible in the three different breads and that sampling location of baked bread might have a limited influence since the average quantitative results of both events after baking were very close to the actual values in the case of broa 1 (prepared with maize semolina). In the other two maize breads subjected to the same baking treatment, the contents of MON810 maize were considerably underestimated, leading to the conclusion that heat-processing was not the responsible parameter for that distortion, but the size of particle and mechanical processing of raw maize play also a major role in GMO quantification.     

A cotton‐specific gene,stearoyl‐ACP desaturase,used as a reference for qualitative and real‐time quantitative polymerase chain reaction detection of genetically modified organisms

Biotechnology has permitted the modification of agricultural materials in a very precise way to improve productivity and yields. Polymerase chain reaction (PCR)‐based methods have been the first choice of most analytical laboratories for routine use in the detection of genetically modified organisms (GMO) and their derived products. These methods rely on the amplification of transgenic sequences and quantification of the transgenic DNA by comparison with an amplified reference gene. This paper describes the specific primers and probe for the cotton stearoyl‐ACP desaturase (sad1) gene, and PCR cycling conditions suitable for the use of this sequence, which acts as an endogenous reference gene in both qualitative and quantitative PCR assays. The two methods were tested with 18 cotton varieties and identical amplification products were obtained with all of them. No amplification products were detected when DNA samples from other species, including soybean, rapeseed, tobacco, maize, tomato, potato, cucumber, pea, red pepper, sunflower, sesame, rice, peach, banana, apple, pumpkin, barley and carrot, were used as templates, which demonstrates that this system is specific for cotton. In real‐time quantitative PCR analysis, the detection limit was as low as 6 pg of DNA, which indicates that this method is suitable for application to processed food samples that contain very low copies of target DNA. Southern blot analysis confirmed that the sad1 gene was a single copy in the tested cotton varieties. Copyright © 2006 Society of Chemical Industry     

Parallelised real-time PCR for identification of maize GMO events

Identification of specific material derived from genetically modified organisms (GMO) present in food, feed or seed samples screened positive for the presence of genetic modification(s) is mandatory for the official food and feed control in the European Union. Since the introduction of regulation (EC) No 1829/2003 in 2004, the number of maize GMO events either approved in the EU or with a pending application grew constantly. By the sheer multitude of events and crossed events (stacks), maize poses a special challenge on official food and feed control. We developed a modular qualitative detection system for the parallel identification of maize GMO events to cope with the increasing number of GMO potentially present in routine samples. This system is based on validated real-time PCR assays in a microtitre plate format grouped modularly by crop species. The maize module identifies in parallel, i.e. simultaneously, 15 maize events and RoundupReady soy in a single analytical run of approximately 2 h. Maize modules can be conveniently prepared in advance and stored at −20 °C until use. Ready-to-use reference DNA mixtures serve as positive controls. The modular approach is flexible as it allows easy change or addition of individual detection reactions, if necessary, e.g. when new validated methods become available. 23 food, 14 feed and 8 seed samples were successfully analysed with the maize module. The parallel detection of nine different GMO maize and soy events in single routine samples demonstrated the usefulness of the parallelised modular approach for routine GMO analysis.     

A multiplex PCR assay for the identification of five commercially important Portunid crabs: Portunus pelagicus,P. gladiator,P. sanguinolentus,Charybdis natator,and C. feriatus

Portunid crabs of the genus Portunus: P. pelagicus, P. gladiator and P. sanguinolentus and the genus Charybdis: C. natator and C. feriatus are economically important species for many tropical countries. An ongoing problem in the crab industry is involved with food labelling or food fraud in which many food manufacturers may have substituted the cheaper crabmeat for the more expensive ones due to the difficulty of species identification after many steps of food processing. To solve this problem, a convenient and accurate multiplex PCR assay using a species-specific primer set KUGEN_PORTspec was developed based on the nucleotide variation of cytochrome b and 28S ribosomal RNA. The primer set specifically amplified fragments of 286, 348, 418, 124 and 481 bp in P. pelagicus, P. gladiator, P. sanguinolentus, C. natator and C. feriatus, respectively, as well as a 220 bp positive control fragment. Specificity and sensitivity tests showed consistency in product sizes and absence of cross-species amplification with 0.1 ng DNA template limit of detection. Validation of the multiplex PCR assay on crabmeat prepared by steaming, mixing, freezing and canning was done and visualized by either agarose gel electrophoresis or automated capillary electrophoresis. The results indicated that the multiplex PCR assay using KUGEN_PORTspec is an effective tool for portunid species identification from both high- and low-quality DNA obtained from processed food. This newly developed primer set is an effective tool for crabmeat species identification to be used in future food industry and consumer protection programs.     

Quantitative competitive PCR for the detection of genetically modified soybean and maize

 The surveillance of food labelling concerning genetically modified organisms (GMOs) requires DNA-based analytical techniques. Present assay systems allow the detection of GMO in food; however, they do not permit their quantitation. In this study, we report the development of quantitative competitive polymerase chain reaction (QC-PCR) systems for the detection and quantitation of the Roundup Ready soybean (RRS) and the Maximizer maize (MM) in food samples. Three DNA fragments that differ from the GMO-specific sequences by an insertion were constructed and used as internal standards in the PCR. These standards were calibrated by co-amplifying with mixtures containing RRS DNA and MM DNA, respectively. The calibrated QC-PCR systems were applied to nine commercial food samples containing RRS DNA and to three certified RRS flour mixtures in order to elucidate whether these food samples contain more or less than 1% RRS DNA. Finally, the GMO contents of four samples that were found to contain more than 1% RRS were determined by QC-PCR using various amounts of standard DNA. Received: 13 January 1998 / Revised version: 4 March 1998