Comparative studies of the quantification of genetically modified organisms in foods processed from maize and soy using trial producing

Development and Performance Evaluation of a New Test Kit for Quantifying the Degree of DNA Fragmentation

BACKGROUND

PCR-based genetic testing of agricultural products and foods is widely used for detecting various analytical targets such as genetically modified organisms and food allergens. However, it is difficult to obtain accurate genetic testing results from processed foods because DNA is fragmented by heat and pressure during food processing. Thus, we previously developed an analytical method to quantitatively evaluate the degree of DNA fragmentation for the purpose of QC of genetic testing for processed foods.

OBJECTIVE

Our previous analytical method requires four PCR primer sets, resulting in high reagent costs and heavy analytical workloads. Therefore, we attempted to develop an easy-to-use test kit for quantifying the degree of DNA fragmentation and to evaluate its analytical performance.

METHODS

To simplify the analysis procedure, we used only two primer sets. In addition, no-fragmentation control templates were prepared to obtain stable measurement results. The precision of the simplified analysis was evaluated through blind tests between laboratories.

RESULTS

It was confirmed that plant species and extracted DNA concentrations had little effect on analysis with the newly developed test kit. In addition, the analytical values indicating the degree of DNA fragmentation exhibited small variability between laboratories.

CONCLUSION

We confirmed the high practicality of the developed test kit. Because DNA fragmentation in cells is a universal phenomenon, we anticipate that the test kit will be used not only for QC of genetic testing but also for food testing, medical diagnostics, and other applications in a range of fields.

HIGHLIGHTS

The newly developed test kit enables quantitative evaluation of the degree of DNA fragmentation in a simple manner.

Advances on the rapid and multiplex detection methods of food allergens

With the gradually increasing prevalence of food allergy in recent years, food allergy has become a major public health problem worldwide. The clinical symptoms caused by food allergy seriously affect people's quality of life; there are unknown allergen components in novel food and hidden allergens caused by cross contamination in food processing, which pose a serious risk to allergy sufferers. Thus, rapid and multiplex detection methods are required to achieve on-site detection or examination of allergic components, so as to identify the risk of allergy in time. This paper reviews the progress of high-efficiency detection of food allergens, including enhanced traditional detection techniques and emerging detection techniques with the ability high-throughput detection or screening potential food allergen, such as xMAP, biosensors, biochips, etc. focusing on their sensitivity, applicability of each method in food, along with their pretreatment, advantages, limitation in the application of food analysis. This paper also introduces the challenges faced by these high-efficiency detection technologies, as well as the potential of customized allergen screening methods and rapid on-site detection technology as future research directions.

Comparison of DNA extraction methods for sweet corn and processed sweet corns

DNA was extracted from sweet corn and its processed products using four DNA extraction methods: the CTAB method, the DNeasy Plant Maxi kit, GM Quicker 3, and Genomic-tip 20/G. DNA was successfully extracted from raw sweet corn and baby corn samples using all four methods. Meanwhile, from frozen, canned, and dry pack products, DNA was well extracted using the DNeasy Plant Maxi kit, GM Quicker 3, and Genomic-tip 20/G, but not enough with the CTAB method. The highest yield of DNA was obtained with Genomic-tip 20/G. The degree of degradation of extracted DNA was observed to increase in the order of raw, frozen, canned, dry pack, and baby corn samples. To evaluate the quality of extracted DNA, real-time PCR analyses were conducted using three maize endogenous genes. The DNAs extracted using GM Quicker 3 had high purity, suggesting that GM Quicker 3 would be the most suitable method for DNA extraction from processed sweet corn products.

Establishment of quantitative analysis method for genetically modified maize using a reference plasmid and novel primers

For the quantitative analysis of genetically modified (GM) maize in processed foods, primer sets and probes based on the 35S promoter (p35S), nopaline synthase terminator (tNOS), p35S-hsp70 intron, and zSSIIb gene encoding starch synthase II for intrinsic control were designed. Polymerase chain reaction (PCR) products (80~101 bp) were specifically amplified and the primer sets targeting the smaller regions (80 or 81 bp) were more sensitive than those targeting the larger regions (94 or 101 bp). Particularly, the primer set 35F1-R1 for p35S targeting 81 bp of sequence was even more sensitive than that targeting 101 bp of sequence by a 3-log scale. The target DNA fragments were also specifically amplified from all GM labeled food samples except for one item we tested when 35F1-R1 primer set was applied. A reference plasmid pGMmaize (3 kb) including the smaller PCR products for p35S, tNOS, p35S-hsp70 intron, and the zSSIIb gene was constructed for real-time PCR (RT-PCR). The linearity of standard curves was confirmed by using diluents ranging from 2×10¹~10⁵ copies of pGMmaize and the R² values ranged from 0.999~1.000. In the RT-PCR, the detection limit using the novel primer/probe sets was 5 pg of genomic DNA from MON810 line indicating that the primer sets targeting the smaller regions (80 or 81 bp) could be used for highly sensitive detection of foreign DNA fragments from GM maize in processed foods.

Interlaboratory validation of quantitative duplex real-time PCR method for screening analysis of genetically modified maize

To reduce the cost and time required to routinely perform the genetically modified organism (GMO) test, we developed a duplex quantitative real-time PCR method for a screening analysis simultaneously targeting an event-specific segment for GA21 and Cauliflower Mosaic Virus 35S promoter (P35S) segment [Oguchi et al., J. Food Hyg. Soc. Japan, 50, 117-125 (2009)]. To confirm the validity of the method, an interlaboratory collaborative study was conducted. In the collaborative study, conversion factors (Cfs), which are required to calculate the GMO amount (%), were first determined for two real-time PCR instruments, the ABI PRISM 7900HT and the ABI PRISM 7500. A blind test was then conducted. The limit of quantitation for both GA21 and P35S was estimated to be 0.5% or less. The trueness and precision were evaluated as the bias and reproducibility of the relative standard deviation (RSD(R)). The determined bias and RSD(R) were each less than 25%. We believe the developed method would be useful for the practical screening analysis of GM maize.

Testing the interaction between analytical modules: an example with Roundup Ready soybean line GTS 40-3-2

BACKGROUND

The modular approach to analysis of genetically modified organisms (GMOs) relies on the independence of the modules combined (i.e. DNA extraction and GM quantification). The validity of this assumption has to be proved on the basis of specific performance criteria.

RESULTS

An experiment was conducted using, as a reference, the validated quantitative real-time polymerase chain reaction (PCR) module for detection of glyphosate-tolerant Roundup Ready(R) GM soybean (RRS). Different DNA extraction modules (CTAB, Wizard and Dellaporta), were used to extract DNA from different food/feed matrices (feed, biscuit and certified reference material [CRM 1%]) containing the target of the real-time PCR module used for validation. Purity and structural integrity (absence of inhibition) were used as basic criteria that a DNA extraction module must satisfy in order to provide suitable template DNA for quantitative real-time (RT) PCR-based GMO analysis. When performance criteria were applied (removal of non-compliant DNA extracts), the independence of GMO quantification from the extraction method and matrix was statistically proved, except in the case of Wizard applied to biscuit. A fuzzy logic-based procedure also confirmed the relatively poor performance of the Wizard/biscuit combination.

CONCLUSIONS

For RRS, this study recognises that modularity can be generally accepted, with the limitation of avoiding combining highly processed material (i.e. biscuit) with a magnetic-beads system (i.e. Wizard).

Investigation of residual DNAs in sugar from sugar beet (Beta vulgaris L.)

Genetically modified (GM) sugar beets have been bred for use as food and animal feed. To evaluate the applicability of GMO analyses to beet sugar products, we investigated residual DNA in eight sorts of in-process beet sugar samples and commercial beet sugar products. Polymerase chain reaction (PCR) analyses with taxon-specific primers indicated that sugar beet DNA was degraded at an early stage of sugar processing, and no PCR amplification was detected from the investigated sugar products because of low DNA recovery and/or PCR inhibition.

Evaluating precision and accuracy when quantifying different endogenous control reference genes in maize using real-time PCR

The agricultural biotechnology industry routinely utilizes real-time quantitative PCR (RT-qPCR) for the detection of biotechnology-derived traits in plant material, particularly for meeting the requirements of legislative mandates that rely upon the trace detection of DNA. Quantification via real-time RT-qPCR in plant species involves the measurement of the copy number of a taxon-specific, endogenous control gene exposed to the same manipulations as the target gene prior to amplification. The International Organization for Standardization (ISO 21570:2005) specifies that the copy number of an endogenous reference gene be used for normalizing the concentration (expressed as a % w/w) of a trait-specific target gene when using RT-qPCR. For this purpose, the copy number of a constitutively expressed endogenous reference gene in the same sample is routinely monitored. Real-time qPCR was employed to evaluate the predictability and performance of commonly used endogenous control genes (starch synthase, SSIIb-2, SSIIb-3; alcohol dehydrogenase, ADH; high-mobility group, HMG; zein; and invertase, IVR) used to detect biotechnology-derived traits in maize. The data revealed relatively accurate and precise amplification efficiencies when isogenic maize was compared to certified reference standards, but highly variable results when 23 nonisogenic maize cultivars were compared to an IRMM Bt-11 reference standard. Identifying the most suitable endogenous control gene, one that amplifies consistently and predictably across different maize cultivars, and implementing this as an internationally recognized standard would contribute toward harmonized testing of biotechnology-derived traits in maize.