Event‐specific analytical methods for biotech maize MIR 604 and DAS‐59122‐7

BACKGROUND: It is very important to develop analytical methods for genetically modified organism (GMO) labelling systems and living modified organism (LMO) management. The polymerase chain reaction (PCR) is the most efficient DNA‐based analytical method for identifying and quantifying biotech crops. Qualitative PCR methods have been developed to detect the presence of biotech crops, while quantitative PCR methods have been developed to analyse the content of biotech crops. Analytical methods are now required for new biotech maize events, MIR 604 and DAS‐59122‐7. RESULTS: The event‐specific primers and probes were developed for qualitative and quantitative analysis of biotech maize MIR 604 and DAS‐59122‐7 based on the 3′ flanking regions. As a reference molecule, single standard plasmid was developed. The specificity of the qualitative primers was confirmed by the single PCR product, with limits of detection (sensitivity) of 0.01 and 0.05% respectively. In‐house validation of the quantitative methods was performed using six levels of mixing samples (0.1–10% w/w). As a result, the biases from the true value and the relative standard deviations were within the range of ± 30%. The limits of quantitation of the quantitative methods were all 0.1% for real time PCRs of MIR 604 and DAS‐59122‐7. CONCLUSION: In this study, event‐specific analytical methods were developed and applied to the qualitative and quantitative analysis of biotech maize MIR 604 and DAS‐59122‐7. Copyright © 2009 Society of Chemical Industry     

标准分子构建及其在转基因玉米59122定量检测中的应用

根据转基因作物59122的外源基因与玉米基因组之间的左侧侧翼序列设计具品系特异性的荧光探针及引物,以实时荧光PCR技术建立59122的品系特定量检测方法,以重组PCR技术成功获得了标准分子(整合了内标基因序列与左侧翼序列)梯度范围为101～105,定量范围为0.01%～100%;建立了玉米内源基因与侧翼序列的标准曲线,变异系数CV值、标准偏差SD以及相关系数R2均可接受;检测5个已知转基因含量(0.1%、0.5%、1%、2%、5%)的混合样品中的转基因含量,结果分别为0.12%、0.56%、1.04%、1.61%、4.66%,实验误差小于25%,结果可信。     

Development and in‐house validation of the event‐specific qualitative and quantitative PCR detection methods for genetically modified cotton MON15985

BACKGROUND: To implement genetically modified organism (GMO) labeling regulations, an event‐specific analysis method based on the junction sequence between exogenous integration and host genomic DNA has become the preferential approach for GMO identification and quantification. RESULTS: In this study, specific primers and TaqMan probes based on the revealed 5′‐end junction sequence of GM cotton MON15985 were designed, and qualitative and quantitative polymerase chain reaction (PCR) assays were established employing the designed primers and probes. In the qualitative PCR assay, the limit of detection (LOD) was 0.5 g kg^?1 in 100 ng total cotton genomic DNA, corresponding to about 17 copies of haploid cotton genomic DNA, and the LOD and limit of quantification (LOQ) for quantitative PCR assay were 10 and 17 copies of haploid cotton genomic DNA, respectively. Furthermore, the developed quantitative PCR assays were validated in‐house by five different researchers. Also, five practical samples with known GM contents were quantified using the developed PCR assay in in‐house validation, and the bias between the true and quantification values ranged from 2.06% to 12.59%. CONCLUSION: This study shows that the developed qualitative and quantitative PCR methods are applicable for the identification and quantification of GM cotton MON15985 and its derivates. Copyright © 2009 Society of Chemical Industry     

实时荧光定量PCR检测转基因玉米59122的方法建立及测量不确定度评估

为了准确定量检测非故意扩散的转基因玉米59122,建立转基因玉米59122及产品的实时荧光定量聚合酶链式反应（polymerase chain reaction,PCR）检测方法,并用特异性、准确度、灵敏度以及测量不确定度等指标评价该方法。结果显示,利用该方法只能检出转基因玉米59122;16 次重复测量含量为1%的转基因玉米59122样品,平均测量值（0.9%）接近真实值（1%）,相对误差为10%,测试回收率为90%,测量不确定度为0.002;能检测到最低含量为2 拷贝的59122分子片段;除去3 次偏离平均值较大的测量值外,13 次重复测量值的变异系数为0.05。因此,实验建立的转基因玉米59122实时荧光定量PCR方法具有较高的特异性、准确度、灵敏度、精密度,较低的测量不确定度。     

A simple DNA extraction method suitable for PCR detection of genetically modified maize

BACKGROUND: The polymerase chain reaction (PCR) is a powerful tool that is being increasingly used for detection of transgenic DNA. PCR requires only a minute quantity of template, but sensitive and accurate testing requires DNA of sufficient purity and free from inhibitors such as plant polysaccharides. Several standard protocols are available for this purpose, but they usually involve several steps, imply destruction of the maize kernel, or are time‐consuming. Our aim was to develop a fast and simple extraction method to isolate a raw DNA‐containing solution from maize tissues suitable for use as a template in a PCR‐based detection assay with specific oligonucleotides directed to the identification of event MON810. RESULTS: The NaOH‐based DNA extraction method we report here is time‐saving (5 min) and can be used to isolate DNA‐containing solutions from a small maize leaf portion (down to 1 mg) or from a single overnight‐germinated kernel. PCR performed with selected primers yielded reproducible detection of transgenic DNA. CONCLUSION: The main advantages of the procedure are the quick extraction step, the possibility of non‐destructive testing of maize kernels, and the robustness of the PCR‐based detection, a consequence of the selection of MON810‐matching oligonucleotides yielding intense and highly specific amplicons. Copyright © 2007 Society of Chemical Industry     

Detection and identification of genetically modified EE‐1 brinjal (Solanum melongena) by single,multiplex and SYBR® real‐time PCR

BACKGROUND: Brinjal is an important vegetable crop. Major crop loss of brinjal is due to insect attack. Insect‐resistant EE‐1 brinjal has been developed and is awaiting approval for commercial release. Consumer health concerns and implementation of international labelling legislation demand reliable analytical detection methods for genetically modified (GM) varieties. RESULTS: End‐point and real‐time polymerase chain reaction (PCR) methods were used to detect EE‐1 brinjal. In end‐point PCR, primer pairs specific to 35S CaMV promoter, NOS terminator and nptII gene common to other GM crops were used. Based on the revealed 3′ transgene integration sequence, primers specific for the event EE‐1 brinjal were designed. These primers were used for end‐point single, multiplex and SYBR‐based real‐time PCR. End‐point single PCR showed that the designed primers were highly specific to event EE‐1 with a sensitivity of 20 pg of genomic DNA, corresponding to 20 copies of haploid EE‐1 brinjal genomic DNA. The limits of detection and quantification for SYBR‐based real‐time PCR assay were 10 and 100 copies respectively. CONCLUSION: The prior development of detection methods for this important vegetable crop will facilitate compliance with any forthcoming labelling regulations. Copyright © 2012 Society of Chemical Industry     

Screening and construct‐specific detection methods of transgenic Huafan No 1 tomato by conventional and real‐time PCR

Genetically modified (GM) tomatoes have been approved for commercialization in many countries since the first GM tomato FLAVR SAVR was permitted for planting in 1994. In China, GM tomato Huafan No 1 with a character of long shelf‐life was the first GM plant which was approved for commercialization in 1996. To meet the requirement of the GM tomatoes labeling policy that has been actualized in China since 2001, screening and construct‐specific PCR detection methods for detecting the universal elements transformed into tomato, such as cauliflower mosaic virus 35S (CaMV35s) promoter and the nopaline synthase (NOS) terminator of Agrobacterium tumefaciens, and the specifically inserted heterologous DNA sequence between CaMV35s promoter and anti‐sense ethylene‐forming enzyme (EFE) gene were set up. To make the detection methods normative, a novel single copy tomato gene LAT52 was also used as an endogenous reference gene in the PCR detection systems. The limit of detection of screening and construct specific detection methods for Huafan No 1 was 68 haploid genome copies in conventional PCR detection, and three copies in TaqMan real‐time PCR detection. The limit of quantitation of screening quantitative PCR assays for Huafan No 1 was three copies and was 25 copies for construct‐specific quantitative PCR. Two samples with known Huafan No 1 tomato content were detected using the established conventional and real‐time PCR systems, and these results also indicated that the established Huafan No 1 screening and construct‐specific PCR detection systems were reliable, sensitive and accurate. Copyright © 2005 Society of Chemical Industry     

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     

Simple,sensitive, accurate multiplex quantitative competitive PCR with capillary electrophoresis detection for the determination of genetically modified maize

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 simple and accurate capillary electrophoresis multiplex quantitative competitive PCR (ce-mqcPCR) method for event-specific quantification of the five novel GM maize events DAS59122, LY038, MON88017, MIR604 and Event 3272. The method combines the simplicity of constructing multiple competitors in silico with the high resolution and sensitivity of fluorescence capillary electrophoresis and the use of an internal template reference amplicon. The competitors are synthesised commercially and added in equal amounts as a restriction enzyme-digested plasmid insert to the multiplex PCR. Quantification is performed by analysing the relative amounts of GMO and GMO competitor fragment pairs after capillary electrophoresis and correcting for differences in maize DNA by comparing with the internal reference gene amplicon. Since the competitors employ the same primers as their corresponding targets, all existing qualitative multiplex PCRs can in principle easily be converted to quantitative assays without changing primer sets or amplification conditions. The ce-mqcPCR method correctly determined 120 GMO templates in known mixed samples. No false-positive or false-negative signals were obtained.     

转基因玉米59122品系的特异性检测

使用反向聚合酶链式反应(PCR)技术克隆了转基因玉米59122的外源基因与玉米基因组之间的两段侧翼序列,并据其左侧侧翼序列设计了具品系特异性的引物,运用半巢式PCR技术建立了59122的品系特异性二重PCR检测方法,扩增片段100bp,横跨pat终止子与转基因玉米侧翼基因之间。以转基因玉米59122、MON863、MON810、GA21、NK603,转基因大豆Roundup Ready和转基因油菜GT73等为材料,证明本方法与其他转基因作物具有高特异性。本方法在检测59122时,确定出连接体系中线性DNA的最佳质量浓度为1ng/μL左右,检出限达到0.1%,灵敏度为38个单倍体基因组拷贝数。因此可准确、快速、高效地检测转基因玉米及其产品,或作为常规PCR定性检测后的验证方法。     

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.     

Development of a real‐time PCR for quantification of the family Syntrophomonadaceae in pit mud from Chinese Luzhou‐flavour liquor distilleries

Syntrophomonadaceae was previously identified to be the predominant bacteria in Chinese Luzhou‐flavour liquor pit mud. In this work, a real‐time quantitative PCR assay was first employed to monitor the variation of the family Syntrophomonadaceae in the pit mud. The specific primers SynF and SynR were designed based on the 16S rDNA gene. A single specific fragment of about 161 bp was amplified in each positive sample, while no signal or a high cycle threshold (Cq) value (>36) was detected in the negative controls. The correlation coefficient (R²) and amplification efficiency (E) of the standard curve were 0.9997 and 106%, respectively. In addition, the sensitivity was 6.0 × 10² copies/μL and the mean recovery rate was 103%. All of these results indicate that the method is rapid, specific, sensitive and accurate. The quantitative results provide further understanding of the time differences and spatial differences in the family Syntrophomonadaceae in pit mud. Copyright © 2015 The Institute of Brewing & Distilling     

Application of host‐specific source‐tracking tools for rapid identification of fecal contamination in fresh produce by humans and livestock

BACKGROUND: Fecal contamination in fresh produce is a public health concern because it may contain human pathogens. We introduced host‐specific quantitative real‐time polymerase chain reaction (qPCR) assays for the rapid detection and identification of fecal contamination sources from humans and farm animals (cow, pig, chicken) in fresh produce. Each composite fecal sample was spiked on lettuce at two contamination levels (0.2 mg or 2 mg feces g^?1), followed by qPCR assays for detecting each host‐specific genetic marker: BoBac (cow); PF163 (pig); CP3‐49 (chicken); and HF183 and gyrB (human). Two commercial DNA extraction kits were compared to evaluate DNA recovery yields and removal of PCR inhibition. Sketa2 assay was conducted to assess the presence of PCR inhibition in the contaminated lettuce. RESULTS: All the qPCR assays yielded reliable detection from contaminated lettuce (2 mg feces g^?1), where their target gene numbers were 1.5–5.0 × 10³ (HF183), 0.8–2.2 × 10³ (gyrB), 0.6–1.6 × 10³ (BoBac), 1.6–3.0 × 10³ (CP3‐49) and 1.1–2.2 × 10³ (PF163) copies g^?1 of lettuce. Among the two extraction kits, QIAamp DNA Stool Kit resulted in 2–3 times higher sensitivity and 20% less PCR inhibition than the PowerFood^? kit. CONCLUSION: This study provides information on the optimized host‐specific qPCR assay in identifying sources of fecal contamination in fresh produce and is useful for tracking the contamination source and improving agricultural practice. © 2012 Society of Chemical Industry     

副溶血性弧菌实时荧光定量PCR标准模板的构建和检测方法的建立

目的:构建肉制品副溶血性弧菌实时荧光定量PCR的标准阳性模板和检测方法.方法:以副溶血性弧菌toxR基因上特异性片段为目标,设计并合成引物及Taqman探针,将目标片段连接到PGM-T载体上构建重组质粒,建立实时荧光定量检测体系,并考察方法的灵敏性、特异性、重复性和准确性.结果:构建出副溶血性弧菌荧光定量PCR检测方法的标准模板并建立了相应的检测方法,获得的标准曲线方程为:Y=-3.151 lgX+42.86,灵敏度40copies/反应体系,对副溶血性弧菌具有特异性,同时,该方法具有良好的重复性,变异系数小于5％.结论:使用基于Taqman探针技术的荧光定量PCR检测方法能够对食品中致病性副溶血性弧菌进行快速、简便、准确、高效的定量检测.     

微滴式数字PCR定量检测转基因玉米品系VCO-01981-5

建立基于QX100微滴式数字聚合酶链式反应(polymerase chain reaction,PCR)平台的我国未批准转基因玉米品系VCO-01981-5的二重微滴式数字PCR定量检测方法。该方法选择基因组中单拷贝的玉米内源基因hmg和VCO-01981-5品系边界序列为定量靶序列,分别设计不同的PCR扩增引物和TaqMan探针,并对两种探针用不同的荧光进行标记,然后将上述探针和引物置于同一个PCR反应体系中以同时定量两个靶标序列。特异性实验结果显示该法只有VCO-01981-5品系的两个靶序列才都有扩增信号。灵敏度、线性和准确性实验结果显示在定量结果相对标准偏差不大于25%时,最低可稳定定量5个拷贝的VCO-01981-5品系特异性序列分子和4个拷贝的内源基因hmg分子;而在高达50 ng模板DNA以下范围内,PCR反应模板量与测定样品拷贝数之间呈高度正相关,相关系数达0.99以上;平均误差小于10%。结果表明本研究建立的该玉米品系定量方法特异性强,稳定性好,精确性、准确性以及灵敏度高,定量范围广,可用于进、出口农产品和食品中该转基因玉米品系成分的定量检测。此外,该法还可为其他转基因玉米品系及其他转基因作物品系建立类似定量检测方法提供参考。     

基于内参的大肠埃希氏菌O157∶H7实时荧光定量PCR快速检测方法的建立

针对大肠埃希氏菌O157∶H7 rfbE和Flic靶基因保守序列,设计特异性引物和探针,优化反应体系,并加入内参（internal amplification control,IAC）,建立能够实时监控反应过程的荧光定量聚合酶链式反应（polymeasechain reaction,PCR）检测方法。结果表明,该方法对E. coli O157∶H7基因组DNA的最低检测限为1 pg/μL;对含有靶基因质粒的最低检测限为103 copies/μL;对细菌的最低检测限为5×103 CFM/mL;Ct值与模板拷贝数均呈良好的线性关系（R2=0.999）。人工污染实验结果表明,在初始菌量为7 CFM/25 g时,采用水洗加试剂盒法提取DNA,E. coli O157∶H7在增菌6 h后即可检出;而采用水煮法提取DNA,则在增菌10 h后方可检出。建立的E. coli O157∶H7实时荧光定量PCR方法,既能有效检测食品中O157∶H7,又能实时监测PCR反应过程,有效防止“假阴性”的发生。     

A peach (Prunus persica)-specific gene, Lhcb2, used as an endogenous reference gene for qualitative and real-time quantitative PCR to detect fruit products

Among the methods used to detect food adulteration, the amplification of endogenous reference genes is particularly important. Endogenous reference genes for many different species, such as cotton, papaya, maize and others, have been reported, yet an endogenous reference gene for the peach is still lacking. In this paper, the chlorophyll a/b-binding protein (Lhcb2) gene was identified as a species-specific gene for the peach. Lhcb2 was assayed in 4 species of peaches and 8 non-peach species by both qualitative and quantitative PCR. No amplification was observed in other species. The detection limit of quantitative PCR was as low as 5 pg of DNA, equal to 9 copies, and Southern blot analysis confirmed that the Lhcb2 gene was present in a single copy in the peach genome. All of these experiments indicated that the Lhcb2 gene is a useful endogenous reference gene for the detection of peach material via both qualitative and quantitative PCR assays, even in the processed food samples such as juices containing peach.     

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.     

Characterisation of the 5′ integration site and development of an event-specific real-time PCR assay for NK603 maize from a low starting copy number

Genetically modified (GM) maize event NK603 is in the pipeline for authorisation in the EU and is likely to become a dominating GM maize on the world market. The 5 integration junction was characterised from a small quantity of commercially available genomic DNA. Specific primers and a probe were designed targeting the 5 integration junction in the plant, amplifying a 102 bp DNA fragment. A method for specific detection and quantification of NK603 using event-specific real-time PCR based on the identified and cloned sequence is described. The assay was specificity tested against five different GM maizes, one non-GM maize and one GM soya bean. Plasmids were constructed for use as external standards in calibration curves. Due to the lack of certified or other suitable commercial reference material for quantification of NK603, the quantifications were performed on non-target DNA spiked with plasmid DNA containing the cloned NK603 5 integration junction. The plasmid was detectable down to one copy per PCR. The limits of detection (LOD) and quantitation (LOQ) are estimated to be comparable to those of state-of-the-art methods applied for other GM events.