A multiplex degenerate PCR analytical approach targeting to eight genes for screening GMOs

Reliable and rapid identification of glyphosate-resistance in the invasive weed Amaranthus palmeri in China

BACKGROUND

Glyphosate-resistant invasive plants, including Amaranthus palmeri S. Watson, have greatly challenged management of new invasions. Elucidating their glyphosate resistance levels rapidly and accurately will better inform management strategies. Quantitative real-time PCR (qPCR) has been used to identify glyphosate resistance in A. palmeri by detecting gene copy numbers of 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), an enzyme inhibited by glyphosate. However, qPCR can only indirectly determine copy numbers because it requires a calibrator sample; it also lacks standardization, thus limiting its usefulness. Droplet digital PCR (ddPCR) is a new method to detect copy number directly and precisely. We evaluated ddPCR as a tool to determine glyphosate-resistance level while using qPCR and glyphosate dose response (GDR) assays as reference technologies to compare performance and efficiency between methods.

RESULTS

We identified seven susceptible and seven resistant populations of A. palmeri using the GDR assay. Resistant levels detected by qPCR and ddPCR were generally consistent with the GDR results. Although detected values obtained by qPCR and ddPCR were highly correlated (R2  = 0.94), ddPCR results had a lower proportion of non-ideal values (36%) with better accuracy (100%) and specificity (100%) than those of qPCR results.

CONCLUSIONS

Our findings demonstrate that ddPCR offers improved accuracy and specificity in detecting EPSPS gene copy numbers and is a robust and rapid method for glyphosate-resistance identification in A. palmeri. Our research is the first to measure glyphosate resistance in A. palmeri by ddPCR assay and will shed light on future applications of ddPCR in identifying herbicide resistance in other invasive weeds. © 2022 Society of Chemical Industry.

A New Reference Plasmid “pGMT27” Provides an Efficient Transgenic Detection Method for Flue-Cured Tobacco

Owing to the economic value of its foliage, tobacco (Nicotiana tabacum) is cultivated all across the world. For the detection of genetically modified (GM) tobacco, there is a lack of universal standard material which ultimately limits the detection methods because the accuracy and comparability of the results cannot be ensured. Here, we prepared a reference plasmid “pGMT27” for the detection of GM tobacco, which was 18,296 bp in length harboring two of the tobacco endogenous and seven exogenous genes. By using qualitative PCR test for the nine genes, 10 copies were used for plasmid sensitivity. In the quantitative real-time PCR (qPCR) assays with pGMT27 as a calibrator, the reaction efficiencies for P-35S and NR were 101.427% and 98.036%, respectively, whereas the limit of detection (LOD) and limit of quantification (LOQ) were 5 copies and 10 copies per reaction. For standard deviation (SD) and relative standard deviation (RSD) of the Ct values, the repeatability values were from 0.04 to 0.42 and from 0.18% to 1.29%, respectively; and the reproducibility values were from 0.04 to 0.39 and from 0.18% to 1.14%, respectively. For the unknown sample test, the average conversion factor (Cf) was 0.39, and the accuracy bias was from −15.55% to 1.93%; for precision, the SD values ranged from 0.02 to 0.62, while RSD values were from 1.34% to 10.6%. We concluded that using the pGMT27 plasmid as a calibrator provided a highly efficient transgenic detection method for flue-cured tobacco.

Rapid and Accurate Screening of Lysine-Producing Edible Mushrooms via the Homocitrate Synthase Gene as a Universal Molecular Marker

Edible mushrooms are important nutraceutical sources of foods and drugs, which can produce various nutritional ingredients including all essential amino acids. The method of rapid screening for the strains producing specific functional components is very indispensable. Homocitrate synthase is one of the key enzymes in the α-aminoadipate pathway for lysine biosynthesis and has preferable sequence conservation in Agaricales. Based on the blast of homocitrate synthase homologous genes of strains of Agaricales, we achieved combinations of degenerate primers as molecular markers to rapidly screen the lysine-producing edible mushrooms. The experimental results revealed that the consistency between PCR amplification and HPLC analysis attained 82 and 75% in strains of Agaricales and Polyporales, respectively. The finding showed that the molecular marker has higher universality for screening edible mushroom resources of Agaricales. This PCR-based approach shows excellent potential in evaluating and discriminating edible wild-grown mushrooms with high lysine content in Agaricales.

2-Hydroxymelatonin induced nutritional orchestration in Cucumis sativus under cadmium toxicity: modulation of non-enzymatic antioxidants and gene expression

2-Hydroxymelatonin (2-OHMT) is an important metabolite produced through melatonin interaction with oxygenated compounds. 2-OHMT pretreated seeds (50 µM, 100 µM, and 150 µM) were grown in soil contaminated with 50 mg kg^-1 cadmium. Cadmium imposed stress reduced seed germination, growth, biomass production, and chlorophyll (Chl) content in Cucumis sativus seedlings. 2-OHMT application emphatically revamped germination, shoot length, root length, and plant biomass production. The 2-OHMT pretreatment modulated expression levels of plasma membrane H⁺-ATPase genes of C. sativus including CsHA2, CsHA3, CsHA4, CsHA8, and CsHA9. This biomolecule amplified the accumulation of antioxidants such as glutathione, proline, phenolics, and flavonoids. The reduced Cd-uptake in 2-OHMT treated C. sativus seedlings encouraged uptake of essential plant nutrients. Furthermore, conjugated increase of indole acetic acid contents and ethylene production rate were observed in 2-OHMT treated seedlings in a dose-dependent manner. The improved nutritional content in 2-OHMT applied seedlings was ascribed to enhanced expression of H⁺-ATPase regulating genes besides increased amount of non-enzymatic antioxidants in Cd-stressed plants. The present novel study elucidates the potential of 2-OHMT in improving nutritional content in cucumber plants by modulation of non-enzymatic antioxidants and gene expression.

Development and Testing of an Individual Kernel Detection System for Genetically Modified Soybean Events in Non-identity-preserved Soybean Samples

A genetically modified (GM) soybean kernel detection system using combination of DNA preparation from individual soybean kernels and event-specific real-time PCR was developed to simultaneously identify GM soybean events authorized for food after safety assessments in Japan. Over 100 kernels in the non-identity-preserved soybean samples imported from the United States of America (two U.S.A. lots) and Brazil (one lot) were randomly selected and examined. In total, 98 and 96% of the two independent U.S.A. lots, and 100% of the Brazilian lot contained GM soybean kernels. Herbicide-tolerant events, MON89788 (trade name Genuity® Roundup Ready 2 Yield™), GTS 40-3-2 (trade name Roundup Ready™ soybean) and A2704-12 (trade name Liberty Link® soybean), were detected similarly in both U.S.A. lots. In the Brazilian lot, in addition to GTS 40-3-2, a stacked GM event, MON87701 × MON89788, having insect-resistance and herbicide-tolerance, was detected. There were no unauthorized GM soybeans comingled, and the ratio of GM soybean events detected was consistent with statistical reports on the cultivated GM soybean events in both countries.

Halotolerant plant-growth promoting rhizobacteria modulate gene expression and osmolyte production to improve salinity tolerance and growth in Capsicum annum L

Some rhizobacteria have demonstrated a noteworthy role in regulation of plant growth and biomass production under biotic and abiotic stresses. The present study was intended to explicate the ameliorative consequences of halotolerant plant growth-promoting rhizobacteria (HPGPR) on growth of capsicum plants subjected to salt stress. Salt stress was ascertained by supplementing 1 and 2 g NaCl kg^-1 soil. The HPGPR positively invigorated growth attributes, chlorophyll, protein contents, and water use efficiency (WUE) of supplemented capsicum plants under salinity stress conditions. Bacillus fortis strain SSB21 caused highest significant increase in shoot length, root length, and fresh and dry biomass production of capsicum plants grown under saline conditions. This multi-trait bacterium also increased biosynthesis of proline and up-regulated the expression profiles of stress related genes including CAPIP2, CaKR1, CaOSM1, and CAChi2. On the other hand, B. fortis strain SSB21 inoculated plants exhibited reduced level of ethylene, lipid peroxidation, and reactive oxygen species (ROS). All these together contribute to activate physiological and biochemical processes involved in the mitigation of the salinity induced stress in capsicum plants.

Boosted Electrochemical Immunosensing of Genetically Modified Crop Markers Using Nanobody and Mesoporous Carbon

The problems of environmental security and the potential risks of human health caused by transgenic crops have attracted much attention. Recent studies reveal 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) from Agrobacterium sp. strain CP4 protein (CP4-EPSPS), which shows very high resistance to herbicide glyphosate, is a typical biomarker of genetically modified (GM) crops. For this reason, it is highly anticipated to devise a sensitive and convenient strategy to detect CP4-EPSPS protein in crops. Herein, we report a simple electrochemical immunosensor by coupling nanobody, ordered mesoporous carbon (OMC), and thionine (Th). As a capture agent, the nanobody was screened out from an immunized Bactrian camel, and exhibited superior properties with respect to conventional antibody, such as higher stability and stronger heat resistance. Moreover, OMC offered an effective platform with high surface area, electrical conductivity, and biocompatibility, which greatly facilitated the assembly of redox probe Th, and further coupling of large amount of capture nanobodies. As a result, the CP4-EPSPS protein could be determined with high sensitivity and efficiency by differential pulse voltammetry (DPV) in a wide linear range from 0.001 to 100 ng·mL^-1 with a low detection limit of 0.72 pg·mL^-1, which was more than 3 orders of magnitude lower than those of previously reported works. As an example, the proposed electrochemical immunosensor was successfully applied to spiked samples, demonstrating its great potential in CP4-EPSPS screening and detection.

One Novel Multiple-Target Plasmid Reference Molecule Targeting Eight Genetically Modified Canola Events for Genetically Modified Canola Detection

Multiple-target plasmid DNA reference materials have been generated and utilized as good substitutes of matrix-based reference materials in the analysis of genetically modified organisms (GMOs). Herein, we report the construction of one multiple-target plasmid reference molecule, pCAN, which harbors eight GM canola event-specific sequences (RF1, RF2, MS1, MS8, Topas 19/2, Oxy235, RT73, and T45) and a partial sequence of the canola endogenous reference gene PEP. The applicability of this plasmid reference material in qualitative and quantitative PCR assays of the eight GM canola events was evaluated, including the analysis of specificity, limit of detection (LOD), limit of quantification (LOQ), and performance of pCAN in the analysis of various canola samples, etc. The LODs are 15 copies for RF2, MS1, and RT73 assays using pCAN as the calibrator and 10 genome copies for the other events. The LOQ in each event-specific real-time PCR assay is 20 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and PEP assays are between 91% and 97%, and the squared regression coefficients (R²) are all higher than 0.99. The quantification bias values varied from 0.47% to 20.68% with relative standard deviation (RSD) from 1.06% to 24.61% in the quantification of simulated samples. Furthermore, 10 practical canola samples sampled from imported shipments in the port of Shanghai, China, were analyzed employing pCAN as the calibrator, and the results were comparable with those assays using commercial certified materials as the calibrator. Concluding from these results, we believe that this newly developed pCAN plasmid is one good candidate for being a plasmid DNA reference material in the detection and quantification of the eight GM canola events in routine analysis.

A temperature-tolerant multiplex elements and genes screening system for genetically modified organisms based on dual priming oligonucleotide primers and capillary electrophoresis

High throughput screening systems are the preferred solution to meet the urgent requirement of increasing number of genetically modified organisms (GMOs). In this study, we have successfully developed a multiplex GMO element screening system with dual priming oligonucleotide (DPO) primers. This system can detect the cauliflower mosaic virus 35S (CaMV 35S), terminator of nopaline synthase gene (NOS), figwort mosaic virus 35S (FMV 35S) promoter, neomycin phosphotransferaseII (NPTII), Bt Cry 1Ab, phosphinothricin acetyltransferase genes (bar) and Streptomyces viridochromogenes (pat) simultaneously, which covers more than 90% of all authorized GMO species worldwide. This system exhibits a high tolerance to annealing temperatures, high specificity and a limit of detection equal to conventional PCR. A total of 214 samples from markets, national entry-exit agencies, the Institute for Reference Materials and Measurement (IRMM) and the American Oil Chemists' Society (AOCS) were also tested for applicability. This screening system is therefore suitable for GMO screening.

Photoelectrochemical CaMV35S biosensor for discriminating transgenic from non-transgenic soybean based on SiO2@CdTe quantum dots core-shell nanoparticles as signal indicators

A methodology for detection of the Cauliflower Mosaic Virus 35S(CaMV35S) promoter was developed to distinguish transgenic from non-transgenic soybean samples by using photoelectrochemical (PEC) biosensor. In this PEC biosensing system, the as-prepared gold nanoparticles-reduced graphene oxide acted as a nanocarrier to immobilize the thiol-functional probe (probe1), and the SiO₂@CdTe quantum dots (QDs) core-shell nanoparticles tagged with the amino-functional probe (probe2) acted as signal indicators, respectively. In the presence of target DNA (tDNA) of CaMV35S, the binding of tDNA with probe1 and probe2 through the high specific DNA hybridization led to the fabrication of sandwich structure, and thus the high loading of the signal indicators SiO₂@CdTe QDs at the electrode surface, which increased the PEC signal. The increased PEC signal depended on the concentration of tDNA, and a wide linear range from 0.1pM to 0.5nM with low detection limit of 0.05pM was obtained. In addition, the PEC biosensor has been successfully used for discriminating transgenic soybean from non-transgenic samples, which was consistent with the polymerase chain reaction (PCR) results, suggesting the proposed PEC biosensor is a feasible tool for the further daily genetically modified organism detection.

Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms

As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories.

Development and application of loop-mediated isothermal amplification assays for rapid visual detection of cry2Ab and cry3A genes in genetically-modified crops

The cry2Ab and cry3A genes are two of the most important insect-resistant exogenous genes and had been widely used in genetically-modified crops. To develop more effective alternatives for the quick identification of genetically-modified organisms (GMOs) containing these genes, a rapid and visual loop-mediated isothermal amplification (LAMP) method to detect the cry2Ab and cry3A genes is described in this study. The LAMP assay can be finished within 60 min at an isothermal condition of 63 °C. The derived LAMP products can be obtained by a real-time turbidimeter via monitoring the white turbidity or directly observed by the naked eye through adding SYBR Green I dye. The specificity of the LAMP assay was determined by analyzing thirteen insect-resistant genetically-modified (GM) crop events with different Bt genes. Furthermore, the sensitivity of the LAMP assay was evaluated by diluting the template genomic DNA. Results showed that the limit of detection of the established LAMP assays was approximately five copies of haploid genomic DNA, about five-fold greater than that of conventional PCR assays. All of the results indicated that this established rapid and visual LAMP assay was quick, accurate and cost effective, with high specificity and sensitivity. In addition, this method does not need specific expensive instruments or facilities, which can provide a simpler and quicker approach to detecting the cry2Ab and cry3A genes in GM crops, especially for on-site, large-scale test purposes in the field.

GMO quantification: valuable experience and insights for the future

Cultivation and marketing of genetically modified organisms (GMOs) have been unevenly adopted worldwide. To facilitate international trade and to provide information to consumers, labelling requirements have been set up in many countries. Quantitative real-time polymerase chain reaction (qPCR) is currently the method of choice for detection, identification and quantification of GMOs. This has been critically assessed and the requirements for the method performance have been set. Nevertheless, there are challenges that should still be highlighted, such as measuring the quantity and quality of DNA, and determining the qPCR efficiency, possible sequence mismatches, characteristics of taxon-specific genes and appropriate units of measurement, as these remain potential sources of measurement uncertainty. To overcome these problems and to cope with the continuous increase in the number and variety of GMOs, new approaches are needed. Statistical strategies of quantification have already been proposed and expanded with the development of digital PCR. The first attempts have been made to use new generation sequencing also for quantitative purposes, although accurate quantification of the contents of GMOs using this technology is still a challenge for the future, and especially for mixed samples. New approaches are needed also for the quantification of stacks, and for potential quantification of organisms produced by new plant breeding techniques.

Surface plasmon resonance detection of transgenic Cry1Ac cotton ( Gossypium spp.)

The detection and identification of genetically modified (GM) plants are challenging issues that have arisen from the potential negative impacts of extensive cultivation of transgenic plants. The screening process is a long-term focus and needs specific detection strategies. Surface plasmon resonance (SPR) has been used to detect a variety of biomolecules including proteins and nucleic acids due to its ability to monitor specific intermolecular interactions. In the present study, two high-throughput, label-free, and specific methods based on SPR technology were developed to detect transgenic Cry1Ac cotton ( Gossypium spp.) by separately targeting protein and DNA. In the protein-based detection system, monoclonal anti-Cry1Ac antibodies were immobilized on the surface of a CM5 sensor chip. Conventional cotton samples were used to define the detection threshold. Transgenic cotton was easily identified within 5 min per sample. For the DNA-based model, a 25-mer biotinylated oligonucleotide probe was immobilized on an SA sensor chip. PCR products of Cry1Ac (230 bp) were used to investigate the reaction conditions. The sensitivity of the constructed sensor chip was identified at concentrations as low as 0.1 nM based on its complementary base pairing.