Use of real-time PCR for determining copy number and zygosity in transgenic plants

This review examines how real-time PCR can be used to determine copy number and zygosity in transgenic plants. Distinguishing between plants that harbor one and two copies of a transgene or are hemizygous and homozygous requires the ability to routinely distinguish twofold differences, a detection difference which approaches the resolution of PCR-based quantification methods. After explaining the basic principles, especially the threshold cycle (Ct value) as the basic measuring unit in real-time PCR, we introduce three quantitation methods currently in use. While the absolute and relative standard curve approaches are qualitative methods that distinguish high-copy from low-copy transformants, the comparative ( ) method with double-dye oligonucleotides (TaqMan probes) is able to detect twofold differences. In order to obtain reliable results, Ct values for an amplicon should be below 25 and the standard deviation below 0.3. Although real-time PCR can deliver exact copy number determinations, the procedure is not fail-safe. Therefore, real-time PCR should to be viewed as complementary to—rather than as a replacement of—other methods such as Southern analysis, but it is particularly useful as a preliminary screening tool for estimating copy numbers of a large number of transformants.     

Protein slot blotting: An easy,rapid and reliable technique to identify the expression of a protein in transgenic plants

A technique based on immunological recognition of a foreign protein in transgenic plants has been developed. It allows a quick and reliable screening of many plant samples, improves the accuracy of the results compared to ELISA and is easier to carry out and more sensitive than a western immunoblot. This technique has also been tested to recognize foreign proteins in rice and tobacco leaf extracts.     

Advantages and disadvantages of using PCR techniques to characterize transgenic plants

The polymerase chain reaction (PCR) revolutionized molecular biology to a similar extent as the discovery of plasmids and restriction endonucleases. However, there are some limitations to the use of PCR. Transgenic plants containing potato spindle tuber viroid (PSTVd) cDNA constructs, demonstrated to become de novo methylated upon PSTVd infection, represent a good example to illustrate the advantages of PCR. PSTVd is a 359 nt long autonomously replicating plant pathogenic RNA where all of its enzymatic requirements are entirely provided by the host cell. In addition, viroids that propagate without a DNA intermediate barely tolerate nucleotide substitutions of their RNA genome without losing infectivity. PCR is the method of choice to characterize the sequence context of genome-integrated viroid cDNA or of reverse transcribed PSTVd RNA, and can hardly be replaced by any alternative procedure. Furthermore, the precise examination of DNA methylation patterns (genomic sequencing) is entirely dependent on PCR. In contrast, the use of PCR is critical for the determination of copy number and arrangement of transgene constructs. Here, the advantages and disadvantages of PCR are discussed and protocols for PCR amplification of cDNA, genomic DNA, and bisulfite-treated DNA from transgenic plants are presented.     

Rapid PCR-based determination of transgene copy number in rice

We present a simple, rapid, and low-cost method to determine transgene copy number in rice. More than 100 first- and second-generation transgenic rice plants were tested. The plasmid (pRCopy) used for rice transformation contains the specific gene of interest and a partially deleted cytochrome c gene (cyc), a single-copy gene in rice. A 132-bp segment of the cloned ricecyc was shortened to 108 bp by deleting a 24-bp internal fragment. After PCR amplification of the genomic DNA from transgenic rice harboring pRCopy, the 2 expected bands were found. The 121-bp band corresponds to the endogenouscyc; the 97-bp band comes from the integrated pRCopy. Clear distinctions can be made between single and multiple copies of the transgene by comparing band densities.     

Potential impacts from the release of transgenic plants into the environment

Transformation techniques are making it possible to produce novel and unusual plant phenotypes. When considering the environmental impact of these, it is important to do so in the context of what is known about conventional plant breeding and the thousands of varieties that have been produced during this century and earlier. There has now been over ten years of experience of environmental impact assessment with transgenic plants, and research has enabled that assessment process to be better informed scientifically. There are, however, important challenges for the future. Fundamental changes in plant biology, including enhanced tolerance to stressful environments, may create a class of plants that are different from those that have been produced so far, and there may be lessons to be learnt from the experience worldwide of the release of exotic species into different countries. Scale-dependent effects of transgenic plants in agriculture can only effectively be measured by large scale production and monitoring. The monitoring process presents a number of challenges to provide oversight that is meaningful and helpful in assessing environmental impact. The international transboundary movement of transgenic plants is already a reality, and it is important that our environmental impact assessments take this possibility into account. This includes both intentional transboundary movement, through trade of commodity crops, but also unintentional transboundary movement, including the possibility of seeds being moved by animals, by transportation and by humans across the world. There are some major challenges in devising agricultural strategies for the transgenic crops that will become available in the future. The responsibility for developing agricultural strategy rests at a number of levels. To achieve this, it will be necessary to have effective dialogue between the regulatory authorities, the plant breeding and agrochemical industries, and the farming industry. There are already encouraging moves in this direction and hopefully this will continue.     

Advances in development of transgenic plants for remediation of xenobiotic pollutants

Phytoremediation-the use of plants for cleaning up of xenobiotic compounds-has received much attention in the last few years and development of transgenic plants tailored for remediation will further enhance their potential. Although plants have the inherent ability to detoxify some xenobiotic pollutants, they generally lack the catabolic pathway for complete degradation/mineralization of these compounds compared to microorganisms. Hence, transfer of genes involved in xenobiotic degradation from microbes/other eukaryotes to plants will further enhance their potential for remediation of these dangerous groups of compounds. Transgenic plants with enhanced potential for detoxification of xenobiotics such as trichloro ethylene, pentachlorophenol, trinitro toluene, glycerol trinitrate, atrazine, ethylene dibromide, metolachlor and hexahydro-1,3,5-trinitro-1,3,5-triazine are a few successful examples of utilization of transgenic technology. As more genes involved in xenobiotic metabolism in microorganisms/eukaryotes are discovered, it will lead to development of novel transgenic plants with improved potential for degradation of recalcitrant contaminants. Selection of suitable candidate plants, field testing and risk assessment are important considerations to be taken into account while developing transgenic plants for phytoremediation of this group of pollutants. Taking advantage of the advances in biotechnology and 'omic' technologies, development of novel transgenic plants for efficient phytoremediation of xenobiotic pollutants, field testing and commercialization will soon become a reality.     

An improved method for determination of gene copy numbers in transgenic mice by serial dilution curves obtained by real-time quantitative PCR assay

Precise characterization of transgene insertion is necessary for phenotype interpretation of transgenic animals. To check for the presence of deletions, estimate the number of inserted transgene copies, and in addition, identify the zygosity of transgenic mice, gene copy numbers were determined by real-time quantitative PCR. Instead of correlating tested samples to a single relative standard curve, serial dilution curves were constructed for every mouse sample. A novel statistical approach was designed in which mice with the same copy number were characterized by the adjusted group mean and standard deviation common to the target sequence. This enabled us to characterize the variability of the obtained results, statistically compare different groups of mice and estimate precision and limits of the applied method.     

Site-specific excisional recombination strategies for elimination of undesirable transgenes from crop plants

A major limitation of crop biotechnology and breeding is the lack of efficient molecular technologies for precise engineering of target genomic loci. While transformation procedures have become routine for a growing number of plant species, the random introduction of complex transgenenic DNA into the plant genome by current methods generates unpredictable effects on both transgene and homologous native gene expression. The risk of transgene transfer into related plant species and consumers is another concern associated with the conventional transformation technologies. Various approaches to avoid or eliminate undesirable transgenes, most notably selectable marker genes used in plant transformation, have recently been developed. These approaches include cotransformation with two independent T-DNAs or plasmid DNAs followed by their subsequent segregation, transposon-mediated DNA elimination, and most recently, attempts to replace bacterial T-DNA borders and selectable marker genes with functional equivalents of plant origin. The use of site-specific recombination to remove undesired DNA from the plant genome and concomitantly, via excision-mediated DNA rearrangement, switch-activate by choice transgenes of agronomical, food or feed quality traits provides a versatile “transgene maintenance and control” strategy that can significantly contribute to the transfer of transgenic laboratory developments into farming practice. This review focuses on recent reports demonstrating the elimination of undesirable transgenes (essentially selectable marker and recombinase genes) from the plant genome and concomitant activation of a silent transgene (e.g., a reporter gene) mediated by different site-specific recombinases driven by constitutive or chemically, environmentally or developmentally regulated promoters. These reports indicate major progress in excision strategies which extends application of the technology from annual, sexually propagated plants towards perennial, woody and vegetatively propagated plants. Current trends and future prospects for optimization of excision-activation machinery and its practical implementation for the generation of transgenic plants and plant products free of undesired genes are discussed.     

Analysis of a large number of independent transgenic rice plants produced by the biolistic method

Summary Over 500 independent transgenic rice plants have been obtained by the biolistic method with an average transformation frequency of 9.7% for japonica variety Taipei 309. A tight selection procedure using 50 mg/l of hygromycin B successfully prevented the growth of nontransformed tissues. Analysis of the T0 transgenic rice plants revealed that more than 97% of the transgenic plants were morphologically normal and more than 80% were at least partially fertile. The hyg^r trait was inherited as a dominant trait in a Mendelian manner in 8 out of 11 transgenic events assayed. Thirty-seven out of fifty transgenic plants were estimated to contain no more than five copies of the transgenes. In six out of seven transformation events, unlinked, co-transformed genes co-segregated in the T1 generation. The hyg^r trait has been stably inherited to the T4 generation. No chimerical transgenic plant has been found in an intensive search. Novel phenomena observed in transgenic rice plants are also reported.     

安全转基因植物培育技术研究进展

由于关系到转基因植物的产业化前景,安全型转基因植物培育越来越受到公众的关注。在植物遗传转化体系中,绝大多数选择标记基因来源于细菌,对人类健康和环境安全存在潜在风险,因此无选择标记转基因植物培育受到科研工作者的高度重视。本文综述了安全型转基因植物的培育途径,包括共转化系统、位点特异性重组系统、转座子系统、同源重组系统、不依赖于组织培养的简易转化技术及再生相关基因利用等技术,探讨了各种途径的优缺点,以期推动安全型转基因植物培育和转基因植物产业化进程。     

Benefits and risks of antibody and vaccine production in transgenic plants

Phytopharming, the production of protein biologicals in recombinant plant systems, has shown great promise in studies performed over the past 13 years. A secretory antibody purified from transgenic tobacco was tested successfully in humans, and prevented bacterial re-colonization after topical application in the mouth. Rapid production of patient-tailored anti-lymphoma antibodies in recombinant Tobamovirus-infected tobacco may provide effective cancer therapy. Many different candidate vaccines from bacterial and viral sources have been expressed in transgenic plants, and three human clinical trials with oral delivery of transgenic plant tissues have shown exciting results. The use of crop plants with agricultural practice could allow cheap production of valuable proteins, while providing enhanced safety by avoidance of animal viruses or other contaminants. However development of this technology must carefully consider the means to ensure the separation of food and medicinal products when crop plants are used for phytopharming.     

Modeling the invasion of recessive Bt-resistant insects: an impact on transgenic plants

There is a growing public concern on ecological and evolutionary consequence of the use of genetically modified organisms. We study the impact of Bt-resistant pests on genetically modified Bt crops. We develop and analyse a conceptual reaction-diffusion model of the Bt crop-Bt-susceptible insects-Bt-resistant insects to simulate the invasion of Bt-resistant insects. We show by means of computer simulations that there is a key parameter, which we define as the growth number that characterizes the insects' fitness. We also show that the Bt-resistant insect invasion can lead to inhomogeneity in plant and insect spatial distributions. The plant biomass is found to be essentially dependent on the duration of the Bt-resistant insect reproduction period. There are two types of this dependence. One of them exhibits, respectively, higher plant biomass in comparison with another. The ambiguity in the response of the Bt crop-Bt-susceptible insects system to the invasion of Bt-resistant insects can lead to serious complications in attempts to regulate the dynamics of the system.     

Expression of the rolC gene and nicotine production in transgenic roots and their regenerated plants

Transformation of Nicotiana tabacum cv. Xanthi leaf sections with the pPCV002-ABC (rol genes A, B and C together under the control of their own promoter) or pPCV002-CaMVC (rol gene C alone under the control of the CaMV 35S promoter) construction present in trans-acting Agrobacterium tumefaciens vectors yielded several transgenic root lines. The two types (rolABC and rolC) of transgenic root lines were examined for their nicotine productivity in relation to growth rate and the amount of rolC gene product measured with specific antibodies. In all cases, the changes in the amount of this polypeptide were positively correlated with the capacity of the transgenic roots to grow and produce nicotine. Both capacities were greatly increased when the rolA, rolB and rolC genes were present together, which demonstrates that the activity of the three rol-gene-encoded functions is synergistic. Consistent observations were also made in the corresponding regenerated plants. Received: 22 February 1997 / Revision received: 22 April 1997 / Accepted: 1 June 1997     

An improved method for the detection and quantification of recombinant protein in transgenic plants

A sensitive method has been developed for the detection of recombinant protein produced as a result of gene transfer into plants. This method is based upon antibody binding, which is then visualized using enhanced chemiluminescence and recorded on x-ray film for long-term storage. The technique is simple, rapid and reliable and can be used to screen large numbers of transgenic plants. Several plant species have been successfully tested in this way for a range of recombinant proteins.     

A rapid and efficient DNA minipreparation suitable for screening transgenic plants

We present a modified method for DNA minipreparation suitable for large-scale screening of transgenic plants. The method is rapid and efficient—one person can prepare DNA from approximately 50 samples per day. The average yield was about 40 μg DNA per 100 mg of fresh tissue, and the A₂₆₀/A₂₈₀ was 1.89–2.03. The total DNA extracted by this method could be used for PCR, restriction enzyme digestion, and Southern blotting.     

An efficient method for measuring copy number variation applied to improvement of nematode resistance in soybean

Copy number variation (CNV) is implicated in important traits in multiple crop plants, but can be challenging to genotype using conventional methods. The Rhg1 locus of soybean, which confers resistance to soybean cyst nematode (SCN), is a CNV of multiple 31.2‐kb genomic units each containing four genes. Reliable, high‐throughput methods to quantify Rhg1 and other CNVs for selective breeding were developed. The CNV genotyping assay described here uses a homeologous gene copy within the paleopolyploid soybean genome to provide the internal control for a single‐tube TaqMan copy number assay. Using this assay, CNV in breeding populations can be tracked with high precision. We also show that extensive CNV exists within Fayette, a released, inbred SCN‐resistant soybean cultivar with a high copy number at Rhg1 derived from a single donor parent. Copy number at Rhg1 is therefore unstable within a released variety over a relatively small number of generations. Using this assay to select for individuals with altered copy number, plants were obtained with both increased copy number and increased SCN resistance relative to control plants. Thus, CNV genotyping technologies can be used as a new type of marker‐assisted selection to select for desirable traits in breeding populations, and to control for undesirable variation within cultivars.     

Phosphodiesterase activities in transgenic tobacco plants associated with the movement protein of tobacco mosaic virus

Summary Hydrolytic activities of leaf extracts from normal and transgenic plants, with (+ MP) and without (-MP) the movement protein of tobacco mosaic virus, were examined. In the + MP transgenic plants, as compared with non-transgenic and — MP plants, higher hydrolytic activities were found on the following substrates: bis-(nitrophenyl)-phosphate (BPNPP, phosphodiesterase), p-nitrophenyl-(phenyl)-phosphate (PNPPP, nucleotidephosphodiesterase) and thymidine-3-monophosphate p-nitrophenyl ester (T₃MPP; 3nucleotide phosphodiesterase.) The + MP plant lines, as compared with other transgenic plants, exhibited higher nucleotide-phosphodiesterase activity in the soluble as well as in the membrane fraction. Substrate concentration kinetic studies revealed the presence of a nucleotide-phospho-diesterase with a high substrate affinity in the +MP extracts in addition to the enzyme with a relatively low substrate affinity present also in the — MP transgenic plants. This high affinity enzyme could be removed from the soluble fraction by precipitation with anti-MP serum, indicating its possible association with the movement protein.     

Fungal and bacterial disease resistance in transgenic plants expressing human lysozyme

The human lysozyme gene, which is assembled by the stepwise ligation of chemically synthesized oligonucleotides, was introduced into tobacco (Nicotiana tabacum cv `SR1') by the Agrobacterium-mediated method. The introduced human lysozyme gene was highly expressed under the control of the cauliflower mosaic virus 35S promoter, and the gene product accumulated in the transgenic tobacco plants. The transgenic tobacco plants showed enhanced resistance against the fungus Erysiphe cichoracearum – both conidia formation and mycelial growth were reduced, and the size of the colony was diminished. Microscopic observation revealed that the transgenic tobacco plants carried the resistant phenotype, analogous to that of the resistant cultivar `Kokubu' which had been selected by conventional breeding. Growth of the phytopathogenic bacterium Pseudomonas syringae pv. tabaci was also strongly retarded in the transgenic tobacco, and the chlorotic halo of the disease symptom was reduced to 17% of that observed in the wild-type tobacco. Thus, the introduction of a human lysozyme gene is an effective approach to protect crops against both fungal and bacterial diseases. Received: 9 September 1996 / Revision received: January 9 1997 / Accepted: 20 February 1997     

Demonstration of site-directed recombination in transgenic zebrafish using the Cre/loxP system

To test the Cre/loxP recombination system in zebrafish, a stable transgenic zebrafish line was developed by using a floxed (loxP flanked) gfp(green fluorescent protein) gene construct under the muscle-specific mylz2 promoter. Like our previous non-floxed gfp transgenic line under the same promoter, the new transgenic line expresses GFP reporter faithfully in fast skeletal muscles to the same intensity. To demonstrate the excision of floxed gfp transgene, in vitro synthesized Cre RNA was injected into embryos of floxed gfp transgenic zebrafish and we found a dramatic reduction of GFP expression. To confirm the excision, PCR was performed and a DNA fragment of correct size was amplified as predicted from the Cre/loxP mediated excision. Finally, we cloned the fragment and sequence information confirmed that the excision occurred at the precise site as predicted. Our experiments demonstrated that the Cre/loxP system can function efficiently and accurately in the zebrafish system.