Persistence of transgenes in wild rice populations depends on the interaction between genetic background of recipients and environmental conditions

The persistence of transgenes in wild populations may cause unintended ecological consequences, and the possibility of transgenes' persistence and introgression is dependent on fitness performance of transgenic crop–wild hybrids. To investigate the effects of transgene and genotype × environment on the fitness of crop–wild rice hybrids, a total of 11 cross‐combination progenies between insect‐resistant transgene (CpTI and Bt/CpTI) rice lines and wild rice (Oryza rufipogon) were evaluated at different sites with contrasting insect treatments. The results showed that fitness performance varied between transgenic hybrids having different wild parents and under different environmental conditions, indicating that fitness effects of transgenes on hybrid progenies depend heavily on the genetic background of recipient plants and growing environment. Significant fitness advantages conferred by transgenes were found only in some hybrids under high insect pressure condition, demonstrating that the level of target insects in the field environment influences the persistence and spread of insect‐resistant transgenes in wild rice populations. These findings suggest that evolutionary fate of escaped transgenes is different in wild populations with diverse genetic backgrounds under various environmental conditions.     

Allozymes and fitness: Evolution of a problem

It was expected that studies of electrophoretic variability in natural populations would resolve longstanding controversies concerning the form of natural selection and its effect on genetic variance in fitness. Recent studies of fitness components for allozymes in E. coli and Drosophila, where genetic backgrounds have been rigidly controlled, and experiments designed to detect small selection coefficients, suggest that selection is much weaker than earlier investigations would indicate. However, perturbing the metabolic background associated with specific loci often allows functional differences to be amplified to an experimentally measurable level. Frequencies of null activity variants in natural populations indicate that the fitness consequences of reduced activity in heterozygoles are probably very small. These results are supported by recent theoretical considerations suggesting that the activity variation associated with electrophoretic variation will have little effect on overall flux in many pathways.     

Genetic control of polyamine-dependent susceptibility to skin tumorigenesis

Overexpression of an ornithine decarboxylase (ODC) transgene greatly increases the susceptibility of mouse skin to carcinogen-induced tumor development. Like many phenotypes in transgenic models, this enhanced susceptibility phenotype is strongly influenced by genetic background. We have mapped tumor-modifier genes in intraspecific crosses between transgenic K6/ODC mice on a susceptible strain background (C57Bl/6J), a moderately resistant background (FVB), or a highly resistant background (C3H/HeJ). We identified several quantitative trait loci that influenced either tumor multiplicity or predisposition to the development of squamous cell carcinoma, but not both phenotypes. Because we did not use a tumor-promotion protocol to induce tumors, most of the quantitative trait loci mapped in this study are distinct from skin tumor-susceptibility loci identified previously. The use of a combined transgenic-standard strain approach to genetic analysis has resulted in detection of previously unknown genetic loci affecting skin tumor susceptibility.     

Heterogeneous selection at specific loci in natural environments in Arabidopsis thaliana

Genetic variation for quantitative traits is often greater than that expected to be maintained by mutation in the face of purifying natural selection. One possible explanation for this observed variation is the action of heterogeneous natural selection in the wild. Here we report that selection on quantitative trait loci (QTL) for fitness traits in the model plant species Arabidopsis thaliana differs among natural ecological settings and genetic backgrounds. At one QTL, the allele that enhanced the viability of fall-germinating seedlings in North Carolina reduced the fecundity of spring-germinating seedlings in Rhode Island. Several other QTL experienced strong directional selection, but only in one site and seasonal cohort. Thus, different loci were exposed to selection in different natural environments. Selection on allelic variation also depended upon the genetic background. The allelic fitness effects of two QTL reversed direction depending on the genotype at the other locus. Moreover, alternative alleles at each of these loci caused reversals in the allelic fitness effects of a QTL closely linked to TFL1, a candidate developmental gene displaying nucleotide sequence polymorphism consistent with balancing selection. Thus, both environmental heterogeneity and epistatic selection may maintain genetic variation for fitness in wild plant species.     

Co-silencing of homologous transgenes in tobacco

Two transgenes inserted into different genomic positions can co-inactivate each other when they share homologous sequences while each of the two homologous transgenes is stably expressed in the absence of a second homologous copy. To evaluate the efficiency of such homology-dependent gene silencing (HDGS) effects, we have produced 19 tobacco transformants that contained a stably expressed NPTII transgene inserted into a single genomic locus, and have analysed the stability of each transgene in the presence of a second stably expressed homologous transgene. All transformants shared the coding region of the NPTII gene but individual transformants differed in transgene copy number, expression levels and in the continuity of the transgene homology due to the insertion of introns into the NPTII region as well as the use of different promoters and terminators for the design of the transgene constructs. We generated 189 progeny populations representing all possible dual combinations among the 19 lines and analysed the kanamycin resistance of 400 seedlings of each cross. Our data show (1) that gene silencing occurs at a relative low frequency when transgenic loci sharing an homology at the coding sequence level are combined, and (2) that neither the variation of this homology by insertion of introns in the coding sequence, or by changing the promoter and terminator of the construct, nor the variation in the expression level of the transgene, are decisive parameters modifying the efficiency of co-silencing between two NPTII transgenes.     

Effects of genetic background on response to selection in experimental populations of Arabidopsis thaliana

The extent to which genetic background can influence allelic fitness is poorly understood, despite having important evolutionary consequences. Using experimental populations of Arabidopsis thaliana and map-based population genetic data, we examined a multigeneration response to selection in populations with differentiated genetic backgrounds. Replicated experimental populations of A. thaliana with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were subjected to strong viability and fertility selection by growing individuals from each population at high density for three generations in a growth chamber. Patterns of genome-wide selection were evaluated by examining deviations from expected frequencies of mapped molecular markers. Estimates of selection coefficients for individual genomic regions ranged from near 0 to 0.685. Genomic regions demonstrating the strongest response to selection most often were selected similarly in both genetic backgrounds. The selection response of several weakly selected regions, however, appeared to be sensitive to genetic background, but only one region showed evidence of positive selection in one background and negative selection in another. These results are most consistent with models of adaptive evolution in which allelic fitnesses are not strongly influenced by genetic background and only infrequently change in sign due to variation at other loci.     

Genetic architecture of a selection response in Arabidopsis thaliana

Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life-history and fitness-related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map-based population genetic data to study how selection acts on standing genetic variation in populations.     

Allelic composition and genetic background effects on transgene expression and inheritance in white clover

Allelic composition and genetic background effects on GUS expression and inheritance using a chimeric (cauliflower mosaic virus 35Sp:uidA) transgene were investigated in white clover as a prelude to transgenic cultivar development. Stable expression and Mendelian inheritance of the uidA transgene was observed over two generations when the uidA transgene was maintained in a heterozygous state. Transgenic backcross progeny (BC1) were intercrossed to produce segregating F2 populations. GUS-positive F2 plants were test-crossed with a non-transgenic control plant to determine whether individuals were heterozygous or homozygous for the transgene. Both expected and distorted segregation ratios were observed. Distortion of the segregation ratio was not caused by transgene inactivation or rearrangement, but was influenced by genetic background. BC1, BC2 and F2 populations were found to have similar levels of uidA gene expression. Quantification of GUS expression from progeny of high and low GUS expressing plants indicate that it is possible to alter transgene expression through selection. No difference was found between the level of expression for F2 plants homozygous or heterozygous for the transgene. These results indicate that F2 plants, homozygous for a transgene, might be used to develop a transgenic cultivar. However, progeny testing to determine the influence of genetic background is a prerequisite to such a development.     

Patterns of male sterility in a grasshopper hybrid zone imply accumulation of hybrid incompatibilities without selection

It is now widely accepted that post-zygotic reproductive isolation is the result of negative epistatic interactions between derived alleles fixed independently at different loci in diverging populations (the Dobzhansky-Muller model). What is less clear is the nature of the loci involved and whether the derived alleles increase in frequency through genetic drift, or as a result of natural or sexual selection. If incompatible alleles are fixed by selection, transient polymorphisms will be rare and clines for these alleles will be steep where divergent populations meet. If they evolve by drift, populations are expected to harbour substantial genetic variation in compatibility and alleles will introgress across hybrid zones once they recombine onto a genetic background with which they are compatible. Here we show that variation in male sterility in a naturally occurring Chorthippus parallelus grasshopper hybrid zone conforms to the neutral expectations. Asymmetrical clines for male sterility have long tails of introgression and populations distant from the zone centre show significant genetic variation for compatibility. Our data contrast with recent observations on 'speciation genes' that have diverged as a result of strong natural selection.     

植物转基因整合座位的结构

通过农杆菌和直接DNA转移技术所获得的转基因植株都具有复杂的转基因座位, 转基因整合染色体和染色体区段是随机的, 但组织培养的选择作用表现为非随机性, 偏向整合于染色体的基因富集区。转基因座位除少数含有完整的单拷贝转基因之外, 大多数转基因座位中外源转基因片段、基因组片段和填充DNA相间而存在。转基因座位中转基因及基因组DNA片段产生缺失、重复和染色体的重排, 转基因的完整性对转基因表达具有重要作用。     

Stability of transgene methylation patterns in mice: Position effects,strain specificity and cellular mosaicism

The methylation status of a transgene, which carried the adenovirus type 2 E2A late promoter linked to the chloramphenicol acetyltransferase gene, was studied in three transgenic mouse lines (5–8, 7–1 and 8–1). These lines were analysed over a large number of offspring generations beyond the founder animal. In mating experiments, the influence of the parent-of-origin and strain-specific backgrounds on the transgene methylation patterns were assessed and found to have no effect on the pre-established methylation patterns in mouse lines 5–8 and 8–1. The founder animal 7–1 carried two groups of a total of ten transgenes, which were located on two different chromosomes. These arrays of transgenes could be segregated into separate mouse lines 7-1A and 7-1B. The transgenes of 7-1A animals exhibited cellular mosaic methylation, patterns that were demethylated in approximately 10% of the offspring in a mixed genetic background. Upon further transmission of these transgenes in a mixed genetic background, the grandparental methylation patterns were reestablished in most progeny. Mating to inbred DBA/2 mice resulted in maintenance of the demethylated pattern or in further demethylation of the transgenes in approximately 50% of the offspring. In contrast, an equal number of transgenic siblings from matings to C57BL/6 mice showed a return to the original methylation pattern. The mosaic methylation status of this locus was apparently controlled by mouse-strain-specific factors. The methylation patterns of the 7-1B transgenes were not cellular mosaic and remained stable in all offspring, as with lines 5–8 and 8–1. Hence, the strain-dependent and cellular mosaic transgene methylation patterns of 7-1A animals were probably a consequence of the chromosomal integration site of the transgenes (position effect).     

Transgene stability and dispersal in forest trees

Transgenics from several forest tree species, carrying a number of commercially important recombinant genes, have been produced, and are undergoing confined field trials in a number of countries. However, there are questions and issues regarding stability of transgene expression and transgene dispersal that need to be addressed in long-lived forest trees. Variation in transgene expression is not uncommon in the primary transformants in plants, and is undesirable as it requires screening a large number of transformants in order to select transgenic lines with acceptable levels of transgene expression. Therefore, the current focus of plant transformation is toward fine tuning of transgene expression and stability in the transgenic forest trees. Although a number of studies have reported a relatively stable transgene expression for several target traits, including herbicide resistance, insect resistance, and lignin modification, there was also some unintended transgene instability in the genetically modified (GM) forest trees. Transgene dispersal from GM trees to feral forest populations and their containment remain important biological and regulatory issues facing commercial release of GM trees. Containment of transgenes must be in place to effectively prevent escape of transgenic pollen, seed, and vegetative propagules in economically important GM forest trees before their commercialization. Therefore, it is important to devise innovative technologies in genetic engineering that lead to genetically stable transgenic trees not only for qualitative traits (herbicide resistance, insect resistance), but also for quantitative traits (accelerated growth, increased height, increased wood density), and also prevent escape of transgenes in the forest trees.     

Transgenic trait deployment using designed nucleases

The demand for crops requiring increasingly complex combinations of transgenes poses unique challenges for transgenic trait deployment. Future value‐adding traits such as those associated with crop performance are expected to involve multiple transgenes. Random integration of transgenes not only results in unpredictable expression and potential unwanted side effects but stacking multiple, randomly integrated, independently segregating transgenes creates breeding challenges during introgression and product development. Designed nucleases enable the creation of targeted DNA double‐strand breaks at specified genomic locations whereby repair can result in targeted transgene integration leading to precise alterations in DNA sequences for plant genome editing, including the targeting of a transgene to a genomic locus that supports high‐level and stable transgene expression without interfering with resident gene function. In addition, targeted DNA integration via designed nucleases allows for the addition of transgenes into previously integrated transgenic loci to create stacked products. The currently reported frequencies of independently generated transgenic events obtained with site‐specific transgene integration without the aid of selection for targeting are very low. A modular, positive selection‐based gene targeting strategy has been developed involving cassette exchange of selectable marker genes which allows for targeted events to be preferentially selected, over multiple cycles of sequential transformation. This, combined with the demonstration of intragenomic recombination following crossing of transgenic events that contain stably integrated donor and target DNA constructs with nuclease‐expressing plants, points towards the future of trait stacking that is less dependent on high‐efficiency transformation.     

Monitoring transgene expression levels in different genotypes of field grown maize (Zea mays L.)

Transgenes in commercially available genetically modified plants are generally controlled by strong constitutive promoters to ensure a high level of expression at all stages of cultivation. Constitutive promoters however are influenced by a wide range of factors, and expression profiles of the transgenes in multiple genetic backgrounds have not yet been extensively studied. In this study a powerful expression profiling methodology for transgenic maize (Zea mays L.) is demonstrated on a large scale, analysing thousands of data points from three genotypes of herbicide and insect pest tolerant transgenic maize. Martonvásár inbred lines were crossed with LH244 maize line containing the MON 88017 events, and leaf tissue from the sixth backcross generation was sampled at four relevant phenological phases. Relative expression levels were determined using 18S rRNA as a reference and detailed statistical analysis performed. Expression levels of both transgenes are varied throughout plant development, and the interaction between the genetic background and phenophase are significant (p < 0.05). Expression is present at a significant level throughout all the phenological stages. We found that the genetic background has a significant (p < 0.01) effect on transgene expression levels in the case of the CP4epsps transgene, but not in the case of cry3Bb1, implying that the sensitivity of different constitutive promoter constructs to the effects of the genetic background is different.     

Hybridization between genetically modified Atlantic salmon and wild brown trout reveals novel ecological interactions

Interspecific hybridization is a route for transgenes from genetically modified (GM) animals to invade wild populations, yet the ecological effects and potential risks that may emerge from such hybridization are unknown. Through experimental crosses, we demonstrate transmission of a growth hormone transgene via hybridization between a candidate for commercial aquaculture production, GM Atlantic salmon (Salmo salar) and closely related wild brown trout (Salmo trutta). Transgenic hybrids were viable and grew more rapidly than transgenic salmon and other non-transgenic crosses in hatchery-like conditions. In stream mesocosms designed to more closely emulate natural conditions, transgenic hybrids appeared to express competitive dominance and suppressed the growth of transgenic and non-transgenic (wild-type) salmon by 82 and 54 per cent, respectively. To the best of our knowledge, this is the first demonstration of environmental impacts of hybridization between a GM animal and a closely related species. These results provide empirical evidence of the first steps towards introgression of foreign transgenes into the genomes of new species and contribute to the growing evidence that transgenic animals have complex and context-specific interactions with wild populations. We suggest that interspecific hybridization be explicitly considered when assessing the environmental consequences should transgenic animals escape to nature.     

Extending the coalescent to multilocus systems: the case of balancing selection

Natural populations are structured spatially into local populations and genetically into diverse 'genetic backgrounds' defined by different combinations of selected alleles. If selection maintains genetic backgrounds at constant frequency then neutral diversity is enhanced. By contrast, if background frequencies fluctuate then diversity is reduced. Provided that the population size of each background is large enough, these effects can be described by the structured coalescent process. Almost all the extant results based on the coalescent deal with a single selected locus. Yet we know that very large numbers of genes are under selection and that any substantial effects are likely to be due to the cumulative effects of many loci. Here, we set up a general framework for the extension of the coalescent to multilocus scenarios and we use it to study the simplest model, where strong balancing selection acting on a set of n loci maintains 2n backgrounds at constant frequencies and at linkage equilibrium. Analytical results show that the expected linked neutral diversity increases exponentially with the number of selected loci and can become extremely large. However, simulation results reveal that the structured coalescent approach breaks down when the number of backgrounds approaches the population size, because of stochastic fluctuations in background frequencies. A new method is needed to extend the structured coalescent to cases with large numbers of backgrounds.     

Identification and characterization of QTL controlling Agrobacterium-mediated transient and stable transformation of Brassica oleracea

A commonly encountered difficulty with the genetic engineering of crop plants is that different varieties of a particular species can show great variability in the efficiency with which they can be transformed. This increases the effort required to introduce transgenes into particular genetic backgrounds. The use of Substitution Lines has allowed the finer mapping of three Quantitative Trait Loci (tf1, tf2 and tf3) that explain 26% of the variation in the efficiency of Agrobacterium-mediated transformation in Brassica oleracea. Use of an 'orthogonal set' of genotypes (containing all eight possible combinations of 'positive' and 'negative' alleles at the three QTL), along with time course studies of transgene expression, has allowed the determination of the stages at which these genes have their effects during transformation. With regard to control of the level of transient transgene expression, tf1 (on LGO1) alone has no detectable effect, whilst tf2 (on LGO3) and tf3 (on LGO7) have highly significant effects (P < 0.001). All three loci have highly significant (P < 0.001) effects on the levels of expression of stably integrated transgene. The use of RFLP markers has shown that tf1 and tf2 are in duplicated regions of the B. oleracea genome and appear to be paralogous in origin. Colinearity of these regions with the A. thaliana genome has been identified. The results allow the selection of progeny Brassica oleracea genotypes that are more efficiently transformed than either parent used in the original cross.     

Site-specific modification of the bovine genome using Cre recombinase-mediated gene targeting.

Cre recombinase (Cre)-mediated targeted insertion of a transgene is a powerful technique that can be used to tailor genomes. When combined with somatic cell nuclear transfer it could offer an efficient way to generate transgenic livestock with site-specific genetic modifications that are free of antibiotic selection markers. We have engineered primary bovine fibroblasts to contain a chromosomal acceptor site with incompatible loxP/lox2272 sites for Cre-mediated cassette exchange and show for the first time that Cre-mediated targeting can be applied in these acceptor cells. Molecular characterization of the resulting cell clones revealed Cre-mediated transgene insertion efficiencies of up to 98% when antibiotic selection was used to identify transgene containing cell clones. Most clonal lines also contained random insertions of the targeting and Cre expression plasmids with only about 10% of the clones being exclusively modified by the intended targeted insertion. This targeting efficiency was sufficient to enable the isolation of correctly targeted clones without the help of antibiotic selection. Therefore, this recombinase-mediated insertion strategy has the potential to produce transgenic cattle from antibiotic selection marker-free somatic cells with transgenes inserted into proven genomic loci ensuring reliable expression levels.