Transgene flow: facts, speculations and possible countermeasures

Flying toward a plastic-free world: Can Drosophila serve as a model organism to develop new strategies of plastic waste management?

The last century was dominated by the widespread use of plastics, both in terms of invention and increased usage. The environmental challenge we currently face is not just about reducing plastic usage but finding new ways to manage plastic waste. Recycling is growing but remains a small part of the solution. There is increasing focus on studying organisms and processes that can break down plastics, offering a modern approach to addressing the environmental crisis. Here, we provide an overview of the organisms associated with plastics biodegradation, and we explore the potential of harnessing and integrating their genetic and biochemical features into a single organism, such as Drosophila melanogaster. The remarkable genetic engineering and microbiota manipulation tools available for this organism suggest that multiple features could be amalgamated and modeled in the fruit fly. We outline feasible genetic engineering and gut microbiome engraftment strategies to develop a new class of plastic-degrading organisms and discuss of both the potential benefits and the limitations of developing such engineered Drosophila melanogaster strains.

Plant Biosystems Design Research Roadmap 1.0

Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.

Evaluating the probability of CRISPR-based gene drive contaminating another species

The probability D that a given clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drive element contaminates another, nontarget species can be estimated by the following Drive Risk Assessment Quantitative Estimate (DRAQUE) Equation: D = h y b + t r a n s f × e x p r e s s × c u t × f l a n k × i m m u n e × n o n e x t i n c t with hyb = probability of hybridization between the target species and a nontarget species; transf = probability of horizontal transfer of a piece of DNA containing the gene drive cassette from the target species to a nontarget species (with no hybridization); express = probability that the Cas9 and guide RNA genes are expressed; cut = probability that the CRISPR-guide RNA recognizes and cuts at a DNA site in the new host; flank = probability that the gene drive cassette inserts at the cut site; immune = probability that the immune system does not reject Cas9-expressing cells; nonextinct = probability of invasion of the drive within the population. We discuss and estimate each of the seven parameters of the equation, with particular emphasis on possible transfers within insects, and between rodents and humans. We conclude from current data that the probability of a gene drive cassette to contaminate another species is not insignificant. We propose strategies to reduce this risk and call for more work on estimating all the parameters of the formula.

Transgene Biocontainment Strategies for Molecular Farming

Advances in plant synthetic biology promise to introduce novel agricultural products in the near future. 'Molecular farms' will include crops engineered to produce medications, vaccines, biofuels, industrial enzymes, and other high value compounds. These crops have the potential to reduce costs while dramatically increasing scales of synthesis and provide new economic opportunities to farmers. Current transgenic crops may be considered safe given their long-standing use, however, some applications of molecular farming may pose risks to human health and the environment. Unwanted gene flow from engineered crops could potentially contaminate the food supply, and affect wildlife. There is also potential for unwanted gene flow into engineered crops which may alter their ability to produce compounds of interest. Here, we briefly discuss the applications of molecular farming and explore the various genetic and physical methods that can be used for transgene biocontainment. As yet, no technology can be applied to all crop species, such that a combination of approaches may be necessary. Effective biocontainment is needed to enable large scale molecular farming.

The application of gene splitting technique for controlling transgene flow in rice

Controlling transgene flow in China is important, as this country is part of the center of origin of rice. A gene-splitting technique based on intein-mediated trans-splicing represents a new strategy for controlling transgene flow via biological measures. In this study, the G2-aroA gene which provides glyphosate tolerance was split into an N-terminal and a C-terminal region, which were then fused to intein N and intein C of the Ssp DnaE intein, ultimately forming EPSPSn:In and Ic:EPSPSc fusion genes, respectively. These fusion genes were subsequently transformed into the rice cultivar Zhonghua 11 via the Agrobacterium-mediated method. The two split gene fragments were then introduced into the same rice genome by genetic crossings. Glyphosate tolerance analysis revealed that the functional target protein was reconstituted by Ssp DnaE intein-mediated trans-splicing and that the resultant hybrid rice was glyphosate tolerant. The reassembly efficiency of the split gene fragments ranged from 67 to 91% at the molecular level, and 100% of the hybrid F1 progeny were glyphosate tolerant. Transgene flow experiments showed that when the split gene fragments are inserted into homologous chromosomes, the gene-splitting technique can completely avoid the escape of the target trait to the environment. This report is the first on the reassembly efficiency and effectiveness of transgene flow containment via gene splitting in rice. This study provides not only a new biological strategy for controlling rice transgene flow but also a new method for cultivating hybrid transgenic rice.

Assessment of potential environmental risks of transgene flow in smallholder farming systems in Asia: Brassica napus as a case study in Korea

The cultivation of genetically modified (GM) crops has raised many questions regarding their environmental risks, particularly about their ecological impact on non-target organisms, such as their closely-related relative species. Although evaluations of transgene flow from GM crops to their conventional crops has been conducted under large-scale farming system worldwide, in particular in North America and Australia, few studies have been conducted under smallholder farming systems in Asia with diverse crops in co-existence. A two-year field study was conducted to assess the potential environmental risks of gene flow from glufosinate-ammonium resistant (GR) Brassica napus to its conventional relatives, B. napus, B. juncea, and Raphanus sativus under simulated smallholder field conditions in Korea. Herbicide resistance and simple sequence repeat (SSR) markers were used to identify the hybrids. Hybridization frequency of B. napus × GR B. napus was 2.33% at a 2 m distance, which decreased to 0.007% at 75 m. For B. juncea, it was 0.076% at 2 m and decreased to 0.025% at 16 m. No gene flow was observed to R. sativus. The log-logistic model described hybridization frequency with increasing distance from GR B. napus to B. napus and B. juncea and predicted that the effective isolation distances for 0.01% gene flow from GR B. napus to B. napus and B. juncea were 122.5 and 23.7 m, respectively. Results suggest that long-distance gene flow from GR B. napus to B. napus and B. juncea is unlikely, but gene flow can potentially occur between adjacent fields where the smallholder farming systems exist.

"Born to Run"? Not Necessarily: Species and Trait Bias in Persistent Free-Living Transgenic Plants

The possibility of transgenes from engineered plants ending up in unmanaged populations with undesirable consequences has been a long-term biosafety concern. Experience with traditionally improved plants reveals that most cases of such gene escape have been of little consequence, but on occasion they have led to the evolution of problematic plants or have resulted in an increased extinction risk for wild taxa. Three decades have passed since the first environmental release of transgenic plants, and more than two decades since their first commercialization. Examples of transgenes gone astray are increasingly commonplace. Transgenic individuals have been identified in more than a thousand free-living plant populations. Here I review 14 well-documented consolidated “cases” in which transgenes have found their way into free-living plant populations. Some as transient volunteers; others appear to be persistent transgenic populations. The species involved in the latter are not representative of the current commercialized transgenic crops as whole. They tend to share certain traits that are absent or rare in the transgenic crops that do not exist as persistent populations. The traits commonly occurring in species with persistent transgenic free-living populations are the following, in descending order of importance: (1) a history of occurring as non-transgenic free-living plants, (2) fruits fully or partially shattering prior to harvest, (3) have small or otherwise easily dispersed seeds, either spontaneously or by seed spillage along the supply chain from harvest to consumer, (4) ability to disperse viable pollen, especially to a kilometer or more, (5) perennial habit, and (6) the transgene's fitness effects in the recipient environment are beneficial or neutral. Based on these observations, a thought experiment posits which species might be the next to be reported to occur as free-living transgenic populations.

Overexpressing Exogenous 5-Enolpyruvylshikimate-3-Phosphate Synthase (EPSPS) Genes Increases Fecundity and Auxin Content of Transgenic Arabidopsis Plants

Transgenic glyphosate-tolerant plants overproducing EPSPS (5-enolpyruvylshikimate-3-phosphate synthase) may exhibit enhanced fitness in glyphosate-free environments. If so, introgression of transgenes overexpressing EPSPS into wild relative species may lead to increased competitiveness of crop-wild hybrids, resulting in unpredicted environmental impact. Assessing fitness effects of transgenes overexpressing EPSPS in a model plant species can help address this question, while elucidating how overproducing EPSPS affects the fitness-related traits of plants. We produced segregating T₂ and T₃Arabidopsis thaliana lineages with or without a transgene overexpressing EPSPS isolated from rice or Agrobacterium (CP4). For each of the three transgenes, we compared glyphosate tolerance, some fitness-related traits, and auxin (indole-3-acetic acid) content in transgene-present, transgene-absent, empty vector (EV), and parental lineages in a common-garden experiment. We detected substantially increased glyphosate tolerance in T₂ plants of transgene-present lineages that overproduced EPSPS. We also documented significant increases in fecundity, which was associated with increased auxin content in T₃ transgene-present lineages containing rice EPSPS genes, compared with their segregating transgene-absent lineages, EV, and parental controls. Our results from Arabidopsis with nine transgenic events provide a strong support to the hypothesis that transgenic plants overproducing EPSPS can benefit from a fecundity advantage in glyphosate-free environments. Stimulated biosynthesis of auxin, an important plant growth hormone, by overproducing EPSPS may play a role in enhanced fecundity of the transgenic Arabidopsis plants. The obtained knowledge is useful for assessing environmental impact caused by introgression of transgenes overproducing EPSPS from any GE crop into populations of its wild relatives.

Intragenic modification of maize

The discovery of plant DNA recombination techniques triggered the development of a wide range of genetically modified crops. The transgenics were the first generation of modified plants; however, these crops were quickly questioned due to the artificial combination of DNA between different species. As a result, the second generation of modified plants known as cisgenic and/or intragenic crops arose as an alternative to genetic plant engineering. Cisgenic and/or intragenic crops development establishes the combination of DNA from the plant itself or related species avoiding the introduction of foreign genetic material, such as selection markers and/or reporter genes. Nowadays it has been made successful cisgenic and/or intragenic modifications in crops such as potato and apple. The present study shows the possibility of reaching similar approach in corn plants. This research was focused on achieve intragenic overexpression of the maize Rubisco activase (Rca) protein. The results were compared with changes in the expression of the same protein, in maize plants grown after 23 cycles of conventional selection and open field planting. Experimental evidence shows that maize intragenic modification is possible for increasing specific gene expression, preserving plant genome free of foreign DNA and achieving further significant savings in time and man labor for crop improvement.

Consumer acceptance of food crops developed by genome editing

One of the major problems regarding consumer acceptance of genetically modified organisms (GMOs) is the possibility that their transgenes could have adverse effects on the environment and/or human health. Genome editing, represented by the CRISPR/Cas9 system, can efficiently achieve transgene-free gene modifications and is anticipated to generate a wide spectrum of plants. However, the public attitude against GMOs suggests that people will initially be unlikely to accept these plants. We herein explored the bottlenecks of consumer acceptance of transgene-free food crops developed by genome editing and made some recommendations. People should not pursue a zero-risk bias regarding such crops. Developers are encouraged to produce cultivars with a trait that would satisfy consumer needs. Moreover, they should carefully investigate off-target mutations in resultant plants and initially refrain from agricultural use of multiplex genome editing for better risk-benefit communication. The government must consider their regulatory status and establish appropriate regulations if necessary. The government also should foster communication between the public and developers. If people are informed of the benefits of genome editing-mediated plant breeding and trust in the relevant regulations, and if careful risk-benefit communication and sincere considerations for the right to know approach are guaranteed, then such transgene-free crops could gradually be integrated into society.

Evolutionary and social consequences of introgression of nontransgenic herbicide resistance from rice to weedy rice in Brazil

Several studies have expressed concerns about the effects of gene flow from transgenic herbicide-resistant crops to their wild relatives, but no major problems have been observed. This review describes a case study in which what has been feared in transgenics regarding gene flow has actually changed biodiversity and people's lives. Nontransgenic imidazolinone-resistant rice (IMI-rice) cultivars increased the rice grain yield by 50% in southern Brazil. This increase was beneficial for life quality of the farmers and also improved the regional economy. However, weedy rice resistant to imidazolinone herbicides started to evolve three years after the first use of IMI-rice cultivars. Population genetic studies indicate that the herbicide-resistant weedy rice was mainly originated from gene flow from resistant cultivars and distributed by seed migration. The problems related with herbicide-resistant weedy rice increased the production costs of rice that forced farmers to sell or rent their land. Gene flow from cultivated rice to weedy rice has proven to be a large agricultural, economic, and social constraint in the use of herbicide-resistant technologies in rice. This problem must be taken into account for the development of new transgenic or nontransgenic rice technologies.