Genetic basis and detection of unintended effects in genetically modified crop plants

Application of next-generation sequencing in the detection of transgenic crop

With the rapid development of transgenic technology and the increasing prevalence of genetically modified (GMO) crops, incidents such as illegal importation, environmental contamination, and safety concerns associated with GMOs have risen significantly in recent years. Consequently, there is a growing demand for more advanced methods of GMO crop detection. Traditional molecular detection techniques, which rely on nucleic acids or proteins, are becoming less effective due to the increasing complexity of GMO crop genomes. In contrast, detection technologies based on second- and third-generation high-throughput sequencing offer promising solutions to these challenges. This review provides a comprehensive overview of the latest advancements in GMO crop detection technologies, categorizing and describing various approaches, and comparing their respective strengths and limitations. The article emphasizes the current state, benefits, challenges, and future prospects of high-throughput sequencing in GMO detection, aiming to guide further research and development in this field.

A visible seedling-stage screening system for the Brassica napus hybrid breeding by a novel hypocotyl length-regulated gene BnHL

Rapeseed (Brassica napus) is a globally significant oilseed crop with strong heterosis performance. Recessive genic male sterility (RGMS) is one of the key approaches for utilizing heterosis in B. napus. However, this method faces the inherent challenge of being time-consuming and labour-intensive for removing fertile plants during seed production. Here, we report a hypocotyl length-regulated gene, BnHL, which is closely linked to a known fertility gene, BnMs2, serving as a seedling morphology marker. This marker could be used to identify fertile plants in the breeding of RGMS lines based on hypocotyl traits. By targeting the BnHL gene, both homozygous and heterozygous edited mutants exhibited significantly longer hypocotyls than the wild type (WT). Furthermore, germination experiments revealed that 7 days after seed germination, the difference in hypocotyl length between the mutant and the WT seedlings reached its maximum, effectively distinguishing fertile plants under both white (W) and red/far-red (R/FR) light. Mutations in BnHL did not result in significant changes in main agronomic traits. Thus, this study provides a comprehensive strategy for screening and identifying a new morphological marker gene for early screening in RGMS hybrid breeding with completely non-transgene during the whole production.

MicroRNA396 negatively regulates shoot regeneration in tomato

Numerous studies have been dedicated to genetically engineering crops to enhance their yield and quality. One of the key requirements for generating genetically modified plants is the reprogramming of cell fate. However, the efficiency of shoot regeneration during this process is highly dependent on genotypes, and the underlying molecular mechanisms remain poorly understood. Here, we identified microRNA396 (miR396) as a negative regulator of shoot regeneration in tomato. By selecting two genotypes with contrasting shoot regeneration efficiencies and analyzing their transcriptome profiles, we found that miR396 and its target transcripts, which encode GROWTH-REGULATING FACTORs (GRFs), exhibit differential abundance between high- and low-efficiency genotypes. Suppression of miR396 functions significantly improved shoot regeneration rates along with increased expression of GRFs in transformed T0 explants, suggesting that miR396 is a key molecule involved in the determination of regeneration efficiency. Notably, we also showed that co-expression of a miR396 suppressor with the gene-editing tool can be employed to generate gene-edited plants in the genotype with a low capacity for shoot regeneration. Our findings show the critical role of miR396 as a molecular barrier to shoot regeneration in tomato and suggest that regeneration efficiency can be improved by blocking this single microRNA.

Processes for regulating genetically modified and gene edited plants

Innovation in agriculture has been essential in improving productivity of crops and forages to support a growing population, improving living standards while contributing toward maintaining environment integrity, human health, and wellbeing through provision of more nutritious, varied, and abundant food sources. A crucial part of that innovation has involved a range of techniques for both expanding and exploiting the genetic potential of plants. However, some techniques used for generating new variation for plant breeders to exploit are deemed higher risk than others despite end products of both processes at times being for all intents and purposes identical for the benefits they provide. As a result, public concerns often triggered by poor communication from innovators, resulting in mistrust and suspicion has, in turn, caused the development of a range of regulatory systems. The logic and motivations for modes of regulation used are reviewed and how the benefits from use of these technologies can be delivered more efficiently and effectively is discussed.

Compositional and Morphological Analysis of Salt Stress Tolerant Mannitol-1-phosphate Dehydrogenase (mtlD)-Transgenic Potato Plants

Undesired effects often occur in genetically modified (GM) plants, especially during metabolite engineering. Nevertheless, conducting a comparative study between GM and non-GM plants can identify the unintended alterations and facilitate the risk assessment of GM crops. This research compared the morphology and composition of a transgenic potato plant expressing mannitol-1-phosphate dehydrogenase (mtlD), with its non-transgenic counterpart. The results indicated significant differences in plant height, number of leaves, length and width of leaves, as well as tuber number and weight between the transgenic and non-transgenic plants. However, compositional analysis revealed no significant differences in soluble protein, starch, total sugar, fructose, fiber, and ascorbate contents between mtlD-GM and non-GM potatoes. Nevertheless, sucrose and glucose levels were found to be higher in the transgenic potato tubers and leaves, respectively, when compared to the non-transgenic plants. In addition to ammonium, potassium, chloride, nitrite, and nitrate levels, significant differences were observed in the amino acids asparagine, aspartic acid, glutamic acid, isoleucine, leucine, lysine, serine, and valine between the GM and non-GM plants. Apart from the target gene product, mannitol, all the changes in chemical compositions observed in the transgenic potato plants fell within the ranges of normal variability for potato plants. Moreover, despite some phenotypical differences between the mtlD-GM potato and its non-GM counterpart, it is believed that this variation is a common phenomenon among potato varieties. In conclusion, the morphological and compositional analysis of the mtlD-GM potato plant revealed substantial equivalence with its non-transgenic counterpart.

Nanotechnology and CRISPR/Cas9 system for sustainable agriculture

The clustered regularly interspaced short palindromic repeats (CRISPR-Cas9), a genome editing tool, has gained a tremendous position due to its therapeutic efficacy, ability to counteract abiotic/biotic stresses in plants, environmental remediation and sustainable agriculture with the aim of food security. This is mainly due to their potential of precised genome modification and numerous genetic engineering protocols with versatility as well as simplicity. This technique is quite useful for crop refinement and overcoming the agricultural losses and regaining the soil fertility hampered by hazardous chemicals. Since CRISPR/Cas9 has been widely accepted in genome editing in plants, however, their revolutionised nature and progress enable genetic engineers to face numerous challenges in plant biotechnology. Therefore, nanoparticles have addressed these challenges and improved cargo delivery and genomic editing processes. Henceforth, this barrier prevents CRISPR-based genetic engineering in plants in order to show efficacy in full potential and eliminate all the barriers. This advancement accelerates the genome editing process and its applications in plant biotechnology enable us to sustain and feed the massive population under varying environments. Genome editing tools using CRISPR/Cas9 and nanotechnology are advantageous that produce transgenic-free plants that overcome global food demands. Here, in this review, we have aimed towards the mechanisms/delivery systems linked with CRISPR/Cas9 system. We have elaborated on the applications of CRISPR/Cas9 and nanotechnology-based systems for sustainable agriculture. Moreover, the challenges and limitations associated with genome editing and delivery systems have also been discussed with a special emphasis on crop improvement.

CRISPR Variants for Gene Editing in Plants: Biosafety Risks and Future Directions

The CRISPR genome editing technology is a crucial tool for enabling revolutionary advancements in plant genetic improvement. This review shows the latest developments in CRISPR/Cas9 genome editing system variants, discussing their benefits and limitations for plant improvement. While this technology presents immense opportunities for plant breeding, it also raises serious biosafety concerns that require careful consideration, including potential off-target effects and the unintended transfer of modified genes to other organisms. This paper highlights strategies to mitigate biosafety risks and explores innovative plant gene editing detection methods. Our review investigates the international biosafety guidelines for gene-edited crops, analyzing their broad implications for agricultural and biotechnology research and advancement. We hope to provide illuminating and refined perspectives for industry practitioners and policymakers by evaluating CRISPR genome enhancement in plants.

Impact of Intron and Retransformation on Transgene Expression in Leaf and Fruit Tissues of Field-Grown Pear Trees

Stable and high expression of introduced genes is a prerequisite for using transgenic trees. Transgene stacking enables combining several valuable traits, but repeated transformation increases the risk of unintended effects. This work studied the stability and intron-mediated enhancement of uidA gene expression in leaves and different anatomical parts of pear fruits during field trials over 14 years. The stability of reporter and herbicide resistance transgenes in retransformed pear plants, as well as possible unintended effects using high-throughput phenotyping tools, were also investigated. The activity of β-glucuronidase (GUS) varied depending on the year, but silencing did not occur. The uidA gene was expressed to a maximum in seeds, slightly less in the peel and peduncles, and much less in the pulp of pear fruits. The intron in the uidA gene stably increased expression in leaves and fruits by approximately twofold. Retransformants with the bar gene showed long-term herbicide resistance and exhibited no consistent changes in leaf size and shape. The transgenic pear was used as rootstock and scion, but grafted plants showed no transport of the GUS protein through the graft in the greenhouse and field. This longest field trial of transgenic fruit trees demonstrates stable expression under varying environmental conditions, the expression-enhancing effect of intron and the absence of unintended effects in single- and double-transformed woody plants.

Volunteer Plants' Occurrence and the Environmental Adaptability of Genetically Modified Fodder Corn upon Unintentional Release into the Environment

The number of corn cultivars that have been improved using genetically modified technology continues to increase. However, concerns about the unintentional release of living-modified organisms (LMOs) into the environment still exist. Specifically, there are cases where LMO crops grown as fodder are released into the environment and form a volunteer plant community, which raises concerns about their safety. In this study, we analyzed the possibility of weediness and volunteer plants' occurrence when GMO fodder corn grains distributed in Korea are unintentionally released into the environment. Volunteer plants' occurrence was investigated by directly sowing grains in an untreated field. The results showed that the germination rate was extremely low, and even if a corn seed germinated, it could not grow into an adult plant and would die due to weed competition. In addition, the germination rate of edible and fodder grains was affected by temperature (it was high at 20 °C and 30 °C but low at 40 °C and extremely low at 10 °C), and it was higher in the former than in the latter. And the germination rate was higher in Daehakchal (edible corn grains) than in Gwangpyeongok (fodder corn grains). The environmental risk assessment data obtained in this study can be used for future evaluations of the weediness potential of crops and the development of volunteer plant suppression technology in response to unintentional GMO release.

Spatial Lipidomics of EPSPS and PAT Transgenic and Non-Transgenic Soybean Seeds Using Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging

Herbicide-resistant soybeans are among the most widely planted transgenic crops. The in situ evaluation of spatial lipidomics in transgenic and non-transgenic soybeans is important for directly assessing the unintended effects of exogenous gene introduction. In this study, matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI)-based non-targeted analytical strategies were used for the first time for in situ detection and imaging of endogenous lipid distributions in transgenic (EPSPS and PAT genes) herbicide-resistant soybean (Glycine max Merrill) (S4003.14) and non-transgenic soybean (JACK) seeds. Statistical analysis revealed significant differences in lipids between S4003.14 and JACK seeds. The variable importance of projection analysis further revealed that 18 identified lipids, including six phosphatidylcholines (PCs), four phosphatidylethanolamines (PEs), five triacylglycerols (TAGs), and three cytidine diphosphate-diacylglycerols (CDP-DAGs), had the strongest differential expression between S4003.14 and JACK seeds. Among those, the upregulated expressions of PC(P-36:1), PC(36:2), PC(P-36:0), PC(37:5), PE(40:2), TAG(52:1), TAG(55:5), and CDP-DAG(37:2) and the downregulated expressions of PC (36:1), TAG(43:0), and three PEs (i.e., PE(P-38:1), PE(P-38:0), and PE(P-40:3)) were successfully found in the S4003.14 seeds, compared to these lipids detected in the JACK seeds. Meanwhile, the lipids of PC (44:8), CDP-DAG(38:0), and CDP-DAG(42:0) were uniquely detected in the S4003.14 soybean seeds, and TAG(45:2) and TAG(57:10) were detected as the unique lipids in the JACK seeds. The heterogeneous distribution of these lipids in the soybean seeds was also clearly visualized using MALDI-MSI. MSI results showed that lipid expression was significantly up/downregulated in S4003.14 seeds, compared to that in JACK seeds. This study improves our understanding of the unintended effects of herbicide-resistant EPSPS and PAT gene transfers on spatial lipidomes in soybean seeds and enables the continued progression of MALDI-MSI as an emerging, reliable, and rapid molecular imaging tool for evaluating unintended effects in transgenic plants.

Comparison of the Phenotypic Performance, Molecular Diversity, and Proteomics in Transgenic Rice

The extent of molecular diversity and differentially expressed proteins (DEPs) in transgenic lines provide valuable information to understand the phenotypic performance of transgenic crops compared with their parents. Here, we compared the differences in the phenotypic variation of twelve agronomic and end-use quality traits, the extent of microsatellite diversity, and DEPs of a recurrent parent line with three transgenic rice restorer lines carrying either CRY1C gene on chromosome 11 or CRY2A gene on chromosome 12 or both genes. The three transgenic lines had significantly smaller stem borer infestation than the recurrent parent without showing significant differences among most agronomic traits, yield components, and end-use quality traits. Using 512 microsatellite markers, the three transgenic lines inherited 2.9-4.3% of the Minghui 63 donor genome and 96.3-97.1% of the CH891 recurrent parent genome. As compared with the recurrent parent, the number of upregulated and down-regulated proteins in the three transgenic lines varied from 169 to 239 and from 131 to 199, respectively. Most DEPs were associated with the secondary metabolites biosynthesis transport and catabolism, carbohydrate transport and metabolism, post-translational modification, and signal transduction mechanisms. Although several differentially expressed proteins were observed between transgenic rice and its recurrent parent, the differences may not have been associated with grain yield and most other phenotypic traits in transgenic rice.

No adverse dietary effect of a cisgenic fire blight resistant apple line on the non-target arthropods Drosophila melanogaster and Folsomia candida

Genetic modification of apple cultivars through cisgenesis can introduce traits, such as disease resistance from wild relatives, quickly and without crossing. This approach was used to generate the cisgenic apple line C44.4.146, a 'Gala Galaxy' carrying the fire blight resistance gene FB_MR5. In contrast to traditionally bred apple cultivars, genetically modified (GM) plants need to undergo a regulatory risk assessment considering unintended effects before approval for commercial release. To determine potential unintended effects of C44.4.146, we assessed major leaf components and effects on the fitness of the decomposers Drosophila melanogaster (fruit fly) and Folsomia candida (collembolan), which were fed a diet amended with powdered apple leaf material. Leaf material of 'Gala Galaxy', several natural 'Gala' mutants, and the unrelated apple cultivar 'Ladina' were used for comparison. The genetic modification did not alter major leaf components and did not adversely affect survival, growth, or fecundity of the two decomposers. Consistent with previous studies with other GM crops, the differences between conventionally bred cultivars were greater than between the GM line and its non-GM wild type. These data provide a baseline for future risk assessments.

Principles of risk decision-making

Risk management decisions in public health require consideration of a number of complex, often conflicting factors. The aim of this review was to propose a set of 10 fundamental principles to guide risk decision-making. Although each of these principles is sound in its own right, the guidance provided by different principles might lead the decision-maker in different directions. For example, where the precautionary principle advocates for preemptive risk management action under situations of scientific uncertainty and potentially catastrophic consequences, the principle of risk-based decision-making encourages decision-makers to focus on established and modifiable risks, where a return on the investment in risk management is all but guaranteed in the near term. To evaluate the applicability of the 10 principles in practice, one needs to consider 10 diverse risk issues of broad concern and explore which of these principles are most appropriate in different contexts. The 10 principles presented here afford substantive insight into the process of risk management decision-making, although decision-makers will ultimately need to exercise judgment in reaching appropriate risk decisions, accounting for all of the scientific and extra-scientific factors relevant to the risk decision at hand.

Transcriptomic Analysis of Mature Transgenic Poplar Expressing the Transcription Factor JERF36 Gene in Two Different Environments

During the last several decades, a number of transgenic or genetically modified tree varieties with enhanced characteristics and new traits have been produced. These trees have become associated with generally unsubstantiated concerns over health and environmental safety. We conducted transcriptome sequencing of transgenic Populus alba × P. berolinensis expressing the transcription factor JERF36 gene (ABJ01) and the non-transgenic progenitor line (9#) to compare the transcriptional changes in the apical buds. We found that 0.77% and 1.31% of the total expressed genes were significant differentially expressed in ABJ01 at the Daqing and Qiqihar sites, respectively. Among them, 30%–50% of the DEGs contained cis-elements recognized by JERF36. Approximately 5% of the total number of expressed genes showed significant differential expression between Daqing and Qiqihar in both ABJ01 and 9#. 10 DEGs resulting from foreign gene introduction, 394 DEGs that resulted solely from the environmental differences, and 47 DEGs that resulted from the combination of foreign gene introduction and the environment were identified. The number of DEGs resulting from environmental factors was significantly greater than that resulting from foreign gene introduction, and the combined effect of the environmental effects with foreign gene introduction was significantly greater than resulting from the introduction of JERF36 alone. GO and KEGG annotation showed that the DEGs mainly participate in the photosynthesis, oxidative phosphorylation, plant hormone signaling, ribosome, endocytosis, and plant-pathogen interaction pathways, which play important roles in the responses to biotic and abiotic stresses ins plant. To enhance its adaptability to salt-alkali stress, the transgenic poplar line may regulate the expression of genes that participate in the photosynthesis, oxidative phosphorylation, MAPK, and plant hormone signaling pathways. The crosstalk between biotic and abiotic stress responses by plant hormones may improve the ability of both transgenic and non-transgenic poplars to defend against pathogens. The results of our study provide a basis for further studies on the molecular mechanisms behind improved stress resistance and the unexpected effects of transgenic gene expression in poplars, which will be significant for improving the biosafety evaluation of transgenic trees and accelerating the breeding of new varieties of forest trees resistant to environmental stresses.

Advances in Electrochemical Techniques for the Detection and Analysis of Genetically Modified Organisms: An Analysis Based on Bibliometrics

Since the first successful transgenic plants obtained in 1983, dozens of plants have been tested. On the one hand, genetically modified plants solve the problems of agricultural production. However, due to exogenous genes of transgenic plants, such as its seeds or pollen drift, diffusion between populations will likely lead to superweeds or affect the original traits. The detection technology of transgenic plants and their products have received considerable attention. Electrochemical sensing technology is a fast, low-cost, and portable analysis technology. This review interprets the application of electrochemical technology in the analysis and detection of transgenic products through bibliometrics. A total of 83 research articles were analyzed, spanning 2001 to 2021. We described the different stages in the development history of the subject and the contributions of countries and institutions to the topic. Although there were more annual publications in some years, there was no explosive growth in any period. The lack of breakthroughs in this technology is a significant factor in the lack of experts from other fields cross-examining the subject. Through keyword co-occurrence analysis, different research directions on this topic were discussed. The use of nanomaterials with excellent electrical conductivity allows for more sensitive detection of GM crops by electrochemical sensors. Furthermore, co-citation analysis was used to interpret the most popular reports on the topic. In the end, we predict the future development of this topic according to the analysis results.

Green Revolution to Gene Revolution: Technological Advances in Agriculture to Feed the World

Technological applications in agriculture have evolved substantially to increase crop yields and quality to meet global food demand. Conventional techniques, such as seed saving, selective breeding, and mutation breeding (variation breeding), have dramatically increased crop production, especially during the 'Green Revolution' in the 1990s. However, newer issues, such as limited arable lands, climate change, and ever-increasing food demand, pose challenges to agricultural production and threaten food security. In the following 'Gene Revolution' era, rapid innovations in the biotechnology field provide alternative strategies to further improve crop yield, quality, and resilience towards biotic and abiotic stresses. These innovations include the introduction of DNA recombinant technology and applications of genome editing techniques, such as transcription activator-like effector (TALEN), zinc-finger nucleases (ZFN), and clustered regularly interspaced short palindromic repeats/CRISPR associated (CRISPR/Cas) systems. However, the acceptance and future of these modern tools rely on the regulatory frameworks governing their development and production in various countries. Herein, we examine the evolution of technological applications in agriculture, focusing on the motivations for their introduction, technical challenges, possible benefits and concerns, and regulatory frameworks governing genetically engineered product development and production.

Update of Argentina’s Regulatory Policies on the Environmental Risk Assessment

The Environmental Risk Assessment (ERA) of genetically modified (GM) crops in Argentina is carried out by the National Advisory Commission on Agricultural Biotechnology (CONABIA) and the Innovation and Biotechnology Coordination (CIyB). Both have a large experience with this assessment, since 1991, when CONABIA was created. The continuous support to biotechnology as a state policy and as part of the decision to encourage developers in the regulatory process has helped make progress in the revision of the regulations. The experience gained during the last 30 years and the worldwide scientific advances supported the bases to update the regulatory framework. Focusing on the biosafety strengthening and the improvement of the applicant’s experience in the GM crops evaluation process, during 2020 and 2021, the ERA went through a reviewing process. Some important modifications were made, such as (i) the assessment of stacked GM crops with focus on the possible interactions between transgenes and the expression products, (ii) the strengthening of the ERA taking into account the transportability of data and conclusions from the Confined Field Trials (CFTs), (iii) the adoption of Familiarity and History of Safe Use (HOSU) concepts on the risk assessment of the expression products, (iv) the special considerations for the unintended effects of insertional sites, and (v) as a post commercial release of GM crops, the Insect Resistance Management Plan (IRMP) was reformulated. These novel approaches enhance the ERA; they make it more efficient by applying the science criteria and the accumulated experience and scientific bibliography on the topic.

Stability of Transgene Inheritance in Progeny of Field-Grown Pear Trees over a 7-Year Period

Breeding woody plants is a very time-consuming process, and genetic engineering tools have been used to shorten the juvenile phase. In addition, transgenic trees for commercial cultivation can also be used in classical breeding, but the segregation of transgenes in the progeny of perennial plants, as well as the possible appearance of unintended changes, have been poorly investigated. We studied the inheritance of the uidA gene in the progeny of field-grown transgenic pear trees for 7 years and the physical and physiological parameters of transgenic seeds. A total of 13 transgenic lines were analyzed, and the uidA gene segregated 1:1 in the progeny of 9 lines and 3:1 in the progeny of 4 lines, which is consistent with Mendelian inheritance for one and two transgene loci, respectively. Rare and random deviations from the Mendelian ratio were observed only for lines with one locus. Transgenic seeds' mass, size, and shape varied slightly, despite significant fluctuations in weather conditions during cultivation. Expression of the uidA gene in the progeny was stable. Our study showed that the transgene inheritance in the progeny of pear trees under field conditions occurs according to Mendelian ratio, does not depend on the environment, and the seed vigor of transgenic seeds does not change.

RNA Interference-Based Genetic Engineering Maize Resistant to Apolygus lucorum Does Not Manifest Unpredictable Unintended Effects Relative to Conventional Breeding: Short Interfering RNA, Transcriptome, and Metabolome Analysis

The use of omics techniques to analyze the differences between genetic engineering organisms and their parents can identify unintended effects and explore whether such unintended effects will have negative consequences. In order to evaluate whether genetic engineering will cause changes in crops beyond the changes introduced by conventional plant breeding, we compared the extent of transcriptome and metabolome modification in the leaves of three lines developed by RNA interference (RNAi)-based genetic engineering and three lines developed by conventional breeding. The results showed that both types of plant breeding methods can manifest changes at the short interfering RNA (siRNA), transcriptomic, and metabolic levels. Relative expression analysis of potential off-target gene revealed that there was no broad gene decline in the three RNAi-based genetic engineering lines. We found that the number of DEGs and DAMs between RNAi-based genetic engineering lines and the parental line was less than that between conventional breeding lines. These unique DEGs and DAMs between RNAi-based genetic engineering lines and the parental lines were not enriched in detrimental metabolic pathways. The results suggest that RNAi-based genetic engineering do not cause unintended effects beyond those found in conventional breeding in maize.

Addressing the challenges of non-target feeding studies with genetically engineered plant material - stacked Bt maize and Daphnia magna

Previous studies reported adverse effects of genetically engineered maize that produces insecticidal Cry proteins from Bacillus thuringiensis (Bt) on the water flea Daphnia magna. In the current study, effects of flour, leaves, or pollen from stacked Bt maize that contains six Bt proteins (SmartStax) in two plant backgrounds on life table parameters of D. magna were investigated. Adverse effects were observed for Bt maize flour, originating from different production fields and years, but not for leaves or pollen, produced from plants grown concurrently in a glasshouse. Because leaves contained eight to ten times more Cry protein than flour, the effects of the flour were probably not caused by the Cry proteins, but by compositional differences between the plant backgrounds. Furthermore, considering the natural range of variation in the response of D. magna to conventional maize lines, the observed effects of Bt maize flour were unlikely to be of biological relevance. Our study demonstrates how Cry protein effects can be separated from plant background effects in non-target studies using Bt plant material as the test substance and how detected effects can be judged for their biological relevance.

Genetic Engineering and Genome Editing for Improving Nitrogen Use Efficiency in Plants

Low nitrogen availability is one of the main limiting factors for plant growth and development, and high doses of N fertilizers are necessary to achieve high yields in agriculture. However, most N is not used by plants and pollutes the environment. This situation can be improved by enhancing the nitrogen use efficiency (NUE) in plants. NUE is a complex trait driven by multiple interactions between genetic and environmental factors, and its improvement requires a fundamental understanding of the key steps in plant N metabolism—uptake, assimilation, and remobilization. This review summarizes two decades of research into bioengineering modification of N metabolism to increase the biomass accumulation and yield in crops. The expression of structural and regulatory genes was most often altered using overexpression strategies, although RNAi and genome editing techniques were also used. Particular attention was paid to woody plants, which have great economic importance, play a crucial role in the ecosystems and have fundamental differences from herbaceous species. The review also considers the issue of unintended effects of transgenic plants with modified N metabolism, e.g., early flowering—a research topic which is currently receiving little attention. The future prospects of improving NUE in crops, essential for the development of sustainable agriculture, using various approaches and in the context of global climate change, are discussed.

Evaluation of the effect of transgenic Bt cotton on snails Bradybaena (Acusta) ravida and Bradybaena similaris (Ferussac)

The impact of transgenic crops on non-target organisms is a key aspect of environmental safety assessment to transgenic crops. In the present study, we fed two snail species, Bradybaena (Acusta) ravida (B. ravida) and Bradybaena similaris (Ferussac)(B. similaris), with the leaves of transgenic Bt cotton Zhong 30 (Z30) and control cotton, its parent line zhong 16 (Z16), to assess the environmental safety of Bt cotton to common non-target organisms in the field. Survival, body weight, shell diameter, helix number, reproduction rate, superoxide dismutase (SOD) activity and Bt protein concentration in snails were monitored in 15 days and 180 days experiments. We also monitored the population dynamics of B. ravida and B. similaris in Z30 and Z16 cotton fields for two successive years. Compared to the snails fed on the control cotton Z16, there was no significant difference in survival, growth, reproduction, and SOD activity on Bt cotton Z30. Bt protein concentrations were significantly between different treatments, and Bt protein residues were only detected in the feces of the Z30 treatment. According to the field data, the number of B. ravida and B. similaris fluctuated considerably across seasons over the entire cotton-growing season; however, there were no significant differences between the Bt and control cotton fields at similar time. As the results showed, in our experiments, Bt cotton Z30 had no adverse effects on the two snail species, both in the laboratory and in the fields.

Impacts of the regulatory environment for gene editing on delivering beneficial products

Various genome-editing technologies have been embraced by plant breeders across the world as promising tools for the improvement of different crops to deliver consumer benefits, improve agronomic performance, and increase sustainability. The uptake of genome-editing technologies in plant breeding greatly depends on how governments regulate its use. Some major agricultural production countries have already developed regulatory approaches that enable the application of genome editing for crop improvement, while other governments are in the early stages of formulating policy. Central to the discussion is the principle of "like products should be treated in like ways" and the subsequent utilization of exclusions and exemptions from the scope of GMO regulations for these products. In some countries, the outcomes of genome editing that could also have been achieved through conventional breeding have been defined as not needing GMO regulatory oversight. In this paper, we provide a short overview of plant breeding and the history of plant biotechnology policy development, the different classes of current regulatory systems and their use of exemptions and exclusions for genome-edited plants, and the potential benefits of such approaches as it relates to achieving societal goals.

Sustainable use of CRISPR/Cas in fish aquaculture: the biosafety perspective

Aquaculture is becoming the primary source of seafood for human diets, and farmed fish aquaculture is one of its fastest growing sectors. The industry currently faces several challenges including infectious and parasitic diseases, reduced viability, fertility reduction, slow growth, escapee fish and environmental pollution. The commercialization of the growth-enhanced AquAdvantage salmon and the CRISPR/Cas9-developed tilapia (Oreochromis niloticus) proffers genetic engineering and genome editing tools, e.g. CRISPR/Cas, as potential solutions to these challenges. Future traits being developed in different fish species include disease resistance, sterility, and enhanced growth. Despite these notable advances, off-target effect and non-clarification of trait-related genes among other technical challenges hinder full realization of CRISPR/Cas potentials in fish breeding. In addition, current regulatory and risk assessment frameworks are not fit-for purpose regarding the challenges of CRISPR/Cas notwithstanding that public and regulatory acceptance are key to commercialization of products of the new technology. In this study, we discuss how CRISPR/Cas can be used to overcome some of these limitations focusing on diseases and environmental release in farmed fish aquaculture. We further present technical limitations, regulatory and risk assessment challenges of the use of CRISPR/Cas, and proffer research strategies that will provide much-needed data for regulatory decisions, risk assessments, increased public awareness and sustainable applications of CRISPR/Cas in fish aquaculture with emphasis on Atlantic salmon (Salmo salar) breeding.

Variation in non-target traits in genetically modified hybrid aspens does not exceed natural variation

Genetically modified hybrid aspens (Populus tremula L. x P. tremuloides Michx.), selected for increased growth under controlled conditions, have been grown in highly replicated field trials to evaluate how the target trait (growth) translated to natural conditions. Moreover, the variation was compared among genotypes of ecologically important non-target traits: number of shoots, bud set, pathogen infection, amount of insect herbivory, composition of the insect herbivore community and flower bud induction. This variation was compared with the variation in a population of randomly selected natural accessions of P. tremula grown in common garden trials, to estimate how the "unintended variation" present in transgenic trees, which in the future may be commercialized, compares with natural variation. The natural variation in the traits was found to be typically significantly greater. The data suggest that when authorities evaluate the potential risks associated with a field experiment or commercial introduction of transgenic trees, risk evaluation should focus on target traits and that unintentional variation in non-target traits is of less concern.

Performance of Daphnia magna on flour, leaves, and pollen from different maize lines: Implications for risk assessment of genetically engineered crops

Non-target effects of genetically engineered (GE) plants on aquatic Daphnia magna have been studied by feeding the species with different maize materials containing insecticidal Cry proteins from Bacillus thuringiensis (Bt). The results of those studies were often difficult to interpret, because only one GE plant was compared to one related non-GE control. In such a setting, effects of the Cry proteins cannot be distinguished from plant background effects, in particular when the test species is nutritionally stressed. In the present study, we tested the suitability of three different maize materials, i.e., flour, leaves and pollen, from five diverse non-GE maize lines (including EXP 258, a breeding line that is closely related to a SmartStax Bt maize) as exclusive food sources for D. magna. The parameters recorded included survival, sublethal endpoints such as body size, number of moltings to first offspring, time to first offspring, number of individuals in first clutch, total number of clutches, total number of offspring, average number of offspring per clutch, and population measures such as net reproductive rate R₀, generation time T and intrinsic rate of increase r_m. The results showed that D. magna can survive, grow and reproduce when fed only maize materials, although the performance was poorer than when fed algae, which indicates nutritional stress. Large differences in life table and population parameters of D. magna were observed among the different maize lines. Our results suggest that confounding effects caused by nutritional stress and plant background might explain some of the conflicting results previously published on the effects of Bt crops on D. magna. Using 95% confidence intervals for the means of the five maize lines for all measured parameters of D. magna performance in our study, we captured the natural range of variation. This information is useful for the interpretation of observed differences in D. magna performance between a GE plant and its non-GE comparator as it helps judging whether observed effects are of biological relevance. If differences between a GE and comparator line are observed and their biological relevance needs to be assessed in future risk assessments of GE maize, 1) the data on natural variation of the different parameters generated by previous studies can be informative (e.g. data from our study for maize fed D. magna); 2) for additional experiments the inclusion of multiple unrelated non-GE comparators should be considered; In addition, it should be taken into account that nutritional stress can affect the outcome of the study.

Metabolic Analysis Reveals Cry1C Gene Transformation Does Not Affect the Sensitivity of Rice to Rice Dwarf Virus

Metabolomics is beginning to be used for assessing unintended changes in genetically modified (GM) crops. To investigate whether Cry1C gene transformation would induce metabolic changes in rice plants, and whether the metabolic changes would pose potential risks when Cry1C rice plants are exposed to rice dwarf virus (RDV), the metabolic profiles of Cry1C rice T1C-19 and its non-Bt parental rice MH63 under RDV-free and RDV-infected status were analyzed using gas chromatography–mass spectrometry (GC-MS). Compared to MH63 rice, slice difference was detected in T1C-19 under RDV-free conditions (less than 3%), while much more metabolites showed significant response to RDV infection in T1C-19 (15.6%) and in MH63 (5.0%). Pathway analysis showed biosynthesis of lysine, valine, leucine, and isoleucine may be affected by RDV infection in T1C-19. No significant difference in the contents of free amino acids (AAs) was found between T1C-19 and MH63 rice, and the free AA contents of the two rice plants showed similar responses to RDV infection. Furthermore, no significant differences of the RDV infection rates between T1C-19 and MH63 were detected. Our results showed the Cry1C gene transformation did not affect the sensitivity of rice to RDV, indicating Cry1C rice would not aggravate the epidemic and dispersal of RDV.

Molecular characterization for food safety assessment of a genetically modified late blight resistant potato: an unusual case

Standard food safety assessments of genetically modified crops require a thorough molecular characterization of the novel DNA as inserted into the plant that is intended for commercialization, as well as a comparison of agronomic and nutritional characteristics of the genetically modified to the non-modified counterpart. These characterization data are used to identify any unintended changes in the inserted DNA or in the modified plant that would require assessment for safety in addition to the assessment of the intended modification. An unusual case of an unintended effect discovered from the molecular characterization of a genetically modified late blight resistant potato developed for growing in Bangladesh and Indonesia is presented here. Not only was a significant portion of the plasmid vector backbone DNA inserted into the plant along with the intended insertion of an R-gene for late blight resistance, but the inserted DNA was split into two separate fragments and inserted into two separate chromosomes. One fragment carries the R-gene and the other fragment carries the NPTII selectable marker gene and the plasmid backbone DNA. The implications of this for the food safety assessment of this late blight resistant potato are considered.

Nanotechnology to advance CRISPR-Cas genetic engineering of plants

CRISPR-Cas genetic engineering of plants holds tremendous potential for providing food security, battling biotic and abiotic crop stresses caused by climate change, and for environmental remediation and sustainability. Since the discovery of CRISPR-Cas technology, its usefulness has been demonstrated widely, including for genome editing in plants. Despite the revolutionary nature of genome-editing tools and the notable progress that these tools have enabled in plant genetic engineering, there remain many challenges for CRISPR applications in plant biotechnology. Nanomaterials could address some of the most critical challenges of CRISPR genome editing in plants through improvements in cargo delivery, species independence, germline transformation and gene editing efficiency. This Perspective identifies major barriers preventing CRISPR-mediated plant genetic engineering from reaching its full potential, and discusses ways that nanoparticle technologies can lower or eliminate these barriers. We also describe advances that are needed in nanotechnology to facilitate and accelerate plant genome editing. Timely advancement of the application of CRISPR technologies in plant engineering is crucial for our ability to feed and sustain the growing human population under a changing global climate.

Proteomics analysis reveals that foreign cp4-epsps gene regulates the levels of shikimate and branched pathways in genetically modified soybean line H06-698

Although genetically modified (GM) glyphosate-resistant soybeans with cp4-epsps gene have been widely planted all over the world, their proteomic characteristics are not very clear. In this study, the soybean seeds of a GM soybean line H06-698 (H) with cp4-epsps gene and its non-transgenic counterpart Mengdou12 (M), which were collected from two experiment fields in two years and used as 4 sample groups, were analyzed with label-free proteomics technique. A total of 1706 proteins were identified quantitatively by label-free quantification, and a total of 293 proteins were detected as common differential abundance proteins (DAPs, FC is not less than 1.5) both in two groups or more. Functional enrichment analysis of common DAPs identified from four groups, shows that most up-regulated proteins were clustered into stress response, carbon and energy metabolism, and genetic information processing. Further documentary analysis shows that 15 proteins play important roles in shikimate pathways, reactive oxygen species (ROS) and stress response. These results indicated that the change of protein abundance in different samples were affected by various factors, but except shikimate and branched pathways related proteins, only ROS and stress-related proteins were found to be stably regulated by cp4-epsps gene, and no unexpected and safety-related proteins such as antinutritional factors, allergenic proteins, and toxic proteins were found as DAPs. The influence of foreign genes in genetically modified plants is worthy of attention and this work provides new clues for exploring the regulated proteins and pathways in GM plants.

Comparative proteome analyses of rhizomania resistant transgenic sugar beets based on RNA silencing mechanism

Rhizomania is an economically important disease of sugar beet, which is caused by Beet necrotic yellow vein virus (BNYVV). As previously shown, RNA silencing mechanism effectively inhibit the viral propagation in transgenic sugar beet plants. To investigate possible proteomic changes induced by gene insertion and/or RNA silencing mechanism, the root protein profiles of wild type sugar beet genotype 9597, as a control, and transgenic events named 6018-T3:S6-44 (S6) and 219-T3:S3-13.2 (S3) were compared by two-dimensional gel electrophoresis. The accumulation levels of 25 and 24 proteins were differentially regulated in S3 and S6 plants, respectively. The accumulation of 15 spots were increased or decreased more than 2-fold. Additionally, 10 spots repressed or induced in both, while seven spots showed variable results in two events. All the differentially expressed spots were analyzed by MALDI-TOF-TOF mass spectrometry. The functional analysis of differentially accumulated proteins showed that most of them are related to the metabolism and defense/stress response. None of these recognized proteins were allergens or toxic proteins except for a spot identified as phenylcoumaran benzylic ether reductase, Pyrc5, which was decreased in the genetically modified S6 plant. These data are in favor of substantial equivalence of the transgenic plants in comparison to their related wild type cultivar since the proteomic profile of sugar beet root was not remarkably affected by gene transfer and activation RNA silencing mechanism.

Evaluation of the use of untargeted metabolomics in the safety assessment of genetically modified crops

BACKGROUND

The safety assessment of foods and feeds from genetically modified (GM) crops includes the comparison of key characteristics, such as crop composition, agronomic phenotype and observations from animal feeding studies compared to conventional counterpart varieties that have a history of safe consumption, often including a near isogenic variety. The comparative compositional analysis of GM crops has been based on targeted, validated, quantitative analytical methods for the key food and feed nutrients and antinutrients for each crop, as identified by Organization of Economic Co-operation and Development (OCED). As technologies for untargeted metabolomic methods have evolved, proposals have emerged for their use to complement or replace targeted compositional analytical methods in regulatory risk assessments of GM crops to increase the number of analyzed metabolites.

AIM OF REVIEW

The technical opportunities, challenges and strategies of including untargeted metabolomics analysis in the comparative safety assessment of GM crops are reviewed. The results from metabolomics studies of GM and conventional crops published over the last eight years provide context to enable the discussion of whether metabolomics can materially improve the risk assessment of food and feed from GM crops beyond that possible by the Codex-defined practices used worldwide for more than 25 years.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Published studies to date show that environmental and genetic factors affect plant metabolomics profiles. In contrast, the plant biotechnology process used to make GM crops has little, if any consequence, unless the inserted GM trait is intended to alter food or feed composition. The nutritional value and safety of food and feed from GM crops is well informed by the quantitative, validated compositional methods for list of key analytes defined by crop-specific OECD consensus documents. Untargeted metabolic profiling has yet to provide data that better informs the safety assessment of GM crops than the already rigorous Codex-defined quantitative comparative assessment. Furthermore, technical challenges limit the implementation of untargeted metabolomics for regulatory purposes: no single extraction method or analytical technique captures the complete plant metabolome; a large percentage of metabolites features are unknown, requiring additional research to understand if differences for such unknowns affect food/feed safety; and standardized methods are needed to provide reproducible data over time and laboratories.

Comparative efficacy of gypsy moth (Lepidoptera: Erebidae) entomopathogens on transgenic blight-tolerant and wild-type American, Chinese, and hybrid chestnuts (Fagales: Fagaceae)

American chestnut (Castanea dentata [Marsh.] Borkh.) was once the dominant hardwood species in Eastern North America before an exotic fungal pathogen, Cryphonectria parasitica (Murrill) Barr, functionally eliminated it across its range. One promising approach toward restoring American chestnut to natural forests is development of blight-tolerant trees using genetic transformation. However, transformation and related processes can result in unexpected and unintended phenotypic changes, potentially altering ecological interactions. To assess unintended tritrophic impacts of transgenic American chestnut on plant-herbivore interactions, gypsy moth (Lymantria dispar L.) caterpillars were fed leaf disks excised from two transgenic events, Darling 54 and Darling 58, and four control American chestnut lines. Leaf disks were previously treated with an LD₅₀ dose of either the species-specific Lymantria dispar multiple nucleopolyhedrovirus (LdMNPV) or the generalist pathogen Bacillus thuringiensis subsp. kurstaki (Btk). Mortality was quantified and compared to water blank controls. Tree genotype had a strong effect on the efficacies of both pathogens. Larval mortality from Btk-treated foliage from only one transgenic event, Darling 54, differed from its isogenic progenitor, Ellis 1, but was similar to an unrelated wild-type American chestnut control. LdMNPV efficacy was unaffected by genetic transformation. Results suggest that although genetic modification of trees may affect interactions with other nontarget organisms, this may be due to insertion effects, and variation among different genotypes (whether transgenic or wild-type) imparts a greater change in response than transgene presence.

Are Physicochemical Properties Shaping the Allergenic Potency of Plant Allergens?

This review searched for published evidence that could explain how different physicochemical properties impact on the allergenicity of food proteins and if their effects would follow specific patterns among distinct protein families. Owing to the amount and complexity of the collected information, this literature overview was divided in two articles, the current one dedicated to protein families of plant allergens and a second one focused on animal allergens. Our extensive analysis of the available literature revealed that physicochemical characteristics had consistent effects on protein allergenicity for allergens belonging to the same protein family. For example, protein aggregation contributes to increased allergenicity of 2S albumins, while for legumins and cereal prolamins, the same phenomenon leads to a reduction. Molecular stability, related to structural resistance to heat and proteolysis, was identified as the most common feature promoting plant protein allergenicity, although it fails to explain the potency of some unstable allergens (e.g. pollen-related food allergens). Furthermore, data on physicochemical characteristics translating into clinical effects are limited, mainly because most studies are focused on in vitro IgE binding. Clinical data assessing how these parameters affect the development and clinical manifestation of allergies is minimal, with only few reports evaluating the sensitising capacity of modified proteins (addressing different physicochemical properties) in murine allergy models. In vivo testing of modified pure proteins by SPT or DBPCFC is scarce. At this stage, a systematic approach to link the physicochemical properties with clinical plant allergenicity in real-life scenarios is still missing.

Plant breeding involving genetic engineering does not result in unacceptable unintended effects in rice relative to conventional cross-breeding

Advancements in -omics techniques provide powerful tools to assess the potential effects in composition of a plant at the RNA, protein and metabolite levels. These technologies can thus be deployed to assess whether genetic engineering (GE) causes changes in plants that go beyond the changes introduced by conventional plant breeding. Here, we compare the extent of transcriptome and metabolome modification occurring in leaves of four GE rice lines expressing Bacillus thuringiensis genes developed by GE and seven rice lines developed by conventional cross-breeding. The results showed that both types of crop breeding methods can bring changes at transcriptomic and metabolic levels, but the differences were comparable between the two methods, and were less than those between conventional non-GE lines were. Metabolome profiling analysis found several new metabolites in GE rice lines when compared with the closest non-GE parental lines, but these compounds were also found in several of the conventionally bred rice lines. Functional analyses suggest that the differentially expressed genes and metabolites caused by both GE and conventional cross-breeding do not involve detrimental metabolic pathways. The study successfully employed RNA-sequencing and high-performance liquid chromatography mass spectrometry technology to assess the unintended changes in new rice varieties, and the results suggest that GE does not cause unintended effects that go beyond conventional cross-breeding in rice.

Paraguay's Path Toward the Simplification of Procedures in the Approval of GE Crops

Agricultural biotechnology was first regulated in Paraguay in 1997. The first update to the country's regulatory framework came in 2012, motivated by the need to keep up with current technologies. As part of this process, in late 2012, the Paraguayan Ministry of Agriculture (MAG) joined the Partnership for Biosafety Risk Assessment and Regulation, led by ILSI Research Foundation. The purpose of the program was the development of capacity building activities. As a result, the regulatory authorities in Paraguay incorporated the problem formulation approach to environmental risk assessment into their regulatory processes, leading to improved efficiency, with more timely decisions. Shifting to a problem formulation-based decision-making system was not straightforward, since practice and experience are always required to make professional risk assessors. Despite the continuity of approvals, there was a lag in the response time reflected in the number of events approved. During 2019, a simplified approval procedure for events that have been assessed by sound and experienced regulatory systems was introduced. Acceptance of third-country assessments can allow regulatory systems to make better use of their human, financial, and institutional resources, and stimulate inter-agency cooperation. In this work we aim to present the recent evolution of the regulatory system in Paraguay toward the establishment of a simplified procedure for GE crops that have been already assessed by sound and experienced regulatory systems, taking into account several scientific criteria. Concepts such as the familiarity, history of safe use, substantial equivalence, transportability, problem formulation, and the use of the consensus documents, developed by Organization for Economic Co-operation and Development (OECD), Food and Agriculture Organization of the United Nations (FAO), World Health Organization (WHO) and other institutions, favors the acceptance of decision documents issued by third countries. This requires the commitment of governments to support the stability of the institutions responsible for the regulatory implementation and also encourages countries to put work into the preparation and publication of decision documents, which are the basis for the commercialization of GE events.

Development and characterization of marker-free and transgene insertion site-defined transgenic wheat with improved grain storability and fatty acid content

Development of marker-free and transgene insertion site-defined (MFTID) transgenic plants is essential for safe application of transgenic crops. However, MFTID plants have not been reported for wheat (Triticum aestivum). Here, we prepared a RNAi cassette for suppressing lipoxygenase (LOX) gene expression in wheat grains using a double right border T-DNA vector. The resultant construct was introduced into wheat genome via Agrobacterium-mediated transformation, with four homozygous marker-free transgenic lines (namely GLRW-1, -3, -5 and -8) developed. Aided by the newly published wheat genome sequence, the T-DNA insertion sites in GLRW-3 and GLRW-8 were elucidated at base-pair resolution. While the T-DNA in GLRW-3 inserted in an intergenic region, that of GLRW-8 inactivated an endogenous gene, which was thus excluded from further analysis. Compared to wild -type (WT) control, GLRW-1, -3 and -5 showed decreased LOX gene expression, lower LOX activity and less lipid peroxidation in the grains; they also exhibited significantly higher germination rates and better seedling growth after artificial ageing treatment. Interestingly, the three GLRW lines also had substantially increased contents of several fatty acids (e.g., linoleic acid and linolenic acid) in their grain and flour samples than WT control. Collectively, our data suggest that suppression of grain LOX activity can be employed to improve the storability and fatty acid content of wheat seeds and that the MFTID line GLRW-3 is likely of commercial value. Our approach may also be useful for developing the MFTID transgenic lines of other crops with enhanced grain storability and fatty acid content.

Transgenic Winter Wheat Expressing the Sucrose Transporter HvSUT1 from Barley does not Affect Aphid Performance

Winter wheat expressing the sucrose transporter HvSUT1 from barley (HOSUT) has an increased yield potential. Genetic engineering should improve cultivars without increasing susceptibility to biotic stresses or causing negative impacts on ecosystem services. We studied the effects of HOSUT wheat on cereal aphids that feed on the sugar-rich phloem sap. Three HOSUT winter wheat lines, their conventional parental cultivar Certo, and three conventional cultivars were used. Clip cage experiments in the greenhouse showed no differences in life-table parameters of Rhopalosiphum padi and Sitobion avenae (Hemiptera: Aphididae) on transgenic lines compared to Certo, except higher fecundity of S.avenae on one HOSUT line. Population development of both aphid species over three weeks on caged flowering tillers did not reveal differences between the HOSUT lines and Certo. When aphids were monitored in a Swiss field study over two years, no differences between HOSUT lines and Certo were observed. We conclude that HOSUT wheat did not have consistent effects on aphids compared to the parental cultivar and measured parameters were generally in the range observed for the conventional winter wheat cultivars. Thus, HOSUT wheat is unlikely to suffer from increased aphid damage.

The Rooting of Stem Cuttings and the Stability of uidA Gene Expression in Generative and Vegetative Progeny of Transgenic Pear Rootstock in the Field

Adventitious rooting plays an important role in the commercial vegetative propagation of trees. Adventitious root formation is a complex biological process, but knowledge of the possible unintended effects induced by both the integration/expression of transgenes and in vitro conditions on the rooting is limited. The long-term stability of transgene expression is important both for original transformants of woody plants and its progeny. In this study, we used field-grown pear rootstock GP217 trees transformed with the reporter ß-glucuronidase (uidA) genes with and without intron and re-transformed with the herbicide resistance bar gene as model systems. We assessed the unintended effects on rooting of pear semi-hardwood cuttings and evaluated the stability of transgene expression in progeny produced by generative (seedlings) and vegetative (grafting, cutting) means up to four years. Our investigation revealed that: (1) The single and repeated transformations of clonal pear rootstocks did not result in unintended effects on adventitious root formation in cuttings; (2) stability of the transgene expression was confirmed on both generative and vegetative progeny, and no silenced transgenic plants were detected; (3) yearly variation in the gene expressions was observed and expression levels were decreased in extremely hot and dry summer; (4) the intron enhanced the expression of uidA gene in pear plants approximately two-fold compared to gene without intron. The current study provides useful information on transgene expression in progeny of fruit trees under natural environmental conditions.

Comparative Proteomics of Phytase-transgenic Maize Seeds Indicates Environmental Influence is More Important than that of Gene Insertion

Proteomic differences were compared between phytase-transgenic (PT) maize seeds and nontransgenic (NT) maize seeds through two-dimensional electrophoresis (2-DE) with mass spectrometry (MS). When maize was grown under field conditions, 30 differentially accumulated proteins (DAPs) were successfully identified in PT seeds (PT/NT). Clusters of Orthologous Groups (COG) functional classification of these proteins showed that the largest group was associated with posttranslational modifications. To investigate the effects of environmental factors, we further compared the seed protein profiles of the same maize planted in a greenhouse or under field conditions. There were 76 DAPs between the greenhouse- and field-grown NT maize seeds and 77 DAPs between the greenhouse- and field-grown PT maize seeds However, under the same planting conditions, there were only 43 DAPs (planted in the greenhouse) or 37 DAPs (planted in the field) between PT and NT maize seeds. The results revealed that DAPs caused by environmental factors were more common than those caused by the insertion of exogenous genes, indicating that the environment has much more important effects on the seed protein profiles. Our maize seed proteomics results also indicated that the occurrence of unintended effects is not specific to genetically modified crops (GMCs); instead, such effects often occur in traditionally bred plants. Our data may be beneficial for biosafety assessments of GMCs at the protein profile level in the future.

Risk Assessment and Regulation of Plants Modified by Modern Biotechniques: Current Status and Future Challenges

This review describes the current status and future challenges of risk assessment and regulation of plants modified by modern biotechniques, namely genetic engineering and genome editing. It provides a general overview of the biosafety and regulation of genetically modified plants and details different regulatory frameworks with a focus on the European situation. The environmental risk and safety assessment of genetically modified plants is explained, and aspects of toxicological assessments are discussed, especially the controversial debate in Europe on the added scientific value of untargeted animal feeding studies. Because RNA interference (RNAi) is increasingly explored for commercial applications, the risk and safety assessment of RNAi-based genetically modified plants is also elucidated. The production, detection, and identification of genome-edited plants are described. Recent applications of modern biotechniques, namely synthetic biology and gene drives, are discussed, and a short outlook on the future follows.

Unintended effects of transgenic rice revealed by transcriptome and metabolism

Genetically modified (GM) organisms have been developed for decades. However, unintended effects are the main concerns of safety assessment that needs to be carefully investigated. Here, eight varieties of GM rice that were developed in China were selected to assess the unintended effects through transcriptome and metabolism. There are 2892-8758 differentially expressed genes (DEGs) and 7-50 metabolites at significant level between GM varieties and their isogenic counterparts, which were far fewer than that between traditional rice varieties. The function enrichment analysis showed altered transcription in stress-related pathway and starch and sucrose metabolism. DEGs shared among eight GM samples constitute less than 1% of the genes in the genome, and none of them is reported more than four times. The insertion effect on the nearby gene expression and the associated metabolism is only restricted to 50 genes. All the results provide a comprehensive analysis of unintended effects and indication of difference in Chinese transgenic rice based on their backgrounds, transformation, and insertion elements.

An EU Perspective on Biosafety Considerations for Plants Developed by Genome Editing and Other New Genetic Modification Techniques (nGMs)

The question whether new genetic modification techniques (nGM) in plant development might result in non-negligible negative effects for the environment and/or health is significant for the discussion concerning their regulation. However, current knowledge to address this issue is limited for most nGMs, particularly for recently developed nGMs, like genome editing, and their newly emerging variations, e.g., base editing. This leads to uncertainties regarding the risk/safety-status of plants which are developed with a broad range of different nGMs, especially genome editing, and other nGMs such as cisgenesis, transgrafting, haploid induction or reverse breeding. A literature survey was conducted to identify plants developed by nGMs which are relevant for future agricultural use. Such nGM plants were analyzed for hazards associated either (i) with their developed traits and their use or (ii) with unintended changes resulting from the nGMs or other methods applied during breeding. Several traits are likely to become particularly relevant in the future for nGM plants, namely herbicide resistance (HR), resistance to different plant pathogens as well as modified composition, morphology, fitness (e.g., increased resistance to cold/frost, drought, or salinity) or modified reproductive characteristics. Some traits such as resistance to certain herbicides are already known from existing GM crops and their previous assessments identified issues of concern and/or risks, such as the development of herbicide resistant weeds. Other traits in nGM plants are novel; meaning they are not present in agricultural plants currently cultivated with a history of safe use, and their underlying physiological mechanisms are not yet sufficiently elucidated. Characteristics of some genome editing applications, e.g., the small extent of genomic sequence change and their higher targeting efficiency, i.e., precision, cannot be considered an indication of safety per se, especially in relation to novel traits created by such modifications. All nGMs considered here can result in unintended changes of different types and frequencies. However, the rapid development of nGM plants can compromise the detection and elimination of unintended effects. Thus, a case-specific premarket risk assessment should be conducted for nGM plants, including an appropriate molecular characterization to identify unintended changes and/or confirm the absence of unwanted transgenic sequences.

Plants Developed by New Genetic Modification Techniques-Comparison of Existing Regulatory Frameworks in the EU and Non-EU Countries

The development of new genetic modification techniques (nGMs), also referred to as "new (breeding) techniques" in other sources, has raised worldwide discussions regarding their regulation. Different existing regulatory frameworks for genetically modified organisms (GMO) cover nGMs to varying degrees. Coverage of nGMs depends mostly on the regulatory trigger. In general two different trigger systems can be distinguished, taking into account either the process applied during development or the characteristics of the resulting product. A key question is whether regulatory frameworks either based on process- or product-oriented triggers are more advantageous for the regulation of nGM applications. We analyzed regulatory frameworks for GMO from different countries covering both trigger systems with a focus on their applicability to plants developed by various nGMs. The study is based on a literature analysis and qualitative interviews with regulatory experts and risk assessors of GMO in the respective countries. The applied principles of risk assessment are very similar in all investigated countries independent of the applied trigger for regulation. Even though the regulatory trigger is either process- or product-oriented, both triggers systems show features of the respective other in practice. In addition our analysis shows that both trigger systems have a number of generic advantages and disadvantages, but neither system can be regarded as superior at a general level. More decisive for the regulation of organisms or products, especially nGM applications, are the variable criteria and exceptions used to implement the triggers in the different regulatory frameworks. There are discussions and consultations in some countries about whether changes in legislation are necessary to establish a desired level of regulation of nGMs. We identified five strategies for countries that desire to regulate nGM applications for biosafety-ranging from applying existing biosafety frameworks without further amendments to establishing new stand-alone legislation. Due to varying degrees of nGM regulation, international harmonization will supposedly not be achieved in the near future. In the context of international trade, transparency of the regulatory status of individual nGM products is a crucial issue. We therefore propose to introduce an international public registry listing all biotechnology products commercially used in agriculture.

Scientific mistakes from the agri-food biotech critics

Critics of the use of advanced biotechnologies in the agri-food sector ("New Breeding Techniques", comprising CRISPR) demand a strict regulation of any such method, even more severe than rules applied to so-called "Genetically Modified Organisms" (i.e. recombinant DNA processes and products). But their position is unwarranted, since it relies on faulty arguments.While most life scientists have always explained that the trigger for regulation should be the single product and its phenotypic traits, opponents insist that the target should be certain biotech processes.The antagonists maintain that NBTs are inherently risky: this belief is exactly the opposite of a long-standing, overwhelming scientific consensus. NBTs involve unpredictable effects, but it is the same for the results of any other technique. The critics wrongly equate "unintended" with "harmful" and misunderstand two meanings of "risk": the "risk" of not achieving satisfactory results does not automatically translate into health or environment "risks". Generic claims that allergenic or toxic properties are a hidden danger of outcomes from NBTs are unsubstantiated - as they would be for traditional techniques.Among several errors, we criticize the misuse of the Precautionary principle, a misplaced alarm about "uncontrolled spreading" of genetically engineered cultivars and the groundless comparison of (hypothetical) agricultural products from NBTs with known toxic substances.In order to "save" traditional techniques from "GMO"-like regulations, while calling for the enforcement of similar sectarian rules for the NBTs, the dissenters engage in baseless, unscientific distinctions.Important and necessary socio-economic, ethical and legal considerations related to the use of agri-food biotechnologies (older and newer) are outside the scope of this paper, which mostly deals with arguments from genetics, biology, and evolutionary theory that are provided by those who are suspicious of NBTs. Yet, we will provide some hints on two additional facets of the debate: the possible motivations for certain groups to embrace views which are utterly anti-scientific, and the shaky regulatory destiny of NBTs in the European Union.

Contribution of Untargeted Metabolomics for Future Assessment of Biotech Crops

The nutritional value and safety of food crops are ultimately determined by their chemical composition. Recent developments in the field of metabolomics have made it possible to characterize the metabolic profile of crops in a comprehensive and high-throughput manner. Here, we propose that state-of-the-art untargeted metabolomics technology should be leveraged for safety assessment of new crop products. We suggest generally applicable experimental design principles that facilitate the efficient and rigorous identification of both intended and unintended metabolic alterations associated with a newly engineered trait. Our proposition could contribute to increased transparency of the safety assessment process for new biotech crops.

Assessment of the potential allergenicity of genetically-engineered food crops

An extensive safety assessment process exists for genetically-engineered (GE) crops. The assessment includes an evaluation of the introduced protein as well as the crop containing the protein with the goal of demonstrating the GE crop is "as-safe-as" non-GE crops in the food supply. One of the evaluations for GE crops is to assess the expressed protein for allergenic potential. Currently, no single factor is recognized as a predictor for protein allergenicity. Therefore, a weight-of-the-evidence approach, which accounts for a variety of factors and approaches for an overall assessment of allergenic potential, is conducted. This assessment includes an evaluation of the history of exposure and safety of the gene(s) source; protein structure (e.g. amino acid sequence identity to human allergens); stability of the protein to pepsin digestion in vitro; heat stability of the protein; glycosylation status; and when appropriate, specific IgE binding studies with sera from relevant clinically allergic subjects. Since GE crops were first commercialized over 20 years ago, there is no proof that the introduced novel protein(s) in any commercialized GE food crop has caused food allergy.