A comparative analysis of insertional effects in genetically engineered plants: considerations for pre-market assessments

IPD3, a master regulator of arbuscular mycorrhizal symbiosis, affects genes for immunity and metabolism of non-host Arabidopsis when restored long after its evolutionary loss

Arbuscular mycorrhizal symbiosis (AM) is a beneficial trait originating with the first land plants, which has subsequently been lost by species scattered throughout the radiation of plant diversity to the present day, including the model Arabidopsis thaliana. To explore if elements of this apparently beneficial trait are still present and could be reactivated we generated Arabidopsis plants expressing a constitutively active form of Interacting Protein of DMI3, a key transcription factor that enables AM within the Common Symbiosis Pathway, which was lost from Arabidopsis along with the AM host trait. We characterize the transcriptomic effect of expressing IPD3 in Arabidopsis with and without exposure to the AM fungus (AMF) Rhizophagus irregularis, and compare these results to the AM model Lotus japonicus and its ipd3 knockout mutant cyclops-4. Despite its long history as a non-AM species, restoring IPD3 in the form of its constitutively active DNA-binding domain to Arabidopsis altered expression of specific gene networks. Surprisingly, the effect of expressing IPD3 in Arabidopsis and knocking it out in Lotus was strongest in plants not exposed to AMF, which is revealed to be due to changes in IPD3 genotype causing a transcriptional state, which partially mimics AMF exposure in non-inoculated plants. Our results indicate that molecular connections to symbiosis machinery remain in place in this nonAM species, with implications for both basic science and the prospect of engineering this trait for agriculture.

T-DNA characterization of genetically modified 3-R-gene late blight-resistant potato events with a novel procedure utilizing the Samplix Xdrop® enrichment technology

Before the commercialization of genetically modified crops, the events carrying the novel DNA must be thoroughly evaluated for agronomic, nutritional, and molecular characteristics. Over the years, polymerase chain reaction-based methods, Southern blot, and short-read sequencing techniques have been utilized for collecting molecular characterization data. Multiple genomic applications are necessary to determine the insert location, flanking sequence analysis, characterization of the inserted DNA, and determination of any interruption of native genes. These techniques are time-consuming and labor-intensive, making it difficult to characterize multiple events. Current advances in sequencing technologies are enabling whole-genomic sequencing of modified crops to obtain full molecular characterization. However, in polyploids, such as the tetraploid potato, it is a challenge to obtain whole-genomic sequencing coverage that meets the regulatory approval of the genetic modification. Here we describe an alternative to labor-intensive applications with a novel procedure using Samplix Xdrop® enrichment technology and next-generation Nanopore sequencing technology to more efficiently characterize the T-DNA insertions of four genetically modified potato events developed by the Feed the Future Global Biotech Potato Partnership: DIA_MSU_UB015, DIA_MSU_UB255, GRA_MSU_UG234, and GRA_MSU_UG265 (derived from regionally important varieties Diamant and Granola). Using the Xdrop® /Nanopore technique, we obtained a very high sequence read coverage within the T-DNA and junction regions. In three of the four events, we were able to use the data to confirm single T-DNA insertions, identify insert locations, identify flanking sequences, and characterize the inserted T-DNA. We further used the characterization data to identify native gene interruption and confirm the stability of the T-DNA across clonal cycles. These results demonstrate the functionality of using the Xdrop® /Nanopore technique for T-DNA characterization. This research will contribute to meeting regulatory safety and regulatory approval requirements for commercialization with small shareholder farmers in target countries within our partnership.

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.

Green revolution to genome revolution: driving better resilient crops against environmental instability

Crop improvement programmes began with traditional breeding practices since the inception of agriculture. Farmers and plant breeders continue to use these strategies for crop improvement due to their broad application in modifying crop genetic compositions. Nonetheless, conventional breeding has significant downsides in regard to effort and time. Crop productivity seems to be hitting a plateau as a consequence of environmental issues and the scarcity of agricultural land. Therefore, continuous pursuit of advancement in crop improvement is essential. Recent technical innovations have resulted in a revolutionary shift in the pattern of breeding methods, leaning further towards molecular approaches. Among the promising approaches, marker-assisted selection, QTL mapping, omics-assisted breeding, genome-wide association studies and genome editing have lately gained prominence. Several governments have progressively relaxed their restrictions relating to genome editing. The present review highlights the evolutionary and revolutionary approaches that have been utilized for crop improvement in a bid to produce climate-resilient crops observing the consequence of climate change. Additionally, it will contribute to the comprehension of plant breeding succession so far. Investing in advanced sequencing technologies and bioinformatics will deepen our understanding of genetic variations and their functional implications, contributing to breakthroughs in crop improvement and biodiversity conservation.

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.

Ribosome inactivating proteins - An unfathomed biomolecule for developing multi-stress tolerant transgenic plants

Transgenic crops would serve as a tool to overcome the forthcoming crisis in food security and environmental safety posed by degrading land and changing global climate. Commercial transgenic crops developed so far focus on single stress; however, sustaining crop yield to ensure food security requires transgenics tolerant to multiple environmental stresses. Here we argue and demonstrate the untapped potential of ribosome inactivating proteins (RIPs), translation inhibitors, as potential transgenes in developing transgenics to combat multiple stresses in the environment. Plant RIPs target the fundamental processes of the cell with very high specificity to the infecting pests. While controlling pathogens, RIPs also cause ectopic expression of pathogenesis-related proteins and trigger systemic acquired resistance. On the other hand, during abiotic stress, RIPs show antioxidant activity and trigger both enzyme-dependent and enzyme-independent metabolic pathways, alleviating abiotic stress such as drought, salinity, temperature, etc. RIPs express in response to specific environmental signals; therefore, their expression obviates additional physiological load on the transgenic plants instead of the constitutive expression. Based on evidence from its biological significance, ecological roles, laboratory- and controlled-environment success of its transgenics, and ethical merits, we unravel the potential of RIPs in developing transgenic plants showing co-tolerance to multiple environmental stresses.

MqsR toxin as a biotechnological tool for plant pathogen bacterial control

Type II toxin-antitoxin (TA) systems are widespread in bacteria and are involved in important cell features, such as cell growth inhibition and antimicrobial tolerance, through the induction of persister cells. Overall, these characteristics are associated with bacterial survival under stress conditions and represent a significant genetic mechanism to be explored for antibacterial molecules. We verified that even though Xylella fastidiosa and Xanthomonas citri subsp. citri share closely related genomes, they have different Type II TA system contents. One important difference is the absence of mqsRA in X. citri. The toxin component of this TA system has been shown to inhibit the growth of X. fastidiosa. Thus, the absence of mqsRA in X. citri led us to explore the possibility of using the MqsR toxin to impair X. citri growth. We purified MqsR and confirmed that the toxin was able to inhibit X. citri. Subsequently, transgenic citrus plants producing MqsR showed a significant reduction in citrus canker and citrus variegated chlorosis symptoms caused, respectively, by X. citri and X. fastidiosa. This study demonstrates that the use of toxins from TA systems is a promising strategy to be explored aiming bacterial control.

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.

Dietary Behavior of Drosophila melanogaster Fed with Genetically-Modified Corn or Roundup®

With the rise in concern about GMOs and pesticides on human health, we have utilized Drosophila melanogaster as a model organism for understanding the effects of Roundup-Ready^® GMO diets on health. We recorded dietary behavior during and after exposure to a medium containing GMO or non-GMO corn, Roundup^® in organic corn medium, and sucrose with or without one of the two Roundup^® formulations. No differences in behavior were observed when Drosophila were exposed to a medium containing Roundup-Ready^® GMO or non-GMO corn. Drosophila can detect and refrain from eating sucrose containing one Roundup^® formulation, Ready-to-Use, which contains pelargonic acid in addition to glyphosate as an active ingredient. Drosophila exhibited dose-dependent increased consumption of sucrose alone after exposure to a medium containing either Roundup^® formulation. This may indicate that flies eating a medium with Roundup^® eat less and were thus hungrier when then given sucrose solution; that a medium with Roundup^® is more difficult to digest; or that a medium with Roundup^® is less nutritious, as would be the case if nutritionally important microbes grew on control medium, but not one containing Roundup^®.

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.

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.

Transparency in risk-disproportionate regulation of modern crop-breeding techniques

Despite over 25 years of safe deployment of genetically engineered crops, the number, complexity, and scope of regulatory studies required for global approvals continue to increase devoid of adequate scientific justification. Recently, there have been calls to further expand the scope of study and data requirements to improve public acceptance. However, increased regulation can actually generate consumer distrust due to the misperception that risks are high. We believe risk-disproportionate regulation as a means to advocate for acceptance of technology is counterproductive, even though some regulatory authorities believe it part of their mandate. To help avoid public distrust, the concept of regulatory transparency to demystify regulatory decision-making should be extended to clearly justifying specific regulatory requirements as: 1) risk-driven (i.e., proportionately addressing increased risk compared with traditional breeding), or 2) advocacy-driven (i.e., primarily addressing consumer concerns and acceptance). Such transparency in the motivation for requiring risk-disproportionate studies would: 1) lessen over-prescriptive regulation, 2) save public and private resources, 3) make beneficial products and technologies available to society sooner, 4) reduce needless animal sacrifice, 5) improve regulatory decision-making regarding safety, and 6) lessen public distrust that is generated by risk-disproportionate regulation.

Influence of transgenesis on genome variability in cucumber lines with a thaumatin II gene

The development of new plant varieties by genetic modification aims at improving their features or introducing new qualities. However, concerns about the unintended effects of transgenes and negative environmental impact of genetically modified plants are an obstacle for the use of these plants in crops. To analyze the impact of transgenesis on plant genomes, we analyze three cucumber transgenic lines with an introduced thaumatin II gene. After genomes sequencing, we analyzed the transgene insertion site and performed variant prediction. As a result, we obtained similar number of variants for all analyzed lines (average of 4307 polymorphisms), with high abundance in one region of chromosome 4. According to SnpEff analysis, the presence of genomic variants generally does not influence the genome functionality, as less than 2% of polymorphisms have high impact. Moreover, analysis indicates that these changes were more likely induced by in vitro culture than by the transgenesis itself. The insertion site analysis shows that the region of transgene integration could cause changes in gene expression, by gene disruption or loss of promoter region continuity.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-00990-8.

Hypothesis-based food, feed, and environmental safety assessment of GM crops: A case study using maize event DP-202216-6

Event DP-2Ø2216-6 (referred to as DP202216 maize) was genetically modified to increase and extend the expression of the introduced zmm28 gene relative to endogenous zmm28 gene expression, resulting in plants with enhanced grain yield potential. The zmm28 gene expresses the ZMM28 protein, a MADS-box transcription factor. The safety assessment of DP202216 maize included an assessment of the potential hazard of the ZMM28 protein, as well as an assessment of potential unintended effects of the genetic insertion on agronomics, composition, and nutrition. The history of safe use (HOSU) of the ZMM28 protein was evaluated and a bioinformatics approach was used to compare the deduced amino acid sequence of the ZMM28 protein to databases of known allergens and toxins. Based on HOSU and the bioinformatics assessment, the ZMM28 protein was determined to be unlikely to be either allergenic or toxic to humans. The composition of DP202216 maize forage and grain was comparable to non-modified forage and grain, with no unintended effects on nutrition or food and feed safety. Additionally, feeding studies with broiler chickens and rats demonstrated a low likelihood of unintentional alterations in nutrition and low potential for adverse effects. Furthermore, the agronomics observed for DP202216 maize and non-modified maize were comparable, indicating that the likelihood of increased weediness or invasiveness of DP202216 maize in the environment is low. This comprehensive review serves as a reference for regulatory agencies and decision-makers in countries where authorization of DP202216 maize will be pursued, and for others interested in food, feed, and environmental safety.

Defining the 'HoneySweet' insertion event utilizing NextGen sequencing and a de novo genome assembly of plum (Prunus domestica)

'HoneySweet' plum (Prunus domestica) is resistant to Plum pox potyvirus, through an RNAi-triggered mechanism. Determining the precise nature of the transgene insertion event has been complicated due to the hexaploid genome of plum. DNA blots previously indicated an unintended hairpin arrangement of the Plum pox potyvirus coat protein gene as well as a multicopy insertion event. To confirm the transgene arrangement of the insertion event, 'HoneySweet' DNA was subjected to whole genome sequencing using Illumina short-read technology. Results indicated two different insertion events, one containing seven partial copies flanked by putative plum DNA sequence and a second with the predicted inverted repeat of the coat protein gene driven by a double 35S promoter on each side, flanked by plum DNA. To determine the locations of the two transgene insertions, a phased plum genome assembly was developed from the commercial plum 'Improved French'. A subset of the scaffolds (2447) that were >10 kb in length and representing, >95% of the genome were annotated and used for alignment against the 'HoneySweet' transgene reads. Four of eight matching scaffolds spanned both insertion sites ranging from 157,704 to 654,883 bp apart, however we were unable to identify which scaffold(s) represented the actual location of the insertion sites due to potential sequence differences between the two plum cultivars. Regardless, there was no evidence of any gene(s) being interrupted as a result of the insertions. Furthermore, RNA-seq data verified that the insertions created no new transcriptional units and no dramatic expression changes of neighboring genes.

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.

DP-2Ø2216-6 maize does not adversely affect rats in a 90-day feeding study

Maize plants containing event DP-2Ø2216-6 (DP202216), which confers herbicide tolerance through expression of phosphinothricin acetyltransferase and enhanced grain yield potential via temporal modulation of the native ZMM28 protein, were developed for commercialization. To address current regulatory expectations, a mandatory 90-day rodent feeding study was conducted to support the safety assessment. Diets containing 50% by weight of ground maize grain from DP202216, non-transgenic control, and 3 non-transgenic reference varieties, were fully characterized, along with the grain, and diets were fed to Crl:CD®(SD) rats for at least 90 days. As anticipated, no biologically-relevant effects or toxicologically-significant differences were observed on survival, body weight/gain, food consumption/efficiency, clinical and neurobehavioral evaluations, ophthalmology, clinical pathology (hematology, coagulation, clinical chemistry, urinalysis), organ weights, or gross and microscopic pathology parameters in rats fed a diet containing up to 50% DP202216 maize grain when compared with rats fed diets containing control or reference maize grains. The results of this study support the conclusion that maize grain from plants containing event DP-2Ø2216-6 is as safe and nutritious as maize grain not containing the event and add to the significant existing database of rodent subchronic studies demonstrating the absence of hazards from consumption of edible fractions of genetically modified plants.

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.

Obligatory metabolomic profiling of gene-edited crops is risk disproportionate

It has been argued that the application of metabolomics to gene-edited crops would present value in three areas: (i) the detection of gene-edited crops; (ii) the characterization of unexpected changes that might affect safety; and (iii) building on the track record of rigorous government regulation in supporting consumer acceptance of genetically modified organisms (GMOs). Here, we offer a different perspective, relative to each of these areas: (i) metabolomics is unable to differentiate whether a mutation has resulted from gene editing or from traditional breeding techniques; (ii) it is risk-disproportionate to apply metabolomics for regulatory purposes to search for possible compositional differences within crops developed using the least likely technique to generate unexpected compositional changes; and (iii) onerous regulations for genetically engineered crops have only contributed to unwarranted public fears, and repeating this approach for gene-edited crops is unlikely to result in a different outcome. It is also suggested that article proposing the utility of specific analytical techniques to support risk assessment would benefit from the input of scientists with subject matter expertise in risk assessment.

Event-specific qualitative polymerase chain reaction analysis for two T-DNA copies in genetically modified orange Petunia

In 2017, various orange coloured petunia on the market turned out to be genetically modified (GM) without an official authorization for commercialization. Sequence analysis suggested these undeclared plants most probably originated from a plant transformation experiment performed in the 1980s. For a deeper understanding how GM petunia entered classical breeding programmes worldwide, and whether they originated from a single source or not, we undertook a molecular genetic characterization of the T-DNA integration sites in different GM petunia cultivars and breeding lines. By means of genome walking, we isolated different T-DNA sequences, which are located at the junctions between the T-DNA(s) and the petunia DNA. Based on the results obtained we conclude that there are at least two T-DNA copies of different lengths. This is supported by Southern blot analysis. For T-DNA1, the 3'-junction sequence was isolated, whereas the 5'-junction remained unclear. In contrast, for T-DNA2, the 5'-junction sequence was isolated, whereas the sequence isolated from the 3'-region consists only of T-DNA, but did not include the junction from the T-DNA to the petunia DNA. We developed primers for event-specific PCRs and screened a set of three orange GM petunia cultivars and 126 GM offspring from a commercial breeding program. We show that both T-DNA copies are present in all our tested GM petunia samples, which underpins the assumption of a single transgenic origin of the undeclared GM petunia. Most likely, the two T-DNAs are integrated in close proximity into the petunia genome.

Clarification on "EFSA Genetically Engineered Crop Composition Equivalence Approach: Performance and Consistency"

A recent perspective defends the approach of the European Food Safety Authority (EFSA) for evaluating the compositional normality of genetically engineered (GE) crops using a concurrently grown subset of non-GE varieties within the risk assessment. While the approach of the EFSA manages the risk of falsely claiming equivalence, this is achieved at the expense of low power to detect true equivalence. This generates inconsistent findings and safety conclusions across studies for the same GE event based on the selected non-GE comparators. Because variation in GE crop composition has not been associated with safety, we suggest policy improvements that would better align with consumer protection.

Familiarity in the Context of Risk Assessment of Transgenic Crops: Focus on Some Countries in the Americas

Problem formulation is the formal opening stage of a risk assessment that determines its purpose and scope and hence guides the gathering of information data. The concepts of familiarity and history of safe use are an integral part of problem formulation. These concepts do not replace the case-by-case approach and are not taken as safety standards but are valuable components of the process that shape the generation of plausible, testable risk hypotheses. The International Life Sciences Institutes in Brazil and Argentina have facilitated numerous discussions on the scientific principles for risk assessment of transgenic crops in the Latin American region in the past 5–6 years. The session held at ISBR 15th elaborated on the familiarity concept and derived tools and their role in the evolution of risk evaluation criteria. Examples of how different countries in the Americas interpret and apply these conceptual tools show that familiarity is a valuable concept, although terms are very often confused and vaguely defined. Formalizing these terms with clear definitions and scope of application in guidelines and regulatory documents would reduce ambiguity, enhance predictability, and add transparency to the evaluation processes.

Regulation of genome edited technologies in India

In India, genetically modified organisms and products thereof are regulated under the "Rules for the manufacture, use, import, export and storage of hazardous microorganisms, genetically engineered organisms or cells, 1989" (referred to as Rules, 1989) notified under the Environment (Protection) Act, 1986. These Rules are implemented by the Ministry of Environment, Forest and Climate Change, Department of Biotechnology and State Governments though six competent authorities. The Rules, 1989 are supported by series of guidelines on contained research, biologics, confined field trials, food safety assessment, environmental risk assessment etc. The definition of genetic engineering in the Rules, 1989 implies that new genome engineering technologies including gene editing technologies like CRISPR/Cas9 and gene drives may be covered under the rules. The regulatory authorities if required, may also review the experiences of other countries in dealing with such new and emerging technologies.

Weight of the evidence: independent research projects confirm industry conclusions on the safety of insect-protected maize MON 810

The cumulative weight of the evidence demonstrates the safety and equivalence of genetically engineered (GE) crops compared to the conventional varieties from which they have been derived. Confirmatory toxicology and animal nutrition studies have nevertheless become an expected/mandated component of GE crop safety assessments, despite the lack of additional value these studies provide for product safety assessment. Characterization and safety data (e.g. trait protein safety; molecular, compositional, and agronomic/phenotypic assessments), and animal feeding studies form a weight of the evidence supporting the safety of insect-protected maize MON 810. Independent animal testing has recently confirmed the lack of MON 810 toxicity in subchronic and chronic toxicity studies. These results could have been predicted from the available safety data. Animal testing of GE crops should be supported by testable scientific hypotheses and testing should be consistent with ethical obligations to reduce, refine, and replace (3Rs) animal testing when possible.

Are Market GM Plants an Unrecognized Platform for Bioterrorism and Biocrime?

This article discusses a previously unrecognized avenue for bioterrorism and biocrime. It is suggested that new gene editing technologies may have the potential to create plants that are genetically modified in harmful ways, either in terms of their effect on the plant itself or in terms of harming those who would consume foods produced by that plant. While several risk scenarios involving GMOs-such as antibiotic resistant pathogens, synthetic biology, or mixing of non-GMO seeds with GMO seeds-have previously have been recognized, the new vulnerability is rooted in a different paradigm-that of clandestinely manipulating GMOs to create damage. The ability to actively inflict diseases on plants would pose serious health hazards to both humans and animals, have detrimental consequences to the economy, and directly threaten the food supply. As this is the first study of this kind, the full scope and impact of suck attacks-especially those involving the intended misuse of technologies such as gene-drives-merits further investigation. Herein, the plausibility of some of the new risks will be analyzed by, (1) Highlighting ownership and origination issues (esp. of event-specific GM-plants) as unrecognized risk factors; (2) Investigating the unique role of GMOs, why-and how-certified GMOs could become a new venue for such attacks; (3) Analyzing possible dual-use potentials of modern technologies and research oriented toward the advancement of GMOs, plant breeding and crop improvement. The identification and analysis of harmful genetic manipulations to utilize (covertly modified) plants (GMOs and non-GMOs) as an attack vector show that these concerns need to be taken seriously, raising the prospect not only of direct harm, but of the more likely effects in generating public concern, reputational harm of agricultural biotechnology companies, law-suits, and increased import bans of certain plants or their derived products.

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.

EFSA Genetically Engineered Crop Composition Equivalence Approach: Performance and Consistency

The European Food Safety Authority (EFSA) oversees the safety assessment of genetically engineered (GE) crops in the European Union and has developed a study design and statistical approach for assessing the compositional equivalency between a GE crop and the corresponding non-GE crop on the basis of the results from a small number of concurrently grown reference lines. Confidence limits around the differences in mean analyte composition between the GE variety and the reference lines are compared with equivalence limits on the basis of the variability of the reference lines. Here, we evaluated the performance and consistency of the equivalence conclusions using a non-GE variety that is, by definition, equivalent to the non-GE crop. Using this approach across the same analytes with the same non-GE variety, it was found that equivalence could not be concluded for 19.7, 22.9, 25.4, and 53.5% of the analytes in four separate studies. In addition, equivalency conclusions for the same analyte often differed from study to study. These results call into question the consistency and value of this approach in the risk assessment of GE crops.

The evolving EU regulatory framework for precision breeding

Plant breeding has always relied on progress in various scientific disciplines to generate and enable access to genetic variation. Until the 1970s, available techniques generated mostly random genetic alterations that were subject to a selection procedure in the plant material. Recombinant nucleic acid technology, however, started a new era of targeted genetic alterations, or precision breeding, enabling a much more targeted approach to trait management. More recently, developments in genome editing are now providing yet more control by enabling alterations at exact locations in the genome. The potential of recombinant nucleic acid technology fueled discussions about potentially new associated risks and, starting in the late 1980s, biosafety legislation for genetically modified organisms (GMOs) has developed in the European Union. However, the last decade has witnessed a lot of discussions as to whether or not genome editing and other precision breeding techniques should be encompassed by the EU GMO legislation. A recent ruling from the Court of Justice of the European Union indicated that directed mutagenesis techniques should be subject to the provisions of the GMO Directive, essentially putting many precision breeding techniques in the same regulatory basket. This review outlines the evolving EU regulatory framework for GMOs and discusses some potential routes that the EU may take for the regulation of precision breeding.

Risk-Only Assessment of Genetically Engineered Crops Is Risky

The risks of not considering benefits in risk assessment are often overlooked. Risks are also often evaluated without consideration of the broader context. We discuss these two concepts in relation to genetically engineered (GE) crops. The health, environmental, and economic risks and benefits of GE crops are exemplified and presented in the context of modern agriculture. Misattribution of unique risks to GE crops are discussed. It is concluded that the scale of modern agriculture is its distinguishing characteristic and that the greater knowledge around GE crops allows for a more thorough characterization of risk. By considering the benefits and risks in the context of modern agriculture, society will be better served and benefits will be less likely to be forgone.

Bt rice could provide ecological resistance against nontarget planthoppers

Genetically engineered (GE) rice lines expressing Lepidoptera-active insecticidal cry genes from the bacterium Bacillus thuringiensis (Bt) have been developed in China. Field surveys indicated that Bt rice harbours fewer rice planthoppers than non-Bt rice although planthoppers are not sensitive to the produced Bt Cry proteins. The mechanisms underlying this phenomenon remain unknown. Here, we show that the low numbers of planthoppers on Bt rice are associated with reduced caterpillar damage. In laboratory and field-cage experiments, the rice planthopper Nilapavata lugens had no feeding preference for undamaged Bt or non-Bt plants but exhibited a strong preference for caterpillar-damaged plants whether Bt or non-Bt. Under open-field conditions, rice planthoppers were more abundant on caterpillar-damaged non-Bt rice than on neighbouring healthy Bt rice. GC-MS analyses showed that caterpillar damage induced the release of rice plant volatiles known to be attractive to planthoppers, and metabolome analyses revealed increased amino acid contents and reduced sterol contents known to benefit planthopper development. That Lepidoptera-resistant Bt rice is less attractive to this important nontarget pest in the field is therefore a first example of ecological resistance of Bt plants to nontarget pests. Our findings suggest that non-Bt rice refuges established for delaying the development of Bt resistance may also act as a trap crop for N. lugens and possibly other planthoppers.

The impact of Genetically Modified (GM) crops in modern agriculture: A review

Genetic modification in plants was first recorded 10,000 years ago in Southwest Asia where humans first bred plants through artificial selection and selective breeding. Since then, advancements in agriculture science and technology have brought about the current GM crop revolution. GM crops are promising to mitigate current and future problems in commercial agriculture, with proven case studies in Indian cotton and Australian canola. However, controversial studies such as the Monarch Butterfly study (1999) and the Séralini affair (2012) along with current problems linked to insect resistance and potential health risks have jeopardised its standing with the public and policymakers, even leading to full and partial bans in certain countries. Nevertheless, the current growth rate of the GM seed market at 9.83-10% CAGR along with promising research avenues in biofortification, precise DNA integration and stress tolerance have forecast it to bring productivity and prosperity to commercial agriculture.

Novel Features and Considerations for ERA and Regulation of Crops Produced by Genome Editing

Genome editing describes a variety of molecular biology applications enabling targeted and precise alterations of the genomes of plants, animals and microorganisms. These rapidly developing techniques are likely to revolutionize the breeding of new crop varieties. Since genome editing can lead to the development of plants that could also have come into existence naturally or by conventional breeding techniques, there are strong arguments that these cases should not be classified as genetically modified organisms (GMOs) and be regulated no differently from conventionally bred crops. If a specific regulation would be regarded necessary, the application of genome editing for crop development may challenge risk assessment and post-market monitoring. In the session “Plant genome editing—any novel features to consider for ERA and regulation?” held at the 14th ISBGMO, scientists from various disciplines as well as regulators, risk assessors and potential users of the new technologies were brought together for a knowledge-based discussion to identify knowledge gaps and analyze scenarios for the introduction of genome-edited crops into the environment. It was aimed to enable an open exchange forum on the regulatory approaches, ethical aspects and decision-making considerations.

Comparative compositional analysis of transgenic potato resistant to potato tuber moth (PTM) and its non-transformed counterpart

In this study, the compositions of transgenic potatoes (TPs) resistant to potato tuber moth (Phthorimaea operculella) were compared with those of its non-transgenic (NTP) counterparts. The light inducible promoter, phosphoenolpyruvate carboxylase led to the expression of Cry1Ab only in the leaves and light-treated tubers of the TPs. No significant differences were found in the moisture, ash, dry weight, total soluble protein, carbohydrate, starch, fiber, ascorbate, cations, anions, fatty acids, and glycoalkaloids contents of TP and NTP. Moreover, light treatment significantly affected the contents of ascorbate, acetate and nitrite anions, palmitic, stearic and linolenic fatty acids, α-haconine and α-solanine glycoalkaloids in TP and NTP tubers. While, significant differences were observed in the amino acid contents in light-treated tubers of TPs than the NTP ones. Although, light treatment in potato tubers resulted in marked metabolic changes, all the variations observed in the metabolites compositions were found to be within the desired reference ranges for potato plants. In conclusion, the results indicated that the TPs were substantially and nutritionally equivalent to the NTP counterparts.

Food and feed safety of DAS-444Ø6-6 herbicide-tolerant soybean

DAS-444Ø6-6 soybean was genetically engineered (GE) to withstand applications of three different herbicides. Tolerance to glufosinate and glyphosate is achieved through expression of the phosphinothricin acetyltransferase (PAT) and double-mutated maize 5-enolpyruvyl shikimate-3-phosphate synthase (2mEPSPS) enzymes, respectively. These proteins are expressed in currently commercialized crops and represent no novel risk. Tolerance to 2,4-dichlorophenoxyacetic acid (2,4-D) is achieved through expression of the aryloxyalkanoate dioxygenase 12 (AAD-12) enzyme, which is novel in crops. The safety of the AAD-12 protein and DAS-444Ø6-6 event was assessed for food and feed safety based on the weight of evidence and found to be as safe as non-GE soybean.

Toxicological and Biochemical Analyses Demonstrate the Absence of Lethal or Sublethal Effects of cry1C- or cry2A-Expressing Bt Rice on the Collembolan Folsomia candida

Assessing the potential effects of insect-resistant genetically engineered (GE) plants on collembolans is important because these common soil arthropods may be exposed to insecticidal proteins produced in GE plants by ingestion of plant residues, crop pollen, or root exudates. Laboratory studies were conducted to evaluate the potential effects of two Bacillus thuringiensis (Bt)-rice lines expressing Cry1C and Cry2A in pollen and leaves and of their non-Bt conventional isolines on the fitness of the collembolan Folsomia candida and on the activities of its antioxidant-related enzymes, superoxide dismutase and peroxidase, and of its detoxification-related enzymes, glutathione reductase and glutathione S-transferase. Survival, development, reproduction, and the intrinsic rate of increase (r_m) were not significantly reduced when F. candida fed on the Bt rice pollen or leaf powder than on the non-Bt rice materials; these parameters, however, were significantly reduced when F. candida fed on non-Bt rice pollen or non-Bt leaf-based diets containing the protease inhibitor E-64 at 75 μg/g. The activities of the antioxidant-related and detoxification-related enzymes in F. candida were not significantly affected when F. candida fed on the Bt rice materials, but were significantly increased when F. candida fed on the non-Bt rice materials containing E-64. The results demonstrate that Cry1C and Cry2A are not toxic to F. candida, and also indicate the absence of unintended effects on the collembolan caused by any change in plant tissue nutritional composition due to foreign gene transformation.

Advancing Agrobacterium-Based Crop Transformation and Genome Modification Technology for Agricultural Biotechnology

The last decade has seen significant strides in Agrobacterium-mediated plant transformation technology. This has not only expanded the number of crop species that can be transformed by Agrobacterium, but has also made it possible to routinely transform several recalcitrant crop species including cereals (e.g., maize, sorghum, and wheat). However, the technology is limited by the random nature of DNA insertions, genotype dependency, low frequency of quality events, and variation in gene expression arising from genomic insertion sites. A majority of these deficiencies have now been addressed by improving the frequency of quality events, developing genotype-independent transformation capability in maize, developing an Agrobacterium-based site-specific integration technology for precise gene targeting, and adopting Agrobacterium-delivered CRISPR-Cas genes for gene editing. These improved transformation technologies are discussed in detail in this chapter.

Insect RNAi: Integrating a New Tool in the Crop Protection Toolkit

Protecting crops against insect pests is a major focus area in crop protection. Over the past two decades, biotechnological interventions, especially Bt proteins, have been successfully implemented across the world and have had major impacts on reducing chemical pesticide applications. As insects continue to adapt to insecticides, both chemical and protein-based, new methods, molecules, and modes of action are necessary to provide sustainable solutions. RNA interference (RNAi) has emerged as a significant tool to knock down or alter gene expression profiles in a species-specific manner. In the past decade, there has been intense research on RNAi applications in crop protection. This chapter looks at the current state of knowledge in the field and outlines the methodology, delivery methods, and precautions required in designing targets. Assessing the targeting of specific gene expression is also an important part of a successful RNAi strategy. The current literature on the use of RNAi in major orders of insect pests is reviewed, along with a perspective on the regulatory aspects of the approach. Risk assessment of RNAi would focus on molecular characterization, food/feed risk assessment, and environmental risk assessment. As more RNAi-based products come through regulatory systems, either via direct application or plant expression based, the impact of this approach on crop protection will become clearer.

Ectopic Expression of Xylella fastidiosa rpfF Conferring Production of Diffusible Signal Factor in Transgenic Tobacco and Citrus Alters Pathogen Behavior and Reduces Disease Severity

The pathogenicity of Xylella fastidiosa is associated with its ability to colonize the xylem of host plants. Expression of genes contributing to xylem colonization are suppressed, while those necessary for insect vector acquisition are increased with increasing concentrations of diffusible signal factor (DSF), whose production is dependent on RpfF. We previously demonstrated that transgenic citrus plants ectopically expressing rpfF from a citrus strain of X. fastidiosa subsp. pauca exhibited less susceptibility to Xanthomonas citri subsp. citri, another pathogen whose virulence is modulated by DSF accumulation. Here, we demonstrate that ectopic expression of rpfF in both transgenic tobacco and sweet orange also confers a reduction in disease severity incited by X. fastidiosa and reduces its colonization of those plants. Decreased disease severity in the transgenic plants was generally associated with increased expression of genes conferring adhesiveness to the pathogen and decreased expression of genes necessary for active motility, accounting for the reduced population sizes achieved in the plants, apparently by limiting pathogen dispersal through the plant. Plant-derived DSF signal molecules in a host plant can, therefore, be exploited to interfere with more than one pathogen whose virulence is controlled by DSF signaling.

Stacking transgenic event DAS-Ø15Ø7-1 alters maize composition less than traditional breeding

The impact of crossing ('stacking') genetically modified (GM) events on maize-grain biochemical composition was compared with the impact of generating nonGM hybrids. The compositional similarity of seven GM stacks containing event DAS-Ø15Ø7-1, and their matched nonGM near-isogenic hybrids (iso-hybrids) was compared with the compositional similarity of concurrently grown nonGM hybrids and these same iso-hybrids. Scatter plots were used to visualize comparisons among hybrids and a coefficient of identity (per cent of variation explained by line of identity) was calculated to quantify the relationships within analyte profiles. The composition of GM breeding stacks was more similar to the composition of iso-hybrids than was the composition of nonGM hybrids. NonGM breeding more strongly influenced crop composition than did transgenesis or stacking of GM events. These findings call into question the value of uniquely requiring composition studies for GM crops, especially for breeding stacks composed of GM events previously found to be compositionally normal.

Single-Event Transgene Product Levels Predict Levels in Genetically Modified Breeding Stacks

The concentration of transgene products (proteins and double-stranded RNA) in genetically modified (GM) crop tissues is measured to support food, feed, and environmental risk assessments. Measurement of transgene product concentrations in breeding stacks of previously assessed and approved GM events is required by many regulatory authorities to evaluate unexpected transgene interactions that might affect expression. Research was conducted to determine how well concentrations of transgene products in single GM events predict levels in breeding stacks composed of these events. The concentrations of transgene products were compared between GM maize, soybean, and cotton breeding stacks (MON-87427 × MON-89034 × DAS-Ø15Ø7-1 × MON-87411 × DAS-59122-7 × DAS-40278-9 corn, DAS-81419-2 × DAS-44406-6 soybean, and DAS-21023-5 × DAS-24236-5 × SYN-IR102-7 × MON-88913-8 × DAS-81910-7 cotton) and their component single events (MON-87427, MON-89034, DAS-Ø15Ø7-1, MON-87411, DAS-59122-7, and DAS-40278-9 corn, DAS-81419-2, and DAS-44406-6 soybean, and DAS-21023-5, DAS-24236-5, SYN-IR102-7, MON-88913-8, and DAS-81910-7 cotton). Comparisons were made within a crop and transgene product across plant tissue types and were also made across transgene products in each breeding stack for grain/seed. Scatter plots were generated comparing expression in the stacks to their component events, and the percent of variability accounted for by the line of identity (y = x) was calculated (coefficient of identity, I2). Results support transgene concentrations in single events predicting similar concentrations in breeding stacks containing the single events. Therefore, food, feed, and environmental risk assessments based on concentrations of transgene products in single GM events are generally applicable to breeding stacks composed of these events.

Environmental impacts of genetically modified plants: A review

Powerful scientific techniques have caused dramatic expansion of genetically modified crops leading to altered agricultural practices posing direct and indirect environmental implications. Despite the enhanced yield potential, risks and biosafety concerns associated with such GM crops are the fundamental issues to be addressed. An increasing interest can be noted among the researchers and policy makers in exploring unintended effects of transgenes associated with gene flow, flow of naked DNA, weediness and chemical toxicity. The current state of knowledge reveals that GM crops impart damaging impacts on the environment such as modification in crop pervasiveness or invasiveness, the emergence of herbicide and insecticide tolerance, transgene stacking and disturbed biodiversity, but these impacts require a more in-depth view and critical research so as to unveil further facts. Most of the reviewed scientific resources provide similar conclusions and currently there is an insufficient amount of data available and up until today, the consumption of GM plant products are safe for consumption to a greater extent with few exceptions. This paper updates the undesirable impacts of GM crops and their products on target and non-target species and attempts to shed light on the emerging challenges and threats associated with it. Underpinning research also realizes the influence of GM crops on a disturbance in biodiversity, development of resistance and evolution slightly resembles with the effects of non-GM cultivation. Future prospects are also discussed.

Safety, Security, and Policy Considerations for Plant Genome Editing

Genome editing with engineered nucleases (GEEN) is increasingly used as a tool for gene discovery and trait development in crops through generation of targeted changes in endogenous genes. The development of the CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein), in particular, has enabled widespread use of genome editing. Research to date has not comprehensively addressed genome-editing specificity and off-target mismatches that may result in unintended changes within plant genomes or the potential for gene drive initiation. Governance and regulatory considerations for bioengineered crops derived from using GEEN will require greater clarity as to target specificity, the potential for mismatched edits, unanticipated downstream effects of off-target mutations, and assurance that genome reagents do not occur in finished products. Since governance and regulatory decision making involves robust standards of evidence extending from the laboratory to the postcommercial marketplace, developers of genome-edited crops must anticipate significant engagement and investment to address questions of regulators and civil society.

Re-sequencing transgenic plants revealed rearrangements at T-DNA inserts, and integration of a short T-DNA fragment, but no increase of small mutations elsewhere

KEY MESSAGE

Transformation resulted in deletions and translocations at T-DNA inserts, but not in genome-wide small mutations. A tiny T-DNA splinter was detected that probably would remain undetected by conventional techniques. We investigated to which extent Agrobacterium tumefaciens-mediated transformation is mutagenic, on top of inserting T-DNA. To prevent mutations due to in vitro propagation, we applied floral dip transformation of Arabidopsis thaliana. We re-sequenced the genomes of five primary transformants, and compared these to genomic sequences derived from a pool of four wild-type plants. By genome-wide comparisons, we identified ten small mutations in the genomes of the five transgenic plants, not correlated to the positions or number of T-DNA inserts. This mutation frequency is within the range of spontaneous mutations occurring during seed propagation in A. thaliana, as determined earlier. In addition, we detected small as well as large deletions specifically at the T-DNA insert sites. Furthermore, we detected partial T-DNA inserts, one of these a tiny 50-bp fragment originating from a central part of the T-DNA construct used, inserted into the plant genome without flanking other T-DNA. Because of its small size, we named this fragment a T-DNA splinter. As far as we know this is the first report of such a small T-DNA fragment insert in absence of any T-DNA border sequence. Finally, we found evidence for translocations from other chromosomes, flanking T-DNA inserts. In this study, we showed that next-generation sequencing (NGS) is a highly sensitive approach to detect T-DNA inserts in transgenic plants.