Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants

As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. This Technical Note to the applicants puts together requirements and recommendations for the quality assessment of the methodology, analysis and reporting when DNA sequencing is used for the molecular characterisation of GM plants. In particular, it applies to the use of Sanger sequencing and next-generation sequencing for the characterisation of the inserted genetic material and its flanking regions at each insertion site, the determination of the copy number of all detectable inserts and the analysis of the genetic stability of the inserts. This updated document replaces the EFSA 2018 Technical Note and reflects the current knowledge in scientific-technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. It does not take into consideration the verification and validation of the detection method which remains under the remit of the Joint Research Centre (JRC).

Deciphering the Genetic Basis of Allelopathy in japonica Rice Cultivated in Temperate Regions Using a Genome-Wide Association Study

Allelopathy has been considered as a natural method of weed control. Despite the nature of allelochemical compounds has been studied, little is known about the genetic basis underlying allelopathy. However, it is known that rice exhibits diverse allelopathic potentials across varieties, and breeding for rice plants exhibiting allelopathic potential conferring an advantage against weeds in paddy fields would be highly desirable. Knowledge of the gene factors and the identification of the genomic regions responsible for allelopathy would facilitate breeding programs. Taking advantage of the existing genetic diversity in rice, particularly in temperate japonica rice, we conducted a comprehensive investigation into the genetic determinants that contribute to rice allelopathy. Employing Genome-Wide Association Study, we identified four Quantitative Trait Loci, with the most promising loci situated on chromosome 2 and 5. Subsequent inspection of the genes located within these QTLs revealed genes associated with the biosynthesis of secondary metabolites such as Phenylalanine Ammonia Lyase (PAL), a key enzyme in the synthesis of phenolic compounds, and two genes coding for R2R3-type MYB transcription factors. The identification of these two QTLs associated to allelopathy in rice provides a useful tool for further exploration and targeted breeding strategies.

Updated scientific opinion on plants developed through cisgenesis and intragenesis

In 2012, EFSA issued an opinion on plants developed through cisgenesis and intragenesis. With the development of New Genomic Techniques (NGTs) in the last decade, cisgenic and intragenic plants can now be obtained with the insertion of a desired sequence in a precise location of the genome. EFSA has been requested by European Commission to provide an updated scientific opinion on the safety and the risk assessment of plants developed through cisgenesis and intragenesis, in order to (i) identify potential risks, comparing them with those posed by plants obtained by conventional breeding and Established Genomic Techniques (EGTs) and (ii) to determine the applicability of current guidelines for the risk assessment of cisgenic and intragenic plants. The conclusions of the previous EFSA opinion were reviewed, taking into consideration the new guidelines and the recent literature. The GMO panel concludes that no new risks are identified in cisgenic and intragenic plants obtained with NGTs, as compared with those already considered for plants obtained with conventional breeding and EGTs. There are no new data since the publication of the 2012 EFSA opinion that would challenge the conclusions raised in that document. The conclusions of the EFSA 2012 Scientific Opinion remain valid. The EFSA GMO Panel reiterates from these conclusions that with respect to the source of DNA and the safety of the gene product, the hazards arising from the use of a related plant‐derived gene by cisgenesis are similar to those from conventional plant breeding, whereas additional hazards may arise for intragenic plants. Furthermore, the EFSA GMO Panel considers that cisgenesis and intragenesis make use of the same transformation techniques as transgenesis, and therefore, with respect to the alterations to the host genome, cisgenic, intragenic and transgenic plants obtained by random insertion do not cause different hazards. Compared to that, the use of NGTs reduces the risks associated with potential unintended modifications of the host genome. Thus, fewer requirements may be needed for the assessment of cisgenic and intragenic plants obtained through NGTs, due to site‐directed integration of the added genetic material. Moreover, the GMO panel concludes that the current guidelines are partially applicable and sufficient. On a case‐by‐case basis, a lesser amount of data might be needed for the risk assessment of cisgenic or intragenic plants obtained through NGTs.

This publication is linked to the following EFSA Journal article: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2022.7618/full

Evaluation of existing guidelines for their adequacy for the food and feed risk assessment of genetically modified plants obtained through synthetic biology

Synthetic biology (SynBio) is an interdisciplinary field at the interface of molecular engineering and biology aiming to develop new biological systems and impart new functions to living cells, tissues and organisms. EFSA has been asked by the European Commission to evaluate SynBio developments in agri-food with the aim of identifying the adequacy and sufficiency of existing guidelines for risk assessment and determine if updated guidance is needed. In this context, the GMO Panel has previously adopted an Opinion evaluating the SynBio developments in agri-food/feed and the adequacy and sufficiency of existing guidelines for the molecular characterisation and environmental risk assessment of genetically modified plants (GMPs) obtained through SynBio and reaching the market in the next decade. Complementing the above, in this Opinion, the GMO Panel evaluated the adequacy and sufficiency of existing guidelines for the food and feed risk assessment of GMPs obtained through SynBio. Using selected hypothetical case studies, the GMO Panel did not identify novel potential hazards and risks that could be posed by food and feed from GMPs obtained through current and near future SynBio approaches; considers that the existing guidelines are adequate and sufficient in some Synbio applications; in other cases, existing guidelines may be just adequate and hence need updating; areas needing updating include those related to the safety assessment of new proteins and the comparative analysis. The GMO Panel recommends that future guidance documents provide indications on how to integrate the knowledge available from the SynBio design and modelling in the food and feed risk assessment and encourages due consideration to be given to food and feed safety aspects throughout the SynBio design process as a way to facilitate the risk assessment of SynBio GMPs and reduce the amount of data required.

In vivo and in vitro random mutagenesis techniques in plants

Mutations are changes in the genetic material that may be transmitted to subsequent generations. Mutations appear spontaneously in nature and are one of the underlying driving forces of evolution. In plants, in vivo and in vitro random mutagenesis relies on the application of physical and chemical mutagens to increase the frequency of mutations thus accelerating the selection of varieties with important agronomic traits. The European Commission has requested EFSA to provide a more detailed description of in vivo and in vitro random mutagenesis techniques and the types of mutations and mechanisms involved, to be able to conclude on whether in vivo and in vitro random mutagenesis techniques are to be considered different techniques. To address the European Commission request, a literature search was conducted to collect information on the random mutagenesis techniques used in plants both in vivo and in vitro, on the type of mutations generated by such techniques and on the molecular mechanisms underlying formation of those mutations. The GMO Panel concludes that most physical and chemical mutagenesis techniques have been applied both in vivo and in vitro; the mutation process and the repair mechanisms act at cellular level and thus there is no difference between application of the mutagen in vivo or in vitro; and the type of mutations induced by a specific mutagen are expected to be the same, regardless of whether such mutagen is applied in vivo or in vitro. Indeed, the same mutation and the derived trait in a given plant species can be potentially obtained using both in vivo and in vitro random mutagenesis and the resulting mutants would be indistinguishable. Therefore, the GMO Panel concludes that the distinction between plants obtained by in vitro or in vivo approaches is not justified.

Evaluation of existing guidelines for their adequacy for the molecular characterisation and environmental risk assessment of genetically modified plants obtained through synthetic biology

Synthetic Biology (SynBio) is an interdisciplinary field at the interface of engineering and biology aiming to develop new biological systems and impart new functions to living cells. EFSA has been asked by the European Commission to evaluate SynBio developments in agri-food with the aim of identifying the adequacy of existing guidelines for risk assessment and determine if updated guidance is needed. The scope of this opinion covers the molecular characterisation and environmental risk assessment of such genetically modified plants obtained through SynBio, meant to be for cultivation or food and feed purposes. The previous work on SynBio by the non-food scientific Committees (2014, 2015) was used and complemented with the output of a horizon scanning exercise, which was commissioned by the EFSA to identify the most realistic and forthcoming SynBio cases of relevance to this remit. The horizon scan did not identify other sectors/advances in addition to the six SynBio categories previously identified by the non-food scientific committees of the European Commission. The exercise did show that plant SynBio products reaching the market in the near future (next decade) are likely to apply SynBio approaches to their development using existing genetic modification and genome editing technologies. In addition, three hypothetical SynBio case studies were selected by the working group of the Panel on Genetically Modified Organisms (GMO), to further support the scoping exercise of this Scientific Opinion. Using the selected cases, the GMO Panel concludes that the requirements of the EU regulatory framework and existing EFSA guidelines are adequate for the risk assessment of SynBio products to be developed in the next 10 years, although specific requirements may not apply to all products. The GMO Panel acknowledges that as SynBio developments evolve, a need may exist to adjust the guidelines to ensure they are adequate and sufficient.

Applicability of the EFSA Opinion on site-directed nucleases type 3 for the safety assessment of plants developed using site-directed nucleases type 1 and 2 and oligonucleotide-directed mutagenesis

The European Commission requested the EFSA Panel on Genetically Modified Organisms (GMO) to assess whether section 4 (hazard identification) and the conclusions of EFSA's Scientific opinion on the risk assessment of plants developed using zinc finger nuclease type 3 technique (ZFN-3) and other site-directed nucleases (SDN) with similar function are valid for plants developed via SDN-1, SDN-2 and oligonucleotide-directed mutagenesis (ODM). In delivering this Opinion, the GMO Panel compared the hazards associated with plants produced via SDN-1, SDN-2 and ODM with those associated with plants obtained via both SDN-3 and conventional breeding. Unlike for SDN-3 methods, the application of SDN-1, SDN-2 and ODM approaches aims to modify genomic sequences in a way which can result in plants not containing any transgene, intragene or cisgene. Consequently, the GMO Panel concludes that those considerations which are specifically related to the presence of a transgene, intragene or cisgene included in section 4 and the conclusions of the Opinion on SDN-3 are not relevant to plants obtained via SDN-1, SDN-2 or ODM as defined in this Opinion. Overall, the GMO Panel did not identify new hazards specifically linked to the genomic modification produced via SDN-1, SDN-2 or ODM as compared with both SDN-3 and conventional breeding. Furthermore, the GMO Panel considers that the existing Guidance for risk assessment of food and feed from genetically modified plants and the Guidance on the environmental risk assessment of genetically modified plants are sufficient but are only partially applicable to plants generated via SDN-1, SDN-2 or ODM. Indeed, those guidance documents' requirements that are linked to the presence of exogenous DNA are not relevant for the risk assessment of plants developed via SDN-1, SDN-2 or ODM approaches if the genome of the final product does not contain exogenous DNA.

Genomics of Evolutionary Novelty in Hybrids and Polyploids

It has long been recognized that hybridization and polyploidy are prominent processes in plant evolution. Although classically recognized as significant in speciation and adaptation, recognition of the importance of interspecific gene flow has dramatically increased during the genomics era, concomitant with an unending flood of empirical examples, with or without genome doubling. Interspecific gene flow is thus increasingly thought to lead to evolutionary innovation and diversification, via adaptive introgression, homoploid hybrid speciation and allopolyploid speciation. Less well understood, however, are the suite of genetic and genomic mechanisms set in motion by the merger of differentiated genomes, and the temporal scale over which recombinational complexity mediated by gene flow might be expressed and exposed to natural selection. We focus on these issues here, considering the types of molecular genetic and genomic processes that might be set in motion by the saltational event of genome merger between two diverged species, either with or without genome doubling, and how these various processes can contribute to novel phenotypes. Genetic mechanisms include the infusion of new alleles and the genesis of novel structural variation including translocations and inversions, homoeologous exchanges, transposable element mobilization and novel insertional effects, presence-absence variation and copy number variation. Polyploidy generates massive transcriptomic and regulatory alteration, presumably set in motion by disrupted stoichiometries of regulatory factors, small RNAs and other genome interactions that cascade from single-gene expression change up through entire networks of transformed regulatory modules. We highlight both these novel combinatorial possibilities and the range of temporal scales over which such complexity might be generated, and thus exposed to natural selection and drift.

LTR-TEs abundance, timing and mobility in Solanum commersonii and S. tuberosum genomes following cold-stress conditions

Copia/Ale is the youngest lineage in both Solanum tuberosum and S. commersonii. Within it, we identified nightshade, a new LTR element active in the cultivated potato. From an evolutionary perspective, long-terminal repeat retrotransposons (LTR-RT) activity during stress may be viewed as a mean by which organisms can keep up rates of genetic adaptation to changing conditions. Potato is one of the most important crop consumed worldwide, but studies on LTR-RT characterization are still lacking. Here, we assessed the abundance, insertion time and activity of LTR-RTs in both cultivated Solanum tuberosum and its cold-tolerant wild relative S. commersonii genomes. Gypsy elements were more abundant than Copia ones, suggesting that the former was somehow more successful in colonizing potato genomes. However, Copia elements, and in particular, the Ale lineage, are younger than Gypsy ones, since their insertion time was in average ~ 2 Mya. Due to the ability of LTR-RTs to be circularized by the host DNA repair mechanisms, we identified via mobilome-seq a Copia/Ale element (called nightshade, informal name used for potato family) active in S. tuberosum genome. Our analyses represent a valuable resource for comparative genomics within the Solanaceae, transposon-tagging and for the design of cultivar-specific molecular markers in potato.

On the Importance to Acknowledge Transposable Elements in Epigenomic Analyses

Eukaryotic genomes comprise a large proportion of repeated sequences, an important fraction of which are transposable elements (TEs). TEs are mobile elements that have a significant impact on genome evolution and on gene functioning. Although some TE insertions could provide adaptive advantages to species, transposition is a highly mutagenic event that has to be tightly controlled to ensure its viability. Genomes have evolved sophisticated mechanisms to control TE activity, the most important being epigenetic silencing. However, the epigenetic control of TEs can also affect genes located nearby that can become epigenetically regulated. It has been proposed that the combination of TE mobilization and the induced changes in the epigenetic landscape could allow a rapid phenotypic adaptation to global environmental changes. In this review, we argue the crucial need to take into account the repeated part of genomes when studying the global impact of epigenetic modifications on an organism. We emphasize more particularly why it is important to carefully consider TEs and what bioinformatic tools can be used to do so.

Assessment of genetically modified soybean MON 87751 for food and feed uses under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2014-121)

Soybean MON 87751 was developed through Agrobacterium tumefaciens‐mediated transformation to provide protection certain specific lepidopteran pests by the expression of the Cry1A.105 and Cry2Ab2 proteins derived from Bacillus thuringiensis. The molecular characterisation data and bioinformatic analyses did not identify issues requiring assessment for food and feed safety. None of the compositional, agronomic and phenotypic differences identified between soybean MON 87751 and the conventional counterpart required further assessment. The GMO Panel did not identify safety concerns regarding the toxicity and allergenicity of the Cry1A.105 and Cry2Ab2 proteins as expressed in soybean MON 87751, and found no evidence that the genetic modification might significantly change the overall allergenicity of soybean MON 87751. The nutritional impact of soybean MON 87751‐derived food and feed is expected to be the same as those derived from the conventional counterpart and non‐GM commercial reference varieties. The GMO Panel concludes that soybean MON 87751, as described in this application, is nutritionally equivalent to and as safe as the conventional counterpart and the non‐GM soybean reference varieties tested, and no post‐market monitoring of food and feed is considered necessary. In the case of accidental release of viable soybean MON 87751 seeds into the environment, soybean MON 87751 would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean MON 87751. In conclusion, soybean MON 87751, as described in this application, is as safe as its conventional counterpart and the tested non‐GM soybean reference varieties with respect to potential effects on human and animal health and the environment.

Technical Note on the quality of DNA sequencing for the molecular characterisation of genetically modified plants

As part of the risk assessment (RA) requirements for genetically modified (GM) plants, according to Regulation (EU) No 503/2013 and the EFSA guidance on the RA of food and feed from GM plants (EFSA GMO Panel, 2011), applicants need to perform a molecular characterisation of the DNA sequences inserted in the GM plant genome. The European Commission has mandated EFSA to develop a technical note to the applicants on, and checking of, the quality of the methodology, analysis and reporting covering complete sequencing of the insert and flanking regions, insertion site analysis of the GM event, and generational stability and integrity. This Technical Note puts together requirements and recommendations for when DNA sequencing is part of the molecular characterisation of GM plants, in particular for the characterisation of the inserted genetic material at each insertion site and flanking regions, the determination of the copy number of all detectable inserts, and the analysis of the genetic stability of the inserts, when addressed by Sanger sequencing or NGS. This document reflects the current knowledge in scientific-technical methods for generating and verifying, in a standardised manner, DNA sequencing data in the context of RA of GM plants. From 1 October 2018, this Technical Note will replace the JRC guideline of 2016 (updated April 2017) related to the verification and quality assessment of the sequencing of the insert(s) and flanking regions. It does not take into consideration the verification and validation of the detection method which remains under the remit of the JRC.

Assessment of genetically modified maize Bt11 x MIR162 x 1507 x GA21 and three subcombinations independently of their origin, for food and feed uses under Regulation (EC) No 1829/2003 (application EFSA-GMO-DE-2010-86)

In this opinion, the GMO Panel assessed the four-event stack maize Bt11 × MIR162 × 1507 × GA21 and three of its subcombinations, independently of their origin. The GMO Panel previously assessed the four single events and seven of their combinations and did not identify safety concerns. No new data on the single events or the seven subcombinations leading to modification of the original conclusions were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single events in the four-event stack maize did not give rise to food/feed safety issues. Based on the nutritional assessment of the compositional characteristics of maize Bt11 × MIR162 × 1507 × GA21, foods and feeds derived from the genetically modified (GM) maize are expected to have the same nutritional impact as those derived from non-GM maize varieties. In the case of accidental release of viable grains of maize Bt11 × MIR162 × 1507 × GA21 into the environment, this would not raise environmental safety concerns. The GMO Panel concludes that maize Bt11 × MIR162 × 1507 × GA21 is nutritionally equivalent to and as safe as its non-GM comparator in the context of the scope of this application. For the three subcombinations included in the scope, for which no experimental data were provided, the GMO Panel assessed the likelihood of interactions among the single events and concluded that their combinations would not raise safety concerns. These maize subcombinations are therefore expected to be as safe as the single events, the previously assessed subcombinations and the four-event stack maize. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize Bt11 × MIR162 × 1507 × GA21 and its subcombinations. A minority opinion expressed by a GMO Panel member is appended to this opinion.

Assessment of genetically modified maize 1507 × NK603 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-008)

Following the submission of application EFSA-GMO-RX-008 under Regulation (EC) No 1829/2003 from Pioneer Hi-Bred International, Inc. and Dow AgroSciences LLC, the Panel on Genetically Modified Organisms of the European Food Safety Authority was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the insect-resistant, herbicide-tolerant genetically modified maize 1507 × NK603, for food and feed uses, import and processing, excluding cultivation within the EU. The data received in the context of this renewal application contained a systematic search and evaluation of literature, updated bioinformatic analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. In conclusion, under the assumption that the DNA sequence of the events in maize 1507 × NK603 considered for renewal are identical to the newly reported 1507 sequence and the NK603 sequence of the originally assessed two-event stack maize, the GMO Panel concludes that there is no evidence in the renewal application EFSA-GMO-RX-008 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize 1507 × NK603 (EFSA, 2006).

Assessment of genetically modified maize MON 87411 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2015-124)

Maize MON 87411 was developed to confer resistance to corn rootworms (Diabrotica spp.) by the expression of a modified version of the Bacillus thuringiensis cry3Bb1 gene and a DvSnf7 dsRNA expression cassette, and tolerance to glyphosate‐containing herbicides by the expression of a CP4 5‐enolpyruvylshikimate‐3‐phosphate synthase (cp4 epsps) gene. The molecular characterisation data and bioinformatics analyses did not identify issues requiring assessment for food and feed safety. No statistically significant differences in the agronomic and phenotypic characteristics tested between maize MON 87411 and its conventional counterpart were identified. The compositional analysis of maize MON 87411 did not identify differences that required further assessment except for palmitic acid levels in grains from not treated maize MON 87411. The GMO Panel did not identify safety concerns regarding the toxicity and allergenicity of the Cry3Bb1 and CP4 EPSPS proteins, as expressed in maize MON 87411 and found no evidence that the genetic modification might significantly change the overall allergenicity of maize MON 87411. The nutritional impact of maize MON 87411‐derived food and feed is expected to be the same as those derived from the conventional counterpart and non‐GM commercial reference varieties. The GMO Panel concludes that maize MON 87411, as described in this application, is nutritionally equivalent to and as safe as the conventional counterpart and the non‐GM maize reference varieties tested, and no post‐market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize MON 87411 grains into the environment, maize MON 87411 would not raise environmental safety concerns. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87411. The GMO Panel concludes that maize MON 87411, as described in this application, is as safe as its conventional counterpart and the tested non‐GM maize reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize 4114 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2014-123)

Maize 4114 was developed through Agrobacterium tumefaciens-mediated transformation to provide protection against certain lepidopteran and coleopteran pests by expression of the Cry1F, Cry34Ab1 and Cry35Ab1 proteins derived from Bacillus thuringiensis, and tolerance to the herbicidal active ingredient glufosinate-ammonium by expression of the PAT protein derived from Streptomyces viridochromogenes. The molecular characterisation data did not identify issues requiring assessment for food/feed safety. None of the compositional, agronomic and phenotypic differences identified between maize 4114 and the non-genetically modified (GM) comparator(s) required further assessment. There were no concerns regarding the potential toxicity and allergenicity of the newly expressed proteins Cry1F, Cry34Ab1, Cry35Ab1 and PAT, and no evidence that the genetic modification might significantly change the overall allergenicity of maize 4114. The nutritional value of food/feed derived from maize 4114 is not expected to differ from that derived from non-GM maize varieties and no post-market monitoring of food/feed is considered necessary. In the case of accidental release of viable maize 4114 grains into the environment, maize 4114 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize 4114. The genetically modified organism (GMO) Panel concludes that maize 4114 is as safe as the non-GM comparator(s) and non-GM reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.

Assessment of genetically modified cotton GHB614 × LLCotton25 × MON 15985 for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2011-94)

The three-event stack cotton GHB614 × LLCotton25 × MON 15985 was produced by conventional crossing to combine three single cotton events, GHB614, LLCotton25 and MON 15985. The EFSA GMO Panel previously assessed the three single events and did not identify safety concerns. No new data on the single events that could lead to modification of the original conclusions on their safety were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single events and of the newly expressed proteins in the three-event stack cotton did not give rise to food and feed safety or nutritional issues. Food and feed derived from cotton GHB614 × LLCotton25 × MON 15985 are expected to have the same nutritional impact as those derived from the non-GM comparator. In the case of accidental release of viable GHB614 × LLCotton25 × MON 15985 cottonseeds into the environment, this three-event stack cotton would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton GHB614 × LLCotton25 × MON 15985. In conclusion, the GMO Panel considers that cotton GHB614 × LLCotton25 × MON 15985, as described in this application, is as safe as the non-GM comparator with respect to potential effects on human and animal health and the environment.

Statement complementing the EFSA Scientific Opinion on application (EFSA‐GMO‐DE‐2011‐95) for the placing on the market of genetically modified maize 5307 for food and feed uses, import and processing under Regulation (EC) No 1829/2003 from Syngenta Crop Protection AG taking into consideration an additional toxicological study

The GMO Panel was previously not in the position to complete the food/feed safety assessment of maize 5307 due to an inadequate 28‐day toxicity study necessary for an appropriate assessment of eCry3.1Ab protein. Following a mandate from the European Commission, the GMO Panel assessed a supplementary 28‐day toxicity study in mice on the eCry3.1Ab protein (1,000 mg/kg body weight (bw) per day) to complement its scientific opinion on application EFSA‐GMO‐DE‐2011‐95 for the placing on the market of the maize 5307 for food and feed uses, import and processing. The supplementary 28‐day toxicity study did not show adverse effects. Taking into account the previous assessment and the new information, the GMO Panel concludes that maize 5307, as assessed in the scientific opinion on application EFSA‐GMO‐DE‐2011‐95 (EFSA GMO Panel, 2015) and in the supplementary toxicity study, is as safe and nutritious as its conventional counterpart in the scope of this application.

Assessment of genetically modified maize MON 87403 for food and feed uses, import and processing, under Regulation (EC) No 1829/2003 (application EFSA-GMO-BE-2015-125)

Maize MON 87403 was developed to increase ear biomass at early reproductive phase through the expression of a modified AtHB17 gene from Arabidopsis thaliana, encoding a plant transcription factor of the HD-Zip II family. The molecular characterisation data and bioinformatic analyses did not identify issues requiring assessment for food and feed safety. No statistically significant differences in the agronomic and phenotypic characteristics tested between maize MON 87403 and its conventional counterpart were identified. The compositional analysis of maize MON 87403 did not identify differences that require further assessment. The GMO Panel did not identify safety concerns regarding the toxicity and allergenicity of the AtHB17∆113 protein, as expressed in maize MON 87403. The nutritional value of food and feed derived from maize MON 87403 is not expected to differ from that of food and feed derived from non-genetically modified (GM) maize varieties. Based on the outcome of the studies considered in the comparative analysis and molecular characterisation, the GMO Panel concludes that maize MON 87403 is as safe and nutritious as the conventional counterpart and the non-GM maize reference varieties tested. In the case of accidental release of viable maize MON 87403 grains into the environment, maize MON 87403 would not raise environmental safety concerns. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of maize MON 87403. In conclusion, the GMO Panel considers that maize MON 87403, as described in this application, is as safe as its conventional counterpart and the tested non-GM maize reference varieties with respect to potential effects on human and animal health and the environment.

Assessment of genetically modified maize NK603 x MON810 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-007)

Following the submission of application EFSA-GMO-RX-007 under Regulation (EC) No 1829/2003 from Monsanto, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application of the herbicide-tolerant and insect-resistant genetically modified maize NK603 x MON810. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatic analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the events in maize NK603 x MON810 considered for renewal is identical to the sequence of the originally assessed events, the GMO Panel concludes that there is no evidence in the renewal application EFSA-GMO-RX-007 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize NK603 x MON810.

Risk assessment of information on the subcombination Bt11 × 1507 × GA21, related to the application of Syngenta (EFSA-GMO-DE-2011-99) for authorisation of food and feed containing, consisting and produced from genetically modified maize Bt11 × 59122 × MIR604 × 1507 × GA21

The GMO Panel has previously assessed the single events Bt11, 59122, MIR604, 1507 and GA21 as well as different stacked events corresponding to combinations of these events and no safety concerns were identified. In its assessment of the five‐event maize stack Bt11 × 59122 × MIR604 × 1507 × GA21 (application EFSA‐GMO‐DE‐2011‐99), the GMO Panel also assessed all the subcombinations of these events not previously assessed, including some for which little or no experimental data were provided, including the three‐event stack Bt11 × 1507 × GA21. In line with Article 5 of the decision for authorisation of application EFSA‐GMO‐DE‐2011‐99, the European Commission received from Syngenta information on the levels of the newly expressed proteins in subcombination Bt11 × 1507 × GA21 and tasked EFSA to analyse these data and to indicate whether they have an impact on the previously issued opinion on the five‐event stack Bt11 × 59122 × MIR604 × 1507 × GA21 and its subcombinations. Analyses of the levels of the newly expressed proteins Cry1Ab, PAT, Cry1F and mEPSPS showed that there is no indication of an interaction between the events combined in maize Bt11 × 1507 × GA21 that would affect the levels of the newly expressed proteins. Thus, the GMO Panel is of the opinion that the new information for maize Bt11 × 1507 × GA21 does not alter the conclusions of the scientific opinion on application EFSA‐GMO‐DE‐2011‐99.

Assessment of genetically modified maize 1507 × 59122 × MON810 × NK603 and subcombinations, for food and feed uses, under Regulation (EC) No 1829/2003 (application EFSA-GMO-NL-2011-92)

In this opinion, the GMO Panel assessed the four‐event stack maize 1507 × 59122 ×  MON810 ×  NK603 and its ten subcombinations, independently of their origin. The GMO Panel previously assessed the four single events combined in this four‐event stack maize and five of their combinations and did not identify safety concerns. No new data on the single events or their previously assessed combinations leading to modification of the original conclusions were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single maize events and of the newly expressed proteins in the four‐event stack maize did not give rise to food and feed safety or nutritional issues. The GMO Panel concludes that the four‐event stack maize is as safe and as nutritious as its non‐GM comparator. In the case of accidental release of viable grains of maize 1507 × 59122 × MON810 × NK603 into the environment, this would not raise environmental safety concerns. For four of the subcombinations not previously assessed, protein expression data were provided and did not indicate an interaction affecting the levels of the newly expressed proteins in these subcombinations. The five subcombinations not previously assessed are expected to be as safe as the single maize events, the previously assessed subcombinations and the four‐event stack maize. The GMO Panel considers that post‐market monitoring of maize 1507 × 59122 ×MON810 × NK603 and its subcombinations is not necessary. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of maize 1507 × 59122 × MON810 ×NK603 and its subcombinations.

Assessment of genetically modified oilseed rape MS8, RF3 and MS8×RF3 for renewal of authorisation under regulation (EC) No 1829/2003 (application EFSA-GMO-RX-004)

Following the submission of application EFSA‐GMO‐RX‐004 under Regulation (EC) No 1829/2003 from Bayer CropScience, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application of the genetically modified (GM) herbicide‐tolerant oilseed rape MS8, RF3 and MS8×RF3. The data received in the context of this renewal application contain post‐market environmental monitoring reports, systematic searches and evaluation of literature, updated bioinformatics analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in oilseed rape MS8, RF3 and MS8×RF3 considered for renewed authorisation is identical to the sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in the context of this renewal application for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on oilseed rape MS8, RF3 and MS8×RF3.

Guidance for the risk assessment of the presence at low level of genetically modified plant material in imported food and feed under Regulation (EC) No 1829/2003

This document provides guidance for the risk assessment under Regulation (EC) No 1829/2003 of the unintended, adventitious or technically unavoidable presence in food and feed of low level of genetically modified plant material intended for markets other than in the European Union. In this context, the presence at low level is defined to be maximum 0.9% of genetically modified plant material per ingredient. This guidance is intended to assist applicants by indicating which scientific requirements of Annex II of Regulation (EU) No 503/2013 are considered necessary for the risk assessment of the presence at low levels of genetically modified plant material in food and feed.

This publication is linked to the following EFSA Supporting Publications article: http://onlinelibrary.wiley.com/doi/10.2903/sp.efsa.2017.EN-1329/full

Assessment of genetically modified sugar beet H7-1 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-006)

Following the submission of application EFSA‐GMO‐RX‐006 under Regulation (EC) No 1829/2003 from KWS SAAT SE and Monsanto Company, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application for the herbicide‐tolerant genetically modified sugar beet H7‐1. The data received in the context of this renewal application contained a systematic search and evaluation of literature, updated bioinformatics analyses and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in sugar beet H7‐1 considered for renewal is identical to the originally assessed event, the GMO Panel concludes that there is no evidence in the context of this renewal application for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on sugar beet H7‐1.

Assessment of genetically modified maize GA21 for renewal of authorisation under Regulation (EC) No 1829/2003 (application EFSA-GMO-RX-005)

Following the submission of application EFSA-GMO-RX-005 under Regulation (EC) No 1829/2003 from Syngenta Crop Protection NV/SA, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application of the herbicide-tolerant genetically modified maize GA21. The data received in the context of this renewal application contained post-market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatics analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize GA21 considered for renewal is identical to the corrected sequence of the originally assessed event, the GMO Panel concludes that there is no evidence in the renewal application EFSA-GMO-RX-005 for new hazards, modified exposure or scientific uncertainties that would change the conclusions of the original risk assessment on maize GA21.

Risk assessment of new sequencing information on genetically modified soybean event 305423

The GMO Panel has previously assessed genetically modified (GM) soybean 305423 as a single event and as part of a two‐event stack, 305423 × 40‐3‐2. These soybean events were found to be as safe as their conventional counterparts and other appropriate comparators with respect to potential effects on human and animal health and the environment. On 23 February 2017, European Commission requested EFSA to analyse new nucleic acid sequencing data and updated bioinformatics data for soybean event 305423 and to indicate whether the previous conclusions of the GMO Panel on the previously assessed GM soybeans remain valid. The new sequencing data indicated a four base pair (bp) difference compared to the sequencing data originally provided: one bp located in the genomic 3′ flanking region, two bp located in a gene silencing cassette and one bp in a partial promoter. These bp reported as differences in the new nucleic acid sequencing data on soybean event 305423 were already present in the original plant material used for the risk assessment. Thus, with the exception of bioinformatics analyses, including an off‐target search with the dsRNA expression cassette, the studies performed for the risk assessment of the single event soybean 305423 and the two‐event stack soybean 305423 × 40‐3‐2 remain valid. The new sequencing data and the bioinformatic analyses performed on the new sequence including the RNAi off‐target search, did not give rise to safety issues. Therefore, EFSA concludes that the original risk assessment of the single soybean event 305423 and the two‐event stack soybean 305423 × 40‐3‐2 remains valid.

This publication is linked to the following EFSA Journal article: http://onlinelibrary.wiley.com/doi/10.2903/j.efsa.2017.4968/full

Scientific Opinion on application EFSA-GMO-BE-2013-117 for authorisation of genetically modified maize MON 87427 × MON 89034 × NK603 and subcombinations independently of their origin, for food and feed uses, import and processing submitted under Regulation (EC) No 1829/2003 by Monsanto Company

In this opinion, the EFSA Panel on Genetically Modified Organisms (GMO Panel) assessed the three-event stack maize MON 87427 × MON 89034 × NK603 and its three subcombinations, independently of their origin. The GMO Panel has previously assessed the three single events combined to produce this three-event stack maize and did not identify safety concerns. No new data on the single events, leading to modification of the original conclusions on their safety, were identified. Based on the molecular, agronomic, phenotypic and compositional characteristics, the combination of the single maize events and of the newly expressed proteins in the three-event stack maize did not give rise to issues regarding food and feed safety or nutrition. In the case of accidental release of viable grains of maize MON 87427 × MON 89034 × NK603 into the environment, the three-event stack maize would not raise environmental safety concerns. The GMO Panel concludes that the three-event stack maize is as safe and as nutritious as the non-GM comparator and the tested non-GM reference varieties in the context of its scope. The GMO Panel considered that its previous conclusions on the two-event stack maize MON 89034 × NK603 remain valid. For the two maize subcombinations for which no experimental data were provided the GMO Panel assessed the likelihood of interactions among the single events, and concluded that their combination would not raise safety concerns. These two subcombinations are therefore expected to be as safe as the single events, the previously assessed maize MON 89034 × NK603 and maize MON 87427 × MON 89034 × NK603. Since the post-market environmental monitoring plan for the three-event stack maize does not include any provisions for the two subcombinations not previously assessed, the GMO Panel recommended the applicant to revise the plan accordingly.

Scientific Opinion on application EFSA-GMO-BE-2013-118 for authorisation of genetically modified maize MON 87427 × MON 89034 × 1507 × MON 88017 × 59122 and subcombinations independently of their origin, for food and feed uses, import and processing submitted under Regulation (EC) No 1829/2003 by Monsanto Company

In this opinion, the GMO Panel assessed the five‐event stack maize MON 87427 × MON 89034 ×1507 × MON 88017 × 59122 and its 25 subcombinations, independently of their origin. The GMO Panel has previously assessed the five single events combined to produce this five‐event stack maize and 11 subcombinations of these events and did not identify safety concerns. No new data on the single events or their previously assessed subcombinations, leading to modification of the original conclusions were identified. The combination of the single events and of the newly expressed proteins in the five‐event stack maize did not give rise to issues – based on the molecular, agronomic/phenotypic or compositional characteristics – regarding food and feed safety and nutrition. Considering the scope of this application, the known biological function of the newly expressed proteins and the data available for the five‐event stack maize and its previously assessed maize subcombinations, the GMO Panel considered that different combinations of the single events would not raise environmental concerns. The GMO Panel concludes that the five‐event stack maize is as safe and as nutritious as the non‐genetically modified (GM) comparator and the tested non‐GM reference varieties in the context of its scope. For the 14 maize subcombinations for which no experimental data were provided, the GMO Panel assessed the likelihood of interactions among the single events, and concluded that their combinations would not raise safety concerns. These maize subcombinations are therefore expected to be as safe as the single events, the previously assessed subcombinations and maize MON 87427 ×MON 89034 × 1507 × MON 88017 × 59122. Since the post‐market environmental monitoring plan for the five‐event stack maize does not include any provisions for the 14 maize subcombinations not previously assessed, the GMO Panel recommended the applicant to revise the plan accordingly.

Scientific opinion on an application for renewal of authorisation for continued marketing of maize 59122 and derived food and feed submitted under articles 11 and 23 of Regulation (EC) No 1829/2003 by Pioneer Overseas Corporation and Dow AgroSciences LLC

Following the submission of application EFSA‐GMO‐RX‐003 under Regulation (EC) No 1829/2003 from Pioneer Overseas Corporation and Dow AgroSciences LLC, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the context of the renewal of authorisation application of the insect‐resistant genetically modified maize 59122. The data received in the context of this renewal application contained post‐market environmental monitoring reports, a systematic search and evaluation of literature, updated bioinformatics analyses, and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed these data for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the context of the original application. Under the assumption that the DNA sequence of the event in maize 59122 considered for renewal is identical to the corrected sequence of the originally assessed event, the GMO Panel concludes that no new hazards or modified exposure and no new scientific uncertainties were identified that would change the conclusions of the original risk assessment on maize 59122.

Guidance on allergenicity assessment of genetically modified plants

This document provides supplementary guidance on specific topics for the allergenicity risk assessment of genetically modified plants. In particular, it supplements general recommendations outlined in previous EFSA GMO Panel guidelines and Implementing Regulation (EU) No 503/2013. The topics addressed are non-IgE-mediated adverse immune reactions to foods, in vitro protein digestibility tests and endogenous allergenicity. New scientific and regulatory developments regarding these three topics are described in this document. Considerations on the practical implementation of those developments in the risk assessment of genetically modified plants are discussed and recommended, where appropriate.

Annual post-market environmental monitoring (PMEM) report on the cultivation of genetically modified maize MON 810 in 2015 from Monsanto Europe S.A

Following a request from the European Commission, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) assessed the annual post-market environmental monitoring (PMEM) report for the 2015 growing season of the Cry1Ab-expressing maize event MON 810 provided by Monsanto Europe S.A. The GMO Panel concludes that the insect resistance monitoring data submitted to EFSA do not indicate a decrease in susceptibility of field Iberian populations of corn borers to the Cry1Ab protein during the 2015 season. However, since the methodology for insect resistance monitoring remained unchanged compared to previous PMEM reports, the GMO Panel reiterates its previous recommendations on resistance monitoring to provide sufficient detection sensitivity. Although the farmer alert system to report complaints about product performance could complement the information obtained from the laboratory bioassays, the GMO Panel is currently not in a position to appraise its usefulness, and therefore encourages the consent holder to provide more information on this complementary resistance monitoring tool. The data on general surveillance (GS) do not indicate any unanticipated adverse effects on human and animal health or the environment arising from the cultivation of maize MON 810. The GMO Panel reiterates its previous recommendations on the analysis of farmer questionnaires, and advises the consent holder to provide more detailed information on the conducting and reporting of the literature search in future annual PMEM reports. Moreover, the GMO Panel encourages relevant parties to continue developing a methodological framework to use existing networks in the broader context of environmental monitoring. The GMO Panel concludes that the case-specific monitoring (CSM) and GS activities of maize MON 810 as carried out by the consent holder do not provide evidence that would invalidate previous GMO Panel evaluations on the safety of maize MON 810.

Scientific Opinion on application EFSA-GMO-NL-2013-119 for authorisation of genetically modified glufosinate-ammonium- and glyphosate-tolerant oilseed rape MON 88302 × MS8 × RF3 and subcombinations independently of their origin, for food and feed uses, import and processing submitted in accordance with Regulation (EC) No 1829/2003 by Monsanto Company and Bayer CropScience

In this opinion, the GMO Panel assessed the three‐event stack oilseed rape (OSR) MON 88302 × MS8 × RF3 and its three subcombinations, independently of their origin. The GMO Panel has previously assessed the single events combined to produce this three‐event stack OSR and did not identify safety concerns; no new information that would modify the original conclusions was identified. The combination of the single OSR events and of the newly expressed proteins in the three‐event stack OSR does not give rise to food and feed safety and nutrition issues – based on the molecular, agronomic/phenotypic and compositional characteristics. In the case of accidental release of viable OSR MON 88302 × MS8 × RF3 seeds into the environment, the three‐event stack OSR would not raise environmental safety concerns. The GMO Panel therefore concluded that the three‐event stack OSR is as safe and as nutritious as its conventional counterpart and the tested non‐GM reference varieties in the context of the scope of this application. Since no new safety concerns were identified for the previously assessed two‐event stack OSR MS8 × RF3, the GMO Panel considered that its previous conclusions on this subcombination remain valid. For the two subcombinations MON 88302 × MS8 and MON 88302 × RF3 for which no experimental data were provided, the GMO Panel assessed the likelihood of interactions among the single events, and concluded that their different combinations would not raise safety concerns. These two subcombinations are therefore expected to be as safe as the single events, the previously assessed OSR MS8 × RF3, and OSR MON 88302 × MS8 × RF3. Since the post‐market environmental monitoring plan for the three‐event stack OSR does not include any provisions for two subcombinations not previously assessed, the GMO Panel recommended the applicant to revise the plan accordingly.

Scientific opinion on application EFSA-GMO-NL-2013-120 for authorisation of genetically modified soybean FG72 × A5547-127 for food and feed uses, import and processing submitted in accordance with Regulation (EC) No 1829/2003 by Bayer CropScience LP and M.S. Technologies LLC

In this opinion, the EFSA Panel on Genetically Modified Organisms (GMO) assesses the two‐event stack soybean FG72 × A5547‐127 for food and feed uses, import and processing. The EFSA GMO Panel previously assessed the two single events combined to produce the two‐event stack soybean FG72 × A5547‐127 and did not identify safety concerns. No new data on the single events, leading to modification of the original conclusions on their safety, were identified. The molecular, agronomic, phenotypic and compositional data on soybean FG72 × A5547‐127 did not give rise to safety concerns and no reason to expect interactions between the single events impacting on the food and feed safety of the two‐event stack soybean was identified. Although the EFSA GMO Panel cannot conclude on forage composition, soybean forage is not expected to be imported in a significant amount for use as feed. Considering the routes of exposure and limited exposure levels, the EFSA GMO Panel concludes that soybean FG72 × A5547‐127 would not give rise to safety concerns in the event of accidental release of viable seeds into the environment. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean FG72 × A5547‐127. The EFSA GMO Panel concludes that soybean FG72 × A5547‐127 is as safe as the non‐genetically modified (GM) comparator and non‐GM soybean reference varieties with respect to potential effects on human and animal health and the environment.

Scientific opinion on an application by Monsanto (EFSA-GMO-NL-2013-114) for the placing on the market of a herbicide-tolerant genetically modified cotton MON 88701 for food and feed uses, import and processing under Regulation (EC) No 1829/2003

Cotton MON 88701 was developed through Agrobacterium tumefaciens‐mediated transformation to express the dicamba mono‐oxygenase (DMO) protein, conferring tolerance to dicamba, and the phosphinothricin N‐acetyltransferase PAT protein, conferring tolerance to glufosinate ammonium‐based herbicides. The molecular characterisation data and bioinformatics analyses did not identify issues requiring further assessment for food/feed safety. The agronomic and phenotypic characteristics tested revealed no relevant differences between cotton MON 88701 and its conventional counterpart. Since complete compositional results were reported for only three sites, the EFSA Panel on Genetically Modified Organisms (GMO Panel) is not in the position to complete the assessment of the compositional analysis. Moreover, as no 28‐day toxicity study in rodents on the MON 88701 DMO protein was provided, the GMO Panel is not in the position to complete the safety assessment of this protein in cotton MON 88701. Consequently, the GMO Panel cannot complete the toxicological, allergenicity and nutritional assessment of food/feed derived from cotton MON 88701. The safety assessment identified no concerns regarding the potential toxicity and allergenicity of the PAT protein newly expressed in cotton MON 88701. Considering the routes of exposure and limited exposure levels, the GMO Panel concludes that cotton MON 88701 would not give rise to safety concerns in the event of accidental release of viable seeds into the environment. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of cotton MON 88701. In conclusion, in the absence of an appropriate comparative assessment and an appropriate assessment of the MON 88701 DMO protein, the GMO Panel is not in a position to complete its food/feed risk assessment of cotton MON 88701. The GMO Panel concludes that the cotton MON 88701 is unlikely to have any adverse effect on the environment in the context of the scope of the application.

Risk assessment of information on the subcombination Bt11 × MIR162, related to the application of Syngenta (EFSA-GMO-DE-2009-66) for authorisation of food and feed containing, consisting and produced from genetically modified maize Bt11 × MIR162 × MIR604 × GA21

The EFSA Panel on Genetically Modified Organisms (GMO) has previously assessed the single events Bt11, MIR162, MIR604 and GA21 as well as different stacked events corresponding to combinations of these events. These maize events were found to be as safe as their conventional counterparts and other appropriate comparators with respect to potential effects on human and animal health and the environment. In its assessment of the four‐event maize stack Bt11 × MIR162 × MIR604 × GA21, the GMO Panel also assessed all the subcombinations of these events not previously assessed, including some for which little or no experimental data were provided, including the two‐stack maize event Bt11 × MIR162 (application EFSA‐GMO‐DE‐2009‐66). On 8 November 2016, the European Commission received from Syngenta information on the subcombination Bt11 × MIR162. On 14 December 2016, the European Commission tasked EFSA to analyse these data and to indicate whether they have an impact on the previously issued opinion on the four‐event stack Bt11 × MIR162 × MIR604 × GA21 and its subcombinations. The GMO Panel used the appropriate principles described in its guidelines for the risk assessment of genetically modified (GM) plants to analyse the provided data. The levels of the newly expressed proteins Cry1Ab, PAT, Vip3Aa20 and PMI are similar between the two‐event stack Bt11 × MIR162 and the corresponding single events Bt11 and MIR162. Based on this analysis, there is no indication of an interaction between the events combined in maize Bt11 × MIR162 that would affect the levels of the newly expressed proteins. Thus, the GMO Panel considers that the new information for maize Bt11 × MIR162 does not alter the conclusions of the scientific opinion on application EFSA‐GMO‐DE‐2009‐66.

Scientific opinion on an application by Dow AgroSciences LLC (EFSA-GMO-NL-2012-106) for the placing on the market of genetically modified herbicide-tolerant soybean DAS-44406-6 for food and feed uses, import and processing under Regulation (EC) No 1829/2003

Soybean DAS‐44406‐6 expresses 5‐enolpyruvyl‐shikimate‐3‐phosphate synthase (2mEPSPS), conferring tolerance to glyphosate‐based herbicides, aryloxyalkanoate dioxygenase (AAD‐12), conferring tolerance to 2,4‐dichlorophenoxyacetic acid (2,4‐D) and other related phenoxy herbicides, and phosphinothricin acetyl transferase (PAT), conferring tolerance to glufosinate ammonium‐based herbicides. The molecular characterisation data and bioinformatics analyses did not identify issues requiring assessment for food/feed safety. The agronomic and phenotypic characteristics revealed no relevant differences between soybean DAS‐44406‐6 and its conventional counterpart, except for pod count, seed count and yield. The compositional analysis identified no differences requiring further assessment, except for an increase (up to 31%) in lectin activity in soybean DAS‐44406‐6. Such increase is unlikely to raise additional concerns for food/feed safety and nutrition of soybean DAS‐44406‐6 as compared to its conventional counterpart and non‐GM reference varieties. There were no concerns regarding the potential toxicity and allergenicity of the three newly expressed proteins, and no evidence that the genetic modification might significantly change the overall allergenicity of soybean DAS‐44406‐6. Soybean DAS‐44406‐6 is as nutritious as its conventional counterpart and the non‐GM soybean reference varieties tested. There are no indications of an increased likelihood of establishment and spread of occasional feral soybean DAS‐44406‐6 plants, unless exposed to the intended herbicides. The likelihood of environmental effects from the accidental release of viable seeds from soybean DAS‐44406‐6 into the environment is therefore very low. The post‐market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean DAS‐44406‐6. In conclusion, the GMO Panel considers that the information available for soybean DAS‐44406‐6 addresses the scientific comments raised by Member States and that soybean DAS‐44406‐6, as described in this application, is as safe as its conventional counterpart and non‐GM soybean reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.

Scientific Opinion on an application by Dow AgroSciences LLC (EFSA-GMO-NL-2011-91) for the placing on the market of genetically modified herbicide-tolerant soybean DAS-68416-4 for food and feed uses, import and processing under Regulation (EC) No 1829/2003

Soybean DAS-68416-4 was developed by Agrobacterium tumefaciens-mediated transformation to express the aryloxyalkanoate dioxygenase-12 (AAD-12) protein, conferring tolerance to 2,4-dichlorophenoxyacetic acid (2,4-D) and other related phenoxy herbicides, and the phosphinothricin acetyltransferase (PAT) protein, conferring tolerance to glufosinate ammonium-based herbicides. The molecular characterisation data and bioinformatics analyses did not identify issues requiring further assessment for food/feed safety. The agronomic and phenotypic characteristics tested revealed no relevant differences between soybean DAS-68416-4 and its conventional counterpart, except for 'days to 50% flowering'. The compositional analysis identified no differences requiring further assessment, except for an increase (up to 36%) in lectin activity in soybean DAS-68416-4. Such increase is unlikely to raise additional concerns for food/feed safety and nutrition for soybean DAS-68416-4 as compared to its conventional counterpart and the non-GM reference varieties. There were no concerns regarding the potential toxicity and allergenicity of the two newly expressed proteins, and no evidence that the genetic modification might significantly change the overall allergenicity of soybean DAS-68416-4. Soybean DAS-68416-4 is as nutritious as its conventional counterpart and the non-GM reference varieties. There are no indications of an increased likelihood of establishment and spread of occasional feral soybean DAS-68416-4 plants, unless these are exposed to the intended herbicides. The likelihood of environmental effects resulting from the accidental release of viable seeds from soybean DAS-68416-4 into the environment is therefore very low. The post-market environmental monitoring plan and reporting intervals are in line with the intended uses of soybean DAS-68416-4. The GMO Panel concludes that the information available addresses the scientific comments of the Member States and that soybean DAS-68416-4, as described in this application, is as safe as its conventional counterpart and the tested non-GM reference varieties with respect to potential effects on human and animal health and the environment in the context of the scope of this application.

Scientific opinion on an application for renewal of authorisation for continued marketing of maize 1507 and derived food and feed submitted under Articles 11 and 23 of Regulation (EC) No 1829/2003 by Pioneer Overseas Corporation and Dow AgroSciences LLC

Following the submission of application EFSA‐GMO‐RX‐001 under Regulation (EC) No 1829/2003 from Pioneer Overseas Corporation and Dow Agrosciences LLC, the Panel on Genetically Modified Organisms of the European Food Safety Authority (GMO Panel) was asked to deliver a scientific risk assessment on the data submitted in the frame of a renewal of authorisation application of the insect‐resistant and herbicide‐tolerant genetically modified (GM) maize 1507. The data package received in the frame of this renewal application contained post‐market environmental monitoring reports, a systematic search and evaluation of literature, an updated bioinformatics analysis and additional documents or studies performed by or on behalf of the applicant. The GMO Panel assessed this data package for possible new hazards, modified exposure or new scientific uncertainties identified during the authorisation period and not previously assessed in the frame of the original application. Under the assumption that the DNA sequence of the event in maize 1507 considered for renewal is identical to the corrected sequence of the originally assessed event, the GMO Panel concludes that no new hazards or modified exposure and no new scientific uncertainties were identified for the application for renewal that would change the conclusions of the original risk assessment on maize 1507 (EFSA, 2005b, 2009).

A call for benchmarking transposable element annotation methods

DNA derived from transposable elements (TEs) constitutes large parts of the genomes of complex eukaryotes, with major impacts not only on genomic research but also on how organisms evolve and function. Although a variety of methods and tools have been developed to detect and annotate TEs, there are as yet no standard benchmarks-that is, no standard way to measure or compare their accuracy. This lack of accuracy assessment calls into question conclusions from a wide range of research that depends explicitly or implicitly on TE annotation. In the absence of standard benchmarks, toolmakers are impeded in improving their tools, annotators cannot properly assess which tools might best suit their needs, and downstream researchers cannot judge how accuracy limitations might impact their studies. We therefore propose that the TE research community create and adopt standard TE annotation benchmarks, and we call for other researchers to join the authors in making this long-overdue effort a success.

Next-generation sequencing, FISH mapping and synteny-based modeling reveal mechanisms of decreasing dysploidy in Cucumis

In the large Cucurbitaceae genus Cucumis, cucumber (C. sativus) is the only species with 2n = 2x = 14 chromosomes. The majority of the remaining species, including melon (C. melo) and the sister species of cucumber, C. hystrix, have 2n = 2x = 24 chromosomes, implying a reduction from n = 12 to n = 7. To understand the underlying mechanisms, we investigated chromosome synteny among cucumber, C. hystrix and melon using integrated and complementary approaches. We identified 14 inversions and a C. hystrix lineage-specific reciprocal inversion between C. hystrix and melon. The results reveal the location and orientation of 53 C. hystrix syntenic blocks on the seven cucumber chromosomes, and allow us to infer at least 59 chromosome rearrangement events that led to the seven cucumber chromosomes, including five fusions, four translocations, and 50 inversions. The 12 inferred chromosomes (AK1-AK12) of an ancestor similar to melon and C. hystrix had strikingly different evolutionary fates, with cucumber chromosome C1 apparently resulting from insertion of chromosome AK12 into the centromeric region of translocated AK2/AK8, cucumber chromosome C3 originating from a Robertsonian-like translocation between AK4 and AK6, and cucumber chromosome C5 originating from fusion of AK9 and AK10. Chromosomes C2, C4 and C6 were the result of complex reshuffling of syntenic blocks from three (AK3, AK5 and AK11), three (AK5, AK7 and AK8) and five (AK2, AK3, AK5, AK8 and AK11) ancestral chromosomes, respectively, through 33 fusion, translocation and inversion events. Previous results (Huang, S., Li, R., Zhang, Z. et al., , Nat. Genet. 41, 1275-1281; Li, D., Cuevas, H.E., Yang, L., Li, Y., Garcia-Mas, J., Zalapa, J., Staub, J.E., Luan, F., Reddy, U., He, X., Gong, Z., Weng, Y. 2011a, BMC Genomics, 12, 396) showing that cucumber C7 stayed largely intact during the entire evolution of Cucumis are supported. Results from this study allow a fine-scale understanding of the mechanisms of dysploid chromosome reduction that has not been achieved previously.

Detection of hepatitis delta virus RNA in human liver tissue by non-radioactive in situ hybridization

Several studies have demonstrated the presence of serum HDV-RNA by molecular hybridization in patients with chronic D infection, but there is scarce information about the presence of HDV-RNA in hepatic tissue. The presence of HDV-RNA by in situ hybridization (ISH) with a non-radioactive probe in paraffin-embedded hepatic tissue was studied in 29 patients with chronic delta hepatitis (20 with and 9 without intrahepatic delta antigen) and correlate their presence with the expression of hepatic delta antigen and serum HDV-RNA by dot-blot hybridization. HDV-RNA was detected by in situ hybridization in 18 cases: 16 of the 20 (80%) biopsies with intrahepatic delta antigen and 2 of the 9 (22%) without. HDV-RNA was not detected in any of the control cases. Serum HDV-RNA was found in 19 cases: 18 (90%) of 20 chronic delta hepatitis cases with tissular delta antigen and one of the 9 without intrahepatic delta antigen. All patients except one, who was positive for intrahepatic HDV-RNA, showed serum HDV-RNA. However, in two cases ISH detected hepatic HDV-RNA without tissular HDAg; one of these also had serum HDV-RNA and in the other positivity for hepatic HDV-RNA by ISH was the only marker of viral delta replication. In conclusion, detection of HDV-RNA in hepatic tissue by in situ hybridization with a digoxygenin-labelled probe is a rapid and sensitive method that could be a useful tool for diagnosis of HDV infection in clinical laboratories.

Chronic delta hepatitis: detection of hepatitis delta virus antigen in serum by immunoblot and correlation with other markers of delta viral replication

To investigate the presence of serum hepatitis delta virus antigen by immunoblot and its correlation with other markers of active viral replication (intrahepatic hepatitis D antigen, IgM antibody to hepatitis D and serum hepatitis D virus RNA), we studied serum samples from 50 patients with chronic hepatitis D virus infection (38 with and 12 without intrahepatic hepatitis D antigen). Of the 38 patients with intrahepatic hepatitis D antigen, 27 (71%) had antigen detectable in serum by immunoblot, whereas only two were reactive by conventional enzyme-linked immunosorbent assay. Thirty-one (82%) patients were also positive for serum hepatitis D virus RNA by spot hybridization and 33 (87%) were positive for IgM anti-hepatitis D virus. All markers were simultaneously present in 24 patients. Circulating hepatitis D antigen was detected in one (8%), IgM anti-hepatitis D in seven (58%) and hepatitis D virus RNA in two (17%) of the 12 patients who had anti-hepatitis D in serum but not detectable hepatitis D antigen in liver. Hepatitis D antigen was not detected in serum of any of the 15 control patients. The results suggest that serum hepatitis D antigen as detected by immunoblot and serum hepatitis D virus RNA are similar in sensitivity for detection of active hepatitis D virus replication during chronic infection and constitute useful, sensitive and noninvasive tests for the diagnosis and monitoring of chronic hepatitis D virus infection.