The large size and complex polyploid nature of many genomes has often hampered genomics development, as is the case for several plants of high agronomic value. Isolating single chromosomes or chromosome arms via flow sorting offers a clue to resolve such complexity by focusing sequencing to a discrete and self-consistent part of the whole genome. The occurrence of sufficient differences in the size and or base-pair composition of the individual chromosomes, which is uncommon in plants, is critical for the success of flow sorting. We overcome this limitation by developing a robust method for labeling isolated chromosomes, named Fluorescent In situ Hybridization In suspension (FISHIS). FISHIS employs fluorescently labeled synthetic repetitive DNA probes, which are hybridized, in a wash-less procedure, to chromosomes in suspension following DNA alkaline denaturation. All typical A, B and D genomes of wheat, as well as individual chromosomes from pasta (T. durum L.) and bread (T. aestivum L.) wheat, were flow-sorted, after FISHIS, at high purity. For the first time in eukaryotes, each individual chromosome of a diploid organism, Dasypyrum villosum (L.) Candargy, was flow-sorted regardless of its size or base-pair related content. FISHIS-based chromosome sorting is a powerful and innovative flow cytogenetic tool which can develop new genomic resources from each plant species, where microsatellite DNA probes are available and high quality chromosome suspensions could be produced. The joining of FISHIS labeling and flow sorting with the Next Generation Sequencing methodology will enforce genomics for more species, and by this mightier chromosome approach it will be possible to increase our knowledge about structure, evolution and function of plant genome to be used for crop improvement. It is also anticipated that this technique could contribute to analyze and sort animal chromosomes with peculiar cytogenetic abnormalities, such as copy number variations or cytogenetic aberrations.

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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.

Transfer of alien chromosome segments from various Triticeae species into cultivated wheats, commonly referred to as “chromosome engineering”, is currently benefiting from the recent, impressive advancements in molecular genetics, cytogenetics and genomics, which are providing new insights into the genetic and physical organization of even complex plant genomes, such as those of the Triticeae. The powerful analytical tools presently available are making the assessment of desired genotypes in the course of chromosome engineering far more precise and effective than in the past, thus giving this transfer strategy renewed and increased potential for meaningful practical achievements. Examples are given here of the application of such tools to the engineering of the durum wheat genome with small alien segments containing genes with beneficial impact on disease resistance and quality traits.

Favoured by climate changes, Fusarium head blight (FHB) has recently become a threat also in unusual environments, including those where durum wheat is largely cultivated. Since current durum wheat cultivars are mostly susceptible to FHB, new germplasm is needed, capable of maintaining yield capacity and grain quality under the disease pressure. To achieve this goal, a sustainable approach relies on transfer of resistance from related Triticeae species by means of chromosome engineering. We resorted to this cytogenetic strategy, efficiently complemented with advanced selection systems, to transfer into durum a QTL for FHB resistance (here, temporarily designated Fhb-7el 2 ) previously mapped on the 7el 2 L arm of the wild Thinopyrum ponticum. A bread wheat 7DS.7el 2 L translocation line was employed as donor of Fhb-7el 2 in crosses with previously developed durum wheat 7AS.7AL-7el 1 L recombinant genotypes, carrying genes for rust diseases (Lr19 ? Sr25) as well as for quality-and yieldcontributing traits, deriving from a different Th. ponticum accession. In pentaploid F 1 s, the largely homologous 7el 1 L and 7el 2 L arms showed considerable reduction in pairing and recombination frequency as compared to what observed in a parallel experiment we carried out in a hexaploid context. Nevertheless, pyramiding into durum of target genes/QTL from the two Th. ponticum accessions was successfully achieved. The selected 7el 1 L ? 7el 2 L tetraploid lines exhibited 70-85 % reduction in FHB severity following Fusarium inoculation, and a parallel decrease in fungal biomass in kernels of infected spikes. Similar effects were detected in bread wheat lines carrying the same target gene assembly on 7DL instead of 7AL. Preliminary evidence of good agronomic performance of the novel 7el 1 L ? 7el 2 L recombinant lines paves the way for their straightforward exploitation in breeding.

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Perennial wheatgrass species of the genus Thinopyrum possess several appealing attributes for wheat improvement, contributing to tolerance to biotic and abiotic stresses, as well as to quality and even to yield increase. Major genes or QTLs underlying such traits have been identified on numerous chromosomes of both diploid (Th. elongatum and Th. bessarabicum) and polyploid (mainly Th. intermedium and Th. ponticum) representatives of the genus, having different genome origin (E, J, St/S) and involving several homoeologous groups. Thinopyrum chromosomes sharing homoeology with wheat group 7 chromosomes turned to be particularly rich in beneficial genes; among them, a Th. ponticum group 7 chromosome referred to as 7Ag or 7el has been extensively targeted in various successful attempts of harnessing its attractive gene content. A survey of the several wheat translocation/recombinant lines involving this chromosome in the background of both bread and durum wheat is given. Such lines are described as highly valuable tools for a variety of studies, from development of integrated genetic and physical maps, to the analysis of structural and functional characteristics associated with defined alien chromosome subregions. The validity of Th. ponticum group 7 transfers as breeding materials (notable genes and traits including Lr19, Sr25, Fusarium head blight resistance, yellow pigment content, and even yield) is also highlighted. Finally, examples are given of pyramiding of group 7 Thinopyrum genes through 'precision' breeding strategies of chromosome

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.