Search

Gene drive technology promises to deliver on some of the global challenges humanity faces to-day in healthcare, agriculture and conservation. However, there is a limited understanding of the consequences of releasing self-perpetuating transgenic organisms into the wild populations under complex ecological conditions. In this study, we analyze the impact of three such complexities, mate-choice, mating systems and spatial mating network, on the population dynamics for two distinct classes of modification gene drive systems. All three factors had a high impact on the modelling outcome. First, we demonstrate that distortion based gene drives appear to be more robust against the mate-choice than viability-based gene drives. Second, we find that gene drive spread is much faster for higher degrees of polygamy. Including a fitness cost, the drive is fastest for intermediate levels of polygamy. Finally, the spread of gene drive is faster and more effective when the individuals have fewer connections in a spatial mating network. Our results highlight the need to include mating complexities while modelling the properties of gene drives such as release thresholds, timescales and population-level consequences. This inclusion will enable a more confident prediction of the dynamics of engineered gene drives and possibly even inform on the origin and evolution of natural gene drives.

It is difficult to trace and identify genome-edited food and feed products if relevant information is not made available to competent authorities. This results in major challenges, as genetically modified organism (GMO) regulatory frameworks for food and feed that apply to countries such as the member states of the European Union (EU) require enforcement based on detection. An international anticipatory detection and identification framework for voluntary collaboration and collation of disclosed information on genome-edited plants could be a valuable tool to address these challenges caused by data gaps. Scrutinizing different information sources and establishing a level of information that is sufficient to unambiguously conclude on the application of genome editing in the plant breeding process can support the identification of genome-edited products by complementing the results of analytical detection. International coordination to set up an appropriate state-of-the-art database is recommended to overcome the difficulty caused by the non-harmonized bio-safety regulation requirements of genome-edited food and feed products in various countries. This approach helps to avoid trade disruptions and to facilitate GMO/non-GMO labeling schemes. Implementation of the legal requirements for genome-edited food and feed products in the EU and elsewhere would substantially benefit from such an anticipatory framework.

Small non-coding RNAs are central regulators of genome activity and stability. Their regulatory function typically involves sequence similarity with their target sites, but understanding the criteria by which they specifically recognize and regulate their targets across the genome remains a major challenge in the field, especially in the face of the diversity of silencing pathways involved. The dominance hierarchy among self-incompatibility alleles in Brassicaceae is controlled by interactions between a highly diversified set of small non-coding RNAs produced by dominant S-alleles and their corresponding target sites on recessive S-alleles. By controlled crosses, we created numerous heterozygous combinations of S-alleles inArabidopsis halleriand developed an RT-qPCR assay to compare allele-specific transcript levels for the pollen determinant of self-incompatibility (SCR). This provides the unique opportunity to evaluate the precise base-pairing requirements for effective transcriptional regulation of this target gene. We found strong transcriptional silencing of recessiveSCRalleles in all heterozygote combinations examined. A simple threshold model of base-pairing for the sRNA-target interaction captures most of the variation inSCRtranscript levels. For a subset of S-alleles, we also measured allele-specific transcript levels of the determinant of pistil specificity (SRK) and found sharply distinct expression dynamics throughout flower development betweenSCRandSRK. In contrast toSCR, bothSRKalleles were expressed at similar levels in the heterozygote genotypes examined, suggesting no transcriptional control of dominance for this gene. We discuss the implications for the evolutionary processes associated with the origin and maintenance of the dominance hierarchy among self-incompatibility alleles.

An intensely debated question is whether or how a mandatory environmental risk assessment (ERA) should be conducted for plants obtained through novel genomic techniques, including genome editing (GE). Some countries have already exempted certain types of GE applications from their regulations addressing genetically modified organisms (GMOs). In the European Union, the European Court of Justice confirmed in 2018 that plants developed by novel genomic techniques for directed mutagenesis are regulated as GMOs. Thus, they have to undergo an ERA prior to deliberate release or being placed on the market. Recently, the European Food Safety Authority (EFSA) published two opinions on the relevance of the current EU ERA framework for GM plants obtained through novel genomic techniques (NGTs). Regarding GE plants, the opinions confirmed that the existing ERA framework is suitable in general and that the current ERA requirements need to be applied in a case specific manner. Since EFSA did not provide further guidance, this review addresses a couple of issues relevant for the case-specific assessment of GE plants. We discuss the suitability of general denominators of risk/safety and address characteristics of GE plants which require particular assessment approaches. We suggest integrating the following two sets of considerations into the ERA: considerations related to the traits developed by GE and considerations addressing the assessment of method-related unintended effects, e.g., due to off-target modifications. In conclusion, we recommend that further specific guidance for the ERA and monitoring should be developed to facilitate a focused assessment approach for GE plants.

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

CRISPR/Cas accelerates the development of synthetic gene drive organisms to quickly spread a genetic modification among the target species. Both in academia and politics, the use of CRISPR/Cas gene drive to potentially control disease vectors, plant pests or invasive alien species is controversial, as exemplified by the last Conference of the Parties of the United Nations Convention on Biodiversity (CBD) and the most recent meeting of its scientific expert group on synthetic biology (Ad Hoc Technical Expert Group/AHTEG). While some argue that current risk assessment frameworks can accommodate synthetic gene drives, others call for a moratorium owing to gene drives’ potentially detrimental impact on wildlife. In essence, the question is whether we have sufficient experience and knowledge to handle this technology safely. Experience and knowledge in turn depend on the degree of continuity and novelty of synthetic gene drive organisms (GDO), compared to existing genetically modified organisms (GMO). While gene drives exist in nature, we find that GDO differ from the currently released GMO on five levels. A clear understanding and analysis of these differences is crucial for any risk assessment regime and a socially acceptable and ethical evaluation that is vital for the application of this technology. ### From nature to synthetic biology Gene drive is a natural phenomenon by which a genetic element is transferred to more than 50% of the offspring of a sexually reproducing organism: natural gene drives are selfish genetic elements that sidestep the rules of Mendelian inheritance, resulting in a so‐called super‐Mendelian inheritance. In 2003, Austin Burt proposed to use this natural phenomenon and synthetically engineer gene drives using specific enzymes called “homing endonucleases.” The discovery of the natural bacterial defence system CRISPR/Cas and its application as a highly specific nuclease eventually boosted the development of synthetic gene drives to circumvent Mendelian inheritance of both the gene drive elements itself …

Environmental control of flowering allows plant reproduction to occur under optimal conditions and facilitates adaptation to different locations. At high latitude, flowering of many plants is controlled by seasonal changes in day length. The photoperiodic flowering pathway confers this response in the Brassicaceae, which colonized temperate latitudes after divergence from the Cleomaceae, their subtropical sister family. The CONSTANS (CO) transcription factor of Arabidopsis thaliana, a member of the Brassicaceae, is central to the photoperiodic flowering response and shows characteristic patterns of transcription required for day-length sensing. CO is believed to be widely conserved among flowering plants; however, we show that it arose after gene duplication at the root of the Brassicaceae followed by divergence of transcriptional regulation and protein function. CO has two close homologs, CONSTANS-LIKE1 (COL1) and COL2, which are related to CO by tandem duplication and whole-genome duplication, respectively. The single CO homolog present in the Cleomaceae shows transcriptional and functional features similar to those of COL1 and COL2, suggesting that these were ancestral. We detect cis-regulatory and codon changes characteristic of CO and use transgenic assays to demonstrate their significance in the day-length-dependent activation of the CO target gene FLOWERING LOCUS T. Thus, the function of CO as a potent photoperiodic flowering switch evolved in the Brassicaceae after gene duplication. The origin of CO may have contributed to the range expansion of the Brassicaceae and suggests that in other families CO genes involved in photoperiodic flowering arose by convergent evolution.

In their Policy Forum “Agricultural research, or a new bioweapon system?” (5 October, p. [35][1]), R. G. Reeves et al. explore the implications of developing genetically modified viruses that insects deliver to plants. To develop horizontal environmental genetic alteration agents (HEGAAs), a U.S. Defense Advanced Research Projects Agency (DARPA) program promotes laboratories in the field to confer genetic modifications outside the lab. Lab-in-the-field approaches have already been described for gene drives ([ 1 ][2]–[ 4 ][3]), but the multilayered concepts of HEGAAs go far beyond those in time and space. Each layer is characterized by a high degree of complexity and is often novel to regulators and risk assessors. The combination of examining recombinant DNA incorporated into a plant virus, determining the role of the sap-sucking insects that carry it, and documenting the genetic modification that the virus triggers is beyond any risk assessment ever performed in the field of biotechnology. Even with the option to assess each layer independently, it remains an incalculable task to synthesize these separate results into a reliable overall assessment. Anticipating potential detrimental impacts for HEGAAs in the case of environmental release is paramount. It is remarkable that there has been no public discourse on environmental risks since DARPA published its work plan almost 2 years ago. Given the unprecedented challenges of the HEGAA approach, regulators around the world need to ensure that they are not caught unprepared. In this regard, HEGAAs serve as a prime example of the pressing need for active horizon scanning in the field of synthetic biology. Such an approach would require three steps to ensure sufficient time for public discourse on applications such as HEGAAs: identification of challenging developments by risk assessment experts, evaluation of wider societal implications, and popularization of the results internationally. We believe that active horizon scanning should be carried out under the umbrella of the United Nations Convention on Biological Diversity. 1. [↵][4]1. K. M. Esvelt, 2. A. L. Smidler, 3. F. Catteruccia, 4. G. Church , eLIFE, 10.7554/eLife.03401.001 (2014). 2. 1. K. M. Esvelt, 2. N. J. Gemmell , PLOS Biol. 15, e2003850 (2017). [OpenUrl][5] 3. 1. S. Simon, 2. M. Otto, 3. M. Engelhard , EMBO Rep. 19, e45760 (2018). [OpenUrl][6][FREE Full Text][7] 4. [↵][8]1. B. L. Webber, 2. S. Raghu, 3. O. R. Edwards , Proc. Natl. Acad. Sci. U.S.A. 112, 10565 (2015). [OpenUrl][9][FREE Full Text][10] [1]: http://www.sciencemag.org/content/362/6410/35 [2]: #ref-1 [3]: #ref-4 [4]: #xref-ref-1-1 "View reference 1 in text" [5]: {openurl}?query=rft.jtitle%253DPLOS%2BBiol.%26rft.volume%253D15%26rft.spage%253De2003850%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [6]: {openurl}?query=rft.jtitle%253DEMBO%2BRep.%26rft_id%253Dinfo%253Adoi%252F10.15252%252Fembr.201845760%26rft_id%253Dinfo%253Apmid%252F29650530%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [7]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiRlVMTCI7czoxMToiam91cm5hbENvZGUiO3M6NToiZW1ib3IiO3M6NToicmVzaWQiO3M6MTE6IjE5LzUvZTQ1NzYwIjtzOjQ6ImF0b20iO3M6MjU6Ii9zY2kvMzYyLzY0MTgvMTAwNy4yLmF0b20iO31zOjg6ImZyYWdtZW50IjtzOjA6IiI7fQ== [8]: #xref-ref-4-1 "View reference 4 in text" [9]: {openurl}?query=rft.jtitle%253DProc.%2BNatl.%2BAcad.%2BSci.%2BU.S.A.%26rft_id%253Dinfo%253Adoi%252F10.1073%252Fpnas.1514258112%26rft_id%253Dinfo%253Apmid%252F26272924%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [10]: /lookup/ijlink/YTozOntzOjQ6InBhdGgiO3M6MTQ6Ii9sb29rdXAvaWpsaW5rIjtzOjU6InF1ZXJ5IjthOjQ6e3M6ODoibGlua1R5cGUiO3M6NDoiRlVMTCI7czoxMToiam91cm5hbENvZGUiO3M6NDoicG5hcyI7czo1OiJyZXNpZCI7czoxMjoiMTEyLzM0LzEwNTY1IjtzOjQ6ImF0b20iO3M6MjU6Ii9zY2kvMzYyLzY0MTgvMTAwNy4yLmF0b20iO31zOjg6ImZyYWdtZW50IjtzOjA6IiI7fQ==

Diurnal patterns of gene transcription are often conferred by complex interactions between circadian clock control and acute responses to environmental cues. Arabidopsis thaliana GIGANTEA (GI) contributes to photoperiodic flowering, circadian clock control, and photoreceptor signaling, and its transcription is regulated by the circadian clock and light. We used phylogenetic shadowing to identify three evolutionarily constrained regions (conserved regulatory modules [CRMs]) within the GI promoter and show that CRM2 is sufficient to confer a similar transcriptional pattern as the full-length promoter. Dissection of CRM2 showed that one subfragment (CRM2-A) contributes light inducibility, while another (CRM2-B) exhibits a diurnal response. Mutational analysis showed that three ABA RESPONSE ELEMENT LIKE (ABREL) motifs in CRM2-A and three EVENING ELEMENTs (EEs) in CRM2-B are essential in combination to confer a high amplitude diurnal pattern of expression. Genome-wide analysis identified characteristic spacing patterns of EEs and 71 A. thaliana promoters containing three EEs. Among these promoters, that of FLAVIN BINDING KELCH REPEAT F-BOX1 was analyzed in detail and shown to harbor a CRM functionally related to GI CRM2. Thus, combinatorial interactions among EEs and ABRELs confer diurnal patterns of transcription via an evolutionarily conserved module present in GI and other evening-expressed genes.

Polyploidy is an example of instantaneous speciation when it involves the formation of a new cytotype that is incompatible with the parental species. Because new polyploid individuals are likely to be rare, establishment of a new species is unlikely unless polyploids are able to reproduce through self-fertilization (selfing), or asexually. Conversely, selfing (or asexuality) makes it possible for polyploid species to originate from a single individual—a bona fide speciation event. The extent to which this happens is not known. Here, we consider the origin of Arabidopsis suecica, a selfing allopolyploid between Arabidopsis thaliana and Arabidopsis arenosa, which has hitherto been considered to be an example of a unique origin. Based on whole-genome re-sequencing of 15 natural A. suecica accessions, we identify ubiquitous shared polymorphism with the parental species, and hence conclusively reject a unique origin in favor of multiple founding individuals. We further estimate that the species originated after the last glacial maximum in Eastern Europe or central Eurasia (rather than Sweden, as the name might suggest). Finally, annotation of the self-incompatibility loci in A. suecica revealed that both loci carry non-functional alleles. The locus inherited from the selfing A. thaliana is fixed for an ancestral non-functional allele, whereas the locus inherited from the outcrossing A. arenosa is fixed for a novel loss-of-function allele. Furthermore, the allele inherited from A. thaliana is predicted to transcriptionally silence the allele inherited from A. arenosa, suggesting that loss of self-incompatibility may have been instantaneous.