Plants are essential for human survival. Over the past three decades, work with the reference plant Arabidopsis thaliana has significantly advanced plant biology research. One key event was the sequencing of its genome 25 years ago, which fostered many subsequent research technologies and datasets. Arabidopsis has been instrumental in elucidating plant-specific aspects of biology, developing research tools, and translating findings to crop improvement. It not only serves as a model for understanding plant biology and but also biology in other fields, with discoveries in Arabidopsis also having led to applications in human health, including insights into immunity, protein degradation, and circadian rhythms. Arabidopsis research has also fostered the development of tools useful for the wider biological research community, such as optogenetic systems and auxin-based degrons. This 4th Multinational Arabidopsis Steering Committee Roadmap outlines future directions, with emphasis on computational approaches, research support, translation to crops, conference accessibility, coordinated research efforts, climate change mitigation, sustainable production, and fundamental research. Arabidopsis will remain a nexus for discovery, innovation, and application, driving advances in both plant and human biology to the year 2030, and beyond.

Agricultural improvements that reduce conventional pesticide use and support environmental aims are a priority. Current approaches develop promising alternative products but meet significant challenges in bringing them to market. This article reports findings of an Association of Applied Biologists event at which delegates from relevant industry sectors discussed the establishment of an effective integrated pest management innovation system linking multiple stakeholders. Interrelated recommendations were agreed upon, focused on structured gap analysis, co-design processes reflecting the complete innovation system, the approval process, application equipment, enhancing grower confidence, integrating knowledge exchange activities, promulgation of public good information and the need for an overarching national action plan and supporting legislation.

Visualizing the location of the total cellular mRNA pool can be important to understand how different genes affect cellular physiology. Over the past decade researchers investigating RNA processing, nuclear transport and the function of the nuclear pore complex have used in situ hybridization protocol to visualize and quantify the accumulation of the total mRNA pool within the plant cell nucleus.

This Community Resource paper introduces the range of materials developed by the INDEPTH (Impact of Nuclear Domains on Gene Expression and Plant Traits) COST Action made available through the INDEPTH Academy. Recent rapid growth in understanding of the significance of epigenetic controls in plant and crop science has led to a need for shared, high-quality resources, standardization of protocols, and repositories for open access data. The INDEPTH Academy provides a range of masterclass tutorials, standardized protocols, and teaching webinars, together with a rapidly developing repository to support imaging and spatial analysis of the nucleus and deep learning for automated analysis. These resources were developed partly as a response to the COVID-19 pandemic, but also driven by needs and opportunities identified by the INDEPTH community of ~200 researchers in 80 laboratories from 32 countries. This community report outlines the resources produced and how they will be extended beyond the INDEPTH project, but also aims to encourage the wider community to engage with epigenetics and nuclear structure by accessing these resources.

Twenty years ago, the Arabidopsis thaliana genome sequence was published. This was an important moment as it was the first sequenced plant genome and explicitly brought plant science into the genomics era. At the time, this was not only an outstanding technological achievement, but it was characterized by a superb global collaboration. The Arabidopsis genome was the seed for plant genomic research. Here, we review the development of numerous resources based on the genome that have enabled discoveries across plant species, which has enhanced our understanding of how plants function and interact with their environments.

The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC). Here, we (a) highlight recent research advances made with the reference plant Arabidopsis thaliana; (b) provide summaries from recent reports submitted by MASC subcommittees, projects and resources associated with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis research community.

Successful collaborative research is dependent on excellent ideas and innovative experimental approaches, as well as the provision of appropriate support networks. Collaboration requires venues, infrastructures, training facilities, and, perhaps most importantly, a sustained commitment to work together as a community. These activities do not occur without significant effort, yet can be facilitated and overseen by the leadership of a research network that has a clearly defined role to help build resources for their community. Over the past 20 years, this is a role that the UKRI-BBSRC-funded GARNet network has played in the support of the UK curiosity-driven, discovery-led plant science research community. This article reviews the lessons learnt by GARNet in the hope that they can inform the practical implementation of current and future research networks.

The plant nucleus contains myriad subdomains that define and are defined by the composition of their chromatin. On a whole nucleus scale, this includes regions of active euchromatin and inactive heterochromatin, although the boundaries between these states are blurred. Different loci constantly enter and exit nuclear structures including the nucleolus and transient regulatory nuclear bodies. Chromatin is defined by its complex combinations of epigenetic modifications and variation in its constituent histone proteins. Here we preview articles that describe many of the mechanisms that regulate this dynamic chromatin.

The precise location of chromatin domains within the cell nucleus has seen growing recognition in the past decade as an additional mechanism of controlling gene expression in both plants and animals (Dekker et al., 2017). Consequently, international efforts are devoted to understanding the organising principle of this organelle in plants, and notably the nature and the role of functional compartments on gene expression (Graumann et al., 2013; Sotelo-Silveira et al., 2018). The European cooperation 'Impact of Nuclear Domains on Gene Expression and Plant Traits' (INDEPTH) brings together molecular cell biologists, plant physiologists, bioinformaticians, image analysts and computer scientists. They aim to address the question of how nuclear architecture, chromatin organisation and gene expression are connected in plants, particularly in relation to traits of interest such as biomass, reproduction and resistance to pathogens (https://www.brookes.ac.uk/indepth/). The kick-off meeting of the INDEPTH consortium took place in Clermont-Ferrand, France, on 12-14th March 2018, where more than 80 researchers set the agenda for the coming four years of research and collaboration.

In July 2017, the Society for Experimental Biology hosted a symposium on new breeding technologies (NBTs) in Plant Sciences at the University of Gothenburg. This report summarises the major outcomes of this meeting. Delegates discussed both the technical and policy aspects of NBTs, with a focus on CRISPR-Cas9 gene editing. While NBTs have the potential to revolutionise the future generation of new crop varieties, a major outcome of the meeting was the acceptance that we are at a critical juncture regarding the policy decisions that will govern the future use of plants generated using these technologies. This meeting report offers insights into how scientists can frame their input into the upcoming debate, as well as a discussion about what is technically possible with NBTs. The use of the CRISPR-Cas9 system for precision genome editing (GE) has been regularly described as a ‘game-changing technology’ that allows a more precise targeting of DNA to induce specific nucleotide variations (Belhaj et al. 2015); however, the use of GE in plants for the production of food or feed still faces an uncertain regulatory future. This follows on from a long-standing public distrust of genetically modified organisms (GMOs), an opinion predicated from, amongst other things, controversial yet discredited scientific studies and public miscommunications. Public unease with this technology has guided government policy on the permitted uses of the products of GMOs, such that growth of these crops is now restricted throughout most of the European Union (EU). The plant science community stands at an important crossroads at which the future uses of plants generated by GE technologies will be decided. This issue was a primary concern for the group of 70 international delegates who met in Gothenburg, Sweden, for the Society for Experimental Biology Plant Section Symposium on New Breeding Technologies in July 2017. This meeting was organised in collaboration with the Global Plant Council, GARNet, the Scandinavian Plant Physiology Society and the Australian Society of Plant Scientists, and brought together experts on both the regulatory and technical aspects of using CRISPR-Cas9, the most popular type of GE technology. This special issue of Physiologia Plantarum includes articles from meeting participants on a variety of topics that were discussed at this meeting.

Gene editing (GE) technology is now widely used by plant scientists who work on a range of model and crop species. GARNet, the New Phytologist Trust and the Bristol Centre for Agricultural Innovation (UK) brought a group of global experts to the University of Bristol in March 2018 to discuss current applications, emerging best practice and policy issues that surround use of this technology. One aim of the workshop was to discuss the regulatory and political issues that surround the use of GE. To this end, invited speakers explained developments from the regions of greatest relevance to delegates, namely the UK, other parts of Europe and the USA. At the meeting Dennis Eriksson from the Swedish University of Agricultural Science (Uppsala, Sweden) reported that the situation in European legislation was in limbo as European Union (EU) Member States awaited a decision from the European Court of Justice (ECJ) regarding the regulatory status of crops generated by mutagenesis techniques. He suggested that there was cause for optimism following a published opinion from the Advocate General indicating that plants generated by GE should be regulated in a similar manner to those generated by other forms of mutagenesis (Abbott, 2018). However, since the meeting, the ECJ has now ruled that crops generated by modern mutagenesis techniques (such as GE) should be regulated under the 2001 Genetically Modified Organism (GMO) directive (Curia.europa.eu, 2018). This decision has been criticized by plant scientists as it states that assessments of crop safety should continue to be made on the basis of process rather than product, regardless of the safety of the final variety (EPSO, 2018; Leyser, 2018). Louise Ball from the UK Department of the Environmental and Rural Affairs (DEFRA) spoke positively about the use of GE, and the UK Advisory Committee on Releases to the Environment (ACRE) has approved the application for a field trial of a gene edited Camelina sativa at Rothamsted Research (Harpenden, UK) since the meeting (Rothamsted Research, 2018). In the opening line of its decision, ACRE ‘considers that Camelina sativa plants produced by CRISPR-Cas9 genome-editing could have been produced through traditional breeding techniques’ (GOV UK, 2018). This outcome indicates that UK regulators are well disposed toward the use of GE in the generation of novel crops. Whilst Louise Ball stated that DEFRA will take its lead from the ECJ decision, there may be opportunities for future use of this technology in the UK post-Brexit. The ECJ decision does include provision for EU countries to make their own decisions on use of crops generated by any mutagenesis technique. Therefore, it is likely that the ruling will not be applied evenly across the continent. Stefan Jansson (Umea University, Sweden) provided the opening keynote presentation to the Bristol meeting, outlining how the Swedish Board of Agriculture does not consider GE plants any differently from those generated by conventional mutagenesis techniques (Eriksson, 2018). Stefan has travelled through different Nordic countries to showcase the first GE meal, and highlighted challenges that will arise if countries differently interpret the GMO directive, now encompassing GE plants. Whereas in Sweden the entire GE plant can be grown, in Finland only certain portions of the plant are permitted; whilst Norway, which is not an EU country, but that adheres to the EU GMO directive, only allows plant genetically modified (GM) products but not the actual plant. The Norwegian Biotechnology Advisory Board has recently proposed a set of regulations that would place all mutagenic events (including those used in conventional breeding or GE) and cisgenic events at a regulatory level below that used to regulate transgenic plants. Stefan pointed out that regulatory bodies will not be able to discriminate between CRISPR-edited and mutagenized plants on the basis of end-point sequence data. Professor Gary Marchant from Arizona State University (Tempe, AZ, USA) reported at the meeting that, in contrast to Europe's process-based and heavy-handed regulatory environment, the US regulatory environment for use of gene-edited crops is light-touch. The US Department of Agriculture (USDA) regulation of GM crops centres on whether the plant contains any ‘plant pest DNA’, commonly including viral promotor sequences. If so, approval of the crop requires a laborious and prohibitively expensive process, stifling innovation in small and medium-sized enterprises (SMEs). However, the regulation of GE has taken a surprising twist. As transgene-free GE organisms do not contain plant pest DNA, they cannot be regulated by the USDA, and equally do not fall under the regulatory auspices of any other US regulatory agency such as the Food and Drug Administration (FDA) and the Environmental Protection Agency (EPA). A growing number of gene edited plants have now been approved by the USDA, following verification that they contain no transgenic DNA (USDA, 2018). This rapid approval process might appear attractive to scientists who want to quickly bring products to market, but the consensus from meeting delegates was that risk- and evidence-based regulations are preferable to very light touch or no regulation (Waltz, 2018). If the US regulatory position is taken to its logical conclusion, then a GE plant that generates a known toxin could be approved as it does not contain ‘plant pest DNA’. Therefore, a product that has had little testing may generate unforeseen harmful by-products, which could damage future use of this technology and compromise public confidence. Gary conceded that in the USA, this issue is likely to remain unresolved in the near term. As trading nations take different stances regarding the growth and use of GE crops, and it may be impossible to discriminate between GE crops and crops that have been engineered by mutagenesis or bred by conventional methods, it is likely that cross-border regulation of these products will be unworkable and unenforceable. Irrespective of the earlier mentioned regulatory uncertainty, GE technology provides an unsurpassed opportunity to modify gene function. Transformation of many crops occurs at low efficiency, and many other plants are recalcitrant to genetic transformation. GE has potential to obviate the requirement for genomic transgene integration in the production of stable mutant lines. Whilst DNA delivery into plant cells is a bottleneck in GE, a few speakers reported progress in removing this bottleneck. Heather Whitney at the University of Bristol (UK) gave an enlightening talk on carbon nanodots, which are easy to make, nontoxic and can be functionalized to deliver DNA into plant cells. Her laboratory and colleagues at Bristol are currently trialling use of this technology to express Cas9 and sgRNAs in a range of grass crops including wheat, and there is exciting potential for broad application across the plant tree of life. Choun-Sea Lin (Academica Sinica, Taipei) travelled from Taiwan to discuss a protoplast transformation technique that has shifted the bottleneck in generating mutants from DNA delivery into cells and transformation to efficient regeneration in tissue culture. He discussed polyethylene glycol delivery of DNA into protoplasts, regeneration and editing of 11 species (five grasses, four brassicas, and two nightshades) and has developed methods to screen individual protoplasts for edits (Fig. 1; Lin et al., 2018). Choun-Sea's group is eager to use their expertise on an expanded number of plant species and welcomes collaboration. Although many laboratories are using CRISPR, best practice is not yet fully established. Baptiste Castel from Jonathan Jones’ laboratory at The Sainsbury Laboratory, Norwich (UK) presented a comprehensive assessment of the molecular parameters for using the CRISPR system in Arabidopsis. Their laboratory has determined that either UBI10, YAO or RPS5 promotor-induced expression of a plant-optimized Cas9_3, which includes an internal intron, caused the highest mutation rates. In addition, they produced a more efficient ‘extension-flip’ variety of the guideRNA. Finally, when the Cas9 and guideRNA were positioned head-to-head within a T-DNA, they could isolate more stably edited plants in the T1 generation (Fig. 2). Michaela McGinn (Illinois State University, USA) reported that, in the novel oilseed feedstock crop Pennycress, the source of the Cas9 nuclease partially determined editing efficiency. She found that Staphylococcus aureus Cas9 had higher editing rates than S. pyogenes Cas9, and that Cas9 expression levels as determined by western blot were not predictive of editing efficiency for either nuclease. Michaela McGinn also reported that edits did not always appear in or stabilize in the T1 generation, sometimes appearing in T2 or later generations. Thus, transformed plants that initially showed wild-type (WT) gene activity may, in fact, generate de novo edits that result in mutant phenotypes in the T2 generation (Fig. 3). Such edits were detectable in sequence traces from T1 GE plants, and trace analysis was therefore recommended. Michaela had used CRISPR-Cas9 to reduce the levels of an undesired fatty acid from 40% in WT Pennycress seed to < 1% in GE mutants (McGinn et al., 2018). A potential concern with the use of CRISPR-Cas9 to create new crop varieties involves the generation of off-target edits across the genome. To allay these concerns, Yiping Qi from the University of Maryland (USA) described a remarkable set of experiments that involved conducting whole genome sequencing on almost 70 individual rice plants (Tang et al., 2018). This allowed them to assess the amount of spontaneous mutations in unedited plants in comparison with those that had been edited by either Cas9 or Cpf1 nucleases. Yiping showed that any allele changes could be explained by the rate of spontaneous mutations, and that neither of the nucleases induced additional off-target mutations in the T1 generation. Given the technical challenges of GE, it might be more cost-effective for researchers to engage with a community resource in order to generate edited plants, and a number of these were introduced at the meeting. These include facilities at the National Institute for Agricultural Biology (Cambridge, UK), the University of Bristol, Rothamsted Research, the John Innes Centre (Norwich, UK) and the Vienna Biocentre Core Facility (Austria). Each facility welcomes prospective collaborations. Whilst the meeting focused on GE, novel uses for Cas9 gene targeting were also discussed. Alex Leydon from Jennifer Nemhauser's group at the University of Washington (Seattle, WA, USA) is using repurposed nucleases for transcriptional control. The synthetic HACR protein includes a dCas9 that binds DNA but lacks nuclease activity, a transcriptional repression domain and a hormone-inducible degron (Khakhar et al., 2018). By either replacing the repression domain and/or the degron, the HACR system can provide enormous variation in experimental design. The core dCas9 subunit allows tight gene regulation, and the Nemhauser group has used different degrons to generate a set of hormone biosensors that are responsive to auxin, jasmonate or gibberellic acid (GA). Although at the workshop Alex specifically described research that had modelled the response to GA, enormous potential of the HACR system was clear. This meeting introduced a wide range of projects that are using CRISPR-based GE and highlighted attempts to optimize GE technology. The community is progressing towards the establishment of a set of standardized protocols that will reduce challenges for new users. Rarely has the future use of a technology been so tightly linked to its regulation and this meeting highlighted the policies employed by different countries. Although a global consensus for evidence- and trait-based regulation of gene edited crops seems some way off, differences in how countries apply these rules will hopefully mean that the technology can still be used to develop useful and much needed novel varieties. The GARNet Plant Gene-Editing Workshop was made possible due to generous support from the New Phytologist Trust, the Bristol Centre for Agricultural Innovation and from the UKRI BBSRC- funded GARNet2020 grant (BB/M004376/1). Special thanks to Helen Harper for help organizing the workshop.

The molecular changes that allow plant roots to response to low phosphate levels are poorly understood. A series of three papers investigate this phenomenon and reveal which components of the auxin response are key for transmitting the phosphate signal into changes in root hair phenotypes.

Plant research produces data in a profusion of types and scales, and in ever-increasing volume. What are the challenges and opportunities presented by data management in contemporary plant science? And how can researchers make efficient and fruitful use of data management tools and strategies?

Targeted genome engineering has been described as a “game-changing technology” for fields as diverse as human genetics and plant biotechnology. One technique used for precise gene editing utilises the CRISPR-Cas system and is an effective method for genetic engineering in a wide variety of plants. However, many researchers remain unaware of both the technical challenges that emerge when using this technique or of its potential benefits. Therefore in September 2015, GARNet and OpenPlant organized a two-day workshop at the John Innes Centre that provided both background information and hands-on training for this important technology.

Regulating nucleo-cytoplasmic transport of RNA and protein is a key cellular control point. Perturbing the function of plant nuclear transport components can cause significant developmental defects and in this report we add an important line to this evidence. Overexpression of AtRAN1 or AtNUP62 in Nicotiana benthamiana causes significant damage to leaf tissue. This demonstrates that the precise control of nuclear transport is an important aspect of maintaining tissue integrity.

The nuclear envelope (NE) separates the key mechanisms of transcription and translation, and as such is a critical control point in all eukaryotic cells. In plants, the proteins of the NE influence a number of processes including the control of nucleo-cytoplasmic transport of RNA and protein, chromatin localization to the nuclear periphery, and direct chromatin binding by members of the nuclear pore complex (NPC). In this review I attempt to bring these roles under the umbrella of their effect on gene expression, even though the complex nature of this cellular environment means there is considerable overlap of effects. Although the volume of research in plant cells has greatly improved over recent years, it is clear that our understanding of how the components of the NE either directly or indirectly influence gene expression is still in its infancy.

The nuclear pore complex (NPC) is a multisubunit protein conglomerate that facilitates movement of RNA and protein between the nucleus and cytoplasm. Relatively little is known regarding the influence of the Arabidopsis NPC on growth and development. Seedling development, flowering time, nuclear morphology, mRNA accumulation, and gene expression changes in Arabidopsis nucleoporin mutants were investigated. Nuclear export of mRNA is differentially affected in plants with defects in nucleoporins that lie in different NPC subcomplexes. This study reveals differences in the manner by which nucleoporins alter molecular and plant growth phenotypes, suggesting that nuclear pore subcomplexes play distinct roles in nuclear transport and reveal a possible feedback relationship between the expression of genes involved in nuclear transport.

The plant hormone auxin is thought to provide positional information for patterning during development. It is still unclear, however, precisely how auxin is distributed across tissues and how the hormone is sensed in space and time. The control of gene expression in response to auxin involves a complex network of over 50 potentially interacting transcriptional activators and repressors, the auxin response factors (ARFs) and Aux/IAAs. Here, we perform a large-scale analysis of the Aux/IAA-ARF pathway in the shoot apex of Arabidopsis, where dynamic auxin-based patterning controls organogenesis. A comprehensive expression map and full interactome uncovered an unexpectedly simple distribution and structure of this pathway in the shoot apex. A mathematical model of the Aux/IAA-ARF network predicted a strong buffering capacity along with spatial differences in auxin sensitivity. We then tested and confirmed these predictions using a novel auxin signalling sensor that reports input into the signalling pathway, in conjunction with the published DR5 transcriptional output reporter. Our results provide evidence that the auxin signalling network is essential to create robust patterns at the shoot apex.