13 ERA-CAPS FLOWPLAST

Flowering is precisely controlled by diverse environmental cues. These responses contribute to the adaptation of plants to different environments and to the optimisation of crop yields. Genetic and molecular analyses performed mainly in Arabidopsis thaliana have identified regulatory pathways that confer different responses to the environment and integrate endogenous and environmental cues to control the floral transition. These pathways act in different tissues of the plant but ultimately influence flowering at the shoot meristem. A complete understanding of these pathways and how they are integrated will decipher how plasticity in flowering response is conferred among plants of the same genotype and how genetic variation between varieties impacts on this plasticity. In turn such knowledge will increase our capacity to breed crops for changing environmental conditions. We propose to investigate the molecular basis of plasticity in flowering-time control in A. thaliana, with a focus on two crucial environmental cues, increases in ambient temperature and different day lengths. As the pathways mediating these responses ultimately converge on the shoot meristem to initiate transcriptional reprogramming we will develop the INTACT system to describe the transcriptional changes that occur in defined spatial zones of the meristem through a temporal series in response to changes in day length. Then, we will use the data from the INTACT profiling to address specific issues related to signal integration at the meristem. We will investigate the chromatin landscape at the shoot apical meristem (SAM) during the transition to flowering and correlate this to transcriptional activity and splicing patterns in response to high ambient temperatures. Such analyses will allow comparison of these data with those obtained during the day-length series identifying common and distinct processes. In addition, we will investigate the integration of different signalling pathways in the rib meristem, where photoperiod and gibberellic acid (GA) signalling converge. Thus, this project will employ flowering and advances in genomic technologies as a platform for dissecting basic mechanisms that govern developmental plasticity on a whole-genome scale. Our results will be of interest to a wide audience, and will help to answer the evolutionarily important questions of how environmental signalling pathways are prioritized and integrated at the shoot meristem as well as how much epigenetic regulation and alternative splicing contributes to the floral transition. Ultimately such knowledge will help predict the mechanisms available to plants to manipulate the timing of the floral transition in response to environmental changes and will contribute to sustainable agriculture.

Flowering is precisely controlled by diverse environmental cues that contribute to the adaptation of plants to different environments. Genetic and molecular analyses have identified regulatory pathways that confer different responses to the environment and integrate endogenous and environmental cues to control the floral transition. An understanding of these pathways will decipher how plasticity in flowering response is conferred among plants of the same genotype. Such knowledge will increase our capacity to breed crops for changing environmental conditions. We propose to investigate the molecular basis of plasticity in flowering-time control in A. thaliana, with a focus on ambient temperature and day length. As the pathways mediating these responses ultimately converge on the shoot meristem, we will develop the INTACT system to describe the transcriptional changes that occur in spatial zones of the meristem. We will investigate the chromatin landscape at the shoot apical meristem (SAM) during the transition to flowering and correlate this to transcriptional activity and splicing patterns in response to high ambient temperatures. Such analyses will allow comparison of these data with those obtained during the day-length series identifying common and distinct processes. In addition, we will investigate the integration of different signalling pathways in the rib meristem, where photoperiod and gibberellic acid (GA) signalling converge. Thus, this project will employ flowering and advances in genomic technologies as a platform for dissecting basic mechanisms that govern developmental plasticity on a whole-genome scale.

The overall aim of this project is to perform high-quality scientific research to understand the molecular basis of plant developmental plasticity with a primary focus on the flowering time response.
Since we anticipate a broad interest in the data generated in this project, we intend to give free access to all generated results as soon as possible. Although all work will be done on the model plant A. thaliana, we foresee that the results can be converted to improve yield of important agricultural food and feed crops, making this project of importance to plant breeders and European agriculture. Small increases in temperature have e.g. a negative effect on the quality, yield, and predictability of harvest time in various Brassicacea food crops, such as cauliflower and broccoli; and currently hardly any solutions are available to deal with this problem. A. thaliana is a member of the Brassicaceae, which means that depending on the conservation of the mechanisms, the knowledge generated in this project might be directly applied and implemented to improve this trait in brassica food crops, giving rise to a more sustainable agriculture. Taking all this into account it is of utmost importance to have clear rules for dissemination of results on one hand, versus protection of the results (IP) on the other hand. We intend to use the IPR document provided by ERA-CAPS as a basis and to describe the exact rules for dissemination and protection of results in the Consortium Agreement (CA), which will be based on the template that will be made available by ERA-CAPS, before the start of the project. All relevant background knowledge of the consortium members will be described in an attachment to this CA. To guarantee optimal dissemination, this topic will be a fixed agenda point for the yearly consortium meetings. In this project various large-scale 2nd generation sequencing data sets will be generated that all will be collected, stored and managed by P5. The PI from P5 is the prime responsible person for these activities. The datasets will be freely available for the partners in the consortium via a password-protected web-portal. This web-portal will also include a public-access domain for dissemination of knowledge to both scientific and non-scientific audiences. At the start of the project the database in the protected part of the web-portal will be filled with some essential publicly available datasets and unpublished data from the partners that will be brought into the project as background. The latter will allow P5 to start from the beginning with developing analysis methods based on true data sets. At a later time point these data sets can be used for comparison. Ultimately, we expect to publish all newly generated large-scale datasets. At that moment, we will submit the data to publicly available data depositories (e.g. NCBI GEO). To ensure that publically funded research is widely accessible, we will either publish in open access journals or pay for open access, depending on the journal's policy. In addition, we will disseminate the outcomes of the project by presenting our results at international scientific conferences and by publishing short summaries of the outcomes of our work in laymen style on the publicly accessible part of the web-portal. For dissemination of knowledge towards commercial parties (e.g. breeding industry) we will actively seek for external interest, making use of existing contacts and by approaching potentially interested companies. Several of the partners already have ongoing collaborations with commercial entities (P2: SAATEN Union, Germany; Biobase, Germany; Phytowelt, Germany; P3: Syngenta, UK; Rijk Zwaan, Netherlands; Bejo Seeds, Netherlands; Bayer, Germany; P4: Biobase, Germany; Strube Research GmbH, Germany; P5: Poznan Plant Breeding, Poland; DANKO Plant Breeding, Poland).