Plant growth and organogenesis are coordinated by stem cells located in specialized tissues known as meristems. Virtually all the aerial parts of the plant derive from stem cells located in niches at the shoot apical meristem (SAM), where they process internal and external cues to sustain their function. As cells are continuously produced at SAM, it is essential for plants to precisely regulate the timing of proliferation as development and plant organogenesis occurs over time throughout the life cycle. The circadian clock is the primary timing device that enables an organism to measure the pass of the time to precisely coordinate biological activities with the internal cues and its surrounding environment. Despite the importance of stem cell function, the mechanisms controlling the timing of SAM activity in synchronization with the environment remain essentially unknown. we propose to investigate the role of the circadian clock as a flexible biological metronome orchestrating the SAM activity in plants. The Clock-SAM proposal aims to generate a road-map of clock function, defining circadian similarities and divergences among the different functional states at the SAM and establishing the correlation between the circadian pace of the clock and cell fate and specification. We will follow an ambitious integrative approach combining epigenetic and transcriptional regulatory mechanisms to understand stem cell function. Our studies will thus answer a fundamental question in plant cell biology by determining how the plant is temporally constructed in our rotating world. The results from this proposal will provide a framework that can be tested for regulating plant productivity and survival in different environmental conditions. Hence, in the long term our findings could be applied to crops of agronomical interest.

Rising heatwaves and drought are severely affecting the capacity of crops to retain water and capture CO2 during photosynthesis, resulting in global yield reductions. One of the most promising approaches to enhance crop production in stressful conditions is to synthetically modify the photosynthetic capacity of plants. In nature, some lineages have evolved mechanisms like C4 photosynthesis and the Crassulacean acid metabolism (CAM) to cope with some of these aspects; While C4 species are extremely efficient at CO2 fixation but vulnerable to severe drought, CAM plants are less productive but very capable of coping with significant drought periods. Engineering a joint C4-CAM system that uses CAM features to fight drought, while still relying on the power of C4 can be a game-changer to increase crop resilience. For decades, the coexistence of C4 and CAM was considered incompatible in nature. An exception to the rule is found in the genus Portulaca where C4 species can trigger CAM when droughted. Despite the huge bioengineering potential of Portulaca, the molecular enablers that allow for C4-CAM to exist in this clade remain elusive. Previous phylogenetic and morphological studies across Portulaca indicate the combined C4 (Kranz anatomy) and CAM (succulence) leaf anatomy might be the main facilitator of C4-CAM. By combining anatomical studies, cell specific metabolomics and genomics with synthetic biology, I aim to identify the basic molecular determinants of the C4-CAM switch in Portulaca, and to leverage this knowledge to transfer CAM anatomical features to C4 species outside Portulaca as a proof of principle. This will set the basis for new rounds of engineering to achieve a fully functional C4-CAM switch. METACAM will provide a quantum leap to our understanding on how incompatible metabolic pathways can be designed, built and integrated in multicellular organisms which is broadly applicable to crop engineering.

The rePLANT (Reconstruction Biology in Plant Sciences) Doctoral Training Program is an ambitious research and training initiative coordinated by the Centre for Research in Agricultural Genomics (CRAG; Barcelona, Spain) together with the Max Planck Institute for Plant Breeding Research (MPIPZ; Cologne, Germany) and the John Innes Centre (JIC; Norwich, UK). rePLANT is designed to conduct, and train in, interdisciplinary and intersectoral collaborative research projects between the three participating institutions, with the additional collaboration and support of associated partner organisations (private companies, and research centres and academic institutions), both national and international. The program will offer twenty (20) four-year doctoral fellowships and will be focused on: training in advanced research topics and technologies; training in non-research oriented transferable and transversal skills; collaborative research projects and secondments; and international networking in both the academic and the industrial sectors; all in order to enrich the training of the doctoral students and enhance their professional development while conducting projects of research excellence in the area of reconstruction biology in plant sciences. Reconstruction biology leverages current knowledge on plant traits and their underlying genes and molecules to understand trait diversification and innovation in a phylogenetic framework, i.e. within and between related species. rePLANT will conduct reconstruction biology at three levels of biological organisation: cell-free systems, whole organisms and ecosystems. With rePLANT, we expect to define quantitative trait models and uncover emergent properties, i.e. system features that the individual components do not have, as well as insights into how far a given trait can be diversified without pleiotropic effects.

Crop wild relatives (CWR) are wild plant taxa closely related to a crop. They represent an important source of genetic diversity for the improvement of agronomic traits. In the context of the One Health Initiative, temperate fruit trees are essential for human nutrition and health, yet CWR resources have hitherto been underused. Moreover, fruit tree long lifespan and a current production dominated by a few cultivars make them particularly vulnerable to the effects of global changes. To address this challenge, the FRUITDIV project will monitor, characterise, use, and conserve the diversity of emblematic fruit tree CWR, with a particular emphasis on Malus, Pyrus and Prunus. To better characterise the genetic and phenotypic diversity of CWR fruit trees and identify favourable traits for future introgression into cultivars, FRUITDIV will use a combination of floristic, ethnogeography and population genomics on genebanks and historical European hotspots of diversity. We will then develop new multiomics-based breeding strategies that combine marker-assisted introgression for traits of interest (e.g. resilience, resistance to pests and diseases, fruit quality) with pangenomic prediction and a reduction of CWR-associated genetic load. In addition to breeding programs, FRUITDIV will also work with networks of farmers and associations to help characterise CWR progeny in various pedo-climatic conditions in Europe. An European-wide online platform that provides genotyping and phenotyping data for free will be implemented to promote the use of CWR genitors by breeders and farmers and help disseminate plant material of interest for various usages and cultivation systems. Overall, the FRUITDIV multi-actor approach involving geneticists, forestry officers, germplasm curators, farmers and citizens, will foster the in- and ex-situ conservation of CWR and promote sustainable agricultural practices across Europe.