FFAST aims at describing wheat genotypes functioning through an innovative model-assisted phenotyping strategy. Currently, studies on field phenotyping are mostly focused on exploiting directly structural traits observations (e.g. leaf area, height) to establish statistical models with genetic characteristics. However, structural traits are highly determined by the environment, and such empirical models are insufficient to describe genotypes functioning. FFAST proposes an alternative approach using functional plant models (FPM, also known as crop process-based models) to describe the eco-physiological mechanisms that produce a differentiated response of the genotype to the environment (GxE). This model-assisted strategy consists in assimilating large observational datasets of multiple structural traits over different growing environments to retrieve, for each genotype, a set of varietal parameters of a FPM. These varietal parameters describe the genotype functioning and constitute functional traits, closely linked to its genetic characteristics. The model-assisted phenotyping method will be evaluated in a panel of ten bread wheat genotypes that will be monitored on phenotyping experiments and by satellite. The phenotyping experiments will be conducted in the Toulouse, Clermont-Ferrand and Montpellier sites –part of the PHENOME-EMPHASIS phenotyping infrastructure– during three years. That will permit to acquire high-throughput observations of multiple structural traits (leaf area, canopy height, heading date, ears density…) in different environments. Nevertheless, as a large environmental variability is essential to retrieve accurately functional traits, FFAST will investigate the use of high-resolution satellite platforms to provide additional cost-efficient observations of structural traits for specific genotypes over contrasted environments. Three genotypes of the panel will be monitored by satellite on 40 distant commercial fields over a climatic gradient in eastern France. Images from Sentinel 2 and PlanetScope satellite constellations will be used to retrieve frequent observations of some essential traits like the leaf green area index (GAI) and the fraction of absorbed photosynthetically active radiation (fAPAR). The estimation of functional traits from the observations will rely on a data assimilation framework based on the Sirius Quality FPM, specifically developed for wheat, which will be linked to the architectural model Adel Wheat. This will permit to improve the description of structure-driven processes such as light interception/absorption or evapotranspiration. Bayesian Monte Carlo methods will be used to retrieve varietal parameters of Sirius Quality from the structural traits observations for each genotype. The resulting posterior distribution of varietal parameters for all the genotypes will be analysed to identify those parameters –or groups of parameters characterizing the same mechanism– presenting statistically different posterior distributions among genotypes. Those parameters will constitute functional traits. The approach proposed by FFAST will be validated evaluating the reliability of the functional traits identified to predict the genotype performance in different environments from those used during the assimilation. This will permit to evaluate as well the role of remote sensing observations over different environments in the FFAST approach, compared to expensive multi-site phenotyping experiments. The project results will be disseminated through scientific papers in different domains: phenomics, eco- physiology, crop modelling and remote sensing. The observational datasets collected for the 10 genotypes will be also made public through a data paper. Moreover, the development of a methodology to produce multi-constellation GAI and fAPAR observations suitable for plant phenotyping will permit HIPHEN –enterprise partner in FFAST– to open new commercial services.

Climatic changes are expected to cause more heat, drought or pathogen stress and also to be associated with more extreme variations of environmental factors. Most of those environmental changes can affect the photosynthetic activity of plants. In general, stress-induced inhibition of photosynthesis leads to excess light energy in chloroplasts resulting in excitation/electron transfer to molecular oxygen and hence in the formation of reactive oxygen species (ROS), especially singlet oxygen (1O2). The latter ROS has dual effect: it is toxic, engaging readily with biomolecules, and it functions as a signal molecule that can lead to acclimation to 1O2 stress. The SLOSAM project is aimed at understanding the genetic bases that determine the adaptability of plants to environmental changes that generate 1O2 in chloroplasts. It brings together two partners with complementary expertise: the LEMP at CEA/Cadarache and the LGBP at the Luminy campus of Aix Marseille University. By federating and coordinating the research done in those groups, we think that a strong research spot on photooxidative stress signaling could be established in France through this project. Using two 1O2-overproducing mutants of the model plant Arabidopsis thaliana, the flu and ch1 mutants, the 1O2 signaling pathway leading to acclimation will be investigated from the initial site of 1O2 production in the chloroplasts to the cytosol and the nucleus. The gene responses to 1O2 in the flu and ch1 mutants showed many similarities, but key differences were also observed, suggesting that the site of 1O2 production (photosystems vs. thylakoid membranes) modulates gene responses and emphasizing the necessity to analyze both mutants in a comparative study. Although a few components of the 1O2 signaling pathway have been identified, the mechanisms by which the 1O2 signal is perceived in the chloroplast and conveyed to the nucleus for changes in gene expression remain largely unknown. The main goal of this project is to shed light on many unknown aspects of this pathway. The main source of 1O2 in plants is the reaction center of Photosystem II (PSII), and recent works in the LEMP have identified compounds (such as b-cyclocitral) generated from PSII by 1O2 oxidation of the carotenoid b-carotene as initial messengers of 1O2 stress. The mode of action of these upstream signals will be investigated using a genetic approach based on the screening of Arabidopsis mutants that do not respond to these carotenoid-derived signals. In parallel, we will use a more targeted approach based on previous data on gene expression regulation during acclimation of Arabidopsis to 1O2. Part of our efforts will also be concentrated on downstream steps of the 1O2 signaling pathway at the nuclear DNA level. Based on the recent discovery by the LGBP that Topoisomerase VI is required for the expression of 1O2-responsive genes in the flu mutant, the role of chromatin dynamics in gene responsiveness will be studied during the 1O2-triggered acclimatory response. Another important level of gene regulation which was overlooked in previous works on photooxidative stress is post-transcriptional gene regulation. This aspect will be investigated in the context of acclimation to 1O2, using various approaches including ribosome profiling, analysis of small RNAs and their mRNA targets and bioinformatics. Thus, the main deliveries of the proposed work are a detailed picture of the gene regulation and the identification of essential genes involved in the acclimatory response of plants to 1O2. Considering the central role played by this ROS in the response of plants to abiotic and biotic stresses, the expected results will be important to understand the adaptation of plants to climatic changes and could provide the bases for the development of photosynthetic organisms tolerant to photooxidative stress in order to secure food production in changing environments and improve biofuel production

Understanding how plants adapt to stressing conditions, and what the genetic bases of this adaptation are, is essential to accurately predict plant behaviors in response to environmental changes. Plants in nature and crop fields are simultaneously exposed to numerous environmental stresses that could exert significant selection. As a consequence, plants have adapted their development to a remarkable large range of environmental conditions including biotic and abiotic stresses. Preserving plant growth and development in the climatic change context is a real challenge. It is well-established that a large part of plant development plasticity is related to changes in cell cycle activity, as shown by robust relationships between organ size and their cell number in different species and many environmental scenarios. Identification of the molecular basis controlling cell cycle plasticity could foster a better understanding of how plants respond to their environment. In addition, it could be a potential source of adaptation to stressing conditions by manipulating cell cycle regulation. The molecular network acting at the G1-to-S cell cycle transition is reported as a crucial limiting factor when cell cycle is lengthened by environmental stresses. Abiotic stresses induce the expression of cyclin-dependent kinase inhibitors (CKI) that reduce cyclin-dependent kinase (CDK) activities, reduce cell proliferation and thus, plant growth. In the CKI-stress project, we will focus on this family of genes mainly because some of them have previously been identified as major control of the cell cycle progression in response to stresses. Several complementary genetic and molecular approaches will be combined with the aim to allow a better understanding of the plant CKI role and function in plant stress responses. In particular we will focus our work on salt, drought and temperature stresses. Arabidopsis will be used as a model system to take advantage of available or potential genetic material as well as an automated platform for reproducible phenotyping of plant responses to stress. Multiple loss-of-function mutants affected on KRPs and SIM-related members known to be stress-induced will be subjected to abiotic stress conditions and analysed with a multi-scale phenotyping approach from cellular processes (cell division, endoreduplication…) to whole plant regulation (leaf expansion, floral transition…). These phenotypical analyses will be completed by molecular and biochemical approaches to reveal post-translational regulations on SIM/SMRs in stress responses, including “degron” mapping of selected SIM/SMRs and the identification of novel E3s involved in SIM/SMRs turnover. Thus we aim to identify all members of the SIM/SMR family involved in these abiotic stress responses. Moreover, we will investigate how these genes are regulated by the gibberellin-regulated DELLA proteins and also by ABA or other stress hormones that impact on cell proliferation.

Carotenoids are an important source of bioactive compounds in plants, including phytohormones (abscisic acid, strigolactones). We recently identified new growth regulators and signaling molecules derived from the oxidation of ß-carotene in the chloroplasts of plants under environmental constraints, such as ß-cyclocitral and its oxidized derivative ß-cyclocitric acid. Application of these apocarotenoids to plants triggers defense mechanisms which increase their tolerance against climatic stresses including drought. ApoStress will delineate this newly discovered retrograde signaling pathway connecting photosynthesis to stress acclimation, by identifying the receptor(s) of those apocarotenoids, their signaling pathways and their protective modes of action against drought stress in the model plant Arabidopsis thaliana. We will also investigate the formation and metabolism of these compounds in planta as well as their emission in the atmosphere. An important aspect of this project is to evaluate the potential of those compounds as phytoprotectors in a crop species, grapevine (Vitis vinifera). The diversity of vine varieties will be exploited to further explore the link between carotenoid oxidative cleavage and drought tolerance and to confirm the findings gathered in Arabidopsis plants on ß-cyclocitral metabolism and physiological processes of interest in this crop species. In the long term, this research could provide new bioactive molecules and new gene targets for improving drought tolerance of plants.

Wine is a key component of the French economy, because the quality and the typicity of French wines are largely recognized as a part of the worldwide image of France. Wine quality strongly depends on berry content at harvest. However, climate change is now modifying this content, especially by increasing berry K+ and sugar concentrations at harvest. This trend already observed since several decades in Europe (and farther) results in wines with increasing alcohol contents, more flat, and with decreased ageing potential. The control of the sugar/acid balance of the berries would allow to maintain the typicity, the quality and the market value of French wines. This requires a better understanding of the molecular basis of K+ and sugar accumulations along grape berry development and in response to climate change. SWEETKALIGRAPE aims at characterizing the molecular repertoire of genes and regulatory networks involved in the fine-tuning of the sugar/acid balance of the berries at harvest. To this end, our consortium gathers 3 groups with complementary expertises: (i) a group of plant (electro)physiologists, molecular and cellular biologists who has carried out pioneering work in analysis of molecular mechanisms involved in K+ transport in Arabidopsis, (ii) a group of cellular and molecular biologists working on berry composition (especially sugars), the responses of berry metabolism to environment and the molecular mechanisms involved in these processes and (3) a group of ecophysiologists investigating the adaptation of plants to contrasted climates. The work programme includes five tasks: (i) Analysis of relationships between berry quality and K+ / sugar contents examined under different climatic scenarios. This experiment will be performed using both current widespread cultivars and particular cultivars of physiological relevance (contrasting by acidity or responses to water stress and heat exposure); (ii) Identification of the molecular repertoire of genes expressed in flesh cells and involved in K+ and sugar accumulations under control, water stress or high temperature conditions through RNA-SEQ analysis, followed by the identification of gene regulatory networks through a systems biology approach (iii) Fine mapping of the subcellular pH in flesh cells allowing to precise the role of the subcellular proton distribution in relation with berry quality (iv) Functional characterization of sugar and K+ channels and transporters identified in task 2 (v) Design of a reverse genetic approach based on VIGS (virus induced gene silencing) technology coupled with transient transformation by agro-infiltrations of berries and precise phenotypic analysis of different mutant plants obtained to precise the role played in planta by K+ channels, sugar transporters and the new candidate genes identified in task 2. Thanks to the combination of genetic, molecular, electrophysiology and functional analyses, the project will develop an integrated study allowing to understand the control of the grape berry sugar/acid balance under various environments. Moreover, the implementation of a new tool for functional genomic analyses in grapevine will be a significant breakthrough because transformed berries will be available within one year. Three to four years are usually needed when grapevine classical stable transformation is used to obtain fruits that may be studied. Finally, this work will open new research lines through the analysis of new genes playing an important role in the berry quality and will provide an improved basis for the selection of vines adapted to our future environment.