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.

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.

In perennial species, yield and production quality are impacted by water stress with marked interannual effects. The knowledge of the physiological and genetic mechanisms regulating grapevine responses to WD remain largely insufficient to adapt the viticulture to climatic challenges. Most often, responses to water stress have been studied during a single vegetative cycle, considering traits independently and using a limited range of genetic diversity. The G2WAS project aims to study the responses of grapevine to water deficit on intra- and inter-annual scales, by integrating the dynamics of production, storage and utilization of carbon resources in both vegetative and reproductive systems. This study will be performed with a diversity panel designed to maximize the genetic diversity of the cultivated species (V. vinifera). In order to decipher the genetic and physiological bases of adaptation to drought, and to incorporate them into breeding programs, several innovative approaches will be run: i) advanced phenotyping of vegetative and reproductive organs targeted at several critical developmental stages, with a focus on carbon allocation, ii) identification by exhaustive transcriptomics (RNAseq) of co-regulated gene networks; iii) genotype-phenotype whole genome association (GWAS) analysis applied to a panel of 279 varieties iv) development of a multi-trait and multi-year statistical model to improve prediction accuracy. Performed for the first time in perennials, such a combination of methods will improve the detection of QTL and the prediction of individual genetic values. This multidisciplinary approach will be supported by the G2WAS consortium which brings together specialists in eco-physiology, physiology, quantitative and functional genetics, statistics and breeders. In addition to the coordination (WP1), the project is based on 4 WP: a physiological study (WP2) of 16 contrasting genotypes confronted to a gradient of 10 hydric conditions under tightly controlled environment (PhenoDyn platform) to provide a precise description of the responses to water deficit and to parametrize the conditions to apply to the GWAS panel (WP3) in the semi-automated phenotyping platform (PhenoArch platform); these data will be used for QTL detection and genomic prediction (WP4), using a statistical model specifically developed for this study; finally, the results will be used in ongoing selection programs (WP5). This last step will be one of the first attempts to combine properties of tolerance to water stress and resistance to fungi, in agreement with the 2 major challenges facing viticulture. In addition to an expected breakthrough on the characterization of critical genetic resources which are fundamental for grapevine improvement, this study will provide new clues on the interaction between carbon limitation and hydraulic functioning at the plant scale. This progress will be essential to develop improvement strategies to anticipate some of the drawbacks linked to climate changes, in particular the increase of evaporative demand and the limitation of water resources. This knowledge and methodologies will be potentially transferable to other models of perennial fruit species.