VINICULTURE aims to integrate innovative methods in archeosciences to identify the characteristics and the diversity of grapevines and wines produced in France, since the origins of viticulture to the Middle Ages. Wine plays a major social and symbolic role since Protohistory. It is a prized exchange product carried over lost distances. The grapevine became a major plant species in terms of economy, landscape, culture and symbolism. Great progress has been accomplished lately by French archaeology concerning the history of vine cultivation and wine making: the circulation of wine, extension of vine cultivation under roman rule, production sites and techniques, vineyards and plantation practices. Despite this progress, fundamental aspects remain unclear. Our knowledge of the wines available before the Middle Ages derives mainly from written documents of different origins and sparse inscriptions on amphorae. Concerning the vines, written documents are practically unusable, and the first real information has been provided by archaeobotany. We now take advantage of recent methodological advances (Morphogeometry, Next Generation Sequencing) to put forward a holistic approach, no longer considering grapevines and wine as generic categories, but instead describing their diversity and analyzing their spatial and chronological dynamics in France, from the Neolithic to the Middle Ages. France is an excellent area to observe the evolution of vine cultivation and wine making in the long run, making it possible to integrate most of the major Euro-Meditteranean exchanges concerning wine, such as the Phoenician, Greek and Roman colonial movements and cultural changes linked to the spread of Christianity and Islam. France also offers the perfect background to study the diffusion of viticulture from the Mediterranean to temperate Europe and its implications in terms of adaptation and re-composition of the diversity of vines and wine. We will analyze plant remains as well as archaeological containers (pottery and wood jars) collected according to strict sampling procedures. Our approach will combine archaeobotany, geometric morphometrics, archaeogenetics, biochemistry and experimental archaeology. By exploiting the potential of Database I2AF and the national network of collaborations Bioarcheodat, Archaeobotany will provide access to a large data set and supply the indispensable background for the observation of the dynamics of Grapevine and of its use since the Neolithic. The most expensive analyses will be restricted to the most promising sites and to the period Bronze Age – Middle Ages. Ancien DNA and Morphometry will provide the means to identify the traits of cultivated grapevines (colour, productivity) and their parenthood with wild grapevines and modern cultivars. As a result, it will be possible to enquire about the geographic origins of the archaeological varieties, to trace the pathways of diffusion and evolution mechanisms. Archaeogenetics and Biochemistry applied to the study of wine jars will provide evidence on the type of wines: of grapes and/or of other fruits, colour, use of additives for aroma and conservation. The role of yeast and bacteria in the fermentation process and in wine conservation will be taken in consideration for the first time. Statistics and models, will allow us to combine data obtained at different levels of analysis, with the information provided by other archaeological sources and by the modern genetic diversity of grapevine and microorganisms, aiming at reconstructing the geo-historical dynamics of vines and wines, in relation to environmental and socio-economic changes.

The identification of new variability represents a major tool to face challenges to overcome global warming and improve farming system sustainability. Turnips and cabbages, which largely contribute to food production worldwide, are native of the Mediterranean basin. Wild forms and landraces grow under highly contrasted environments. Taking advantage of this distribution, the objective of BrasExplor is to collect, explore this wide genetic diversity of wild and locally cultivated forms, after discussions with farmers on cultural practices and traditional uses, in order to promote local varieties. Collects will be performed along the climatic gradient with a precise description of contrasted environmental conditions, edaphic and microbiome composition of the soil. From 100 populations of cabbages (Brassica oleracea) and 100 of turnips (B. rapa), we will sequence (Next Generation Sequencing) in bulk each population for genome-wide scans looking for associations between nucleotide polymorphism and environmental variables as well as soil composition in order to search for genetic determinants of adaptation to suboptimal conditions. These data will be confirmed under controlled conditions for water and temperature stress and in contrasted field conditions for different traits: seed germination, root architecture, flowering phenology, self-incompatibility, microbiota diversity, morphology. Genetic data will be also used to infer their population genetic structure and to understand the relationships between the wild and cultivated forms of each species, the impact of farming practices under environmental constraints. Results will allow development of core-collections for in situ/on-farm management strategies and ex situ conservation as well as for promotion of landraces and for first proposal of pre-breeding populations.

The timing of reproduction strongly contributes to fitness and yield in annual and perennial plants. Here, we aim to decipher molecular mechanisms and the regulatory logic that control the switch in meristem identity that occurs during floral transition, and its subsequent stabilization during inflorescence development. We use a comparative approach among annual and perennial species, including an economically important crop, to broaden the relevance of our findings and to determine the flexibility in the underlying mechanisms in different developmental contexts and in response to different environmental and endogenous signals. Floral transition is the first step in plant reproduction, it is controlled by environmental and endogenous cues, and its timing is critical to fitness in natural populations or to yield in agriculture. During floral transition the developmental identity of the shoot apical meristem and/or axillary meristems is altered causing them to switch from vegetative meristems that form leaf primordia to inflorescence meristems that produce floral primordia. This transition is a binary switch that is usually irreversible, so that after the switch the identity of the inflorescence meristem is stable and does not revert back to a vegetative meristem. We propose that a bistable-switch mechanism reinforced by feedback loops acts at the shoot meristem to control the transition, and that the switch mechanism is biased by environmental signals to allow the transition to occur. Our model proposes that APETALA2 (AP2) and APETALA2-LIKE (AP2-LIKE) transcription factors maintain the vegetative state, while the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) and FRUITFULL (FUL) MADS box transcription factors together with the non-coding microRNA172 (miR172) maintain the reproductive state. These two sets of factors form a mutually repressive motif that is biased from the vegetative to reproductive state by environmental cues that induce SOC1, FUL and MIR172 transcription in the shoot meristem. We propose to test this model in annual and perennial crucifer species, Arabidopsis thaliana and Arabis alpina, respectively, as well as in apple trees using state of the art transcriptomics, transgenic and genetic approaches. These experiments will form a basis for quantitative modelling of the floral transition, a crucial stage in plant development. Furthermore, we propose to identify whether there is genetic variability in the switch mechanism in apple trees in relation to the undesired alternate bearing phenomenon. This will have practical significance in manipulating reproduction patterns and yield of crops.

The profitability of deciduous fruit orchards in semi-arid zones, especially in southern and eastern Mediterranean countries, depends on irrigation water availability throughout the growing season. Studies of water stress effects on growth have been mostly conducted on annuals, focusing on crop management and the physiological and molecular mechanisms underpinning water use efficiency. Unlike annuals, whose life cycle only depends on current conditions without investment in perennial structures, fruit tree development in any year strongly depends on the environmental conditions in the preceding years. Still unanswered is the scientific question of how the fruit tree uses water to grow, flower, fruit and at the same time develop buds for the next season. Also, there is a crucial need for irrigation protocols to manage severe and/or temporal reductions in water availability, keeping in mind that water management techniques not only modify growing and fruiting patterns, but also pest dynamics. The drive towards sustainable agriculture by reduced inputs, especially of chemicals, strengthens the idea that pest infestation has to be considered within water management strategies. Our project aims to contribute to develop sustainable fruit production in a context of increasing ecological and climatic stresses. APMed will be centred on two high added-value fruits grown in most Mediterranean countries, Apple and Peach, to gain knowledge on how the fruit tree adapts to water scarcity and what are efficient means to improve fruit production in these contexts, including the possible reduction of aphid infestations. We share the opinion that growing fruit trees in dry zones cannot be solved by disconnected disciplines, thus we will mobilize different research competences to address scientific and applied aspects. First, we will characterize ecophysiological mechanisms (at leaf and stem levels) underlying resistance or tolerance to drought, aiming to improve breeding and selection schemes for drought tolerant cultivars and rootstocks that maintain commercial productivity at a lower water use. Second, we will assess several horticultural practices to optimize water use in orchards: tree training to optimize leaf-fruit ratio; colored hail-nets to combine crop protection with control of tree vigour and water saving capacity; irrigation scheduling strategies building on Regulated Deficit Irrigation (RDI) concepts to avoid excessive water percolation below the root zone and losses to the atmosphere by surface evaporation. These latter concepts have been developed by members of this consortium. A third aspect will focus on the relationships between plant development and aphid infestations. Indeed, plant development is altered by both water stress and aphids, but reciprocally aphid infestation is altered by plant development, leading to non-linear responses of aphid infestations to tree water status and consequently to irrigation management. APMed activities will span 5 Working Packages gathering 5 countries, France as coordinator, Israel, Italy, Morocco and Spain. Seven research teams will be involved with complementary competences on irrigation scheduling in deciduous fruit tree orchards (Israel, Morocco, Spain), fruit tree ecophysiology (France, Italy), and pest infestation (France, Morocco). Furthermore, growers and researchers will collaborate through already established networks in all countries, and collaborative work is foreseen with sub-contractors (e.g. experimental centers and extension services in France).

Floods are responsible for around 60% of all agricultural damage and crop loss (FAO, 2015). The perspective of global climate warming will affect cultivated areas and crop growing conditions, impacting the future of food security in the world. The identification of genes controlling flooding tolerance is one of the keys to the development of submergence-tolerant varieties in cereals, a problem that affects an increasing number of cultivated areas worldwide. Rice has aerenchyma, which are air-filled cavities that connect the aerial parts and roots, allowing them to maintain their respiration and growth under submerged conditions. Aerenchyma formation is an adaptive response to submergence in rice but the gene network controlling aerenchyma and cortex formation is still unknown. The main objective of the project is to identify and characterize transcription factors involved in cortex and aerenchyma tissue differentiation in rice using a systems biology approach. This work will help to identify key genes behind aerenchyma and flooding tolerance in rice. These genes will be future candidates for breeding better-flooding tolerance cultivars in rice but also in cereals.