Low agrobiodiversity and the reduced ability to respond to the increasing climate change-related stresses, are detrimental effects from the current high-input agriculture. Commercial apple orchards are a prime example of intensive pesticide and irrigation practices that counteract the EU’s ambitions to reduce external inputs and reverse agrobiodiversity degradation by 2030. In this context, new breeding and management practices show high potential to break out of this vicious circle and allow the development of divers and resilient agroecosystems that require less pesticides and irrigation. Breeding has been traditionally based on the phenotypic selection of segregating populations. In the last decades, molecular markers and genomic selection have been implemented in breeding schemes. Such tools have been mainly focused on genotype-trait associations. The plant-associated microbiome is long known for its vital contributions to crop performance. However, agricultural practices and breeding have paid little attention to directly regulate and employ host-beneficial microbial functions. AppleBIOME will investigate the combined action of host and microbiome genetics (holobiont approach) under high and low-input management practices to boost the breeding for resilient varieties. AppleBIOME relies in an exceptional germplasm resource representative of the broad genetic diversity of apple in Europe: «the Apple REFPOP». The Apple REFPOP was designed and established as an output of the EU project FruitBreedomics and consists of 534 genotypes (accessions and progenies) planted in 2016 following the same experimental design in six diverse biogeographical regions in Europe (Belgium, France, Italy, Poland, Spain, and Switzerland) with a subset also being managed under low-input practices. The densely SNPgenotyped Apple REFPOP has been successfully used to evaluate genomic predictive abilities of quantitative agronomic traits considering genotype x environment interactions (GxE). AppleBIOME brings together the hosting institutions of the Apple REFPOP to add the management component into the evaluation of the genetic mechanisms for the response to (a)biotic stresses. First, at each location, we will acquire agronomic and disease related parameters (along with climatic data) for either of two management comparisons: high vs low pesticide and high vs low water input. Genome-wide association analysis (GWAS) and genomic prediction models will (i) identify genomic regions contributing to the stress response and (ii) estimate genomic predictive ability of the traits under environmental stress. Second, we will analyze the phyllosphere microbiome in the Apple REFPOP at each site and management practice and in commercial orchards. Microbe amplicon sequences will be analyzed to determine microbiome attributes such as diversity parameters, networks and key taxa that are host-regulated and involved in stress resilience. GWAS and deep learning (DL) predictive models will then be performed to identify new loci and candidate genes that regulate microbiome-mediate stress response. Resulting molecular markers and models will be evaluated together with breeders for their suitability for direct use in current breeding schemes. As a whole, we will build on knowledge of the holobiont functional diversity in apple orchards to exploit microbiome-mediated resistance. Finally, the knowledge gained will be disseminated to stakeholders, and discussion forums will be created to weight the advantages, disadvantages, and challenges and ensure the commercial uptake of the project outcomes. Via these close collaborations with the apple production industry and related dissemination and exploitation activities, AppleBIOME will promote the development of novel varieties that can better respond to climate change-relevant stresses and pave the way towards new agrobiodiversity-based breeding and cultivation systems.

In the context of climate change, it appears essential to unravel the mechanisms governing abiotic stress tolerance in higher plants, in order to build predictive models and use this knowledge to assist selection and design of stress tolerant crops. We have previously uncovered remarkable adaptations in seed mitochondria, which because of the ability of seeds to survive desiccation, display impressive tolerance to abiotic stress. In particular, seed mitochondria accumulate high levels of small heat shock proteins (sHSP) and late embryogenesis abundant proteins (LEA). The sHSP are the most widespread but less conserved HSP. They contribute to the molecular chaperone network that assists protein biogenesis and homeostasis under stress conditions (sHSPs are stress inducible). In eukaryotes, mitochondrial sHSP (M-sHSP) have only been identified in plants and insects. LEA proteins are highly hydrophilic proteins, generally intrinsically disordered, which accumulate in desiccation tolerant organisms, and whose functions still remain largely enigmatic. The MITOZEN project aims at deciphering the molecular function and physiological role of the mitochondrial sHSP and LEA proteins (M-sHSP and M-LEA) in the model plant Arabidopsis thaliana. The genome of Arabidopsis harbors 17 sHSP genes (including 3 M-sHSP) and more that 50 LEA genes, among which we have recently identified 5 M-LEA genes. The molecular functions of the M-sHSP and M-LEA will be explored using biochemical and biophysical approaches to study recombinant proteins produced in Escherichia coli. Their structural features and protective activities (oligomerisation, secondary structure, chaperone activities, membrane protection) will be examined in the context of temperature stress and dehydration using a large panel of techniques and in vitro assays. The goal is to determine the potential molecular functions of the different M-sHSP and M-LEA in the context of stress tolerance (desiccation in seeds, high temperature in seeds and plants). A reverse genetics approach will be developed in Arabidopsis to explore the role of M-M-sHSPs and M-LEAs in the physiology and development of plants. Single and multiple knock-out mutant lines will be constructed, as well as overexpressors using an inducible system. Their phenotypic characterization will focus on seed development and abiotic stress tolerance of plants, including mitochondrial function. The integration of data provided by these multidisciplinary approaches (bioinformatics, biochemistry and biophysics, genetics, physiology) will shed light on the function and importance of the different M-sHSP and M-LEA in the development and stress tolerance of plants. It will also increase knowledge about molecular chaperones and in particular with respect to their yet unexplored role in the context of dehydration, and will shed novel light on the function of LEA proteins.

Living cultural and natural objects, ornamental plants have been reached by the heritage fashion of the 70’s-80’s. Giving value back to old outdated varieties, this heritage fashion is based upon an aesthetic critic of the horticulture supply and of the current commodification trend. Horticulture creation is a hybrid process based on both aesthetic concerns and breeding knowledge. RosesMonde project deals with this creative hybridity and first and foremost with the way it is interwoven with heritage development and commodification trends of the current aesthetic capitalism. Its main focus is the Rose which GVC is at the crossroad of cultural industries and agribusiness. How does rosicole breeding record the tension between commodification and heritage development which are the backbone of contemporary social and political dynamics? To address this question, a strong research team has been set up and associates social scientists from four disciplines (geography, history, sociology and economics) with geneticists. This team shall work through three main entries: varieties, actors and places before dealing with heuristic and synthetic cases studies. Entry by varieties: the genetic diversity will be analyzed on a large sample of 1400 genotypes obtained after 1900. These genotypes will be selected according to their representativeness of the different market sectors and the different date of the rose, were obtained. From the genetic and historical analysis, a sub-ample will be selected (384 individuals) to sequence the genes involved in important esthetical and agronomic traits. These analyses will allow identifying the factors of innovation during the plant breeding, by crossing the data of the genetic basis used by the breeders and their criteria of selection. We will (i) characterize the process of evolution of the genetic diversity used (management of genetic diversity available during the period and the introduction of new progenitors bringing novel traits) and (ii) search if genomic regions have been selected by who and for which use? We will deal with actors –being they breeders, producers, publishers, French, European or African to understand how they build their specifications and prioritize their creative criteria. Crossing economic and sociologic approaches, we shall understand the aesthetic and even ethic logics of the creative activity and how it participates in the commodification/heritage dialectic, how it is paid for through IP and how it affects the garden and cut roses GVCs. In addition an economic enquiry will analyze three data bases (INRA, OCVV, BDV) to understand the economic diversity of creative enterprises. Places will be analyzed using different scales. First the global scale will allow us to map the different production enterprises and clusters and their varietal orientations. Then, through Parisian and Aquitanian examples, we shall reflect at the urban scale in order to map the demand and the marketing side of the creation. The aim is to connect varieties, supply and marketing chains with their social urban contexts, to understand how strong and efficient are the heritage elements. Shorts chains and long supply chains will be compared to underline the way environmental concerns are interweaved with aesthetics requirements to build social distinction and segment the demand. Finally we shall carry out case studies and focus on emblematic varieties, actors and events which embody the heritage dynamics and commodification trends as well as the creation process as co-construction. To sum up RosesMonde is all about creation and the way Roses express our contemporary world’s paradoxes and socio-political ambiguities in the sense that economic empowerment and democratization allow anybody to access distinctive goods but at the same time social distinction always requires more and more segmented supplies which use heritage and sustainability as their main criteria.

The contribution of organellar genomes (mitochondrial, mt and plastid, pt) to fitness and local adaptation of plants is well documented. However, neither the genetic variations involved, both in cytoplasmic and nuclear genomes, have been identified, nor the extent of phenotype variation they confer to adaptive evolution has been evaluated. Moreover, very little knowledge is available about the molecular and physiological integration into the global plant phenotype, such as fitness, of natural genetic variation at the level of organelle genes. In addition, nuclear-cytoplasmic co-adaptation exerts evolutionary constraints on genetic variations in both compartments that are not fully understood. In this project, focused on the model species Arabidopsis thaliana, we will address adaptation at two interdependent levels: the contribution of cytoplasmic variations to plant adaptation to its environment; the co-adaptation of the cytoplasmic and nuclear genetic compartments. We recently described cytoplasmic diversity in a collection of accessions from diverse geographic origins and showed that nucleo-cytoplasmic co-adaptation exists inside the diversity of the species (Moison et al, 2010, Plant J 63:728-38). In addition, genetic variations correlated with adaptation to climatic variables have been recently described for this species (Hancock et al, 2011, Science 34:83-86; Fournier-Level et al, 2011, Science 34:86-89). Interestingly, biological processes related to pt or mt activities, such as photosynthesis and energy metabolism were found to be enriched in the correlated polymorphisms (Hancock et al, 2011). Finally, potentially adaptive traits, such as water use efficiency (WUE), seed dormancy and germination, were impacted in this species by cytoplasmic variations (McKay et al, 2008, Evolution 62:3014-26; Corey et al, 1976, Genetics 82:677-83; our unpublished work). This project will take advantage of a novel genetic resource: 56 cytolines (lines possessing the nuclear genome of an accession and mt and pt genomes of another) produced from the smallest core-collection (n=8) of the Versailles Arabidopsis Stock Centre (VASC) (McKhann et al, 2004, Plant J 38:193-202). These new genetic combinations will be used to: 1. Identify nuclear and cytoplasmic genes involved in cyto-nuclear co-adaptation in A. thaliana. This will exploit a combination of organelle and nuclear genomes leading to male sterility. 2. Evaluate the impact on phenotype of the new genetic combinations, at different levels, for potentially adaptive traits. 3. Correlate measured variable traits at different phenotypic levels 4. Identify genomic regions in the different genetic compartments likely involved in plant adaptation and/or cyto-nuclear co-adaptation

Ketone bodies are produced by the liver from fat during fasting. We have shown that the metabolism of the ketone body acetoacetate (AcAc) restores mitochondrial function and metabolism of monocytes/macrophages exposed to acidosis. As mitochondria regulate cell sensitivity to death, we then observed that AcAc also protects cells from apoptosis and ferroptosis by increasing their reducing potential. Moreover, monocytes cultured in the presence of AcAc acquire a reparative phenotype induced by epigenetic modifications. These data suggest that AcAc behaves as a unique endogenous substrate for enhancing cell resistance to stress. The aim of this project is to characterize the metabolic, molecular and cellular mechanisms associated with this protective potential. We will decipher the metabolic and transcriptional changes that induce increased GSH and nicotinamide synthesis and the acquisition of a reparative phenotype (WP1). We will demonstrate the interest of this molecule in the context of sepsis, a pathology associated with lactic acidosis, mitochondrial dysfunction and massive cell death by (i) evaluating the potential of AcAc to resuscitate ex vivo cells from patients in septic shock (WP2) (ii) the ability of ketone bodies to reduce the severity of sepsis and protect tissues in an experimental sepsis model (WP3). This project will establish a link between metabolic reprogramming and increased tissue capacity to resist stress, and lay the foundations for evaluating its therapeutic potential in pathologies associated with massive cell death.