Lignocellulosic biomass from short-rotation coppice poplar is a renewable resource of interest for producing second generation biofuels. However, current poplar varieties have neither been selected for this specific cultivation system nor for the conversion process of lignocellulose into simple and fermentable sugars (saccharification). The factors affecting biomass yield and chemical properties need thus to be studied. Over the last decades, some efforts in the main riparian poplar species involved in poplar cultivation in Europe have been devoted to the evaluation of the genetic variability of target traits for a bioenergy end-use. Furthermore, several genomic regions underlying this variation (quantitative trait loci – QTL) have been successfully mapped on the reference genome sequence. However, as they have been carried out in bi-parental crosses, the confidence intervals of the QTLs detected in such studies were quite large and their transferability in several backgrounds was rare, limiting severely their use in marker-assisted breeding. Efficient genetic improvement needs population based screenings, for which QTL mapping is rapidly limiting. To overcome such limitation, association mapping – the detection of QTLs in more complex populations – represents an obvious alternative in forest tree species because they are generally characterized by a rapid decay of linkage disequilibrium (LD). As a result, two recent association studies have been carried in two poplar species for biomass quality traits. Despite their novelty, as they were the first association mapping studies in riparian poplar species, both studies were characterized by a relative small number of significant associations and, more importantly, most of the reported associations explained a low proportion of phenotypic variability. Several hypotheses might explain these disappointing results, including the lack of exhaustiveness both in terms of genetic diversity and polymorphism screened, and the complexity of underlying determinisms. This latter point could involve gene by environment and/or gene by gene interactions, as well as rare variants, all of which could not be detected in previous studies as they were not explicitly addressed. By tackling such drawbacks, the proposed project aims at deciphering the genetic architecture of biomass yield and quality as target traits for poplar lignocellulose valorization in biorefinery. More specifically a systems biology approach, integrating polymorphism, expression and phenotypic data, is proposed in natural populations of black poplar (Populus nigra) covering the native range of the species in Western Europe and of specific interest in the French national poplar breeding program. Besides fundamental knowledge on the genetic factors controlling plant cell wall construction and biomass yield, the proposed project will evaluate the feasibility of phenotype prediction using multiple sources of information which can be of direct interest for breeding.

The treatment of Inflammatory Bowel Disease (IBD) represents a major medical challenge. IBD is a highly debilitating disease, which incidence is constantly growing in developed countries. The current therapies are costly, present severe side effects, and a number of patients are resistant to any forms of treatment. Therefore, intensive research has aimed at understanding the mechanisms of those diseases, to define new potential targets. Using pre-clinical models, we have identified previously unknown anti-inflammatory properties for Elafin, a protein naturally expressed in the human gut, that is able to inhibit elastolytic activity. We then have cloned the gene of human Elafin and expressed it in recombinant bacteria that are present in daily food: the Lactococcus lactis, assuming that Elafin delivery to the gut by such a probiotic strain, would exert protective effects against colitis. Treatments with those recombinant bacteria drastically reduced inflammatory symptoms associated with IBD in animal models. However, animal models provide limited knowledge as they have an etiology different from the human disease, and very often do not implicate the same mediators. In addition, the mechanisms by which Elafin delivery to the gut would be protective are unclear. Protease inhibition is probably implicated, but potentially antimicrobial properties and inhibition of nuclear factors are also involved. The cells on which Elafin exerts its anti-inflammatory properties are also undefined. If Elafin-recombinant L. lactis has to be considered as a possible treatment for IBD in human, there is an absolute need to define the mechanisms by which such recombinant L. lactis strains protects against intestinal inflammation, in a context that would be as close as possible to the human disease and its mediators. The general objective of the project is to investigate the mechanisms by which Elafin delivery is protective against intestinal inflammation, and to determine whether Elafin delivery by lactic acid bacteria protects from the deleterious environment present in tissues from IBD patients. Specifically, we aim at determining the effects of Elafin-recombinant L. lactis on three general types of cells that are in contact with the recombinant LAB: 1/ Intestinal Epithelial Cells 2/ Mucosal Immune Cells 3/ Microbiota For all those cellular targets, we will determine whether Elafin’s effects are due to protease inhibition or to other properties, by comparing the effects of wild-type or mutated forms of Elafin recombined in L. lactis. This approach will shed definitive and unique light on the mechanisms of action of Elafin upon mucosal inflammation.

Nitric oxide (NO) is a nitrogen trace gas which is produced by microbes and physico-chemical processes in soils as well as by physiological processes in plants. NO is considered as a major physiological mediator with many functions such as stimulation of the plant innate immune system, stimulation of plant morphogenesis and nutrition, responses to abiotic stresses, antimicrobial agent against pathogens, regulation of nitrogen cycling processes in microorganisms, etc. Despite the relatively high emission of NO quantified from soil and the high concentrations of NO within the soil profile, it remains largely unexplored how organisms below and above ground as well as their interactions respond to variations in NO fluxes and concentrations. Considering the versatile role of NO on both microorganisms and plants, investigating the role of NO in plant-soil systems can lead to a greater understanding of plant-microbe and microbe-microbe interactions. Such interactions and feedbacks between plants and microbial communities are of importance for many soil functions such as plant productivity and health, soil filtration, climate regulation, and nutrient cycling and have therefore rapidly gained a lot of attention since they can offer promising avenues for practical application. The overall objective of this project is to assess the importance of exogenous NO produced either by plants or by soil processes on soil microorganisms and plants as well as their interactions. Our overarching hypothesis is that soil NO concentrations and NO emissions from soil are not only of outstanding importance for atmospheric chemistry but can also affect microbes and plants and therefore regulate plant-soil interactions as well as soil functions. More specifically, the different hypotheses associated with our objective are: (H1) Plants can detect exogenous NO emitted from soil with consequences for plant health and nutrition, (H2) Exogenous NO can affect microbial community composition and interactions, (H3) NO is a regulator of key microbial activities related to soil N- and C-cycling. Therefore, exogenous NO can affect both the abundance and the activity of the corresponding soil microbial guilds as well as indirectly N-acquisition, N-transformation and organic matter decomposition by other soil microorganisms. (H4) Moreover, NO metabolism/ NO production in plants can affect microbial C-/ N-processes in the rhizosphere. In this project, we will use a model soil and the model plant Arabidopsis thaliana. Within a series of defined incubation experiments, we will expose soil micro-organisms, plants, plant-soil systems to defined exogenous NO concentrations and will study physiological, functional and process changes in plants and microbes to NO concentration changes. We will focus on nitrogen-cycling not only because NO is inherently linked to this cycle but also because nitrogen is the nutrient most strongly limiting plant growth in many terrestrial ecosystems

Changing scale in the molecular approach of chicken domestication by undertaking whole genome resequencing for several species is the major ambition of this project. Little is known of the history of chicken domestication at the genome level, in particular the relation with wild species of the genus Gallus. The project involves the four wild species of the genus Gallus: Gallus gallus (red junglefowl), Gallus sonneratii (grey junglefowl), Gallus varius (green junglefowl) and Gallus lafayetii (Sri Lanka junglefowl) and an outgroup species, Bambusicola thoracicus (Chinese bamboo-partridge) known as a sister group of the genus Gallus. The project will use genome sequencing to analyze with an unprecedented resolution the structure of genetic diversity within the genus Gallus, to better understand the make-up of the genome of domestic chickens and to propose molecular tools for the management of wild populations in zoological gardens. Several events of domestication have most probably taken place and a few studies showed that two species, at least, of the genus Gallus could be involved (Gallus gallus and Gallus sonneratii). Our preliminary data suggest that more than 20 regions could have been introgressed from G. sonneratii or G. lafayetii. The identification of such introgression phenomena has a fundamental interest in order to understand to what extent the current structure of the genome of domestic chicken reflects a complex process of domestication. Furthermore, introgression may have involved regions controlling traits of high selective value for breeders. Practical consequences for the management of populations in areas where wild junglefowls and domestic chickens cohabit are expected. A large scale sampling will be undertaken to obtain DNA from genuine wild junglefowls, the absence of recent crossbreeding will be checked with a 60K SNP chip. An array of domestic chickens from different breeds will be sampled to maximise genetic diversity. Sequencing with a very high coverage (95X) will be performed for Bambusicola thoracicus and resequencing with a high coverage (20X) will be done for 48 wild Gallus and 24 domestic chickens. Sequence fragments will be aligned on the reference Gallus gallus sequence. The evolutionary dynamics at the genus level will be addressed with Approximate Bayesian Computation by Population Monte Carlo (ABC-PMC) to uncover qualitative aspects of the complex events (mutations, incomplete lineage sorting, lateral gene transfers...) which shaped the dynamics of the Gallus genus. Footprints left by all types of selection will be searched on coding sequences and non-coding sequences (using outlier approaches based on the XP-EHH score) to increase our understanding of the evolutionary dynamics at play both within the genus during evolutionary timescales and within the domesticated species. We will refine and adapt to the domestic chicken a methodology recently developed to investigate the evolutionary relationships between Neandertals and present-day humans. The local ancestry of domestic chickens along the genome will be modelled with a hidden process. The trajectory of such a process naturally segments the genome and indicates for each segment from which Gallus species it is most likely to derive. Variation in linkage disequilibrium among domestic chickens will be assessed at the same time. A wealth of new sequencing information will be obtained that will be made available for follow-up studies. Annotations of genes in the introgressed regions will also open the way to follow-up functional studies. A specific workshop dedicated to the genomics of domestication will be organised with invited experts working on similar issues in other species. This project will significantly contribute to the international initiative on avian genomes as well as to the 10K vertebrate genomes initiative.

Anti-Müllerian hormone (AMH), also called Müllerian inhibiting substance, is a member of the transforming growth factor beta family synthesized by growing ovarian follicles and involved in the control of follicular development. AMH has been recognized as one of the best hormonal markers of the ovarian reserve and for this reason it is increasingly used in reproductive medicine. However, few data are available on the regulation and the role of AMH in the ovary. The aim of this proposal is to fill the lack of data on normal ovarian AMH physiology and to understand the role of AMH and its specific receptor (AMHR2) in the polycystic ovarian syndrome (PCOS), the most common cause of female infertility. Indeed, some of the features of PCOS include an abnormally rich pool of small follicles which could be due to the dysregulation of the AMH/AMHR2 system. The project is divided in four tasks corresponding to these objectives. More precisely, the two first tasks aim to explore the regulation of the AMH/AMHR2 system. The objective of the Task 1 is to study the regulation of AMH and AMHR2 expression by different hormones of pituitarian (gonadotropins) or ovarian (oestradiol, Bone Morphogenetic Proteins or BMPs) origin in granulosa cells from fully differentiated luteinized and small growing follicles .The Task 2 aims to further explore, at the promoter level, the hormonal regulations studied in Task 1, and to get new insights into their mechanism of action . We will take advantage of species differences of expression and regulation, of in silico analysis of the AMH and AMHR2 coding sequences and promoters and of in vitro comparisons of promoter activity. The third Task is to better understand the effects of AMH on follicular maturation. For that, we plan to identify new AMH target genes involved in this process, in particular those which are regulated in an opposite way to BMPs, and the different signalling pathways activated by AMH in granulosa cells. In the Task 4, we will take advantage of the results obtained in the previous tasks to study the role of the AMH/AMHR2 system in the PCOS. We will try to find out why AMH and AMHR2 are overexpressed in these women and what are the consequences of these high levels of AMH and AMHR2 in PCOS ovaries on AMH signalling pathways and target gene expression. Because the amount of PCOS granulosa cells is limited, and because only luteinized granulosa cells are available in human, we will also work on a prenatally-androgenized sheep model which recapitulates several features of PCOS and allows studying the role of androgens in the aetiology of this syndrome. The novelty of this project comes mainly from the fact that we will work in parallel on human, ovine and porcine material because there are complementary and have characteristics fitting very well with our scientific questions. Moreover, it should lead to numerous new results ranging from basic research to clinical and agronomic applications such as the improvement of reproductive biotechnologies. It will be coordinated by Nathalie di Clemente, a specialist of AMH since 20 years, who heads an Inserm team. It will gather two complementary partners worldwide known in their domain of expertise: an Inserm team specialist of AMH and Reproductive Medicine, and an INRA team specialist of ovarian physiology and AMH/BMPs systems in farm animals. All these aspects make the project feasible in the given time.