Food production systems need to be more efficient and sustainable to tackle the challenges posed by a growing population and a climate crisis. Breeding strategies have proven themselves to be essential in providing genetic gain for livestock, but efforts must go on. Providing quality annotations for animal genomes will be instrumental to further improve genetic gains. The FAANG (functional annotation of animal genomes) initiative aims at gathering a community to foster FAIR data principles in this field (ref 1–3). A data coordination center (DCC) at the EMBL-EBI is developing the FAANG data portal to allow FAANG data to be more findable, accessible, interoperable and foster their reuse (ref 2). This project, VizFaDa, will produce interactive data visualisations of FAANG data through web applications, and we will work with the EMBL-EBI to integrate those visualisations with the existing portal. First we will compute pairwise correlations between FAANG samples (genes expression and epigenetic data), and render the results in the form of interactive, subset-able, clustered correlation heatmaps. Users will be able to upload their processed data to be compared to FAANG samples within seconds. Correlation heatmaps will provide an eagle-eye view of the data available and their similarities. Second, we will integrate epigenetic and transcriptomic data by producing stacked epigenetic profiles near gene starts, gene ends, and middle exons, sorted according to gene expression level or exon inclusion ratio. These attractive visualisations will expose the complex links existing between epigenetic marks and transcription, and will add value to the FAANG dataset. Efforts will be devoted to make the addition of new samples of the dataset as automatic as possible, to ensure the long term stability of the proposal. Development of the web applications will be fully open source. Altogether, we hope our efforts will reinforce the FAANG data portal attractiveness for researchers and breeders, and will foster data reuse.

The aim of the Path2Bos project is to reconstruct the evolutionary path of cattle from its domestication starting about 10,000 years ago in Anatolia, during its later spread into Europe and Africa and up to now, through a paleogenomic analysis of fossils, the direct witnesses of evolution. The goal is to identify genomic regions that were selected at the early stages of domestication, corresponding to basic phenotypes that should be preserved in ongoing genetic selection schemes. The project is based on a previous paleogenetic characterization of a large number (~ 700) of 9,000- to 1,000-year-old archaeological bones of ancient domesticated cattle and their wild ancestors, the aurochs. We have genotyped the mitochondrial genomes and sequenced the hypervariable regions of almost 200 of these ancient bones, allowing us to assign reliably their mitochondrial haplogroups and to follow the evolution of populations from their initial domestication in Anatolia during the Neolithic as well as their spread and evolution in Europe and North Africa until the Middle Ages. Using sequence capture, we obtained complete mitogenomes from 40 of these samples representing the various clades, reconstructed the evolution and timing of radiation of aurochs’ populations, and untangled the impacts on population diversity of both climate changes during the Pleistocene-Holocene transition and initial domestication. We have sequenced the genome of a 9,000-year-old aurochs from the domestication centre in Anatolia that will serve as a reference genome to follow the genomic changes and selective sweeps during the domestication process. We propose to sequence about 30 of these ancient genomes and to compare them with genomes and phenotypic records from modern domestic animals to reconstruct many aspects of the selection pressure exerted during different prehistoric and historic periods. We will also sequence several individuals from modern hardy breeds to generate reference genetic data from breeds that have escaped recent selection schemes or that were selected for alternative phenotypes. Our data will be used in combination with modern genomic data from the 1,000 Bull Genomes consortium in various complementary ways to identify and to date signatures of selection during the cattle domestication process. We will screen for selection events that are either recent or old, complete or ongoing, acting on new variants or on standing variation. Using powerful tools to detect selective sweeps in genomes, ancient genomic data will provide the ability to date the various selection events, to identify the population(s) of origins onto which selection was exerted and to explore the validity of the various demographic models used to detect selective sweeps from modern genomic data. We will also use extensive GWAS data, produced by one of us using modern cattle, to reconstruct the past evolution of complex multigenic traits. Path2Bos will (1) improve the power and accuracy of the identification of genomic regions under selection, (2) estimate the strength of selection and date the origin of the corresponding selective events, (3) identify variants that were selected in the past and that have been lost in modern selection schemes, thereby pinpointing the genetic bases of phenotypic traits that might be useful to preserve for the long-term sustainability of cattle husbandry. Thus, it will provide an original and very useful cattle genome annotation data source to complement the genomic characterization efforts of modern cattle breeds and enrich the current selection strategies. A strong point of Path2Bos is the complementarity of the expertise and resources, including preliminary data, of the consortium partners, in particular paleogenomics and a large collection of characterized archeological samples, involvement in the 1000 Bull Genomes consortium and GWAS, selective sweep method developments and analyses of genomes and a high-throughput sequencing facility.

The current increase in world meat demand together with global changes (climate changes, availability of agricultural resources, societal perception of breeding) require us to rethink our production systems. The pressure of livestock production on ecosystems needs to be reduced, food and health security need to be increased, as well as animal welfare. To achieve these objectives, a better knowledge of the link between genotype and phenotype is necessary. Development of efficient cellular tools are key to address this new challenge because they are more suitable than living farm animals to generate biological data through high-throughput screens (HTS) and to perform functional analysis. Moreover they are more socially and ethically acceptable, safer regarding biosecurity and reduce the need of animal experimentation in agreement with the 3R (Replace, Reduce, Refine) rules. Within the different strategies that can be implemented so far, the production and use of pluripotent stem cells (PSCs) is in perfect agreement with those goals as these cells can differentiate in vitro and in vivo toward all the cell lineages. As such, these cells can be useful as novel cellular tools to evaluate the causality of genetic variants on quantitative traits and specific cell phenotypes. However despite the progress made on mouse and rat models to produce PSCs, the establishment of PSCs in pig is still beset with problems and their pluripotent state still relies on the expression of exogenous factors. This impacts their differential potential and strongly restrict their use for ex vivo and in vitro phenotyping. The fact that producing fully pluripotent cells in pig remains impossible by standard procedures raises numerous concerns on the molecular mechanisms controlling pluripotency in pigs. One possibility is that the signaling pathways necessary to activate the core pluripotency network in mice and humans are inactive or insufficient in this species. Another hypothesis is that induced pluripotent stem cells generated in pigs carry genetic and epigenetic barriers, and are therefore not fully reprogrammed by conventional protocols. We propose to evaluate both hypotheses in pigs, by considering the specific microenvironment of pig embryonic PSCs. We will characterize the epigenomic profiles of preimplantation pig embryos at the unicellular and tissue scales and the proteome of uterine fluids at the corresponding embryonic stages. Together with available transcriptomic profiles we will integrate this “multi-omics” information to infere regulatory networks driving pluripotency in pig blastocysts (Task 1). In parallel we will design and generate fluorescent tagged cell lines for tracing endogenous pluripotency (Task 2) and we will use these innovative tools (reporter cell lines and omics data) to perform a screening of small molecules and cytokines able to sustain pluripotency and cellular self-renewal (Task 4). Once defined, we will use this optimized culture system to improve the reprogramming process. Our aim is to overcome remaining epigenetic barriers through the use of new sets of reprogramming factors and epigenetic modifiers (identified through Task 1) to reach a fully reprogrammed state (Task 3). We finally propose to confirm the pluripotent state of the cell lines produced during this project through a complete molecular characterization and in particular by evaluating their ability to contribute to chimaeras (Task 5). In conclusion, our project integrates different approaches (descriptive, functional and experimental) leading to significant progress towards the production of true pig pluripotent stem cells.

In line with the purpose to elaborate a new agro-food business model and promote Mediterranean local food products, the project aims to establish new knowledge and to explore the feasibility to obtain an innovative product that can contribute to improve human health and to face some of the challenges of the Mediterranean area. In this contest, polyunsaturated fatty acids take part in numerous physiological processes. Moreover, there is evidence that linen derived products (linen plant, linen straw, linseed, linseed bran) and some species of algae, rich in a-linolenic acid, the essential precursor of O-3, may have beneficial effects on human and animal health. An unbalanced diet in terms of O-6/O-3 ratio contributes to increase the cardiovascular diseases, obesity, diabetes and to reduce the human fertility, especially male fertility, in western Countries. On the light of this data, flax and algae supplementation in animal diet is a valid method to increase the productive and reproductive performances, the sanitary conditions of the farm and to produce nutritionally beneficial animal products such as rabbit meat. Finally, these innovative animal products, rich in O-3 and with reduced O-6/O-3 ratio, could be considered an innovative and valid functional food for the improvement of human health and fertility. Thus, the project has the following aims: 1 – to develop specific feeds for reproducing and growing rabbit based on the supplementation of linen derived products and algae, to reach a higher omega-3 fatty acids content in meat, and to assess the role of "omega-3 fixation booster"; 2 - to increase the fertility of rabbits to make more efficient the rabbit farming systems, including in hot climatic conditions also related to “global warming”; 3 – to improve the sanitary status in the rabbit farms through a higher resistance to infectious diseases, by increasing the immunological response of the animals and thus leading to reduce the use of antibiotics and to improve the animal welfare; 4 – to produce a new innovative, high quality and functional food (O rabbit meat) that can be produced by SMEs and can link local agricultural producers to urban, national, and international markets; 5 – to develop an innovative method of packaging that allows a prolongation of the shelf-life of the rabbit meat contributing to its commercialization in the domestic market and also for export (to reverse the import trend in the agricultural sector in some Mediterranean countries); 6 – to create a new market and supply food chain (O rabbit consortium) that includes under its disciplinary and logo, farmers, breeders and research centres that produce O rabbit meat as a guarantee of a high quality product and under the principle “from the farm to the fork”. According to the purpose to strengthen horizontal integration, the Consortium O rabbit includes the whole food chain that produces the innovative functional food: O rabbit meat. The research centers included in the consortium evaluate the quality of the O rabbit meat, the sanitary condition of the animals and their fertility. Another innovative aspect is the devise of a special packaging that can extend the shelf-life of the O rabbit meat. The dissemination of the results may contribute to the launch of this new healthy product in the market (vertical integration). The consortium and the O rabbit meat production may have a positive socio-economic impact for local market, exportation, and knowledge-based job. O Rabbit can increase the protein consumption in some areas and can concur to balance the diet O-6/O-3 ratio in other countries with beneficial effects on human health.

The overall goal of this project is to help improving the efficiency and sustainability of the egg production sector. The approach consists in extending the laying cycle up to 90 weeks from 60-70 weeks currently and improving hen feed efficiency (FE) and laying rate at these advanced ages, all while maintaining good egg quality, both on the nutritional and food safety plans. Eggs are a valuable and cheap source of nutrients for human alimentation all over the world. Their production is steadily increasing worldwide. Extending the laying cycle will ensure sustainability of the sector: i) economically, by reducing the per-egg cost, ii) socially, by reducing the flocks size, their turnover and the number of one-day males killed, iii) environmentally, by reducing the feed inputs. However, the current understanding of the genetic basis of egg productions at these advanced ages is scarce if anything, since almost all the studies are conducted around 30 to 60 weeks. Hence, this project aims at (a) providing a comprehensive view of the genetic basis of the laying rate, feed efficiency and egg quality in layers at a production stage never studied before (90 weeks of age) and (b) evaluating the age effect (60 weeks versus 90 weeks) on this genetic architecture and on the cis-regulation of gene expression in liver at the adult stage in relation to liver-related trait QTL refining. The egg quality will be studied under both the nutritional (yolk lipid quantity and composition) and the food safety (antimicrobial ability of the white against Salmonella enterica serovar Enteritidis, a bacterium of great concern in food safety) aspects. The project is organized in two Parts and 6 working tasks (WT), in addition to a management / dissemination WT). Part 1 (4 tasks) is aimed at gaining genetic knowledge on all the traits of interest at an advanced age. To this end, we will estimate the genetic parameters and map by GWAS the QTL regions for FE and egg rate (WT1), egg nutritional traits (WT3) and antimicrobial ability (WT4). We will also develop a genomic evaluation of FE, trait very costly to measure (WT2). Part 2 (2 tasks) is dedicated at going further into the QTL region characterization, an endeavor known to be challenging. First, in WT5, we will gain knowledge on gene expression regulation in adult liver and its variation between 60 and 90 weeks by detecting cis-eQTLs and new regulatory regions, using cutting-edge genomic methods (ATAC-, ChIP-, DNA-, RNA-seq, RRBS). In particular, we will be able to study a class of regulatory genes, called long noncoding RNA genes (LNC) using a genome annotation enriched in LNC that we recently generated. This task should facilitate the identification of causative genes and perhaps variants (SNPs or INDEL), underlying QTL, notably those related to the egg nutritional quality (in particular lipid content), since the liver is the tissue where egg yolk’s lipids and proteins synthesis takes place. Finally, in WT6 we will prioritize a few regions highlighted in WT5, that we will select for being involved in a trait of interest, affected by the age, and with an effect observable in cell lines for molecular biology validations. From a practical viewpoint, this project will contribute to identify new targeted selection criteria for strategical traits such as FE, egg laying rate, egg nutritional quality and egg safety. From an academic viewpoint, it will contribute to provide a cis-regulation map of gene expression in adult liver and its variation between 60 and 90 weeks, and to identify causative genes and variants controlling QTL detected in Part 1, with a particular attention to yolk lipid related traits. The consortium is composed of 5 INRAE groups specialized in chicken genetics, genomics, bioinformatics, feed efficiency, food quality and security, one French international chicken breeding company and one platform specialized in lipidomic, thus gathering the expertise required for this project.