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 future challenge in animal production will be to provide food to a growing human population by respecting a balance between quality products, consumer acceptance and safety, as well as animal welfare. In a perspective of safe and sustainable food systems, reducing the use of antibiotics in livestock is a major concern. In fact, antibiotic resistance is one of the major medical challenges of the 21st century. The transfer of genes conferring resistance through the environment and the food chain, the potential for development of resistant bacteria and the appearance of therapeutic failures in human medicine, notably due to zoonotic bacteria, constitute major health issues for livestock farming sectors. In the pig breeding industry, the weaning period is often accompanied by a decreased growth rate caused by disparate food intake and diarrhoea due to digestive disorders that might be associated with bacterial population disequilibrium (i.e. dysbiosis) and/or opportunistic intestinal infections. Alarmingly, during this transition period the prophylactic use of antibiotics is still very frequent in order to limit piglet morbidity and mortality. Thus, reducing the prophylactic use of antibiotics in weaning pigs is a main issue and there is a strong need for alternatives. In this context, we have built a public-private partnership that gathers INRA scientists and industries from economic sectors of both animal feeding and pig breeding. PigletBiota is a precompetitive project that will study the physiological and genetic bases of the piglet sensitivity at weaning, as a prerequisite to identify innovative actions to adapt animals and pig production systems to a reduction of antibiotic use. The global aim of the PIGLETBIOTA project is to develop research that will contribute to adapt pig production systems to a reduction of antibiotics. The project proposes an integrative biology approach to determine the main factors influencing the variability of the individual’s robustness at weaning. We will monitor piglets for health, immune, stress and zootechnical traits and will characterize the intestinal microbiota diversity and composition as well as the contribution of host’s genotypes. The experimental design will combine various environments, including experimental and commercial farms, and ages at weaning and all animals will be fed without antibiotics. Animals (n~1000) will be clinically surveyed, measured for various traits related to production, immunity and stress, and genotyped with high-density SNP chips. The genetic parameters of the sensitivity at weaning will be estimated and genetic association studies performed. Faecal samples before and after the weaning date will be collected for characterizing the dynamics of the gut microbiota and studying its influence on the individual sensitivity at weaning. Animal and microbiota data will be vertically integrated in order to better understand the interplay between the these two levels of this biological system, and to develop robust indicators of weaning sensitivity. Finally, a functional screening using INRA platforms dedicated to human studies will be performed in order to detect active molecules to be tested in vivo and by using an axenic pigs model. The PigletBiota public-private consortium will favor translational research and innovation.

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.

MICROFEED will study a generally ignored partner of livestock, the gut microbiota, to refund the improvement of production efficiency and robustness in pig breeding. The gut microbiota is an essential contributor to the availability of nutrients in the animal gut, contributing to its growth, health and immunity. MICROFEED will explore the gut microbiota component and its link with the genetic and genomic of feed efficiency and robustness of the host in two unique designs developed to study the pig feed efficiency. The first design relies on 10 generations of divergent selection for feed efficiency in two pig lines fed a conventional diet, to identify and quantify the impact of the gut microbiota potentially co-selected in response to genetic improvement for feed efficiency. The second design is based on a commercial population currently selected for production by the French pig breeders, from which the divergent lines were selected. It will be divided into two sub-designs of related pigs fed either a conventional diet or a high dietary fibers diet more difficult to digest. This second design is the result of collaboration between INRA and the pig breeders grouped in FGPorc in the frame of the H2020 Feed-a-Gene project to study the pig feed efficiency in response to lowered feed quality. In a first step, MICROFEED will produce new data (phenotypes, genotypes) in the two designs (908 pigs in Design 1 and 1700 in Design 2), together with feces samples for partial sequencing (16S) of the gut microbiota (600 + 1600 samples) to evaluate quantitatively the contribution of the gut microbiota to the variability of pig feed efficiency, and to test the effect of diet changes on this contribution. Prediction equations from the gut microbiota and host genomic data will be established. In a second step, whole-metagenome sequencing of 96 samples representing key microbiota profiles for extreme feed efficiency phenotypes, and whole-genome sequencing of 40 pigs best representing the two designs diversity will be obtained. These will be combined to identify the host and gut microbiota genes and functions involved in the feed efficiency of the pig and its robustness to diet changes, and to dissect the underlying biological mechanisms. Finally, external feces samples, genotypes and phenotypes available among the consortium from other projects, including different breeds, feeds, breeding conditions, will be used for validating the prediction equations established in the first step, to test their robustness to these factors and to then propose new selection and management strategies for pig breeding. By identifying which microbes contribute to feed efficiency and which are robustness to feed changes, MICROFEED will propose new genomic tools to jointly pilot the gut microbiota composition and the host genetic in terms of genetic selection for pig breeders, but also in terms of nutrition and feeding for the feeding industry. MICROFEED is structured in eight tasks, including one for the project management (Task 0) and one for the dissemination and transfer (Task 7). The two first tasks will concern data acquisition, the three following tasks will concentrate on acquisition of new knowledge on the relationships between host, gut microbiota and feed. Task 6 will validate these results and propose new strategies for selection and feeding. The consortium is composed of seven INRA groups specialized in pig genetics and genomics, feed efficiency and gut microbiota, plus two private partners from the French pig breeding industry representing more than 75% of the French pig genetic market. The total cost of MICROFEED is 1.4 million euros (not including INRA salaries), comprising a contribution of 258 k€ from the private companies and a demand to the ANR of 719 k€, for a labor of 227 person.months during 4 years.