GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors. The activation status of functional genome sequences varies across time and space, and in response to environmental perturbations. In full coordination and synergy with global effort and ongoing projects of the Functional Annotation of ANimal Genomes (FAANG) community, we will characterize the dynamics (“switches”) of the functional genome from embryo (chicken) and fetus (pig) to adult life by targeting a panel of tissues relevant to sustainable production. New expression QTL data in pigs and existing high-resolution QTL data in chicken will be used for developing innovative genomic predictive models that integrate functional annotations, and these models will be validated in commercial pig and poultry populations. In addition, nutritional epigenetic data will allow evaluation of the influence of maternal diet on the epigenome of the pig fetus and whether such effects persist until post-weaning. These open-shared datasets will conform fully with FAANG standards and add valuable knowledge on genetic and epigenetic variation of functional elements to FAANG. A comprehensive plan of dissemination and outreach activities to a large audience of stakeholders will be implemented. The GENE-SWitCH consortium brings together partners representing pan-European excellence (including the academic institutions which pioneered FAANG) and world-leading animal breeding and biotech industry in a true co-creation effort. Overall, GENE-SWitCH will contribute to the global FAANG effort considerably, demonstrate how functional annotation of genomes can foster the advancement of genomic selection for immediate benefit to the breeding industry, and produce cutting-edge research paving the way to new studies and strategies for sustainable productions.

SmartCow integrates key European cattle research infrastructures, to promote their coordinated use and development and thereby help the European cattle sector face the challenge of sustainable production. Covering all the relevant scientific fields and the diversity of cattle types and production systems, SmartCow will provide the academic and private research communities with easy access to 11 major research infrastructures from 7 countries (18 installations) of high quality services and resources. These are needed to develop innovative and ethical solutions for efficient use of animal and feed resources that promote animal welfare and healthy livestock, as well as sustainable competitiveness. SmartCow combines strong scientific and technical skills in animal nutrition (in vivo methods for nutrient utilisation and emissions measurements), genetics (genotyped animals, phenotyping capabilities), health and welfare (sensors and automatic recordings of physiological and behavioural traits) and ethics in animal experimentation. A central promotion and management of transnational access to the research infrastructures will provide access to around 10,000 cow.weeks and facilitate up to 33 research projects involving 59 users. Networking activities will harmonise and standardise procedures especially in animal care and measurements, design of experiments, data recording and analysis thanks to a cloud-based data-platform specifically developed in the project. Joint research activities will produce refined methods and proxies to evaluate feed efficiency and emissions, develop new protocols to reduce the use of animals and produce new methods to exploit sensor data for cattle husbandry. Promotion of transnational access and dissemination of SmartCow outcomes and innovations for maximum impact will be supported by a Stakeholder Platform composed of pre- and post-farm gate industry, farmer organisations, NGOs, policy makers at national and EU levels.

More sustainable breeding programs and linked technologies need to be in line with social demand and to take into account genetic diversity as well as required adaption to climate change. Towards these aims, RUMIGEN will ensure engagement of a variety of stakeholders to assess social perception of breeding objectives and related technologies in ruminants. It will define “rooms of acceptance” which will be implemented in sustainable breeding scenarios that will then be assessed through multi-actor panels. To define new breeding programs, RUMIGEN, which brings together partners representing pan-European leaders on ruminant breeding, will question trade-offs and pleiotropic effects through adaptation to environmental stressors such as heat stress. Cosmopolitan and local dairy cattle breeds will be analysed evaluating mid to long term effects as well as impact on next generation (fetal programming). This work will rely on large-scale data from commercial farms combined with climatic data, taking advantage of the large panel of situations across Europe and of a unique design involving half-sister cows raised in contrasted conditions, Denmark and India. Diversity will be also studied with new breed genome assemblies. Methods will be developed to account for rare alleles and to maintain diversity. An epigenotyping platform will be designed to (i) explore sperm epigenome influences on bull fertility and progeny, (ii) decipher underlying mechanisms of epigenetic inheritance and (iii) evaluate how much epigenetic biomarkers improve phenotype prediction. RUMIGEN will answer questions on genome editing specificity and safety issues, assessing its potential to preserve genetic diversity and increase genetic gains. Overall, RUMIGEN will develop models combining genomics, epigenomics and biotechnologies to improve genomic selection, preserve genetic biodiversity and avoid genetic load. Improved phenotype prediction will pave the way to new management indexes for precision farming.