RUMIGEN has the following objectives:
- Manage within- and across-breed genetic diversity in cosmopolitan and local bovine breeding populations
Breed specific genome assemblies will be produced to describe the diversity of the bovine genome, including breed-specific variations which are overlooked using the current Hereford reference genome assembly. Methods will be developed to take advantage of this newly discovered genetic diversity and other state-of-the-art genomic tools in order to in vivo preserve endangered and non-endangered genetic resources, aiming to maintain genetic diversity, avoid unintentional genetic drift of functional trait values, avoid genetic load and improve resilience and adaptation.
- Examining transmission of paternal epigenetic information
Accumulating evidence suggests that sperm biomolecules and epigenome influence early embryonic development and affects the long-term development of progeny up to adulthood. RUMIGEN will analyse to what extent the sperm epigenome impacts the offspring’s subsequent development and production (embryo and cattle), considering both genetic-dependent (i.e epigenetic biomarkers under genetic control) and -independent (environmentally induced epigenetic marks) mechanisms.
- Evaluate to what extent epigenetic biomarkers may help to predict cattle phenotypes
Mixed model methods including both genetic value and epigenome effects will be used to assess to what extent the epigenome information explains trait variability and can improve individual performance predictions.
- Evaluate the impact of heat stress on cattle trade-offs between production and reproduction
Reaction norm models will be used to estimate the trajectory of the genetic parameters, especially correlations between traits, across climatic and other environmental conditions, in order to predict the cattle resilience to future conditions.
- Evaluate the impact of intrauterine heat stress on offspring epigenome and phenotypes
Foetal programming through intra-uterine heat stress can induce structural and functional changes in the foetus that may persist through adulthood. RUMIGEN will explore this phenomenon both statistically to refine susceptibility windows and experimentally to highlight epigenetic changes associated with immunity and health.
- Assess the potential of Genome Editing (GE) to speed up introgression
Across breeds introgression of one health-related allele will be assessed to compare the efficiency of genome editing versus marker-assisted mating for animal welfare.
- Develop cost-effective generic tools to assess the cattle epigenome
RUMIGEN will set up a cattle custom methylation chip (epiCHIP) and a sncRNA quantification platform, in order to efficiently fulfil the two previous objectives with data and to prepare ready-to-use tools for future selection.
- Assess the security of embryo biotechnologies and Genome Editing
RUMIGEN will compare several breeding tools, artificial insemination and new breeding strategies (in vitro embryo transfers, with or without prior genome editing) in terms of genome integrity under these different conditions.
- Assess the social acceptability of breeding and related technologies through a multi-actor approach
RUMIGEN will develop and make use of highly advanced models for societal dialogue to define the “room of acceptance” of breeding goals, genomic selection, reproductive biotechnologies and new breeding techniques. This process will engage farmers, industry, CSO’s/NGO’s, a diversity of experts, policy-makers, and citizens from at least 8 countries, providing also guidelines for policy options.
- Redesign new sustainable genomic selection schemes taking into account present and future environmental effects
RUMIGEN will design new breeding approaches for each farming system/environment/breed specific context. These approaches will combine breeding goals and technologies, taking the “room of acceptance” into account, in order to guarantee long-term efficiency in future conditions, genetic diversity preservation, social acceptability and adequacy to regulation.