H2020 BovReg Project: BovReg: Identification of functionally active genomic traits relevant to phenotypic diversity and plasticity in cattle

Genomic Approaches for Better Livestock Breeding Understanding the biological mechanisms behind genetic variations could help farmers breed livestock efficiently and improve animal welfare. Genomic information (the cellular data an organism needs to grow and function) has been analyzed and used for some time to breed more resilient and healthy livestock. A key drawback is that the biological mechanisms underlying certain genetic variants are still not widely understood.

Therefore, the consequences for the health and welfare of livestock can be unpredictable, as certain genetic traits can have unforeseen side effects. The BovReg project sought to move toward a more biology-based approach, where the function of a specific genetic variant is better understood. "This is still a very unknown area," says Christa Kuehn, BovReg project coordinator, currently at the Friedrich-Loeffler Institute in Germany. "However, we know that more than 95% of the genome that is not translated into proteins must have some function; otherwise, evolution would not have maintained it for millions of years." Investigating the Regulatory Regions of the Genome Kuehn and her colleagues wanted to investigate these regulatory regions of the genome. To uncover these mechanisms, the project, coordinated by the Research Institute of Farm Animal Biology in Germany, generated huge amounts of shared functional genomic data from bovine tissue and frequently used cell lines. The goal was to establish a much more detailed understanding of traits related to the robustness and health of livestock.

To this end, the project also developed bioinformatics pipelines to ensure that data analysis was reproducible and interoperable across different platforms. “A huge amount of data was generated, which was also usable for biomedical research,” explains Kuehn. “We wanted to ensure that this information was usable and accessible.” All data will be incorporated into a global public data portal. “We also conducted ethical mapping to graphically represent societal perceptions about genomic reproduction,” adds Kuehn. “Research can sometimes cause social disruption or reluctance, so we wanted to anticipate and analyze its potential implications for society.” Functional Annotation of Animal Genomes The results of the BovReg project have also informed the global FAANG (Functional Annotation of Animal Genomes) project, an organization that brings together genomic research on farm animals worldwide. The FAANG community operates in parallel with the ENCODE initiative, which is dedicated to characterizing the function of the human genome. BovReg co-created EuroFAANG, an umbrella initiative of six related EU-funded projects, which have agreed on common data channels and overarching protocols, ensuring that knowledge is disseminated as widely as possible.

Building on this EuroFAANG umbrella, further EU funding was secured two years ago for a project called EuroFAANG Research Infrastructure, which will establish the necessary infrastructure to continue this cooperation in the future. “One of the main challenges after a project like BovReg is keeping people together and ensuring the community continues,” says Kuehn. Improving livestock breeding practices Kuehn and his team believe that the pioneering work of the BovReg project will help improve breeding practices. “The more we know about genomic function, the more we can avoid harmful side effects of breeding,” he notes. “This could save resources and improve animal welfare.” Better genomic information could also lead to more targeted animal management and veterinary intervention. “Some animal populations might benefit more from personalized treatment than others,” adds Kuehn. “Advancing our understanding of genomic functions can help us understand the real needs of animals.”