BovReg clustered with five other EU H2020 funded projects to build the EuroFAANG node for harmonization and sharing of resources across core functional genome annotation projects (WP9 and WP11).
For five bovine cell lines, genomic (structural) variation, expression catalogue, epigenetic landscape and DNA-DNA interaction (WPs 1, 2, 5) were profiled. This information fed into functional validation work within WP6 and now is a valuable resource of information for the community.
From comprehensive RNAseq data sets on BovReg tissue samples, an improved annotation catalogue was generated for coding and non-coding transcribed elements in the bovine genome. Further functional assays established the epigenetic landscape (histone modifications, open chromatin, tissue-specific cytosine methylation pattern) in those samples (WPs 2, 5).
New Nextflow and nf-core-based pipelines were established to achieve highly standardized and reproducible bioinformatic tools for genome annotation (WP2, 3, 4). In parallel, the FAANG data coordination centre was further expanded with improved utilities and an extended ontology (WPs 3, 10).
Meta GWAS studies on BovReg target traits and plasma metabolites yielded large numbers of trait-associated variants. The eQTL analysis demonstrated the value of the new BovReg transcriptome annotation (WP2) by highlighting significant cis eQTL for previously unannotated loci (WP4).
An intersection of trait-associated genetic variants and functional regulatory potential prediction resulted in lists of annotated candidate regulatory SNPs as potential causal variants (WP4, 6).. Luciferase assays and genome editing editing with new protocols confirmed the regulatory role of predicted genetic variants/genomic regions in in-vitro studies with the characterized cell lines.
Whole transcriptome and epigenomic analyses of embryos produced in-vitro with sperm samples from heat-stressed sires revealed an indication of intergenerational response pattern for heat stress (WP5). Integration with generated data on open chromatin from respective embryo samples enable an improved understanding of the environmentally induced transgenerational epigenomic modulation.
Feature models using Bayesian Variable Selection methods were developed for the integration of biological functional information (WPs 2, 4, 5) into genomic evaluation schemes (WP7). Low-pass sequencing followed by reference-guided variant discovery showed a new cost-effective approach to obtain highly accurate genotypes for whole-genome sequence variants for genomic predictions.
The study of the societal and ethical contexts of livestock genomics (WP8) included interviews with diverse stakeholders on modern cattle breeding techniques. To continue engagement with publics outside of stakeholder communities (WPs 8, 9), the finalised content of the DEMOCS game was printed in English and Finnish, played with groups of publics, and their opinions and insights analysed. The game available for download and widely distributed (also in German and French).
Training, communication and efficient knowledge transfer within BovReg was done continuously, including 30 open-access peer-reviewed publications, participation to 23 conferences/workshops with 32 presentations and 6 posters, organization of 3 conference sessions, 4 training courses and 4 industry workshops,; the project web site had 146.211 total visits while related social media activities were significant (Twitter/X 429 followers, Facebook 85 followers, Linkedin 313 followers, Zenodo 577 downloads, YouTube 136 subscribers) (WP9).
Joint activities with the EuroFAANG cluster of projects, global FAANG initiatives, collaboration with the FAANG Communications Group, and the breeding industry culminated in a public final conference (120 participants with 34 presentations and a panel discussion), the third in a series of conferences linked to the FAANG 10-year jubilee (WPs 9, 10).
