Periodic Reporting for period 3 - BovReg (BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle)
Reporting period: 2022-09-01 to 2024-02-29
Despite the revolution in functional genome analysis, a wide gap remains in understanding associations between the (epi)genome and complex phenotypes of interest, which impedes the efficient use of annotated genomes. BovReg brought together an interdisciplinary team of experts from the EU, Canada and Australia. BovReg provided a comprehensive map of functionally active genomic features based on FAANG core assays in cattle and how their (epi)genetic variation in beef and dairy breeds translates into phenotypes. This constitutes key knowledge for biology-driven genomic prediction needed by scientific and industrial livestock communities. BovReg generated this functional genome data from bovine tissues covering different ontological stages and phenotypes by applying novel bioinformatic pipelines. BovReg addressed the following specific objectives focusing on three key phenotypic traits: biological efficiency (nutrient conversion, greenhouse gas emission), disease susceptibility (mastitis) and robustness (fertility) in dairy and beef cattle.
BovReg aimed to:
1. Establish laboratory and bioinformatics tools for functional annotation of the bovine genome and in other species
2. Annotate functionally active genomic regions in the bovine genome
3. Map functional parameters (ranging from molecular to agricultural phenotypes) to newly annotated genomic features
4. Develop prototype models for integrating biological knowledge on regulatory variation in the bovine genome (biology-driven genomic prediction tools) into genomic selection schemes for local and global beef and dairy cattle breeds (WP7)
5. Provide targeted training, dissemination and communication activities in the use of the new resources and knowledge applying FAIR principles to ensure reproducibility and ensure long-term data storage (WP3, 9 and 10)
6. Develop a Democs card game to engage with lay publics and stakeholders on issues related to livestock breeding and genomics, and establish an ethical framework for scientific and corporate cultures (WP8)
BovReg aimed to:
1. Establish laboratory and bioinformatics tools for functional annotation of the bovine genome and in other species
2. Annotate functionally active genomic regions in the bovine genome
3. Map functional parameters (ranging from molecular to agricultural phenotypes) to newly annotated genomic features
4. Develop prototype models for integrating biological knowledge on regulatory variation in the bovine genome (biology-driven genomic prediction tools) into genomic selection schemes for local and global beef and dairy cattle breeds (WP7)
5. Provide targeted training, dissemination and communication activities in the use of the new resources and knowledge applying FAIR principles to ensure reproducibility and ensure long-term data storage (WP3, 9 and 10)
6. Develop a Democs card game to engage with lay publics and stakeholders on issues related to livestock breeding and genomics, and establish an ethical framework for scientific and corporate cultures (WP8)
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).
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).
The BovReg project will make a long-lasting contribution to knowledge of genome function in cattle with the following impacts.
• BovReg datasets and its functional annotation map, together with the expanded FAANG data coordination center and new bioinformatic pipelines will provide FAIR resources for biology-informed genotype–to–phenotype prediction.
• The newly established and tested feature models will also enable small and rare breeds to benefit from the progress in modern breeding technologies to support the goal of EU Farm-to-Fork strategy to foster biodiversity in farming systems.
• Epigenomic results, including those transmitted across generations, will impact responses to climate change effects on farmed animals for improving breeding and husbandry.
• BovReg adheres to the concept of responsible research and innovation (RRI). Partners are proactively engaged with stakeholders and with the public to obtain a comprehensive view of the societal implications of the new cattle breeding technologies.
These impacts will provide much-needed input to the emerging EuroFAANG Research Infrastructure (https://eurofaang.eu/) initiated with substantial BovReg contribution, consolidating farmed animal genotype to phenotype research worldwide, which started in January 2023.
• BovReg datasets and its functional annotation map, together with the expanded FAANG data coordination center and new bioinformatic pipelines will provide FAIR resources for biology-informed genotype–to–phenotype prediction.
• The newly established and tested feature models will also enable small and rare breeds to benefit from the progress in modern breeding technologies to support the goal of EU Farm-to-Fork strategy to foster biodiversity in farming systems.
• Epigenomic results, including those transmitted across generations, will impact responses to climate change effects on farmed animals for improving breeding and husbandry.
• BovReg adheres to the concept of responsible research and innovation (RRI). Partners are proactively engaged with stakeholders and with the public to obtain a comprehensive view of the societal implications of the new cattle breeding technologies.
These impacts will provide much-needed input to the emerging EuroFAANG Research Infrastructure (https://eurofaang.eu/) initiated with substantial BovReg contribution, consolidating farmed animal genotype to phenotype research worldwide, which started in January 2023.