Periodic Reporting for period 2 - BovReg (BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle)
Berichtszeitraum: 2021-03-01 bis 2022-08-31
Despite the revolution in functional genome analysis, currently a wide gap remains in understanding associations between the (epi)genome and complex phenotypes of interest, and this impedes the efficient use of annotated genomes, e.g. for precision breeding of farm animals.
BovReg brings together an interdisciplinary team of experts encompassing bioinformatics, molecular and quantitative genetics, animal breeding, reproductive physiology, ethics and social science from the EU, Canada and Australia.
BovReg will provide a comprehensive map of functionally active genomic features data 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 is generating functional genome data from representative bovine tissues, which cover different ontological stages and phenotypes, applying novel bioinformatic pipelines. BovReg addresses 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.
It aims 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 based on a comprehensive catalogue of 24 tissues that are highly relevant for the BovReg target traits, five ontogenetic stages and both genders from dairy and beef breeds
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 to ensure that the science developed is responsive to these issues (WP8)
BovReg brings together an interdisciplinary team of experts encompassing bioinformatics, molecular and quantitative genetics, animal breeding, reproductive physiology, ethics and social science from the EU, Canada and Australia.
BovReg will provide a comprehensive map of functionally active genomic features data 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 is generating functional genome data from representative bovine tissues, which cover different ontological stages and phenotypes, applying novel bioinformatic pipelines. BovReg addresses 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.
It aims 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 based on a comprehensive catalogue of 24 tissues that are highly relevant for the BovReg target traits, five ontogenetic stages and both genders from dairy and beef breeds
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 to ensure that the science developed is responsive to these issues (WP8)
BovReg has clustered with five other EU H2020 funded projects (GENE-SWitCH, AQUA-FAANG, RUMIGEN, GEroNIMO, HoloRuminant) 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 the expression catalogue, epigenetic landscape, DNA-DNA interaction and genetic variants (WPs 1, 2, 5) were profiled. This information feeds into functional validation work within WP6 and is a valuable resource of information for the community.
From comprehensive RNAseq data sets on BovReg tissue samples, an improved comprehensive annotation catalogue was generated for coding and non-coding transcribed elements in the bovine genome. Further assays (ChIPseq, ATACseq, RRBS, WGMS) established the epigenetic landscape (histone modifications, open chromatin, tissue-specific CpG methylation pattern) in those samples (WPs 2, 5).
New Nextflow and nf-core-based pipelines (e.g. ChIPseq, ATACseq, microRNA, eQTL or TWAS analyses) were established to achieve highly standardized and reproducible bioinformatic tools for genome annotation (WP2, 3, 4). In parallel, the FAANG data coordination centre (FAANG DCC) was further expanded with improved utilities (WPs 3, 10).
Meta GWAS studies on BovReg target traits and plasma metabolites yielded up to 91,774 or and 5,592 trait-associated variants (p<1e-6), respectively. The eQTL analysis demonstrated the value of the new BovReg transcriptome annotation (WP2), because it highlighted significant cis eQTL for previously unannotated loci (WP4).
An intersection of eQTL, meta-GWAS, TWAS and functional regulatory potential prediction resulted in lists of annotated candidate rSNPS as potential causal variants (WP4s 6). For their functional validation via CRISPR/Cas9, protocols were established in the characterized cell lines (WP6).
Whole transcriptome and RRBS analyses of embryos produced in-vitro with sperm samples from heat-stressed sires revealed indication on intergenerational response pattern for heat stress (WP5). Integration with generated ATACseq from respective embryo samples will 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 resulting in three published papers. To further engage with the public outside of stakeholder communities (WPs 8, 9), the finalised content of the DEMOCS game has been printed for playing with the public and is translated into Finnish and German.
Training, communication and efficient knowledge transfer within BovReg is done continuously, including open-access peer-reviewed publications, workshops, organization of conference sessions, training courses or social media activities (WP9). Joint activities with the EuroFAANG cluster of projects, global FAANG initiatives, collaboration with the FAANG Communications Group, and the breeding industry are ongoing and contribute to sustainability of the BovReg project (WPs 9, 10).
For five bovine cell lines the expression catalogue, epigenetic landscape, DNA-DNA interaction and genetic variants (WPs 1, 2, 5) were profiled. This information feeds into functional validation work within WP6 and is a valuable resource of information for the community.
From comprehensive RNAseq data sets on BovReg tissue samples, an improved comprehensive annotation catalogue was generated for coding and non-coding transcribed elements in the bovine genome. Further assays (ChIPseq, ATACseq, RRBS, WGMS) established the epigenetic landscape (histone modifications, open chromatin, tissue-specific CpG methylation pattern) in those samples (WPs 2, 5).
New Nextflow and nf-core-based pipelines (e.g. ChIPseq, ATACseq, microRNA, eQTL or TWAS analyses) were established to achieve highly standardized and reproducible bioinformatic tools for genome annotation (WP2, 3, 4). In parallel, the FAANG data coordination centre (FAANG DCC) was further expanded with improved utilities (WPs 3, 10).
Meta GWAS studies on BovReg target traits and plasma metabolites yielded up to 91,774 or and 5,592 trait-associated variants (p<1e-6), respectively. The eQTL analysis demonstrated the value of the new BovReg transcriptome annotation (WP2), because it highlighted significant cis eQTL for previously unannotated loci (WP4).
An intersection of eQTL, meta-GWAS, TWAS and functional regulatory potential prediction resulted in lists of annotated candidate rSNPS as potential causal variants (WP4s 6). For their functional validation via CRISPR/Cas9, protocols were established in the characterized cell lines (WP6).
Whole transcriptome and RRBS analyses of embryos produced in-vitro with sperm samples from heat-stressed sires revealed indication on intergenerational response pattern for heat stress (WP5). Integration with generated ATACseq from respective embryo samples will 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 resulting in three published papers. To further engage with the public outside of stakeholder communities (WPs 8, 9), the finalised content of the DEMOCS game has been printed for playing with the public and is translated into Finnish and German.
Training, communication and efficient knowledge transfer within BovReg is done continuously, including open-access peer-reviewed publications, workshops, organization of conference sessions, training courses or social media activities (WP9). Joint activities with the EuroFAANG cluster of projects, global FAANG initiatives, collaboration with the FAANG Communications Group, and the breeding industry are ongoing and contribute to sustainability of the BovReg project (WPs 9, 10).
The BovReg project will make a long-lasting contribution to knowledge of genome function in cattle. The FAANG CC and data portal is continuously improving together with Nextflow and nf-core based bioinformatic pipelines, which together with the BovReg datasets will provide FAIR resources for biology-informed genotype–to–phenotype prediction for the community in the future. The 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.
Members of the EuroFAANG cluster under the lead of UEDIN and FBN recently submitted a proposal for establishing an infrastructure to consolidate farmed animal genotype to phenotype research in Europe and beyond, which was positively evaluated by the European Commission and is planned to start in January 2023.
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.
Members of the EuroFAANG cluster under the lead of UEDIN and FBN recently submitted a proposal for establishing an infrastructure to consolidate farmed animal genotype to phenotype research in Europe and beyond, which was positively evaluated by the European Commission and is planned to start in January 2023.