BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle

Informazioni relative al progetto

BovReg

ID dell’accordo di sovvenzione: 815668

DOI

10.3030/815668

Progetto chiuso

Data della firma CE 10 Maggio 2019

Data di avvio 1 Settembre 2019

Data di completamento 29 Febbraio 2024

Finanziato da

• SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy

Costo totale

€ 6 033 458,83

Contributo UE

€ 5 993 458,83

Coordinato da

FORSCHUNGSINSTITUT FUR NUTZTIERBIOLOGIE
Germany

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Risultati finali

Documents, reports (58)

Inter- and transgenerational epigenetic marks

Lists and maps of inter- and transgenerational paternally transmitted effects on the embryonic intermediate phenotype (transcriptome) and epigenetic characteristics and marks (T5.3)

Final report on BovReg data production

Final report on BovReg data production (T3.4)

Genomic prediction for feed efficiency in single and multi-breed context

D7.4 Genomic prediction for feed efficiency in single and multi-breed context

Training course/hackathon on bioinformatics methods

Report on course/hackathon on bioinformatics methods at CRG premises (T9.2)

Reports on 3 dissemination workshops

Reports on 3 dissemination workshops (T9.4)

Differentially expressed genes in bovine embryos

Lists of differentially expressed genes affected by different culture conditions temperature increased fatty acid concentrations in bovine embryos T52

Report on ontologies used across BovReg

Report on ontologies used across BovReg (T3.3)

Report on promoting Democs game to specific target groups

Report on promoting Democs game to specific target groups (T9.3)

Spatial DNA-DNA interaction map

A spatial DNADNA interaction map of the bovine genome T23

Final version of the cow evolutionary annotation

Final version of the cow genome evolutionary annotation (T3.5)

List of antibodies for ChIP-seq on bovine tissues

List of antibodies suitable for ChIPSeq on bovine tissues T12

Map of open chromatin regions, 4 specific histone marks, CTCF binding sites across bovine cell-lines

A map of open chromatin regions four specific histone marks of CTCF binding sites of the bovine genome across the five bovine celllines T22

Final report on cluster cooperation activities

Final report on cluster cooperation activities (T9.1)

Communication Plan

Communication Plan (T9.3)

Agreed Statutes of the EEAB

Agreed Statutes of the EEAB (T11.3)

Article on the societal context and ethical dimension

Journal article on societal context and ethical dimensions T81

Training on methodology for biology-driven selection

Report on course on methodology for biology-driven selection (T9.2)

Audit on required and available pipelines

Audit on required and available pipelines across the consortium (T3.1)

Genomic prediction for mastitis in Nordic breeds

D7.5 Genomic prediction for mastitis in Nordic breeds

Demonstration of performance of the mastitis feature model in the Nordic cattle breeding programme

Demonstration of performance of the mastitis feature model in the Nordic cattle breeding program (T9.4)

Public report on ethical dimensions of innovations in livestock genomics

Public Report on the ethical dimensions (T8.1)

Public report: on societal context of innovations in livestock genomics

Public Report: Societal context of innovations in livestock genomics (T8.1)

Policy seminar for all relevant stakeholder

Policy seminar for all relevant stakeholders (T8.3)

BAM files for CAGE libraries

144 BAM files for CAGE libraries (T2.1)

Project sessions at international conferences and final conference

Reports on 3 project sessions at international conferences and final conference (T9.3)

Mid project report on BovReg data production

Mid project report on BovReg data production T34

First version of the cow evolutionary annotation

First version of the cow genome evolutionary annotation T35

Bayesian multi-feature genomic prediction model with overlapping features

Development and evaluation of Bayesian multi-feature genomic prediction model with overlapping features (T7.1)

Training course on new laboratory methods

Report on course on new laboratory methods at UNLIM premises (T9.2)

Single-cell analysis results of key tissues
Maps of chromatin architecture in bovine embryos

Maps of culture conditionspecific chromatin architecture in bovine embryos T52

lncRNA-DNA interaction map

A map of features in the bovine genome interacting with selected long lncRNAs (T2.3)

First prototype of a normalized ENCODE pipeline

First prototype of a normalized ENCODE pipeline (T3.2)

Map of open chromatin regions, 4 specific histone marks and CTCF binding sites for 24 tissues

A map of open chromatin regions four specific histone marks and CTCF binding sites of the bovine genome for 24 tissues across three breeds two sexes and two developmental stages T22

Communication tools, the website and communication package

Communication tools, including the project website (concept, screenshots) and the project communication package (logo, flyer, poster) (T9.3)

A comprehensive functional annotation map

A comprehensive map of functional annotation of the bovine genome (T2.5)

Establishment of novel bovine cell lines

Establishment of novel bovine cell lines T11

6-monthly reports on BovReg data releases

6-monthly reports on BovReg data releases (T10.2)

150 BAM files for ATAC-seq & ChIP-seq libraries

150 BAM files for each of the ATACseq and ChIPseq H3K4me3 H3K4me1 H3K27me3 H3K27ac and CTCF libraries T22

Ontology improvements

D3.11 Ontology improvements updating and extending D3.3, the report on ontologies used across BovReg, in collaboration with the EuroFAANG cluster partnes

Framework to enable professionals to address societal dimensions of livestock breeding

Framework to enable professionals to address societal dimensions of livestock breeding (T8.3)

Final report on normalized pipelines

Final report on normalized pipelines (T3.2)

Plan to achieve synergies with cluster projects

Collaboration plan (T9.1)

Bayesian Variable Selection models with SNP- specific a-priori inclusion probabilities

Development and evaluation of Bayesian Variable Selection models with SNPspecific a priori inclusion probabilities T71

Contribution of annotations to heritability

Contribution of different functional annotations to the heritability of BovRegs key traits T44

A panel of tests at selected MGE insertions

A panel of tests for presence of copies of selected MGE insertions in the available breeds (T2.4)

Mid-term report on cluster cooperation activities

Midterm report on cluster cooperation activities T91

Report of final GA meeting

Approved Minutes of final GA meeting, including EEAB meeting (T11.2 &3)

Genomic prediction using functional annotations and QTL features in small dairy breeds

D7.3 Genomic prediction using functional annotations and QTL features in small dairy breeds

Mid project report on normalized pipelines

Mid project report on normalized consortium pipelines T32

List of genotypes at each MGE insertion site

A list of genotypes of whole-genome sequenced animals at each MGE insertion site (T2.4)

Deployment procedure for optimized pipeline

Cloud deployment procedure for normalized pipeline T32

Report on results of playing Democs games

Report on results of playing Democs game in English and Finnish (T8.2)

Maps of tissue and cell line specific DNA methylation

Genome wide maps of tissue and cell line specific DNA methylation T51

BAM files for PolyA+,Total and small RNA

144 BAM files for RNA transcripts from PolyA Total and small RNA libraries T21

Genomic data of novel bovine cell lines

Genomic data of novel bovine cell lines T11

Map of fully annotated bovine transcriptomes

A map of fully annotated bovine transcriptome for 24 tissues across three breeds two sexes and two developmental stages T21

Catalogue of MGE insertion sites

A catalogue of MGE insertion sites across the cattle genome (T2.4)

Open Research Data Pilot (1)

Data management plan

Data management plan (T10.1)

Other (2)

A collection of registered pipelines

A collection of pipelines registered in the main repository (T10.3)

Democs game, boxed and downloadable forms

Democs game in boxed and downloadable forms (T8.2)

Websites, patent fillings, videos etc. (1)

Data Portal (website)

Dedicated portal website to access and publish the BovReg metadata T102

Pubblicazioni

Peer reviewed articles (30)

High-resolution structural variation catalogue in a large-scale whole genome sequenced bovine family cohort data

Autori: Young-Lim, Lee; Mirte, Bosse; Haruko, Takeda; Gabriel Costa Monteiro, Moreira; Latifa, Karim; Tom, Druet; Claire, Oget-Ebrad; Wouter, Coppieters; Roel F, Veerkamp; Martien A M, Groenen; Michel, Georges; Aniek C, Bouwman; Carole, Charlier
Pubblicato in: BMC Genomics, Numero 24, Article number: 225 (2023), 2023, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-023-09259-8

Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species.

Autori: Annie Robic; Chloé Cerutti; Christa Kühn; Christa Kühn; Thomas Faraut
Pubblicato in: Frontier Genetics, Numero 4, 2021, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2021.665153

The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

Autori: Audald Lloret-Villas, Hubert Pausch, Alexander S. Leonard
Pubblicato in: Genetics Selection Evolution, Numero 55, 2023, ISSN 1297-9686
Editore: Springer Nature
DOI: 10.1186/s12711-023-00809-y

Using Breeding Technologies to Improve Farm Animal Welfare: What is the Ethical Relevance of Telos?

Autori: Kramer, K.; Meijboom, F. L.B.; AISS Sustainable Animal Stewardship; dASS BW-2; LS Wijsgerige Ethiek; OFR - Ethics Institute
Pubblicato in: Journal of Agricultural and Environmental Ethics, Numero 34 (1), 2021, ISSN 1187-7863
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10806-021-09843-6

Molecular quantitative trait loci in reproductive tissues impact male fertility in cattle

Autori: Mapel, Kadri, et al.
Pubblicato in: Nature Communications, Numero 15, Article number: 674, 2024, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-024-44935-7

Sequence-based GWAS meta-analyses for beef production traits

Autori: Marie-Pierre Sanchez; Thierry Tribout; Naveen K. Kadri; Praveen K. Chitneedi; Steffen Maak; Chris Hozé; Mekki Boussaha; Pascal Croiseau; Romain Philippe; Mirjam Spengeler; Christa Kühn; Yining Wang; Changxi Li; Graham Plastow; Hubert Pausch; Didier Boichard
Pubblicato in: Genetics Selection Evolution, Numero 55, Article number: 70 (2023), 2023, Pagina/e Springer Nature, ISSN 1297-9686
Editore: Springer
DOI: 10.1186/s12711-023-00848-5

How Do Technologies Affect How We See and Treat Animals? Extending Technological Mediation Theory to Human-animal Relations

Autori: Koen Kramer; Franck L. B. Meijboom
Pubblicato in: Ethical Theory and Moral Practice, 2022, ISSN 1386-2820
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10677-022-10305-9

Establishment of a cloning-free CRISPR/Cas9 protocol to generate large deletions in the bovine MDBK cell line

Autori: Joanna Stojak; Dominique Rocha; Caroline Mörke; Christa Kühn; Veronique Blanquet; Hiroaki Taniguchi
Pubblicato in: Journal of Applied Genetics, Numero Volume 65, 2024, ISSN 1234-1983
Editore: Polska Akademia Nauk
DOI: 10.1007/s13353-024-00846-3

Ensembl 2021

Autori: Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Lea
Pubblicato in: Nucleic Acids Research, Numero 49/D1, 2020, Pagina/e D884-D891, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa942

Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle

Autori: Jiyuan Li, Robert Mukiibi, Yining Wang, Graham S. Plastow, Changxi Li
Pubblicato in: BMC Genomics, Numero 22, 2021, Pagina/e 823, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-021-08064-5#ack1

Ensembl 2024

Autori: Peter W Harrison; M Ridwan Amode; Olanrewaju Austine-Orimoloye; Andrey G Azov; Matthieu Barba; If Barnes; Arne Becker; Ruth Bennett; Andrew Berry; Jyothish Bhai; Simarpreet Kaur Bhurji; Sanjay Boddu; Paulo R Branco Lins; Lucy Brooks; Shashank Budhanuru Ramaraju; Lahcen I Campbell; Manuel Carbajo Martinez; Mehrnaz Charkhchi; Kapeel Chougule; Alexander Cockburn; Claire Davidson; Nishadi H De Silva;
Pubblicato in: Nucleic Acids Research, Numero Volume 52, Numero D1, 2024, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkad1049

Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

Autori: Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries and Hubert Pausch
Pubblicato in: BMC Genomics, Numero 22, 2021, Pagina/e 363, ISSN 1471-2164
Editore: BioMed Central
DOI: 10.1186/s12864-021-07554-w

Single-cell RNA sequencing of freshly isolated bovine milk cells and cultured primary mammary epithelial cells

Autori: Doreen Becker, Rosemarie Weikard, Frieder Hadlich, Christa Kühn
Pubblicato in: Scientific Data, Numero 8, 2022, ISSN 2052-4463
Editore: Springer Nature
DOI: 10.1038/s41597-021-00972-1

Accounting for overlapping annotations in genomic prediction models of complex traits

Autori: Mollandin, Fanny
Pubblicato in: BMC Bioinformatics, Numero 23, Article number: 365, 2022, ISSN 1471-2105
Editore: BioMed Central
DOI: 10.1186/s12859-022-04914-5

The European Nucleotide Archive in 2020

Autori: Peter W Harrison, Alisha Ahamed, Raheela Aslam, Blaise T F Alako, Josephine Burgin, Nicola Buso, Mélanie Courtot, Jun Fan, Dipayan Gupta, Muhammad Haseeb, Sam Holt, Talal Ibrahim, Eugene Ivanov, Suran Jayathilaka, Vishnukumar Balavenkataraman Kadhirvelu, Manish Kumar, Rodrigo Lopez, Simon Kay, Rasko Leinonen, Xin Liu, Colman O’Cathail, Amir Pakseresht, Youngmi Park, Stephane Pesant, Nadim Rahm
Pubblicato in: Nucleic Acids Research, Numero 49/D1, 2020, Pagina/e D82-D85, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkaa1028

Ensembl 2022

Autori: Fiona Cunningham, James E Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis, Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tama
Pubblicato in: Nucleic Acids Research, Numero Volume 50, Numero D1, 2022, ISSN 1362-4962
Editore: Oxford University Press
DOI: 10.1093/nar/gkab1049

Summer heat during spermatogenesis reduces in vitro blastocyst rates and affects sperm quality of next generation bulls

Autori: Jens Vanselow, Claudia Wesenauer, Anja Eggert, Arpna Sharma, Frank Becker.
Pubblicato in: Andrology, 2024, ISSN 2047-2927
Editore: Wiley
DOI: 10.1111/andr.13627

Metabogenomic analysis to functionally annotate the regulatory role of long non-coding RNAs in the liver of cows with different nutrient partitioning phenotype

Autori: Wietje Nolte, Rosemarie Weikard, Elke Albrecht, Harald M.Hammon, Christa Kühn
Pubblicato in: Genomics, Numero Volume 114 Numero 1, 2022, Pagina/e Pages 202-214, ISSN 0888-7543
Editore: Academic Press
DOI: 10.1016/j.ygeno.2021.12.004

From FAANG to fork: application of highly annotated genomes to improve farmed animal production

Autori: Emily L. Clark, Alan L. Archibald, Hans D. Daetwyler, Martien A. M. Groenen, Peter W. Harrison, Ross D. Houston, Christa Kühn, Sigbjørn Lien, Daniel J. Macqueen, James M. Reecy, Diego Robledo, Mick Watson, Christopher K. Tuggle, Elisabetta Giuffra
Pubblicato in: Genome Biology, Numero 21/1, 2020, ISSN 1474-760X
Editore: Springer nature
DOI: 10.1186/s13059-020-02197-8

MeSCoT: the tool for quantitative trait simulation through the mechanistic modeling of genes’ regulatory interactions

Autori: Viktor Milkevych, Emre Karaman, Goutam Sahana, Luc Janss, Zexi Cai, Mogens Sandø Lund
Pubblicato in: G3 Genes|Genomes|Genetics, Numero 21601836, 2021, ISSN 2160-1836
Editore: Genetics Society of America
DOI: 10.1093/g3journal/jkab133

The Ethics of Innovations in Genomic Selection: On How to Broaden the Scope of Discussion

Autori: Kramer, K.; Meijboom, F. L.B.; dASS BW-2; AISS Sustainable Animal Stewardship; LS Wijsgerige Ethiek; OFR - Ethics Institute
Pubblicato in: Journal of Agricultural and Environmental Ethics, Numero Volume 35, Numero 2, 2022, ISSN 1187-7863
Editore: Kluwer Academic Publishers
DOI: 10.1007/s10806-022-09883-6

Bull fertility and semen quality are not correlated with dairy and production traits in Brown Swiss cattle

Autori: Xena Marie Mapel; Maya Hiltpold; Naveen Kumar Kadri; Ulrich Witschi; Hubert Pausch
Pubblicato in: JDS Communications, Numero Vol 3, Iss 2, 2022, ISSN 2666-9102
Editore: Elsevier
DOI: 10.3168/jdsc.2021-0164

A 12 kb multi-allelic copy number variation encompassing a GC gene enhancer is associated with mastitis resistance in dairy cattle

Autori: Lee YL, Takeda H, Costa Monteiro Moreira G, et al.
Pubblicato in: Plos Genetics, 2021, ISSN 1553-7390
Editore: Public Library of Science
DOI: 10.1371/journal.pgen.1009331

Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle

Autori: Jiyuan Li; Yining Wang; Robert Mukiibi; Brian Karisa; Graham S. Plastow; Changxi Li
Pubblicato in: Scientific Reports, Numero vol. 12 , no. 1, 2022, ISSN 2045-2322
Editore: Nature Publishing Group
DOI: 10.1038/s41598-022-06567-z

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using CAGE sequencing

Autori: M. Salavati; R. Clark; D. Becker; C. Kühn; G. Plastow; S. Dupont; G.C.M. Moreira; C. Charlier; E.L. Clark
Pubblicato in: G3 Genes|Genomes|Genetics, Numero Volume 13, Numero 8, 2023, ISSN 2160-1836
Editore: Genetics Society of America
DOI: 10.1093/g3journal/jkad108

The intronic branch point sequence is under strong evolutionary constraint in the bovine and human genome.

Autori: Naveen Kumar Kadri; Xena M. Mapel; Hubert Pausch
Pubblicato in: Communications Biology, Numero Vol 4, Numero 1, 2021, Pagina/e Pp 1-13, ISSN 2399-3642
Editore: Springer Nature
DOI: 10.1038/s42003-021-02725-7

The FAANG Data Portal: Global, Open-Access, “FAIR”, and Richly Validated Genotype to Phenotype Data for High-Quality Functional Annotation of Animal Genomes

Autori: Peter W. Harrison; Alexey Sokolov; Akshatha Nayak; Jun Fan; Daniel R. Zerbino; Guy Cochrane; Paul Flicek
Pubblicato in: Frontiers in Genetics, Numero Vol 12, 2021, ISSN 1664-8021
Editore: Frontiers Media
DOI: 10.3389/fgene.2021.639238

Comparative cryopreservation of bovine and porcine primary hepatocytes

Autori: Andres S, Bartling B, Stiensmeier V, Starke A, Schmicke M.
Pubblicato in: Frontiers in Veterinary Science, Numero Volume 10 - 2023, 2023, ISSN 2297-1769
Editore: Frontiers Media
DOI: 10.3389/fvets.2023.1211135

An evaluation of the predictive performance and mapping power of the BayesR model for genomic prediction

Autori: Fanny Mollandin, Andrea Rau, Pascal Croiseau
Pubblicato in: G3 Genes|Genomes|Genetics, Numero Volume 11, Numero 11, 2021, ISSN 2160-1836
Editore: Genetics Society of America
DOI: 10.1093/g3journal/jkab225

Ensembl 2023

Autori: Fergal J Martin; M Ridwan Amode; Alisha Aneja; Olanrewaju Austine-Orimoloye; Andrey G Azov; If Barnes; Arne Becker; Ruth Bennett; Andrew Berry; Jyothish Bhai; Simarpreet Kaur Bhurji; Alexandra Bignell; Sanjay Boddu; Paulo R Branco Lins; Lucy Brooks; Shashank Budhanuru Ramaraju; Mehrnaz Charkhchi; Alexander Cockburn; Luca Da Rin Fiorretto; Claire Davidson; Kamalkumar Dodiya; Sarah Donaldson; Bilal
Pubblicato in: Nucleic Acids Research, Numero Volume 51, Numero D1, 2022, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gkac958