BovReg - Identification of functionally active genomic features relevant to phenotypic diversity and plasticity in cattle | BovReg | Project | Results | H2020 | CORDIS

Livrables

Training course/hackathon on bioinformatics methods

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

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)

Spatial DNA-DNA interaction map

A spatial DNADNA interaction map of the bovine genome T23

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

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

Audit on required and available pipelines

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

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)

BAM files for CAGE libraries

144 BAM files for CAGE libraries (T2.1)

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)

Maps of chromatin architecture in bovine embryos

Maps of culture conditionspecific chromatin architecture in bovine embryos T52

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)

Establishment of novel bovine cell lines

Establishment of novel bovine cell lines T11

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

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

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

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)

Data management plan

Data management plan (T10.1)

Data Portal (website)

Dedicated portal website to access and publish the BovReg metadata T102

Democs game, boxed and downloadable forms

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

Publications

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

Auteurs: 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
Publié dans: BMC Genomics, Numéro 24, Article number: 225 (2023), 2023, ISSN 1471-2164
Éditeur: BioMed Central
DOI: 10.1186/s12864-023-09259-8

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

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

Auteurs: Annie Robic; Chloé Cerutti; Christa Kühn; Christa Kühn; Thomas Faraut
Publié dans: Frontier Genetics, Numéro 4, 2021, ISSN 1664-8021
Éditeur: Frontiers Media
DOI: 10.3389/fgene.2021.665153

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

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

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

Auteurs: Mapel, Kadri, et al.
Publié dans: Nature Communications, Numéro 15, Article number: 674, 2024, ISSN 2041-1723
Éditeur: Nature Publishing Group
DOI: 10.1038/s41467-024-44935-7

Sequence-based GWAS meta-analyses for beef production traits

Auteurs: 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
Publié dans: Genetics Selection Evolution, Numéro 55, Article number: 70 (2023), 2023, Page(s) Springer Nature, ISSN 1297-9686
Éditeur: Springer
DOI: 10.1186/s12711-023-00848-5

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

Auteurs: Joanna Stojak; Dominique Rocha; Caroline Mörke; Christa Kühn; Veronique Blanquet; Hiroaki Taniguchi
Publié dans: Journal of Applied Genetics, Numéro Volume 65, 2024, ISSN 1234-1983
Éditeur: Polska Akademia Nauk
DOI: 10.1007/s13353-024-00846-3

Ensembl 2021

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 49/D1, 2020, Page(s) D884-D891, ISSN 0305-1048
Éditeur: 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

Auteurs: Jiyuan Li, Robert Mukiibi, Yining Wang, Graham S. Plastow, Changxi Li
Publié dans: BMC Genomics, Numéro 22, 2021, Page(s) 823, ISSN 1471-2164
Éditeur: BioMed Central
DOI: 10.1186/s12864-021-08064-5#ack1

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

Ensembl 2024

Auteurs: 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;
Publié dans: Nucleic Acids Research, Numéro Volume 52, Numéro D1, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad1049

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

Auteurs: Audald Lloret-Villas, Meenu Bhati, Naveen Kumar Kadri, Ruedi Fries and Hubert Pausch
Publié dans: BMC Genomics, Numéro 22, 2021, Page(s) 363, ISSN 1471-2164
Éditeur: BioMed Central
DOI: 10.1186/s12864-021-07554-w

Accounting for overlapping annotations in genomic prediction models of complex traits

Auteurs: Mollandin, Fanny
Publié dans: BMC Bioinformatics, Numéro 23, Article number: 365, 2022, ISSN 1471-2105
Éditeur: BioMed Central
DOI: 10.1186/s12859-022-04914-5

The European Nucleotide Archive in 2020

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro 49/D1, 2020, Page(s) D82-D85, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkaa1028

Ensembl 2022

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro Volume 50, Numéro D1, 2022, ISSN 1362-4962
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkab1049

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

Auteurs: Koen Kramer; Franck L. B. Meijboom
Publié dans: Ethical Theory and Moral Practice, 2022, ISSN 1386-2820
Éditeur: Kluwer Academic Publishers
DOI: 10.1007/s10677-022-10305-9

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

Auteurs: Doreen Becker; Rosemarie Weikard; Frieder Hadlich; Christa Kühn; Christa Kühn
Publié dans: Scientific Data, Numéro 7, 2021, ISSN 2052-4463
Éditeur: Springer Nature
DOI: 10.1038/s41597-021-00972-1

Sequence-based GWAS meta-analyses for beef production traits

Auteurs: 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
Publié dans: Genetics Selection Evolution, Numéro 55, Article number: 70 (2023), 2023, ISSN 1297-9686
Éditeur: Springer Nature
DOI: 10.1186/s12711-023-00848-5

Ensembl 2023

Auteurs: 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; B
Publié dans: Nucleic Acids Research, Numéro Volume 51, Numéro D1, 2022, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkac958

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

Auteurs: Wietje Nolte, Rosemarie Weikard, Elke Albrecht, Harald M.Hammon, Christa Kühn
Publié dans: Genomics, Numéro Volume 114 Numéro 1, 2022, Page(s) Pages 202-214, ISSN 0888-7543
Éditeur: Academic Press
DOI: 10.1016/j.ygeno.2021.12.004

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

Auteurs: A. Lloret-Villas; H. Pausch; A.S. Leonard
Publié dans: Genetics Selection Evolution, Numéro 55, Article number: 33 (2023), 2023, ISSN 1297-9686
Éditeur: Springer Nature
DOI: 10.1186/s12711-023-00809-y

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

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

Auteurs: 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
Publié dans: Genome Biology, Numéro 21/1, 2020, ISSN 1474-760X
Éditeur: Springer nature
DOI: 10.1186/s13059-020-02197-8

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

Auteurs: Viktor Milkevych, Emre Karaman, Goutam Sahana, Luc Janss, Zexi Cai, Mogens Sandø Lund
Publié dans: G3 Genes|Genomes|Genetics, Numéro 21601836, 2021, ISSN 2160-1836
Éditeur: Genetics Society of America
DOI: 10.1093/g3journal/jkab133

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

Auteurs: Kramer, K.; Meijboom, F. L.B.; dASS BW-2; AISS Sustainable Animal Stewardship; LS Wijsgerige Ethiek; OFR - Ethics Institute
Publié dans: Journal of Agricultural and Environmental Ethics, Numéro Volume 35, Numéro 2, 2022, ISSN 1187-7863
Éditeur: 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

Auteurs: Xena Marie Mapel; Maya Hiltpold; Naveen Kumar Kadri; Ulrich Witschi; Hubert Pausch
Publié dans: JDS Communications, Numéro Vol 3, Iss 2, 2022, ISSN 2666-9102
Éditeur: Elsevier
DOI: 10.3168/jdsc.2021-0164

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

Auteurs: Fanny Mollandin, Andrea Rau, Pascal Croiseau
Publié dans: G3 Genes|Genomes|Genetics, Numéro Volume 11, Numéro 11, 2021, ISSN 2160-1836
Éditeur: Genetics Society of America
DOI: 10.1093/g3journal/jkab225

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

Auteurs: Jiyuan Li; Yining Wang; Robert Mukiibi; Brian Karisa; Graham S. Plastow; Changxi Li
Publié dans: Scientific Reports, Numéro vol. 12 , no. 1, 2022, ISSN 2045-2322
Éditeur: 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

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

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

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

Auteurs: Naveen Kumar Kadri; Xena M. Mapel; Hubert Pausch
Publié dans: Communications Biology, Numéro Vol 4, Numéro 1, 2021, Page(s) Pp 1-13, ISSN 2399-3642
Éditeur: 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

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

Comparative cryopreservation of bovine and porcine primary hepatocytes

Auteurs: Andres S, Bartling B, Stiensmeier V, Starke A, Schmicke M.
Publié dans: Frontiers in Veterinary Science, Numéro Volume 10 - 2023, 2023, ISSN 2297-1769
Éditeur: Frontiers Media
DOI: 10.3389/fvets.2023.1211135

Ensembl 2024

Auteurs: 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 S
Publié dans: Nucleic Acids Research, Numéro Volume 52, Numéro D1, 2024, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkad1049

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

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

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

Ensembl 2023

Auteurs: 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
Publié dans: Nucleic Acids Research, Numéro Volume 51, Numéro D1, 2022, ISSN 0305-1048
Éditeur: Oxford University Press
DOI: 10.1093/nar/gkac958

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

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