Towards improvement of ruminant breeding through genomic and epigenomic approaches

Project Information

RUMIGEN

Grant agreement ID: 101000226

DOI

10.3030/101000226

Project closed

EC signature date 5 May 2021

Start date 1 June 2021

End date 31 May 2026

Funded under

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

Total cost

€ 7 474 892,75

EU contribution

€ 6 998 851,50

Coordinated by

INSTITUT NATIONAL DE RECHERCHE POUR L'AGRICULTURE, L'ALIMENTATION ET L'ENVIRONNEMENT
France

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Deliverables

Documents, reports (18)

Practice Abstracts - batch 1

This deliverable contains 3 practice abstracts. Leader: EFFAB / R / PU

Map of inbreeding depression, deleterious variants and genetic load.
Effects of GS on gain, diversity and drift.
Report on the effect of heat stress on production and fertility traits
Report on the impact of sperm epigenome on progeny phenotype
Outreach dissemination and training plan (ODPT) (updates at M13, M25; M37; M49; M60)
Report on novel statistical methods predicting future performance based on genomic, epigenomic and environmental data
Room of acceptance of future livestock breeding
Room of acceptance ex-ante.
Report on novel statistical tools and breeding strategies for mitigating trade-offs between production, efficiency and resilience
Position paper on GE.

Position paper on GE

Genomic selection method that manage genetic drift, inbreeding depression, rare alleles, and genetic load.
Communication package
Report on the effect of heat stress of the pregnant dam on the performances of her progeny.
Scenarios for acceptable future livestock breeding.
Report on the genetic control of DNA methylation
Report on novel statistical tools and breeding strategies for balancing short/long-term response and maintaining genetic diversity
Report on the trajectory of genetic and genomic correlations between production and fertility across heat conditions.

Other (1)

Anonymised raw data from citizen consultations.

Publications

Peer reviewed articles (18)

Assembly of a pangenome uncovers novel non-reference unique insertion sequences in cattle highlighting their genetic diversity

Author(s): Valentin Sorin, Florian Besnard, Aurélien Capitan, Cécile Grohs, Maulana Mughitz Naji, Clémentine Escouflaire, Sébastien Fritz, Joanna Lledo, Camille Eché, Carole Iampietro, Cécile Donnadieu, Denis Milan, Laurence Drouilhet, Gwenola Tosser-Klopp, Didier Boichard, Christophe Klopp, Marie-Pierre Sanchez, Mekki Boussaha
Published in: Journal of Animal Science and Biotechnology, 2026, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.64898/2025.12.02.691810

A Recursive Model Approach to Include Epigenetic Effects in Genetic Evaluations Using Simulated <scp>DNA</scp> Methylation Effects

Author(s): Adrián López‐Catalina, Mohamed Ragab, Antonio Reverter, Oscar González‐Recio
Published in: Journal of Animal Breeding and Genetics, Issue 142, 2025, Page(s) 550-559, ISSN 0931-2668
Publisher: Blackwell Publishing Inc.
DOI: 10.1111/jbg.12925

Stress-induced epigenetic effects driven by maternal lactation in dairy cattle: a comethylation network approach

Author(s): Adrián López-Catalina, Antonio Reverter, Pamela A. Alexandre, Loan T. Nguyen, Oscar González-Recio
Published in: Epigenetics, Issue 19, 2024, ISSN 1559-2294
Publisher: Landes Bioscience
DOI: 10.1080/15592294.2024.2381856

Genetic regulation of sperm DNA methylation in cattle through meQTL mapping

Author(s): Corentin Fouéré, Valentin Costes, Chris Hozé, Amrita Raja Ravi Shankar, Florian Besnard, Gabriel Costa Monteiro Moreira, Valentin Sorin, Chrystelle Le Danvic, Aurélie Chaulot-Talmon, Francesca Ali, Marie Christine Deloche, Aurélie Bonnet, Eliaou Sellem, Hélène Jammes, Sébastien Fritz, Mekki Boussaha, Didier Boichard, Hélène Kiefer, Marie-Pierre Sanchez
Published in: BMC Genomics, Issue 26, 2025, ISSN 1471-2164
Publisher: BioMed Central
DOI: 10.1186/s12864-025-11934-x

Effect of temperature-humidity index on the evolution of trade-offs between fertility and production in dairy cattle

Author(s): Aurélie Vinet, Sophie Mattalia, Roxane Vallée, Christine Bertrand, Anne Barbat, Julie Promp, Beatriz C. D. Cuyabano, Didier Boichard
Published in: Genetics Selection Evolution, Issue 56, Article number: 23 (2024), 2024, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-024-00889-4

Long-lasting effects of in utero heat stress on subsequent performances of heifers and primiparous cows

Author(s): A. Vinet, C. Fouéré, B.C.D. Cuyabano, S. Mattalia, R. Vallée, A. Barbat, C. Bertrand, C. Hoze, D. Boichard
Published in: Journal of Dairy Science, Issue 107, 2025, Page(s) 11065-11077, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2024-25168

Breeding for thermotolerance in dairy cattle: Production versus fertility traits

Author(s): M.J. Carabaño, C. Díaz, M. Ramón
Published in: Journal of Dairy Science, Issue 108, 2026, Page(s) 9915-9929, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2025-26258

Linkage- and ROH-based genomic relationship matrices for IBD based management of genetic diversity

Author(s): Oda B. Wæge, Xijiang Yu, Peer Berg, Theo Meuwissen
Published in: Genetics Selection Evolution, Issue 58, 2026, ISSN 1297-9686
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s12711-026-01044-x

Comprehensive detection of structural variations in long and short reads dataset of French cattle

Author(s): Maulana Mughitz Naji, Christophe Klopp, Thomas Faraut, Camille Eché, Arnaud Di Franco, Clément Birbes, Camille Marcuzzo, Amandine Suin, Carole Iampietro, Claire Kuchly, Caroline Vernette, Sébastien Fritz, Cécile Grohs, Christine Gaspin, Denis Milan, Cécile Donnadieu, Didier Boichard, Marie-Pierre Sanchez, Mekki Boussaha
Published in: Scientific Reports, 2026, ISSN 2692-8205
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2025.05.22.654398

CRISPR/Cas9-editing of PRNP in Alpine goats.

Author(s): Aurélie Allais-Bonnet, Christophe Richard, Marjolaine André, Valérie Gelin, Marie-Christine Deloche, Aurore Lamadon, Gwendoline Morin, Béatrice Mandon-Pépin, Eugénie Canon, Dominique Thépot, Johann Laubier, Katayoun Moazami-Goudarzi, Ludivine Laffont, Olivier Dubois, Thierry Fassier, Patrice Congar, Olivier Lasserre, Tiphaine Aguirre-Lavin, Jean-Luc Vilotte, Eric Pailhoux
Published in: Veterinary Research, 2025, ISSN 1297-9716
Publisher: BioMed Central
DOI: 10.21203/rs.3.rs-5173836/v1

Oxford nanopore sequencing as an alternative to reduced representation bisulphite sequencing for the identification of CpGs of interest in livestock populations

Author(s): Adrián López-Catalina, Valentin Costes, Ramón Peiró-Pastor, Hélène Kiefer, Oscar González-Recio
Published in: Livestock Science, Issue 279, 2025, Page(s) 105377, ISSN 1871-1413
Publisher: Elsevier BV
DOI: 10.1016/j.livsci.2023.105377

Impact of genomic selection on genetic diversity in 5 local European cattle breeds

Author(s): R. Bonifazi, T.H.E. Meuwissen, P. Croiseau, G. Restoux, S. Minéry, J. Vandenplas, J.J. Windig
Published in: Journal of Dairy Science, Issue 109, 2026, Page(s) 5475-5498, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2025-27562

Genetic analysis of the impact of heat stress on fertility traits in dairy cows in the Netherlands

Author(s): Tijesunimi O. Ojo, Jeremie Vandenplas, Han A. Mulder, Mathijs L. van Pelt, Mario P.L. Calus
Published in: Journal of Dairy Science, Issue 108, 2025, Page(s) 1699-1713, ISSN 0022-0302
Publisher: American Dairy Science Association
DOI: 10.3168/jds.2024-25316

Pangenome-based association testing between a structural variant located upstream of the KIT gene and head depigmentation across a diverse panel of cattle breeds

Author(s): V. Sorin, M. P. Sanchez, L. Drouilhet, G. Tosser-Klopp, M. M. Naji, D. Boichard, H. Pausch, M. Boussaha, A. S. Leonard
Published in: Genetics Selection Evolution, Issue 58, 2026, ISSN 1297-9686
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s12711-026-01037-w

Estimation of genotype by temperature-humidity index interactions on milk production and udder health traits in Montbeliarde cows

Author(s): Aurélie Vinet, Sophie Mattalia, Roxane Vallée, Christine Bertrand, Beatriz C. D. Cuyabano, Didier Boichard
Published in: Genetics Selection Evolution, Issue 55, 4 (2023), 2023, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-023-00779-1

"Modifications ciblées du génome (""genome editing"") chez les animaux d’élevage : ou en est-on en France et en Europe ?"

Author(s): Eric Pailhoux, Jean-Luc Vilotte
Published in: Bulletin de l'Académie Vétérinaire de France, Issue 176, 2023, ISSN 0001-4192
Publisher: PERSEE Program
DOI: 10.3406/bavf.2023.71031

Empowering bioinformatics communities with Nextflow and nf-core

Author(s): Björn E. Langer, Andreia Amaral, Marie-Odile Baudement, Franziska Bonath, Mathieu Charles, Praveen Krishna Chitneedi, Emily L. Clark, Paolo Di Tommaso, Sarah Djebali, Philip A. Ewels, Sonia Eynard, James A. Fellows Yates, Daniel Fischer, Evan W. Floden, Sylvain Foissac, Gisela Gabernet, Maxime U. Garcia, Gareth Gillard, Manu Kumar Gundappa, Cervin Guyomar, Christopher Hakkaart, Friederike Hanssen
Published in: Genome Biology, Issue 26, 2025, ISSN 1474-760X
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s13059-025-03673-9

Haplotype‐Resolved Genome Assemblies for Norwegian Red Cattle

Author(s): Thea Johanna Hettasch, Matthew Peter Kent, Arne Bjørke Gjuvsland, Mariann Árnyasi, Dag Inge Våge
Published in: Animal Genetics, Issue 57, 2026, ISSN 0268-9146
Publisher: Blackwell Publishing Inc.
DOI: 10.1002/age.70087