GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics

Informations projet

GEroNIMO

N° de convention de subvention: 101000236

DOI

10.3030/101000236

Projet clôturé

Date de signature de la CE 6 Mai 2021

Date de début 1 Juin 2021

Date de fin 31 Mai 2026

Financé au titre de

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

Coût total

€ 7 065 713,25

Contribution de l’UE

€ 6 999 962,25

Coordonné par

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

CORDIS fournit des liens vers les livrables publics et les publications des projets HORIZON.

Les liens vers les livrables et les publications des projets du 7e PC, ainsi que les liens vers certains types de résultats spécifiques tels que les jeux de données et les logiciels, sont récupérés dynamiquement sur OpenAIRE .

Livrables

Other (2)

Practice Abstracts - batch 1

This deliverable contains at least 2 practice abstracts.

Adaptation of the optiSel R Package

Adaptation of the optiSel R Package to account for major genes.

Documents, reports (9)

Report on the surveys assessing management schemes of local breeds over Europe in monogastrics

A compilation of the answers of different breeds and species will be performed.

Characterization of DNA methylation in pig and chicken

Analysis of DNA methylation data and estimation of DNA methylation heritability to be used in WP4.

Comprehensive phenotype recording for ELP traits in pig and chicken

Large-scale phenotype recording will be made available for traits related to quality (egg, sperm and meat), egg production, feed efficiency, health and growth.

Simulation study of breeding strategies for a dual-purpose breed

A simulation study of different breeding strategies for establishing a dual-purpose breed from two divergently selected chicken breeds, incorporating optimum contributions selection to control for genetic diversity, will be reported.

Characterization of feed and heat stress on epigenetic variation in chicken and pig

Differential methylated regions between control and stressed individuals will be detected in different breeds of pigs and chickens and integrated with transcriptomes and phenotypes for better understanding epi/genetic adaptation to feed and heat stresses.

Identification of methylation lifetime changes in relation to welfare in chicken

Epigenetic variation throughout chicken lifetime will be estimated and will be correlated with behavioural and welfare traits phenotypic variation.

The importance of national and regional dimensions on the societal and ethical concerns of genomics innovations

An analysis of national and regional dimensions for the societal and ethical concerns will be delivered, tailored to the context of genomics innovation and animal breeding.

Interviews and focus groups feedbacks about the evaluation of genomics innovations

A report on the results of the interviews and focus groups in four countries will be made available.

Characterization of the seasonality impact on epigenetic variation in pig

Data integration of methylation patterns with other data (RNA-seq, phenotypes and climate indices) will be performed to identify significant correlations between epigenetic variation, seasonality in relation to female prolificacy and male sperm quality.

Publications

Conference proceedings (63)

Influence of early rearing system on later performance of commercial laying hens

Auteurs: Q. Berger, N. Bedere, P. Le-Roy, S. Lagarrigue, T. Burlot, T. Zerjal
Publié dans: Book of abstracts of 74th European Federation of Animal Science Annual Meeting, Numéro August 2023, 2023
Éditeur: Proceedings EAAP https://doi.org/10.3920/978-90-8686-936-7

Body weight variation is a good proxy of abdominal fat weight in laying hens at 90 weeks of age

Auteurs: Hubert A., Bedere N., Degalez F., Allain C., Becot L., Berger Q., Burlot T., Emily M., Ferry A., Lagoutte L., Lebez B., Sanchez M.-P., Tribout T., Pitel F., Zerjal T., Allais S., Lagarrigue S.
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

Studying husbandry and nutrition in Krškopolje pig: Implications for fat deposition and meat quality with insights into metabolism and gene expression

Auteurs: Martin Škrlep, Klavdija Poklukar, Bojana Savić, Marjeta Čandek-Potokar
Publié dans: "Proceedings of the 15th International Symposium ""Modern Trends in Livestock Production"" - zbornik radova", 2025, Page(s) 174-186
Éditeur: Institute of Animal Husbandry, Belgrade-Zemun
DOI: 10.5937/animtrend25174s

Transgenerational response to the ingestion of an endocrine disruptor: phenotypic, genetic, and epigenetic analyses in quail

Auteurs: Stacy Rousse, Sophie Leroux, David Gourichon, Ludovic Calandreau, Remi Seraphin, Ingrid David, Alexandre Hubert, Guillaume Cossard, Ole Madsen, Marta Godia Perello, Tatiana Zerjal, Sandrine Lagarrigue, Frédérique Pitel, Sonia E Eynard
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

Unravelling gene switches for the regulation of litter size through the study of swine with high and low prolificacy

Auteurs: Endika Varela-Martínez, Beatrice Tadeu-Querido, Fábio Teixeira, Graça Ferreira-Dias, Jordana lopes, Elisa Bettencourt, Pamela Valente, Maria Salomé Gonçalves, Luís Telo da Gama, Carlos Bettencourt, Branco, Sofia VanHarten, Kiala Sebastino, Hermenegildo Chiaia, Maria Cristina Bressan, Luísa Mateus, Andreia J. Amaral
Publié dans: Book of Abstracts of the 76th Annual Meeting of the European Federation of Animal Science, 2025, Page(s) 625
Éditeur: EAAP

Genetic architecture of the persistency of production, quality, and efficiency traits in laying hens

Auteurs: Q. Berger, N. Bedere, P. Le-Roy, S. Lagarrigue, T. Burlot, T. Zerjal
Publié dans: Book of abstracts of 74th European Federation of Animal Science Annual Meeting, Numéro August 2023, 2023
Éditeur: Proceedings EAAP https://doi.org/10.3920/978-90-8686-936-7

811. Estimating vertical path coefficients of transmission of non-genetic inherited effects from a similarity matrix

Auteurs: I. David, C. Larzul, A. Ricard
Publié dans: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2023
Éditeur: Wageningen Academic Publishers
DOI: 10.3920/978-90-8686-940-4_811

The effect of on-farm hatching on spatial traits in a quasi-commercial barn

Auteurs: M. B. Petelle, C. M. Montalcini, M. J. Toscano
Publié dans: European's Poultry Conference Journal - The Book of Abstracts, Numéro 24th-28th June 2024, 2024
Éditeur: meap

Gene Polymorphism Frequencies in Krskopolje Pig Breed

Auteurs: K. Poklukar, M. Čandek-Potokar, N. Batorek Lukač, MJ. Mercat, D. Picard Druet, M. Škrlep
Publié dans: Book of abstracts of the 14th International Symposium Modern Trends in Livestock Production, Numéro October 2023, 2023, ISBN 978-86-82431-80-0
Éditeur: Proceedings of the 14th International Symposium Modern Trends in Livestock Production

Growth potential of Krškopolje pigs in different production systems.

Auteurs: BATOREK LUKAČ, Nina, ČANDEK-POTOKAR, Marjeta
Publié dans: Book of abstracts of the XIth International Symposium on Mediterranean Pig, Numéro October 11-13, 2022, 2022, Page(s) 43-44, ISBN 978-953-8276-35-4
Éditeur: University of Zagreb

Leveraging local breeds and landscape genomics to detect adaptive genes

Auteurs: Carl Kroger, Romuald Rouger, Michel Sourdioux, Michèle Tixier-Boichard, Tatiana Zerjal, Gwendal Restoux
Publié dans: Abstract book of the 13th ESPG, 2025, Page(s) 40
Éditeur: WPSA

The effect of PRKAG3 and RYR1 genes on meat quality traits in the local Krskopolje pig breed

Auteurs: K. Poklukar, M. Čandek-Potokar, N. Batorek Lukač, MJ. Mercat, D. Picard Druet, M. Škrlep
Publié dans: Book of abstracts of the 14th International Symposium Modern Trends in Livestock Production, Numéro October 2023, 2023, ISBN 978-86-82431-80-0
Éditeur: Proceedings of the 14th International Symposium Modern Trends in Livestock Production

Modelling genetic and epigenetic selection signatures from pool sequencing.

Auteurs: Sonia E Eynard, Kossi-Julien Kowou, Cécile Donnadieu, Loïc Flatres-Grall, Carole Iampietro, Sandrine Lagarrigue, Sophie Leroux, Joanna Lledo, Marie-José Mercat, Juliette Riquet, Céline Vandecasteele, Frédérique Pitel, Bertrand Servin
Publié dans: Book of Abstracts EAGS 2026, 2026, Page(s) 21
Éditeur: France Génomique

Modelling genetic and epigenetic selection signatures from pool sequencing

Auteurs: Sonia E Eynard, Kossi-Julien Kowou, Cécile Donnadieu, Loïc Flatres-Grall, Carole Iampietro, Sandrine Lagarrigue, Sophie Leroux, Joanna Lledo, Marie-José Mercat, Juliette Riquet, Céline Vandecasteele, Frédérique Pitel, Bertrand Servin
Publié dans: Booklet of abstracts of the Zurich EPIGENETIC INHERITANCE SYMPOSIUM 2025, 2025, Page(s) 19
Éditeur: ETH Zurich

Using functional annotation and individual omics in genomic prediction

Auteurs: M. P. L. Calus, B. C. Perez, J. de Vos, O. Madsen, L. Ayres, H. Bovenhuis, M. Ballester, MJ. Mercat, M. C. A. M. Bink
Publié dans: Book of abstracts of 39th International Society for Animal Genetics Conference, Numéro July 2023, 2023, Page(s) 45
Éditeur: ISAG

Taming the Genome: Epigenetic Contributions to Domestication and Sex-Specific Regulation in Chickens

Auteurs: C. Guerrero-Bosagna
Publié dans: Book of Abstracts of the Congress of the European Society for Evolucionary Biology 2025 (ESEB2025), Numéro 17th-22th August 2025, 2025, Page(s) p30
Éditeur: Sociedad Española de Biologia Evolutiva (Sesbe)

The effect of low protein diet on adipose tissue transcriptome in Krškopolje pig breed

Auteurs: K. Poklukar, M. Čandek-Potokar, N. Batorek Lukač, M. Vrecl, G. Fazarinc, M. Škrlep
Publié dans: Book of abstracts of the 1st Regional Meeting of The European Federation of Animal Science, Numéro April 2024, 2024
Éditeur: 1st Regional Meeting of The European Federation of Animal Science

Transgenerational response to endocrine disruptor: phenotypic, genotypic and epigenotypic analyses in quail

Auteurs: S. Rousse, S. Leroux, D. Gourichon, L. Calandreau, C. Cerutti, G. Devailly, T. Zerjal, S. Lagarrigue, F. Pitel, S. E. Eynard
Publié dans: Book of abstracts of the Environmental and Agronomical Genomics Symposium, Numéro February 2024, 2024
Éditeur: France Genomic

The impact of chronic heat stress on DNA methylation and gene expression in laying hens

Auteurs: Marie Courbariaux, Odile Rogier, Remi Seraphin, Sonia E Eynard, Sophie Leroux, Laetitia Lagoutte, Florence Jaffrezic, Andrea Rau, Thierry Burlot, Frédérique Pitel, Sandrine lagarrigue, Tatiana Zerjal 
Publié dans: 2025
Éditeur: EAAP- 76th Annual meeting

Using henomic and transcriptomic information for complex trait prediction

Auteurs: V. Haas, R. Wellmann, M. P. L. Calus, J. Bennewitz
Publié dans: Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (EAAP), Numéro 1st-5th September 2024, 2024
Éditeur: EAAP

HenTrack: Improving breeding programs with superior behavior and welfare phenotypes

Auteurs: M. Toscano
Publié dans: Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (EAAP), Numéro 1st-5th September 2024, 2024
Éditeur: EAAP

The Banija Spotted Pig: Current Population Status, Genetic Diversity and Prospects for Sustainable Conservation

Auteurs: Dubravko Škorput, Ana Kaić, Danijel Karolyi, Krešimir Salajpal, Zoran Luković, Ivona Djurkin Kušec, Marie-Jose Mercat, Klavdija Poklukar, Marjeta Čandek-Potokar, Martin Škrlep
Publié dans: Abstracts of the 35th Annual Meeting and International Conference of the International Association for the Conservation of Animal Breeds in the Danube Region, 2026
Éditeur: International Association for the Conservation of Animal Breeds in the Danubian Region

Transcriptomic profiling of laying hen livers in relation to age and interaction with early liferearing conditions

Auteurs: Guillaume Cossard, Alexandre Hubert, Laetitia Lagoutte, Bénédicte Lebez, Coralie Allain, Fabien Degalez, Alexandre Ferry, Lorry Becot, Thierry Burlot, Frédérique Pitel, Tatiana Zerjal, Sandrine Lagarrigue
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

Assessing multiphase feeding sequencing plan designed for fatty type pigs in indoor and outdoor heavy pig production systems by modeling: an example of Krškopolje pig.

Auteurs: BATOREK LUKAČ, Nina, ŠKRLEP, Martin, POKLUKAR ŽNIDARŠIČ, Klavdija, MILLET, Sam, ČANDEK-POTOKAR, Marjeta.
Publié dans: Book of abstracts of the 7th EAAP International Symposium on Energy and Protein Metobolism and Nutrition (ISEP), Numéro September 12-15, 2022, 2022
Éditeur: EAAP

Characterization of DNA methylation patterns and genomic regulation of DNA methylation of skeletal muscle in three commercial pig breeds.

Auteurs: Maria Luigi-Sierra, Marta Gòdia, Ole Madsen, Peter Karlskov-Mortensen
Publié dans: Book of Abstracts of the 76th annual meeting of the European Federation of Animal Science, 2025, Page(s) 624
Éditeur: EAAP

Integrating Multi-Omics Data in Deep Learning Prediction of Pig Production Traits

Auteurs: Ioanna-Theoni Vourlaki, Maria Gracia Luigi-Sierra, Levi Ayres, Yuliaxis Ramayo-Caldas, Mario P.L. Calus, Peter Karlskov-Mortensen, Miriam Piles
Publié dans: 2026
Éditeur: WCGALP
DOI: 10.31274/wcgalp.23672

Stakeholders’ perception of the local breeds’ sector in six European countries - a survey by the GEroNIMO project

Auteurs: Marie-José MERCAT, Andreia AMARAL, Riccardo BOZZI, Marjeta ČANDEK-POTOKAR, Pedro FERNANDES, Jetsabell GUTIERREZ VALLEJOS, Danijel KAROLYI, Denis LALOë, Zoran LUKOVIć, Gwendal RESTOUX, António VICENTE, Virginia RIBEIRO, Tamara RODRIGUEZ SILVA, Romuald ROUGER, Dubravko ŠKORPUT, Martin ŠKRLEP
Publié dans: Book of abstracts of the XIth International Symposium on the Mediterranean pig, Numéro October 11-13, 2022, 2022, Page(s) 87-88, ISBN 978-953-8276-35-4
Éditeur: UNIZG

GEroNIMO (Genome and Epigenome eNabled breedIng in MOnogastrics)

Auteurs: S. Lagarrigue, F. Pitel, T. Zerjal for the GEroNIMO consortium
Publié dans: Book of abstracts of 74th European Federation of Animal Science Annual Meeting, Numéro August 2023, 2023
Éditeur: Proceedings EAAP https://doi.org/10.3920/978-90-8686-936-7

Perceptions of stakeholders involved in preserving local breeds - a survey by the GEroNIMO project

Auteurs: MJ. Mercat, A. Amaral, R. Bozzi, M. Candek-Potokar, P. Fernandes, J. Gutierrez Vallejos, D. Karolyi, D. Laloë, Z. Lukovic, H. Lenoir, G. Restoux, A. Vicente, V. Ribeiro, T. Rodriguez Silva, R. Rouger, D. Skroput, M. Skrlep
Publié dans: Journées de la Recherche Porcine, Numéro 9, 2023
Éditeur: Ifip; Inrae,

NIRS Prediction of Pork Intramuscular Fat for Future Use in Genetic Evaluation of Local Breeds

Auteurs: M.J Mercat, A. Vautier, P. Ganier, S. Dare, G. Flého, K. Poklukar, M. Škrlep, H. Lenoir, J. Magadray, G. Lenoir, B. Ligonesche, D. Karolyi, D. Škorput, A. Amaral, M. Čandek-Potokar and B. Lebret
Publié dans: 2026
Éditeur: 2026 World Congress on Genetics Applied to Livestock Production
DOI: 10.31274/wcgalp.23839

Unravelling the genetic architecture of persistence in production, quality, and efficiency traits in laying hens at late production stages

Auteurs: Quentin Berger, Nicolas Bedere, Sandrine Lagarrigue, Thierry Burlot, Pascale Le-Roy, Thierry Tribout, Tatiana Zerjal
Publié dans: British Poultry Science, 2026
Éditeur: openRxiv
DOI: 10.1101/2025.02.26.640268

A IncRNA gene-enriched atlas for GRCg7b chicken genome gathering EMBL-EBI EnsembI, NCBI-RefSeq and two FAANG databases

Auteurs: F. Degalez, M. Charles, S. Foissac, H. Zhou, D. Guan, L. Fang, C. Klopp, C. Alain, L. Lagoutte, B. Lebez, F. Lecerf, B. Vourch, T. Zerjal, F. Pitel, S. Lagarrigue
Publié dans: Book of abstracts of 74th European Federation of Animal Sciences Annual Meeting, Numéro August 2023, 2023
Éditeur: Proceedings EAAP https://doi.org/10.3920/978-90-8686-936-7

Whole genome sequencing and epigenotyping for multiple generations of selection using Oxford Nanopore Technology

Auteurs: S. E. Eynard, C. Donnadieu, L. Flatres-Grall, C. Iampietro, S. Lagarrigue, S. Leroux, J. Lledo, J. Riquet, B. Servin, C. Vandecasteele, T. Zerjal, F. Pitel
Publié dans: Book of abstracts of Environmental and Agronomical Genomics Symposium, Numéro February 2024, 2024
Éditeur: EAGS

Multi-omics approaches for understanding efficient pig production traits

Auteurs: Maria Luigi-Sierra, Marta Gòdia, Ole Madsen, Peter Karlskov-Mortensen
Publié dans: Proceedings of the 40th International Conference on Animal Genetics, 2025, Page(s) 139
Éditeur: ISAG

Association between melanocortin 4-receptor (MC4R) polymorphism with carcass and meat quality traits in local Krškopolje pig breed

Auteurs: K. Poklukar, M. Čandek-Potokar, MJ. Mercat, M. Škrlep
Publié dans: 32nd Internaltional Sysposium Animal Science Days 2024 Book of Abstracts, Numéro 2nd-4th October 2024, 2024
Éditeur: Universitat fur Bodenkultur

Unraveling gene switches for the regulation of litter size through the study of swine with high and low prolificacy

Auteurs: E. Varela-Martínez, B. Tadeu-Querido, F. Teixeira, G. Ferreira-Dias, J. Lopes , E. Bettencourt, P. Valente, M.S. Gonçalves, L.T. Gama, C. Bettencourt, S. Branco, S.
Publié dans: 40th International Society for Animal Genetics Conference, ISAG.  , 2025
Éditeur: 40th International Society for Animal Genetics Conference, ISAG.  

Assessing the genetic contribution to intramuscular fat content in local Krškopolje pig

Auteurs: Poklukar K., Čandek-Potokar M., Mercat M.-J., Banville M., Taussat S.,  Škrlep M.
Publié dans: Book of Abstracts of the 76th annual meeting of the European Federation of Animal Science, 2025, Page(s) 629
Éditeur: EAAP

Using the transmissibility model to demonstrate transgenerational transmission of environmental effects in quails

Auteurs: Keyvan Karami, Stacy Rousse, Frederique Pitel, Sonia Eynard, David Gourichon, Sophie Leroux, Anne Ricard, Ingrid David
Publié dans: Book of abstracts of the Zurich Epigenetic Inheritance Symposium 2025, 2025, Page(s) 25
Éditeur: ETH Zurich

Exploring the Landscape of Local and Distant Intra-vs. Inter-Chromosomal eQTLs Using TensorQTL and GCTA: A case study from 459 Liver Transcriptomes of Aged Laying Hens

Auteurs: Alexandre Hubert, Fabien Degalez, Coralie Allain, Thierry Burlot, Louis Calvez, Marta Gòdia, Laetitia Lagoutte, Bénédicte Lebez, Frédéric Lecerf, Ole Madsen, Tatiana Zerjal, Frédérique Pitel, Mathieu Emily, Sophie Allais, Sandrine Lagarrigue
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

From womb to bloom: conception, early life and maternal effects on boar semen production

Auteurs: P. Sá, R. M. Godinho, M. Gòdia, C. A. Sevillano, B. Harlizius, O. Madsen, H. Bovenhuis
Publié dans: Bookf of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (EAAP), Numéro 1st-5th September 2024, 2024
Éditeur: EAAP

Integrating Transcriptomics and Epigenomics for Enhanced Breeding Programs in Pigs

Auteurs: M. Luigi, P. Karlskov-Mortensen
Publié dans: 5th Annual congress of Young Researchers (ACYR), Numéro 10th-11th March 2025, 2025
Éditeur: ACYR

Influence of rearing systems on the liver transcriptome profile of krškopolje pigs: indoor vs. outdoor conditions

Auteurs: Poklukar K., Čandek-Potokar M., Savić B., Škrlep M.
Publié dans: Book of Abstracts of the 76th annual meeting of the European Federation of Animal Science, 2025, Page(s) 649
Éditeur: EAAP

Polymorphisms of selected genes in Banija spotted and Turopolje pig

Auteurs: D. Karolyi, K. Poklukar, K. Salajpal, D. Skorput, Z. Lukovic, MJ. Mercat, M. Candek-Potokar, M. Skrlep
Publié dans: 32nd International Symposium Animal Science Days 2024, Book of Abstracts, Numéro 2nd-4th October 2024, 2024
Éditeur: Universitat fur Bodenkultur

Banija spotted pig – from science to practise

Auteurs: Zoran Luković, Dubravko Škorput, Krešimir Salajpal, Sven Menčik, Danijel Karolyi
Publié dans: Book of abstracts of the XIth International Symposium on the Mediterranean pig, Numéro October 11-13, 2022, 2022, Page(s) 51-52, ISBN 978-953-8276-35-4
Éditeur: UNIZG

On the genetic basis of porcine semen traits: a large-scale genome-wide study on a synthetic line

Auteurs: P. Sá, R. M. Godinho, M. Gòdia, C. A. Sevillano, B. Harlizius, O. Madsen, H. Bovenhuis
Publié dans: Book of abstracts of 39th International Society for Animal Genetics Conference, Numéro July 2023, 2023, Page(s) 18
Éditeur: ISAG

Comparison of haematological profiles between Alentejano and commercial (LWxLR) pigs

Auteurs: Luísa Mateus, Graça Ferreira Dias, Maria Salomé, Gonçalves, Pamela Valente, Elisa Bettencourt, Luís Telo da Gama, Carlos Bettencourt, Andreia J. Amaral
Publié dans: Book of abstracts of the CIISA Congress 2022 Lisbon, Portugal)., Numéro November 2022, 2022, Page(s) 150
Éditeur: CIISA

Integrated analysis of methylome and transcriptome highlights limited impact of DNA methylation on age-related gene regulation in laying hens

Auteurs: Guillaume Cossard, Alexandre Hubert, Fabien Degalez, Coralie Allain, Thierry Burlot, Sonia Eynard, Marta Gòdia, Mathieu Emily, Laetitia Lagoutte, Bénédicte Lebez, Ole Madsen, Andrea Rau, Stacy Rousse, Remi Seraphin, Tatiana Zerjal, Frederique Pitel, Sandrine Lagarrigue
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

Transgenerational response to an endocrine disruptor ingestion: phenotypic, genetic and epigenetic analyses in quail

Auteurs: Rousse S., Leroux S., Gourichon D., Calandreau L., Zerjal T., Lagarrigue S., Pitel F., Eynard S.
Publié dans: Book of Abstracts of the 76th annual meeting of the European Federation of Animal Science, 2025, Page(s) 624
Éditeur: EAAP

Combining LD-Guided QTL Refinement, GEGA Annotation, and Tissue-Specific eQTL for Candidate Gene Prioritization

Auteurs: Hubert A., Degalez F., Allain C., Becot L., Burlot T., Ferry A., Lagoutte L., Lebez B., Zerjal T., Allais S., Pitel F., Lagarrigue S.
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

Local breeds and landscape genomics: A powerful combination for detecting adaptive genes

Auteurs: Carl Kroger, Michel Sourdioux, Romuald Rouger, Michele Tixier-Boichard, Tatina Zerjal, Gwendal Restoux 
Publié dans: Book of Abstracts of the 76th annual meeting of the European Federation of Animal Science, 2025, Page(s) 413
Éditeur: EAAP

Stakeholders’ perception of the local breeds’ sector in six European countries - a survey by the GEroNIMO project

Auteurs: Marie-José MERCAT, Andreia AMARAL, Riccardo BOZZI, Marjeta ČANDEK-POTOKAR, Pedro FERNANDES, Jetsabell GUTIERREZ VALLEJOS, Danijel KAROLYI, Denis LALOë, Zoran LUKOVIć, Gwendal RESTOUX, António VICENTE, Virginia RIBEIRO, Tamara RODRIGUEZ SILVA, Romuald ROUGER, Dubravko ŠKORPUT, Martin ŠKRLEP
Publié dans: Book of abstracts of the XI International Symposium on the Mediterranean pig, Numéro 4, 2022, ISBN 978-953-8276-35-4
Éditeur: University of Zagreb Faculty of Agriculture
DOI: 10.5281/zenodo.14870239

Lipid traits related to body reserves and egg yolks of laying hens at 90 weeks of age: QTL detection and genetic correlations with production traits

Auteurs: Alexandre Hubert, Fabien Degalez, Nicolas Bedere, Coralie Allain, Lorry Becot, Quentin Berger, Thierry Burlot, Mathieu Emily, Alexandre Ferry, Laetitia Lagoutte, Alexandre Langon, Bénédicte Lebez, Marie-Pierre Sanchez, Thierry Tribout, Frédérique Pitel, Tatiana Zerjal, Sophie Allais, Sandrine Lagarrigue
Publié dans: Abstracts of PAG33, 2026
Éditeur: PAG

Feed stress-induced transcriptomic changes in the liver of Krškopolje pigs reared in the outdoor system

Auteurs: K. Poklukar, M. Čandek-Potokar, M. Vrecl, M. Škrlep
Publié dans: Book of Abstracts of the 3rd Regional Meeting of the European Federation of Animal Science (EAAP), Numéro 9th-11th April 2025, 2025
Éditeur: EAAP

A single-locus quantitative generic model to include DNA methylation information

Auteurs: L. Ayres, M. P. L. Calus, H. Bovenhuis
Publié dans: Book of abstracts 7th International Conference of Quantitative Genetics, Numéro 22nd-26th July 2024, 2024
Éditeur: Institute of Science and Technology Austria (ISTA)

The evolution of epigenetics across multiple generations

Auteurs: S. E. Eynard, C. Donnadieu, L. Flatres-Grall, C. Iampietro, S. Lagarrigue, S. Leroux, J. Lledo, J. Riquet, B. Servin, C. Vandecasteele, T. Zerjal, F. Pitel
Publié dans: Book of abstracts of Epigenetic Trangenerational Inheritance Meeting, Numéro September 2023, 2023
Éditeur: Epigenetic Trangenerational Inheritance Meeting

A IncRNA gene-enriched atlas for GRCg7b chicken genome & its functional annotation across 47 tissues

Auteurs: F. Degalez, M. Charles, S. Foissac, H. Zhou, D. Guan, L. Fang, C. Klopp, C. Alain, L. Lagoutte, B. Lebez, F. Lecerf, B. Vourch, T. Zerjal, F. Pitel, S. Lagarrigue
Publié dans: Book of abstracts of 39th International Society for Animal Genetics Conference, Numéro July 2023, 2023, Page(s) 49
Éditeur: ISAG

Genetic polymorphisms in Krškopolje pig breed

Auteurs: K. Poklukar, M. Čandek-Potokar, MJ. Mercat, M. Škrlep
Publié dans: Zadravčevi-Erjavčevi Dnevi 2024, Numéro 14th November 2024, 2024
Éditeur: ZED

Incorporating genomic and transcriptomic effects in linear and structural models for predicting complex traits in pigs

Auteurs: I. T. Vourlaki, M. Ballester, T. Jove, Y. Ramayo-Caldas, M. Piles
Publié dans: ISAG 2025 Abstract Book, 2025, Page(s) 146
Éditeur: ISAG

Estimating the heritability of meat quality traits in Krškopolje pigs

Auteurs: K. Poklukar, M. Čandek-Potokar, MJ. Mercat, M. Banville, M. Škrlep
Publié dans: Book of Abstracts of the 3rd Regional Meeting of the European Federation of Animal Science (EAAP), Numéro 9th-11th April 2025, 2025
Éditeur: EAAP

Added value of functional annotation and individual omics in genomic prediction

Auteurs: M. P. L. Calus
Publié dans: AGBT: Agricultural Meeting, Numéro April 2024, 2024
Éditeur: AGBT Ag; DOI not available

Transmission of DNA methylation: genetic or epigenetic ? A transgenerational case study in quails

Auteurs: Stacy Rousse, Sophie Leroux, Remi Seraphin, David Gourichon, Marta Godia Perello, Ole Madsen, Frédérique Pitel, Sonia E Eynard
Publié dans: Book of Abstracts EAGS 2026, 2026, Page(s) 23
Éditeur: France Génomique

Local pig and chicken breeds: weaknesses, strengths and challenges by Italian stakeholder concept

Auteurs: Parrini S., Mercat M.J., Amaral De Jesus A., Karolyi D., Căndek Potokar M., Restoux G., Fabbri M.C., Crovetti A., Sirtori F., Bozzi R.
Publié dans: ASPA 25th Congress Book of Abstract, Italian Journal of Animal Science, 24:sup1, 1-463, 2025, Page(s) 241
Éditeur: Animal Science and Production Association

Transmission of DNA methylation: genetic or epigenetic? A transgenerational case study in quails

Auteurs: Stacy Rousse, Sophie Leroux, David Gourichon, Marta Godia Perello, Ole Madsen, Frédérique Pitel, Sonia E Eynard
Publié dans: Booklet of abstracts of the Zurich EPIGENETIC INHERITANCE SYMPOSIUM 2025, 2025, Page(s) 31
Éditeur: ETH Zurich

Book chapters (2)

Perceptions of stakeholders involved in preserving local breeds - a survey by the GEroNIMO project

Auteurs: MJ. Mercat, A. Amaral, R. Bozzi, M. Candek-Potokar, P. Fernandes, J. Gutierrez Vallejos, D. Karolyi, D. Laloë, Z. Lukovic, H. Lenoir, G. Restoux, A. Vicente, V. Ribeiro, T. Rodriguez Silva, R. Rouger, D. Skroput, M. Skrlep
Publié dans: Journées de la Recherche Porcine, Numéro January 2023, 2023, ISSN 2772-283X
Éditeur: INRAE, IFIP
DOI: 10.1016/j.anscrio.2023.06.089

Attitudes towards genome editing in farmed animals: An interview study

Auteurs: L. Borgdorf, F.L.B. Meijboom
Publié dans: Back to the future: Sustainable innovations for ethical food production and Consumption, 2024
Éditeur: Brill Publishers
DOI: 10.3920/978-90-0471-550-9_44

Peer reviewed articles (23)

O197 Assessing multiphase feeding sequencing plan designed for fatty type pigs in indoor and outdoor heavy pig production systems by modeling – an example of Krškopolje pig

Auteurs: N. Batorek-Lukač, M. Škrlep, K. Poklukar, S. Millet, M. Čandek-Potokar
Publié dans: Animal - science proceedings, Numéro 13, 2023, Page(s) 495-496, ISSN 2772-283X
Éditeur: Elsevier BV
DOI: 10.1016/j.anscip.2022.07.207

Detection of quantitative trait loci and genetic correlations of lipid reserves and production traits in aging laying hens

Auteurs: Alexandre Hubert, Fabien Degalez, Nicolas Bedere, Coralie Allain, Lorry Becot, Quentin Berger, Thierry Burlot, Mathieu Emily, Alexandre Ferry, Laetitia Lagoutte, Alexandre Langon, Bénédicte Lebez, Marie-Pierre Sanchez, Thierry Tribout, Frédérique Pitel, Tatiana Zerjal, Sophie Allais, Sandrine Lagarrigue
Publié dans: Poultry Science, Numéro 105, 2026, Page(s) 106963, ISSN 0032-5791
Éditeur: Poultry Science Association Inc.
DOI: 10.1016/j.psj.2026.106963

Genetic architecture of backfat thickness in laying hens: implications for extended egg production

Auteurs: Nicolas Bédère, Frédéric Hérault, Lorry Bécot, Thierry Burlot, Christian Diot, Sandrine Lagarrigue, Pascale Le Roy
Publié dans: Genetics Selection Evolution, Numéro 58, 2026, ISSN 1297-9686
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s12711-026-01036-x

Turopolje Pig: Between Conservation and Sustainability

Auteurs: D. Skorput, A. Kaic, M. Spehar, D. Karolyi, Z. Lukovic
Publié dans: Sustainability, 2024, ISSN 2071-1050
Éditeur: MDPI Open Access Publishing
DOI: 10.3390/su16051786

Enriched atlas of IncRNA and protein-coding genes for the GRCg7b chicken assembly and its functional annotation across 47 tissues

Auteurs: F. Degalez, M. Charles, S. Foissac, H. Zhou, D. Guan, L. Fang, C. Klopp, C. Allain, L. Lagoutte, F. Lecerf, H. Acloque, E. Giuffra, F. Pitel, S. Lagarrigue
Publié dans: Scientific Reports, 2024, ISSN 2045-2322
Éditeur: Nature Publishing Group
DOI: 10.1038/s41598-024-56705-y

A single-locus quantitative genetic model incorporating DNA methylation

Auteurs: L. Ayres, H. Bovenhuis, M.P.L. Calus
Publié dans: Journal of Theoretical Biology, Numéro 607, 2025, Page(s) 112110, ISSN 0022-5193
Éditeur: Academic Press
DOI: 10.1016/j.jtbi.2025.112110

Incorporating transcriptomic data into genomic prediction models to improve the prediction accuracy of phenotypes of efficiency traits

Auteurs: Valentin P. Haas, Robin Wellmann, Pascal Duenk, Michael Oster, Siriluck Ponsuksili, Jörn Bennewitz, Mario P. L. Calus
Publié dans: Genetics Selection Evolution, Numéro 57, 2025, ISSN 1297-9686
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s12711-025-01008-7

Co-occurring microbial guilds in pig fecal microbiota: key drivers and effects on host performance

Auteurs: Ioanna-Theoni Vourlaki, Raquel Rio-Lopez, Adrià Clavell-Sansalvador, Lino C. Ramírez-Ayala, Maria Ballester, Juan P. Sanchez, Miriam Piles, Raquel Quintanilla, Angela C. da Fonseca de Oliveira, Leandro Batista Costa, Antoni Dalmau, Yuliaxis Ramayo-Caldas
Publié dans: Genetics Selection Evolution, Numéro 57, 2025, ISSN 1297-9686
Éditeur: BioMed
DOI: 10.1186/s12711-025-00979-x

The effect of aging on genetic parameters of boar semen traits

Auteurs: Pedro Sá, Rodrigo M Godinho, Marta Gòdia, Claudia A Sevillano, Barbara Harlizius, Ole Madsen, Henk Bovenhuis
Publié dans: Journal of Animal Science, Numéro 103, 2025, ISSN 0021-8812
Éditeur: American Society of Animal Science
DOI: 10.1093/jas/skaf257

Growth Performance, Carcass Quality, and Lipid Metabolism in Krškopolje Pigs and Modern Hybrid Pigs: Comparison of Genotypes and Evaluation of Dietary Protein Reduction

Auteurs: Martin Škrlep, Klavdija Poklukar, Milka Vrecl, Jana Brankovič, Marjeta Čandek-Potokar
Publié dans: Animals, Numéro 14, 2025, Page(s) 3331, ISSN 2076-2615
Éditeur: MDPI AG
DOI: 10.3390/ani14223331

Transmissibility model to evaluate transgenerational transmission of environmental effects in quails

Auteurs: K. Karami, S. Rousse, F. Pitel, S. Eynard, D. Gourichon, S. Leroux, A. Ricard, I. David
Publié dans: animal, Numéro 19, 2026, Page(s) 101636, ISSN 1751-7311
Éditeur: Cambridge University Press
DOI: 10.1016/j.animal.2025.101636

Genetic parameters and parental and early-life effects of boar semen traits

Auteurs: Pedro Sá, Rodrigo M. Godinho, Marta Gòdia, Claudia A. Sevillano, Barbara Harlizius, Ole Madsen, Henk Bovenhuis
Publié dans: Genetics Selection Evolution, Numéro 57, 2025, ISSN 1297-9686
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s12711-025-00954-6

Attitudes towards Genome Editing in Farmed Animals – a Cross-Cultural Study

Auteurs: Leon Borgdorf, Elsa Delanoue, Meta Candek-Potokar, Valentin P. Haas, Koen Kramer, Franck L.B. Meijboom
Publié dans: Food Ethics, Numéro 11, 2026, ISSN 2364-6853
Éditeur: Springer Science and Business Media LLC
DOI: 10.1007/s41055-026-00205-4

The Effect of Reduced Dietary Protein on Adipose Tissue in Local Krškopolje Pigs

Auteurs: Klavdija Poklukar, Marjeta Čandek-Potokar, Milka Vrecl, Jana Brankovič, Matjaž Uršič, Martin Škrlep
Publié dans: International Journal of Molecular Sciences, Numéro 26, 2025, Page(s) 4440, ISSN 1422-0067
Éditeur: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms26094440

ASPA 25th Congress Book of Abstract

Auteurs: Manuela Renna
Publié dans: Italian Journal of Animal Science, Numéro 24, 2026, Page(s) 1-463, ISSN 1828-051X
Éditeur: Informa UK Limited
DOI: 10.1080/1828051x.2025.2520034

Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression: a pilot study

Auteurs: Keyvan Karami, Jules Sabban, Chloé Cerutti, Guillaume Devailly, Sylvain Foissac, David Gourichon, Alexandre Hubert, Jean-Noël Hubert, Sophie Leroux, Tatiana Zerjal, Sandrine Lagarrigue, Frédérique Pitel
Publié dans: Environmental Epigenetics, Numéro 11, 2025, ISSN 2058-5888
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/eep/dvaf009

Reducing Protein Levels in Diets for Local Pig Breeds: A Case Study on Fat-Type Krškopolje Pig

Auteurs: Martin Škrlep, Klavdija Poklukar, Sam Millet, Marjeta Čandek-Potokar
Publié dans: Animal Science Journal, Numéro 96, 2025, Page(s) e70077, ISSN 1740-0929
Éditeur: Wiley
DOI: 10.1111/asj.70077

Incorporating genomic and transcriptomic effects in joint linear and non-linear structural models for predicting complex traits in pigs

Auteurs: I-T. Vourlaki, M. Piles, T. Jové-Juncà, Y. Ramayo-Caldas, R. Quintanilla, M. Ballester
Publié dans: animal, Numéro 20, 2026, Page(s) 101765, ISSN 1751-7311
Éditeur: Cambridge University Press
DOI: 10.1016/j.animal.2026.101765

A genome-wide association study reveals additive and recessive alleles affecting male fertility in pigs

Auteurs: Pedro Sá, Marta Gòdia, Rodrigo M. Godinho, Claudia A. Sevillano, Barbara Harlizius, Ole Madsen, Henk Bovenhuis
Publié dans: Journal of Animal Science and Biotechnology, Numéro 16, 2025, ISSN 2049-1891
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s40104-025-01312-8

Simulation of dual-purpose chicken breeding programs implementing gene editing

Auteurs: E. Y. S. Chuang, R. Wellmann, F. L. B. Meijboom, J. Tetens, J. Bennewitz
Publié dans: Genetics Selection Evolution, 2024, ISSN 0999-193X
Éditeur: BioMed Central
DOI: 10.1186/s12711-023-00874-3

GEGA (Gallus Enriched Gene Annotation): an online tool providing genomics and functional information across 47 tissues for a chicken gene-enriched atlas gathering Ensembl and Refseq genome annotations

Auteurs: Fabien Degalez, Philippe Bardou, Sandrine Lagarrigue
Publié dans: NAR Genomics and Bioinformatics, Numéro 6, 2024, ISSN 2631-9268
Éditeur: Oxford University Press (OUP)
DOI: 10.1093/nargab/lqae101

Empowering bioinformatics communities with Nextflow and nf-core

Auteurs: 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
Publié dans: Genome Biology, Numéro 26, 2025, ISSN 1474-760X
Éditeur: Springer Science and Business Media LLC
DOI: 10.1186/s13059-025-03673-9

An improved transmissibility model to detect transgenerational transmitted environmental effects

Auteurs: I. David, A. Ricard
Publié dans: Genetics Selection Evolution, 2023, ISSN 0999-193X
Éditeur: BioMed Central
DOI: 10.1186/s12711-023-00833-y

Non-peer reviewed articles (1)

Adipose tissue transcriptome profiles of local Krškopolje pig and modern hybrids receiving reduced protein diets

Auteurs: K. Poklukar, M. Čandek-Potokar, B. Savić, M. Škrlep
Publié dans: animal, Numéro 20, 2026, Page(s) 101864, ISSN 1751-7311
Éditeur: Cambridge University Press
DOI: 10.1016/j.animal.2026.101864

Other (2)

Transmission of an environmental modification in quails across three generations: changes in the contribution to phenotypic variability

Auteurs: Stacy Rousse, Sophie Leroux, David Gourichon, Ludovic Calandreau, Andrea Rau, Sandrine Lagarrigue, Tatiana Zerjal, Frédérique Pitel, Sonia E. Eynard
Publié dans: 2026
Éditeur: openRxiv
DOI: 10.1101/2025.07.04.663137

Growth potential of Krškopolje pigs in different production systems.

Auteurs: BATOREK LUKAČ, Nina, ČANDEK-POTOKAR, Marjeta
Publié dans: Book of abstracts. XIth International Symposium on Mediterranean Pig, Numéro 5, 2022, ISBN 978-953-8276-35-4
Éditeur: University of Zagreb, Faculty of agriculture