GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics

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Deliverables

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

Multi-actor Approach Report

Report summarizing main activities done with stakeholders including an assessment of main problems faced by partners working with stakeholders and contingency measures implemented to tackle and resolve them. Update at M60 includes an assessment of the impact and effectiveness of Stakeholders participation in the project.

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.

Outreach, Dissemination and Training Plan (ODTP)

ODTP will be submitted at M6 and will be regularly updated in the course of the project depending on the project progress, newly available opportunities for communication and dissemination activities.

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

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

Author(s): Q. Berger, N. Bedere, P. Le-Roy, S. Lagarrigue, T. Burlot, T. Zerjal
Published in: Book of abstracts of 74th European Federation of Animal Science Annual Meeting, Issue August 2023, 2023
Publisher: Proceedings EAAP https://doi.org/10.3920/978-90-8686-936-7

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

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

Author(s): I. David, C. Larzul, A. Ricard
Published in: Proceedings of 12th World Congress on Genetics Applied to Livestock Production (WCGALP), 2023
Publisher: 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

Author(s): M. B. Petelle, C. M. Montalcini, M. J. Toscano
Published in: European's Poultry Conference Journal - The Book of Abstracts, Issue 24th-28th June 2024, 2024
Publisher: meap

Gene Polymorphism Frequencies in Krskopolje Pig Breed

Author(s): K. Poklukar, M. Čandek-Potokar, N. Batorek Lukač, MJ. Mercat, D. Picard Druet, M. Škrlep
Published in: Book of abstracts of the 14th International Symposium Modern Trends in Livestock Production, Issue October 2023, 2023, ISBN 978-86-82431-80-0
Publisher: Proceedings of the 14th International Symposium Modern Trends in Livestock Production

Growth potential of Krškopolje pigs in different production systems.

Author(s): BATOREK LUKAČ, Nina, ČANDEK-POTOKAR, Marjeta
Published in: Book of abstracts of the XIth International Symposium on Mediterranean Pig, Issue October 11-13, 2022, 2022, Page(s) 43-44, ISBN 978-953-8276-35-4
Publisher: University of Zagreb

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

Using functional annotation and individual omics in genomic prediction

Author(s): 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
Published in: Book of abstracts of 39th International Society for Animal Genetics Conference, Issue July 2023, 2023, Page(s) 45
Publisher: ISAG

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

Author(s): C. Guerrero-Bosagna
Published in: Book of Abstracts of the Congress of the European Society for Evolucionary Biology 2025 (ESEB2025), Issue 17th-22th August 2025, 2025, Page(s) p30
Publisher: Sociedad Española de Biologia Evolutiva (Sesbe)

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

Author(s): K. Poklukar, M. Čandek-Potokar, N. Batorek Lukač, M. Vrecl, G. Fazarinc, M. Škrlep
Published in: Book of abstracts of the 1st Regional Meeting of The European Federation of Animal Science, Issue April 2024, 2024
Publisher: 1st Regional Meeting of The European Federation of Animal Science

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

Author(s): S. Rousse, S. Leroux, D. Gourichon, L. Calandreau, C. Cerutti, G. Devailly, T. Zerjal, S. Lagarrigue, F. Pitel, S. E. Eynard
Published in: Book of abstracts of the Environmental and Agronomical Genomics Symposium, Issue February 2024, 2024
Publisher: France Genomic

Using henomic and transcriptomic information for complex trait prediction

Author(s): V. Haas, R. Wellmann, M. P. L. Calus, J. Bennewitz
Published in: Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (EAAP), Issue 1st-5th September 2024, 2024
Publisher: EAAP

HenTrack: Improving breeding programs with superior behavior and welfare phenotypes

Author(s): M. Toscano
Published in: Book of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (EAAP), Issue 1st-5th September 2024, 2024
Publisher: EAAP

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.

Author(s): BATOREK LUKAČ, Nina, ŠKRLEP, Martin, POKLUKAR ŽNIDARŠIČ, Klavdija, MILLET, Sam, ČANDEK-POTOKAR, Marjeta.
Published in: Book of abstracts of the 7th EAAP International Symposium on Energy and Protein Metobolism and Nutrition (ISEP), Issue September 12-15, 2022, 2022
Publisher: EAAP

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

Author(s): 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
Published in: Book of abstracts of the XIth International Symposium on the Mediterranean pig, Issue October 11-13, 2022, 2022, Page(s) 87-88, ISBN 978-953-8276-35-4
Publisher: UNIZG

GEroNIMO (Genome and Epigenome eNabled breedIng in MOnogastrics)

Author(s): S. Lagarrigue, F. Pitel, T. Zerjal for the GEroNIMO consortium
Published in: Book of abstracts of 74th European Federation of Animal Science Annual Meeting, Issue August 2023, 2023
Publisher: 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

Author(s): 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
Published in: Journées de la Recherche Porcine, Issue 9, 2023
Publisher: Ifip; Inrae,

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

Author(s): 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
Published in: Book of abstracts of 74th European Federation of Animal Sciences Annual Meeting, Issue August 2023, 2023
Publisher: 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

Author(s): 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
Published in: Book of abstracts of Environmental and Agronomical Genomics Symposium, Issue February 2024, 2024
Publisher: EAGS

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

Author(s): K. Poklukar, M. Čandek-Potokar, MJ. Mercat, M. Škrlep
Published in: 32nd Internaltional Sysposium Animal Science Days 2024 Book of Abstracts, Issue 2nd-4th October 2024, 2024
Publisher: Universitat fur Bodenkultur

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

Author(s): P. Sá, R. M. Godinho, M. Gòdia, C. A. Sevillano, B. Harlizius, O. Madsen, H. Bovenhuis
Published in: Bookf of Abstracts of the 75th Annual Meeting of the European Federation of Animal Science (EAAP), Issue 1st-5th September 2024, 2024
Publisher: EAAP

Integrating Transcriptomics and Epigenomics for Enhanced Breeding Programs in Pigs

Author(s): M. Luigi, P. Karlskov-Mortensen
Published in: 5th Annual congress of Young Researchers (ACYR), Issue 10th-11th March 2025, 2025
Publisher: ACYR

Polymorphisms of selected genes in Banija spotted and Turopolje pig

Author(s): D. Karolyi, K. Poklukar, K. Salajpal, D. Skorput, Z. Lukovic, MJ. Mercat, M. Candek-Potokar, M. Skrlep
Published in: 32nd International Symposium Animal Science Days 2024, Book of Abstracts, Issue 2nd-4th October 2024, 2024
Publisher: Universitat fur Bodenkultur

Banija spotted pig – from science to practise

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

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

Author(s): P. Sá, R. M. Godinho, M. Gòdia, C. A. Sevillano, B. Harlizius, O. Madsen, H. Bovenhuis
Published in: Book of abstracts of 39th International Society for Animal Genetics Conference, Issue July 2023, 2023, Page(s) 18
Publisher: ISAG

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

Author(s): Luísa Mateus, Graça Ferreira Dias, Maria Salomé, Gonçalves, Pamela Valente, Elisa Bettencourt, Luís Telo da Gama, Carlos Bettencourt, Andreia J. Amaral
Published in: Book of abstracts of the CIISA Congress 2022 Lisbon, Portugal)., Issue November 2022, 2022, Page(s) 150
Publisher: CIISA

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

Author(s): 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
Published in: Book of abstracts of the XI International Symposium on the Mediterranean pig, Issue 4, 2022, ISBN 978-953-8276-35-4
Publisher: University of Zagreb Faculty of Agriculture
DOI: 10.5281/zenodo.14870239

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

Author(s): K. Poklukar, M. Čandek-Potokar, M. Vrecl, M. Škrlep
Published in: Book of Abstracts of the 3rd Regional Meeting of the European Federation of Animal Science (EAAP), Issue 9th-11th April 2025, 2025
Publisher: EAAP

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

Author(s): L. Ayres, M. P. L. Calus, H. Bovenhuis
Published in: Book of abstracts 7th International Conference of Quantitative Genetics, Issue 22nd-26th July 2024, 2024
Publisher: Institute of Science and Technology Austria (ISTA)

The evolution of epigenetics across multiple generations

Author(s): 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
Published in: Book of abstracts of Epigenetic Trangenerational Inheritance Meeting, Issue September 2023, 2023
Publisher: Epigenetic Trangenerational Inheritance Meeting

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

Author(s): 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
Published in: Book of abstracts of 39th International Society for Animal Genetics Conference, Issue July 2023, 2023, Page(s) 49
Publisher: ISAG

Genetic polymorphisms in Krškopolje pig breed

Author(s): K. Poklukar, M. Čandek-Potokar, MJ. Mercat, M. Škrlep
Published in: Zadravčevi-Erjavčevi Dnevi 2024, Issue 14th November 2024, 2024
Publisher: ZED

Estimating the heritability of meat quality traits in Krškopolje pigs

Author(s): K. Poklukar, M. Čandek-Potokar, MJ. Mercat, M. Banville, M. Škrlep
Published in: Book of Abstracts of the 3rd Regional Meeting of the European Federation of Animal Science (EAAP), Issue 9th-11th April 2025, 2025
Publisher: EAAP

Added value of functional annotation and individual omics in genomic prediction

Author(s): M. P. L. Calus
Published in: AGBT: Agricultural Meeting, Issue April 2024, 2024
Publisher: AGBT Ag; DOI not available

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

Attitudes towards genome editing in farmed animals: An interview study

Author(s): L. Borgdorf, F.L.B. Meijboom
Published in: Back to the future: Sustainable innovations for ethical food production and Consumption, 2024
Publisher: Brill Publishers
DOI: 10.3920/978-90-0471-550-9_44

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

Author(s): N. Batorek-Lukač, M. Škrlep, K. Poklukar, S. Millet, M. Čandek-Potokar
Published in: Animal - science proceedings, Issue 13, 2023, Page(s) 495-496, ISSN 2772-283X
Publisher: Elsevier BV
DOI: 10.1016/j.anscip.2022.07.207

Turopolje Pig: Between Conservation and Sustainability

Author(s): D. Skorput, A. Kaic, M. Spehar, D. Karolyi, Z. Lukovic
Published in: Sustainability, 2024, ISSN 2071-1050
Publisher: 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

Author(s): 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
Published in: Scientific Reports, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-56705-y

A single-locus quantitative genetic model incorporating DNA methylation

Author(s): L. Ayres, H. Bovenhuis, M.P.L. Calus
Published in: Journal of Theoretical Biology, Issue 607, 2025, Page(s) 112110, ISSN 0022-5193
Publisher: Academic Press
DOI: 10.1016/j.jtbi.2025.112110

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

Author(s): 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
Published in: Genetics Selection Evolution, Issue 57, 2025, ISSN 1297-9686
Publisher: BioMed
DOI: 10.1186/s12711-025-00979-x

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

Author(s): Martin Škrlep, Klavdija Poklukar, Milka Vrecl, Jana Brankovič, Marjeta Čandek-Potokar
Published in: Animals, Issue 14, 2025, Page(s) 3331, ISSN 2076-2615
Publisher: MDPI AG
DOI: 10.3390/ani14223331

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

Author(s): Pedro Sá, Rodrigo M. Godinho, Marta Gòdia, Claudia A. Sevillano, Barbara Harlizius, Ole Madsen, Henk Bovenhuis
Published in: Genetics Selection Evolution, Issue 57, 2025, ISSN 1297-9686
Publisher: Springer Science and Business Media LLC
DOI: 10.1186/s12711-025-00954-6

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

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

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

Author(s): Martin Škrlep, Klavdija Poklukar, Sam Millet, Marjeta Čandek-Potokar
Published in: Animal Science Journal, Issue 96, 2025, Page(s) e70077, ISSN 1740-0929
Publisher: Wiley
DOI: 10.1111/asj.70077

Simulation of dual-purpose chicken breeding programs implementing gene editing

Author(s): E. Y. S. Chuang, R. Wellmann, F. L. B. Meijboom, J. Tetens, J. Bennewitz
Published in: Genetics Selection Evolution, 2024, ISSN 0999-193X
Publisher: 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

Author(s): Fabien Degalez, Philippe Bardou, Sandrine Lagarrigue
Published in: NAR Genomics and Bioinformatics, Issue 6, 2024, ISSN 2631-9268
Publisher: Oxford University Press (OUP)
DOI: 10.1093/nargab/lqae101

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

An improved transmissibility model to detect transgenerational transmitted environmental effects

Author(s): I. David, A. Ricard
Published in: Genetics Selection Evolution, 2023, ISSN 0999-193X
Publisher: BioMed Central
DOI: 10.1186/s12711-023-00833-y

Growth potential of Krškopolje pigs in different production systems.

Author(s): BATOREK LUKAČ, Nina, ČANDEK-POTOKAR, Marjeta
Published in: Book of abstracts. XIth International Symposium on Mediterranean Pig, Issue 5, 2022, ISBN 978-953-8276-35-4
Publisher: University of Zagreb, Faculty of agriculture

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