Periodic Reporting for period 3 - GEroNIMO (GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics)
Période du rapport: 2024-06-01 au 2025-05-31
In response to increasing societal demands for sustainable animal production and the challenges posed by climate change and environmental fluctuations, GEroNIMO seeks to improve livestock breeding in pigs and chickens by integrating comprehensive genetic, epigenetic, and phenotypic data. GEroNIMO approach aims to unravel the biological mechanisms driving efficient and resilient livestock production and to develop advanced genomic selection models that enhance breeding accuracy and sustainability, maintaining genetic diversity.
A central focus of the project is understanding how organisms respond to environmental variations through epigenetic modifications that influence gene expression and shape phenotypes. Environmental factors during various life stages, including prenatal development, can have long-lasting effects on production traits, behaviour and adaptive capacity. To investigate these processes, GEroNIMO uses diverse experimental strategies across species, including chicken, pig, and quail, to identify epigenetic signatures of environmental stressors such as changes in feed composition, heat stress, and seasonal fluctuations in outdoor farming. GEroNIMO results will advance our understanding of how the breeding environment affects DNA methylation patterns and regulatory elements involved in stress response and resilience, ultimately providing insights into how breeding and environmental exposures influence traits variation over time.
Beyond scientific and technical advances, GEroNIMO addresses ethical and societal implications of emerging genomic technologies. The project emphasizes transparent communication, stakeholder engagement, and aligning breeding innovations with public values on sustainability, animal welfare, and food security. By fostering open dialogue among researchers, breeders, policymakers, and the wider public, GEroNIMO aims to maximize its findings’ practical impact, ensuring responsible and socially acceptable improvements in livestock breeding and production systems.
A central focus of the project is understanding how organisms respond to environmental variations through epigenetic modifications that influence gene expression and shape phenotypes. Environmental factors during various life stages, including prenatal development, can have long-lasting effects on production traits, behaviour and adaptive capacity. To investigate these processes, GEroNIMO uses diverse experimental strategies across species, including chicken, pig, and quail, to identify epigenetic signatures of environmental stressors such as changes in feed composition, heat stress, and seasonal fluctuations in outdoor farming. GEroNIMO results will advance our understanding of how the breeding environment affects DNA methylation patterns and regulatory elements involved in stress response and resilience, ultimately providing insights into how breeding and environmental exposures influence traits variation over time.
Beyond scientific and technical advances, GEroNIMO addresses ethical and societal implications of emerging genomic technologies. The project emphasizes transparent communication, stakeholder engagement, and aligning breeding innovations with public values on sustainability, animal welfare, and food security. By fostering open dialogue among researchers, breeders, policymakers, and the wider public, GEroNIMO aims to maximize its findings’ practical impact, ensuring responsible and socially acceptable improvements in livestock breeding and production systems.
GEroNIMO has made major strides in understanding genomic and epigenetics control of phenotype diversity. It also allowed to better understand the extent of environmental influence on epigenetic modifications. Extensive data from pig and chicken populations—including phenotypes, gene expression, DNA methylation, and genetic profiles—have been collected. QTL analyses have identified key genes linked to traits like growth, meat quality, sperm quality, egg production, etc. Moreover, genomic and landscape studies in local chickens have pinpointed genes involved to environmental adaptation. Finally, integrated multi-omics models are being developed to improve the accuracy of trait prediction, which is essential for effective breeding strategies. Progress included also the calibration of devices to measure intramuscular fat in local pig breeds, enabling more precise selection for meat quality.
Efforts have been invested to investigate the influence of environmental factors on epigenetic modifications. Ten experiments were proposed to explore how rearing conditions, stressors, and life stages affect methylation patterns. Rearing systems were shown to affect later performance in pig and chicken. Transcriptomic data notably revealed differences in lipid metabolism genes due to rearing environments.
To support this work, the project assessed and optimized methylation analysis techniques. GBS-MeDIP was selected for within population comparisons, while RRBS was used for between population comparisons and for studies linking genetics and epigenetics. Large methylation and transcriptomic datasets have been generated, and analyses are underway to gaining an integrated view of the different omics layers involved in Efficient Livestock Production trait variation.
Ethical and societal research across multiple countries revealed varied public attitudes toward genomic innovation, reinforcing the need for responsible development. Outreach, training, and stakeholder engagement have helped ensure knowledge transfer and collaboration across science, policy, and industry.
Despite some delays in epigenetic data generation, the project has successfully met its overall goals and continues to contribute valuable insights for improving animal breeding.
Efforts have been invested to investigate the influence of environmental factors on epigenetic modifications. Ten experiments were proposed to explore how rearing conditions, stressors, and life stages affect methylation patterns. Rearing systems were shown to affect later performance in pig and chicken. Transcriptomic data notably revealed differences in lipid metabolism genes due to rearing environments.
To support this work, the project assessed and optimized methylation analysis techniques. GBS-MeDIP was selected for within population comparisons, while RRBS was used for between population comparisons and for studies linking genetics and epigenetics. Large methylation and transcriptomic datasets have been generated, and analyses are underway to gaining an integrated view of the different omics layers involved in Efficient Livestock Production trait variation.
Ethical and societal research across multiple countries revealed varied public attitudes toward genomic innovation, reinforcing the need for responsible development. Outreach, training, and stakeholder engagement have helped ensure knowledge transfer and collaboration across science, policy, and industry.
Despite some delays in epigenetic data generation, the project has successfully met its overall goals and continues to contribute valuable insights for improving animal breeding.
The GEroNIMO project advances livestock breeding by integrating multi-omics data as genomics, epigenomics, transcriptomics with a large range of phenotypes to unravel the complex biology behind trait variation. It also shed light on how environmental factors can induce lasting epigenetic changes. These results are valuable resources for boosting the accuracy of breeding value predictions beyond traditional models.
Progress includes the development of innovative models that incorporate epigenetic information, revealing non-genetic inheritance patterns, which have potential applications also in plant and human studies. Calibration of novel tools like devices for intramuscular fat prediction in local pig breeds supports precision breeding efforts in previously under-characterized populations. Furthermore, landscape genomics combined with epigenetic analyses in local breeds opens new avenues for conserving functional genetic diversity adapted to changing environments.
On the ethical and societal side, the project identified limitations in current debates and broadened the dialogue by engaging diverse stakeholders and organizing international public focus groups on breeding and gene editing. This is helping to shape more inclusive, responsible innovation pathways.
Outreach and dissemination activities have been highly effective, with wide-ranging communication, stakeholder engagement, and training across Europe. GEroNIMO’s visibility and impact are expanding through multimedia content, regional workshops, and collaborations with EU networks, ensuring the project's results are well integrated into science, policy, and practice.
The expected results of the project include innovative genomic selection models that incorporate epigenetic profiles to boost breeding efficiency and robustness under climate variability. These models aim to provide breeders with better tools for an efficient livestock production while maintaining genetic diversity and animal welfare. The project also plans to deliver comprehensive guidelines addressing societal and ethical dimensions, fostering responsible innovation and public acceptance of genome-enabled breeding technologies.
Progress includes the development of innovative models that incorporate epigenetic information, revealing non-genetic inheritance patterns, which have potential applications also in plant and human studies. Calibration of novel tools like devices for intramuscular fat prediction in local pig breeds supports precision breeding efforts in previously under-characterized populations. Furthermore, landscape genomics combined with epigenetic analyses in local breeds opens new avenues for conserving functional genetic diversity adapted to changing environments.
On the ethical and societal side, the project identified limitations in current debates and broadened the dialogue by engaging diverse stakeholders and organizing international public focus groups on breeding and gene editing. This is helping to shape more inclusive, responsible innovation pathways.
Outreach and dissemination activities have been highly effective, with wide-ranging communication, stakeholder engagement, and training across Europe. GEroNIMO’s visibility and impact are expanding through multimedia content, regional workshops, and collaborations with EU networks, ensuring the project's results are well integrated into science, policy, and practice.
The expected results of the project include innovative genomic selection models that incorporate epigenetic profiles to boost breeding efficiency and robustness under climate variability. These models aim to provide breeders with better tools for an efficient livestock production while maintaining genetic diversity and animal welfare. The project also plans to deliver comprehensive guidelines addressing societal and ethical dimensions, fostering responsible innovation and public acceptance of genome-enabled breeding technologies.
