Periodic Reporting for period 2 - GEroNIMO (GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics)
Reporting period: 2022-12-01 to 2024-05-31
The monogastric livestock sector is affected by the consequences of climate change and society’s demands, and is in seek of animals capable to adapt to various stresses. The overall response of organisms to environmental changes involves, in addition to genetic variability, epigenetics alterations potentially affecting phenotypes, even in subsequent generations. In GEroNIMO these questions are addressed by producing comprehensive phenotypic, genetic, epigenetic and gene expression data in diverse animal designs, across various environments. Each of these data types and their combination will provide enriched knowledge on the molecular mechanisms related to efficient livestock production (ELP) traits, helping to dissect the impact of genetic background, inheritance and non-genetic factors on trait variation. This will provide the foundation for developing genomic selection models that can entail better breeding towards sustainable and environmental robust animal production. Genomic evaluation models developed in GEroNIMO integrate individual epigenetic information, and evaluate whether or not this improves accuracy of predicted genomic breeding values for several important traits.
GEroNIMO also investigates the genetic and epigenetic architecture in a broad panel of pig and poultry local breeds, considered as reservoir of genetic and epigenetic variability that could help improve the animals’ ability to adapt to future environmental changes, and propose tools and methods to improve breeding schemes.
To address the societal and ethical dimensions associated to innovations in genomics, GEroNIMO integrates an interdisciplinary approach that combines innovative work done on the project’ activities using methods from philosophical and bioethics, ethics and social sciences.
Dialogue with stakeholders and existing networks is a critical point of the project’s communication & dissemination strategies that intend to strengthen the interaction and exchange between researchers and stakeholders, in order to contribute to the diversity and sustainability of livestock production.
GEroNIMO also investigates the genetic and epigenetic architecture in a broad panel of pig and poultry local breeds, considered as reservoir of genetic and epigenetic variability that could help improve the animals’ ability to adapt to future environmental changes, and propose tools and methods to improve breeding schemes.
To address the societal and ethical dimensions associated to innovations in genomics, GEroNIMO integrates an interdisciplinary approach that combines innovative work done on the project’ activities using methods from philosophical and bioethics, ethics and social sciences.
Dialogue with stakeholders and existing networks is a critical point of the project’s communication & dissemination strategies that intend to strengthen the interaction and exchange between researchers and stakeholders, in order to contribute to the diversity and sustainability of livestock production.
Comprehensive sampling of tissue and ELP phenotypes have been achieved for chicken and pig’ populations. We thoroughly evaluated DNA methylation assays (GBS-MeDIP and RRBS), and chose to use one or the other depending on the scientific question. All molecular analyses are ongoing, and the first results of gene expression analysis have been obtained. The heritability was estimated for some traits, and genomic regions associated to different ELP traits were identified.
The interest in collectively build a rich sample collection with chemical measurements, in order to have a wide diversity of intramuscular fat and consolidate predictions, was established and NIRS devices will be valuable tools for stakeholders. Implementation difficulties in 2 local breeds showed that setting up conservation or genetic improvement programs of local breeds can remain challenging. Rich datasets were built up in 2 pig breeds, and blood sampling was conducted in 30 local breeds (pig, chicken) for epigenetic studies.
A model that considers the effect of DNA methylation on gene expression and subsequently the phenotype, has been theoretically developed; an RShiny application for the computation of different epigenetic relationships is available for use. Enhancements to the transmissibility model have been made to better model environmental influences on the phenotype. Empirical analyses have started to predict pig phenotypic traits using multi-omics data, as well as to demonstrate improved prediction accuracy using transcriptomic data in Japanese quail.
A literature review of the current debate on the ethical and societal dimensions of novel breeding technologies showed that there is a need to broaden the debate, including ways to improve public engagement. Semi-structured interviews were conducted with scientists, breeders and other experts, to complement the picture emerging from the literature. In general, the results of the interviews reflect the themes found in the literature. Focus group discussions with the general public were organised in 4 countries: although animal breeding and technological innovation are characterised by global developments, the assessment is less uniform and influenced by national or regional dimensions. A stochastic simulation protocol was developed to model a breeding programme for dual-purpose chicken lines and the potential role of gene editing, taking into account the ethical and societal dimensions from the start. These analyses are essential to answer the question of whether - if at all - genomic innovations can be responsibly introduced into pig and poultry breeding.
Since the beginning of GEroNIMO’ project, the communication efforts have been continuously enhanced by updating the dissemination materials, social medial campaigns and presentations at international events. Additional training workshops, targeting scientists and breeders, have been set up to ensure the transfer of knowledge and project sustainability. Efficient exploitation strategy and stakeholder engagement have been ensured through meetings, specific documents and ongoing communication efforts.
The interest in collectively build a rich sample collection with chemical measurements, in order to have a wide diversity of intramuscular fat and consolidate predictions, was established and NIRS devices will be valuable tools for stakeholders. Implementation difficulties in 2 local breeds showed that setting up conservation or genetic improvement programs of local breeds can remain challenging. Rich datasets were built up in 2 pig breeds, and blood sampling was conducted in 30 local breeds (pig, chicken) for epigenetic studies.
A model that considers the effect of DNA methylation on gene expression and subsequently the phenotype, has been theoretically developed; an RShiny application for the computation of different epigenetic relationships is available for use. Enhancements to the transmissibility model have been made to better model environmental influences on the phenotype. Empirical analyses have started to predict pig phenotypic traits using multi-omics data, as well as to demonstrate improved prediction accuracy using transcriptomic data in Japanese quail.
A literature review of the current debate on the ethical and societal dimensions of novel breeding technologies showed that there is a need to broaden the debate, including ways to improve public engagement. Semi-structured interviews were conducted with scientists, breeders and other experts, to complement the picture emerging from the literature. In general, the results of the interviews reflect the themes found in the literature. Focus group discussions with the general public were organised in 4 countries: although animal breeding and technological innovation are characterised by global developments, the assessment is less uniform and influenced by national or regional dimensions. A stochastic simulation protocol was developed to model a breeding programme for dual-purpose chicken lines and the potential role of gene editing, taking into account the ethical and societal dimensions from the start. These analyses are essential to answer the question of whether - if at all - genomic innovations can be responsibly introduced into pig and poultry breeding.
Since the beginning of GEroNIMO’ project, the communication efforts have been continuously enhanced by updating the dissemination materials, social medial campaigns and presentations at international events. Additional training workshops, targeting scientists and breeders, have been set up to ensure the transfer of knowledge and project sustainability. Efficient exploitation strategy and stakeholder engagement have been ensured through meetings, specific documents and ongoing communication efforts.
Understanding the biological mechanisms underlying efficient livestock production (ELP) traits is of high relevance for breeding companies to meet society’s demands for sustainable animal production and to enable stable animal production under changing environmental conditions. A comprehensive understanding of the involvement of different omics layers toward different ELP trait variations and development of methodologies for combined analysis of many omics data will help to develop models that enable to better disentangle the impact of inheritance, genetics, and the environment on phenotypes. These models, and our demonstration of their abilities, are expected to have an impact beyond livestock breeding alone, including applications in plant breeding, but also the prediction of genetic predisposition to certain diseases in human genetics. GEroNIMO will also expand the knowledge of how environment can induce persistent changes in epigenomes, potentially enabling the quantification of farm animal welfare through an epigenetic toolbox.
GEroNIMO will propose new methods and tools to implement breeding programs to improve the quality of the products while managing genetic diversity and, in pigs, eliminating an undesirable allele affecting meat quality and welfare. Knowledge on epigenetic diversity will shed light on the functional diversity and could lead to the establishment of new policies for the conservation of local breeds.
We aim to broaden the debate on the ethical and societal dimensions by interviewing experts from different disciplinary and members of the general public. Our objective is to translate the results into tools that enable professionals in research, breeding and policy makers to deal with the societal dimensions of genomics innovations including genome and epigenomics editing.
GEroNIMO’ communication, dissemination and exploitation strategy has successfully established an interactive network of regional, national, and international players in animal breeding and genome and epigenome research. Efforts will continue to ensure that the project’s innovative methods are effectively adopted by end-users. The aim will be to maximise the project’s socio-economic impact and wider societal implications.
GEroNIMO will propose new methods and tools to implement breeding programs to improve the quality of the products while managing genetic diversity and, in pigs, eliminating an undesirable allele affecting meat quality and welfare. Knowledge on epigenetic diversity will shed light on the functional diversity and could lead to the establishment of new policies for the conservation of local breeds.
We aim to broaden the debate on the ethical and societal dimensions by interviewing experts from different disciplinary and members of the general public. Our objective is to translate the results into tools that enable professionals in research, breeding and policy makers to deal with the societal dimensions of genomics innovations including genome and epigenomics editing.
GEroNIMO’ communication, dissemination and exploitation strategy has successfully established an interactive network of regional, national, and international players in animal breeding and genome and epigenome research. Efforts will continue to ensure that the project’s innovative methods are effectively adopted by end-users. The aim will be to maximise the project’s socio-economic impact and wider societal implications.
