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GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics

Periodic Reporting for period 1 - GEroNIMO (GEroNIMO: Genome and Epigenome eNabled breedIng in MOnogastrics)

Reporting period: 2021-06-01 to 2022-11-30

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. These companies are using traditional genetic models, in which all factors other than genetics are included as nuisance factors, whereas the impact of the environment on phenotypic variation is largely mediated by interactions between genetic and non-genetic components.
GEroNIMO addresses these challenges by producing comprehensive phenotypic, genetic, epigenetic and gene expression data in pig and chicken, providing the basis for developing genomic selection models that will improve selection towards sustainable and environmental robust animal production.
European pig and chicken production is mainly based on a few selected lines reared under controlled conditions and representing a narrow sample of the genetic diversity of the species. Local breeds are characterised by small effective population sizes and are considered robust and resilient as adapted to the natural rearing condition. Thus, they may represent a reservoir of genetic and epigenetic variability and could help improve the animals’ ability to adapt to future environmental changes. GEroNIMO will investigate the genetic and epigenetic architecture in a broad panel of pig and poultry breeds, and propose tools and methods to improve breeding schemes, including the implementation of cost-effective phenotyping, meeting expectations raised by the breeders and preserving genetic diversity.
Innovations in genomics, including genome / epigenomics editing, raise questions about the societal context in which they take place. GEroNIMO aims to evaluate new genome-enabled breeding techniques from a societal and ethical perspective and contribute to a better societal understanding of how breeding can improve animal welfare, 'feed the world', and improve animal production in general.
In the first reporting period, comprehensive sampling of tissues and ELP phenotypes have been achieved for several thousand chickens and pigs. First results show that contrasted rearing conditions impact a variety of traits in chicken, and that the rearing system has an effect on growth, fat and muscle composition in pig. Genomics regions related to some traits were found thanks to genetic information provided by the commercial partners. Protocols for isolating high-quality DNA/RNA have been optimized. A course was held to familiarize the different partners with an original and inexpensive method to assay DNA methylation.
A wide survey was carried out among stakeholders of pig and chicken local breeds (550 participants), providing an overview of the management programs of 126 breeds: most of the production system of local breeds is carried out without selection program, using natural mating. Interestingly, in both species, the stakeholders’ first motivation is the interest for genetic conservation. Most stakeholders are concerned about the sustainability of local breeds mainly because of risks related to economics or legal regulation. They express expectations for more public support. A R package was adapted to control the frequencies of major genes in addition to maximising the genetic diversity and the genetic gain. A SNP panel was developed to assign parentage, design mating plans and describe the genetic diversity in a chicken breed. NIRS spectra were acquired on several hundred of eggs and pork meat samples with the aim to calibrate devices for large-scale phenotyping of the intramuscular fat content (pork) or fine composition (eggs).
Research has started to investigate how non-genetic inheritance of traits can be modelled, and to identify publicly available datasets that can be used to start evaluating the models that will be developed.
A literature study on the ethical and societal dimensions on novel breeding technologies was performed, showing a need to broaden the debate, including ways to enhance public engagement. Semi-structured interviews with scientists, breeders, and other professionals have been performed, reflecting in general the themes found in the literature study. First optimizations of mRNA transfection protocols have been made for in vitro epigenetic editing in pig intestinal cell lines and organoids.
For dissemination, exploitation and outreach, we prepared the project website (>2.5K users), 5 social media accounts (649 followers) and a Hackathon. Various communication materials have been produced, and GEroNIMO partners presented the project at 14 international and national events. GEroNIMO joined the EuroFAANG Initiative. A First IP Workshop and the Exploitation Plan were realized. A Round Table was held during a GEroNIMO & GENE-SWitCH Joint Stakeholder Event. Multi-actor Approach guidelines and a stakeholder community (747 active members) were created. The Stakeholders’ Advisory Board was set up and a private SAB area published on the website. Several training activities and videos were performed.
GEroNIMO will expand the knowledge of how environment can induce persistent changes in epigenomes, potentially enabling the quantification of farm animal welfare through an epigenetic toolbox. It will also allow to estimate the shaping of the epigenetic landscape by generations of selection, and the extent of non-genetic inheritance. More broadly, a comprehensive understanding of the different omics layers involved in ELP trait variations will help develop models that enable to better disentangle the impact of inheritance, genetics, and the environment on phenotypes. These models are expected to be more accurate in predicting breeding values, as needed to perform selection in sustainable livestock breeding programs, and should have an impact beyond livestock, including applications in plant breeding, or in the prediction of genetic predisposition to certain diseases in human genetics.
The first activity period has strengthened or expanded links between local breed stakeholders and research. Awareness-raising and training activities for breeders will continue. Large-scale phenotyping tools will be calibrated and available for actors of pork and eggs chains. All this should support the implementation of improved management or selection programs to optimize the genetic diversity and improve key ELP traits in both pigs and poultry. In addition, the genome and epigenome of about thirty local breeds of pigs or poultry will be characterized, paving the way to propose new models to maintain optimal population genetic and epigenetic diversity.
Our first literature study indicates that the current debate on the ethical and societal dimensions is too narrow, and often do not include the whole variety of morally relevant aspects. To widen it we will include inputs from national discussions, developing a case study that integrates ethics and research innovation and 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. We will continue to maximize the impact by promoting exchanges with stakeholders.
First Annual Meeting Consortium photo