The GENE-SWitCH Project

GENE-SWitCH aims to deliver new underpinning knowledge on the functional genomes of two main monogastric farm species (pig and chicken) and to enable immediate translation to the pig and poultry sectors. The activation status of functional genome sequences varies across time and space, and in response to environmental perturbations.

In full coordination and synergy with global effort and ongoing projects of the Functional Annotation of ANimal Genomes (FAANG - www.faang.org) community, the dynamics (“switches”) of the functional genome from embryo (chicken) and fetus (pig) to adult life will be characterized by targeting a panel of tissues relevant to sustainable production. New expression QTL data in pigs and existing high-resolution QTL data in chicken will be used for developing innovative genomic predictive models that integrate functional annotations, and these models will be validated in commercial pig and poultry populations. In addition, nutritional epigenetic data will allow evaluation of the influence of maternal diet on the epigenome of the pig fetus and whether such effects persist until post-weaning. These openshared datasets will conform fully with FAANG standards and add valuable knowledge on genetic and epigenetic variation of functional elements to FAANG.

A comprehensive plan of dissemination and outreach activities to a large audience of stakeholders will be implemented. The GENE-SWitCH consortium brings together partners representing pan-European excellence (including the academic institutions which pioneered FAANG) and world-leading animal breeding and biotech industry in a true co-creation effort. Overall, GENE-SWitCH will contribute to the global FAANG effort considerably, demonstrate how functional annotation of genomes can foster the advancement of genomic selection for immediate benefit to the breeding industry, and produce cutting-edge research paving the way to new studies and strategies for sustainable productions.

Aims of the project

The aims of GENE-SWitCH are:

1. to characterise the functional elements of the genomes (coding and regulatory) of the pig and chicken with a particular emphasis on tissues of relevance to sustainable production;
2. in coordination with the global FAANG initiative to share and disseminate this knowledge as richly annotated high-quality reference genome sequences; and
3. to enable the use of this knowledge to further improve the effectiveness of genomic selection in the pig and poultry sectors. The activation status of functional genome sequences varies not only between cells and tissues but also over time. Thus, we will characterise the dynamics (“switches”) of the functional genome in the target tissues from embryo/fetus to adult life.
4. As the genome is dynamic also in response to environmental perturbations, a further aim is to identify the effects of maternal diet on the porcine fetal epigenome (“diet x epigenetics”) and to assess the persistence of these epigenome states until post-weaning. GENE-SWitCH will deliver new knowledge and tools for immediate translation in the pig and poultry sectors that have a strong track record in using such resources to improve the sustainability of production. The diet x epigenetic approach will deliver underpinning information that will pave the way to more studies for future precision breeding strategies.​

The elements of the genome that are functional vary across time and space (i.e. cells and tissues) and in response to environmental perturbations. Thus, annotation that is built upon functional data derived from adult tissues alone or from only unperturbed cells will not provide comprehensive functional annotation.

As characterising the functional genomics elements across all cells, tissues, timepoints and a range of perturbation states is not affordable within a single project, coordination between FAANG-related projects working on the same species is essential to maximise the coverage of functional annotation for the species.
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GENE-SWitCH will contribute to the global FAANG effort in the two foremost sources of meat – pigs and chickens as illustrated in the Figure.