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The regulatory GENomE of SWine and CHicken: functional annotation during development

Project description

Genomic selection practices in the farming industry

Functional annotation of the genome provides an indication of which genes are transcriptionally active across space and time. Identification of the regulatory regions or elements responsible for this gene activation is important not only for the well-being of humans but in the farming and biotech industries. The EU-funded GENE-SWitCH project focusses on the genome of swine and poultry and aims to discover genetic loci that can contribute to sustainable animal breeding and production. Insight into the epigenetic influence of maternal diet will help optimise existing practices with immediate benefit to the farming sector.


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) community, we will characterize the dynamics (“switches”) of the functional genome from embryo (chicken) and fetus (pig) to adult life 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 open-shared 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.

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Net EU contribution
€ 1 184 073,00
75007 Paris

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Ile-de-France Ile-de-France Paris
Activity type
Research Organisations
Total cost
€ 1 286 962,50

Participants (12)