FEEDTHEPIG

Coordinator: DISTAL

Scientific Officer: Francesca Bertolini

Duration: 30/11/2023 - 29/11/2025

Research group: Francesca Bertolini, Paolo Zambonelli.

Feed efficiency (FE) is a key driver of sustainability in pig production because feed represents the major production cost and a substantial contributor to environmental burden. Genetic selection for improved FE can reduce feed consumption, production costs, and environmental emissions, but FE remains a complex and expensive trait to measure. The FEEDTHEPIG project investigated the biological mechanisms underlying FE in Italian heavy pigs, the genetic foundation of PDO dry-cured ham production. Using phenotypic records, biological samples, and 60K SNP genotypes from a large cohort of animals, pigs from the extreme tails of the Feed Conversion Ratio (FCR) distribution were characterized through untargeted metabolomics, metabolite Genome-Wide Association Studies (mGWAS), and liver transcriptomic analyses. The project aimed to identify FE-related biomarkers, investigate their genetic regulation, and evaluate their integration into advanced breeding programs.

Results achieved

Untargeted metabolomic analyses identified metabolites significantly associated with FCR divergence, highlighting pathways involved in energy metabolism, amino acid turnover, lipid metabolism, and mitochondrial function. Metabolite Genome-Wide Association Studies (mGWAS) demonstrated that several FE-related metabolites are under genetic control and identified genomic regions associated with their abundance, supporting their use as genetically anchored intermediate phenotypes. Liver transcriptomic analyses identified differentially expressed genes between high- and low-efficiency pigs, with functional annotation suggesting the involvement of metabolic, muscle-related, and immune pathways. Multi-omic integration highlighted biological networks associated with nutrient utilization and metabolic efficiency. Simulation studies demonstrated that incorporating multi-omic biomarkers into genomic selection schemes can improve the accuracy of genetic prediction for FE. Metabolomic information proved particularly valuable as an indirect predictor of FE, and the combined use of direct phenotypes and molecular biomarkers yielded the highest expected genetic gains while maintaining performance for production traits relevant to PDO dry-cured ham production.

Funding

Funded by the European Union - NextGenerationEU under the National Recovery and Resilience Plan (PNRR) - Mission 4 Education and research - Component 2 From research to business - Investment 1.1 Notice PRIN 2022 PNRR (DD N. 1409 del 14/09/2022), entitled "An integrated metabolomic, transcriptomic and genomic approach to identify new markers for the genetic improve-ment of feed efficiency in Italian pigs", proposal code  P2022FZMJ9 - CUP J53D23018310001.