Multi-omics dissection of lipid metabolism in Italian heavy pig breeds

Metabolomics can provide a comprehensive overview of circulating metabolites in animals, considered as endophenotypes or molecular phenotypes. These molecules are the products of various metabolic pathways controlled, modified or catalysed by a wide range of enzymes, regulators and other protein products. Metabolites can be used to dissect more complex phenotypes that have direct or indirect economic value in animal breeding. The lipid fraction of the animal metabolome can help describe the lipidome, providing new insights into the genetic and physiological mechanisms underlying fat related traits. Fat deposition and composition traits are particularly important in the Italian heavy pig production sector, due to their impact on carcass, meat quality and production traits. In this study, we combined genomic and lipidomic information from approximately 700 Italian Large White (ILW) and 300 Italian Duroc (IDU) pigs to analyse genetic factors affecting the pig plasma lipidome. These pigs were genotyped with a 60,000 single nucleotide polymorphism (SNP) panel and their lipid profiles, consisting of ~300 lipids and derived metabolites, were analysed. Lipidomic profiles were initially compared between the two breeds using multivariate approaches. A total of 30 sphingolipids were found to be differentially abundant in the plasma of pigs from these two breeds. Additionally, genome wide association studies identified significant SNPs for 78 and 54 molecules in ILW and IDU pigs, respectively. The same QTL identified in both breeds had opposite allele frequencies, suggesting that lipid related metabolism is controlled by different genetic mechanisms in these breeds. The research was supported by: (1) PRIN2017 PigPhenomics that has received funding from the Italian MUR (for the production metabolomic data); (2) the Horizon Europe Re-Livestock pro-ject that has received funding from the European Union's Horizon Europe research and innovation programme under the grant agreement No. 01059609; (3) the European Union Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) – MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 – D.D. 1032 17/06/2022, CN00000022).