Towards the Development of Nutrigenetic Concepts in Pigs by Merging Genomics, Transcriptomics and Metabolomics

In a context of system biology concepts applied to livestock, animal nutrition can be considered as the netwotk interconnecting metabolic, physiologic and genetic aspects. The aim of this Thesis was to detect markers associated with productive traits and metabolic pathways in pigs, merging analyses on pig genome, transcriptome and metabolome. Several approaches of target metabolomics, target re-sequencing of pig genome portions and RNA-seq have been performed, adding classical lab validations. Analysis of the variability in pig genes related to metabolism like bitter taste receptors genes (TAS2R), fatty acids receptors genes (GPR120), KMO and others have been carried out in different pig populations, including commercial breeds (Large White, Duroc, Landrace, Pietran, Meishan) and Italian local pig breeds (Mora Romagnola, Nero Siciliano, Apulo-Calabrese, Casertana and Cinta Senese) as well as wild boars. Moreover, genome wide association analyses based on metabolites and, for most metabotypes, significant SNPs were close or within genes directly involved in the catabolic or anabolic pathways of the targeted metabolites. A few of these markers were associated (P nominal value <0.01) with production and carcass traits. According to our results, the development of precision feeding strategies focused on specific amino acid needs of the animals according to their genotype in genes involved in the amino acid metabolism pathways would be one of the envisaged perspectives of application in pig nutrigenetics and, more generally, in livestock nutrition.