Identification of biomarkers for feed efficiency and growth rate by exploring the plasma metabolome of divergent heavy pigs

Feed represents the largest expense in pig farming and significantly affects the sustainability of the production system. Therefore, enhancing feed efficiency is a key strategy to mitigate these costs and environmental impacts. This is particularly relevant in the context of the heavy pig system in which animals are slaughtered at a heavier live weight than in many other production systems to follow the rules of Protected Designation of Origin (PDO) value chains. Since growth rate is correlated with feed efficiency, and under PDO rules, pigs cannot reach the slaughter weight earlier than a set age limit, the daily gain of the pigs needs to be controlled. In this study, we used untargeted metabolomics to identify plasma metabolites in Italian Large White heavy pigs that may differentiate between animals with divergent feed efficiency and growth rate, and that may constitute biomarkers for one or the other trait. From a starting cohort of 672 performance-tested pigs, two partially overlapping datasets of 200 pigs each, extreme and divergent for feed conversion ratio (FCR) and average daily gain (ADG), were selected. Approximately 700 metabolites were analysed in the plasma of these pigs. Metabolomic data were analysed with the Boruta machine learning algorithm. Discriminant metabolites were further evaluated through univariate and multivariate analyses. Boruta identified 10 and 7 metabolites that differentiate between FCR and ADG extreme pigs, respectively, with an additional metabolite shared by the two datasets. Most metabolites selected in the FCR dataset still show significant abilities to discriminate among high and low ADG pigs, even if they have not been selected in the Boruta analysis, showing medium to high values of Area Under the Curve, and highly significant Mann-Whitney test U P-values, while the opposite was not true. Among the metabolites detected, L-carnitine and O-adipoylcarnitine, both involved in fatty acid metabolism, were significantly higher in pigs with high FCR. Isoleucylhydroxyproline and prolylhydroxyproline, linked to collagen turnover, were higher in low FCR pigs, potentially reflecting more efficient protein metabolism. Other metabolites linked to gut microbiome activity significantly differentiate between high and low FCR and ADG pigs, suggesting a potential role of the microbiota in nutrient utilisation. The identified metabolomic profiles confirm that feed efficiency and growth rate are related yet distinct traits, whose independent consideration will enhance the accuracy of biomarker discovery and genetic selection in Italian heavy pigs.