Simple Summary
In this study, we investigated the genetic basis of key feed efficiency traits, namely residual feed intake, feed conversion ratio, and average daily feed intake in a commercial line of heavy pigs. Using a Bayesian case–control genome-wide association approach, we identified, for each trait, multiple SNPs with high posterior probability for the direction of their effects, confirming that feed efficiency traits are polygenic. Potential candidate genes involved in feed efficiency, as well as in nutrient transport and absorption, metabolic homeostasis, immune functions, cellular signaling, energy sensing, neurological processes, and other processes, were identified. These findings highlight the complexity of feed efficiency and contribute to expanding current knowledge of the biological mechanisms underlying this trait in pigs.
Abstract
Feed efficiency traits are increasingly important in pig production for improving profitability and environmental sustainability. Understanding their genetic basis is crucial for uncovering underlying biological mechanisms and informing selection strategies. In this study, we analyzed residual feed intake (RFI), feed conversion ratio (FCR), and average daily feed intake (ADFI) in 201 animals. Three separate Bayesian GWASs were conducted using 29,844 SNPs in a case–control design, with the lowest and highest 15% of the phenotypic distribution selected as controls and cases (N = 30 per group), respectively, for each trait. The results confirmed the polygenic nature of the traits, identifying 4 SNPs for RFI on Sus scrofa chromosomes (SSC) 3, 13, and 15 with high posterior probability for the direction of their effects; 4 SNPs for FCR on SSC 8, 14, and 17; and 8 SNPs for ADFI on SSC 1, 2, 6, 8, and 11. A candidate gene search identified 41 potential genes involved in diverse biological processes, including feed efficiency, intestinal development, tissue remodeling and integrity, nutrient transport and absorption, metabolic homeostasis, cellular signaling, energy sensing, and neurological regulation. These genes formed a highly interconnected network, highlighting the complexity of feed efficiency and the interplay among multiple physiological, metabolic, and regulatory pathways.