<b>Transcriptome and proteome analysis revealed the key genes and major pathways that social genetic effects influence pig RFI</b>

Background: Social genetic effects (SGEs), also known as indirect genetic effects (IGEs), refer to heritable components within the environment that impact an individual’s phenotype through social interactions with conspecifics. SGEs play a significant role in feeding behaviour and related production performance phenotypes, although the underlying mechanisms remain unclear. In this study, we examined the feeding behaviour and growth performance of two groups of pigs with extreme values of SGEs on residual feed intake. Additionally, we conducted combined proteomics and transcriptomics analysis of the liver and ileum in these two pig groups using transcriptome sequencing and ITRAQ technology to investigate the underlying mechanisms and major pathways involved. Results: We found that individuals with higher social genetic effects spent a longer time but had fewer visits in the feeder, they also consumed a lesser overall amount of food but had a higher intake per feeding. We also identified the differentially expressed genes in the liver and ileum. Through functional enrichment analysis, we found that the differentially expressed genes in the liver were mainly associated with mitochondrial oxidative phosphorylation, while the differentially expressed genes in the ileum were primarily associated with fatty acid metabolism and absorption, as well as amino acid metabolism. Afterwards, we identified potential key genes through a combined analysis of transcriptome and proteome data. Core genes in the liver were mainly enriched in mitochondria and involved in oxidative phosphorylation and respiratory electron transport. Core genes in the ileum were primarily associated with fat digestion and absorption, as well as cholesterol metabolism. Conclusions: In conclusion, pigs with different values of SGEs exhibit distinct feeding patterns, and mitochondrial oxidative phosphorylation, fat digestion and absorption, and amino acid metabolism are the primary pathways through which SGEs influence residual feed intake. Our study offers valuable insights into understanding the regulatory mechanisms of SGEs on RFI.