# Transcriptomic and Proteomic Analyses of the Liver and Ileum Identify Key Genes and Pathways Associated with Low and High Groups of Social Genetic Effect of Residual Feed Intake

## TL;DR

This study explores how the genes of other pigs affect individual feed efficiency, finding differences in feeding behavior and biological pathways in pigs with high or low genetic effects.

## Contribution

The study identifies key genes and pathways in liver and ileum tissues linked to social genetic effects on feed intake in pigs.

## Key findings

- Pigs with high SGE values showed distinct feeding patterns, spending more time at the feeder but consuming less overall.
- Differentially expressed genes in the liver were linked to energy processes, while ileum genes were related to fat digestion and cholesterol metabolism.
- Integrated transcriptomic and proteomic analysis revealed key genes involved in mitochondrial functions and oxidative phosphorylation.

## Abstract

Social genetic effects (SGEs) are how the genes of other animals affect an individual’s traits, such as the feed efficiency within a group. This study investigated the processes involved in SGEs related to the residual feed intake (RFI) in pigs. Pigs with high and low SGE values for RFI were selected, and their feeding behavior, growth performance, and gene and protein expression in the liver and ileum were analyzed. The study found that pigs with higher SGE values had unique feeding habits, spending more time at the feeder but consuming less food overall. Specific genes and proteins were identified: genes in the liver were linked to energy processes, while those in the ileum were related to fat digestion and cholesterol metabolism. These results suggest that pigs in different SGE groups have different feeding behaviors and use various biological pathways to manage feed intake. This research could help improve feed efficiency in pig production.

Social genetic effects (SGEs) refer to how the genotypes of other individuals impact an individual’s phenotype within a population. These effects significantly influence the feeding behavior and production performance in pigs, though their mechanisms are not well understood. This study examined two pig groups with extreme SGE values for residual feed intake (RFI), analyzing their feeding behavior and the molecular mechanisms involved using transcriptomics and proteomics analysis of liver and ileum tissues. Pigs with higher SGE values exhibited distinct feeding patterns, spending more time at the feeder but making fewer visits. They consumed less overall feed but had a higher intake per visit. Differentially expressed genes and proteins were identified in the liver and ileum and were associated with processes such as mitochondrial functions, oxidative phosphorylation, and cholesterol metabolism. Integrated analysis supported these findings. Combined transcriptome and proteome analysis identified potential key genes that were associated with processes including mitochondrial processes, oxidative phosphorylation, fat digestion and absorption, and cholesterol metabolism. The results showed that pigs with differing SGE values display different feeding behaviors and utilize distinct molecular pathways affecting RFI. These findings offer valuable insights into how SGEs influence feed efficiency and shed light on the fundamental mechanisms underlying it.