# Multi-Omics Integration Reveals Key Genes, Metabolites and Pathways Underlying Meat Quality and Intramuscular Fat Deposition Differences Between Tibetan Pigs and Duroc × Tibetan Crossbred Pigs

## TL;DR

This study identifies genes and metabolites that influence meat quality and fat deposition differences between Tibetan pigs and their crossbred offspring with Duroc pigs.

## Contribution

The study provides new insights into the molecular mechanisms affecting meat quality through multi-omics analysis in Tibetan pigs and their crossbreds.

## Key findings

- Tibetan pigs have higher intramuscular fat and monounsaturated fatty acids compared to crossbreds.
- Genes like IL6, GPX1, and metabolites like betaine and carnosine are linked to meat quality differences.
- Crossbred pigs retain high productivity while inheriting superior meat traits from Tibetan pigs.

## Abstract

Tibetan pigs are a valuable local pig breed in China, known for their excellent meat quality. However, their slow growth and low production efficiency limit large-scale breeding. Crossbreeding with Duroc pigs is a promising strategy to balance meat quality and production performance. Yet, the molecular mechanisms underlying the differences in meat quality and intramuscular fat deposition between TPs and DZs remain unclear. Our study addresses this gap through phenotype detection and multi-omics analysis.

The sensory quality of pork constitutes a complex phenotype that arises from the interplay between genetic factors and environmental conditions. As a local pig breed in China, Tibetan pigs (TPs) are known for their high-quality meat. However, their slow growth rate and low production efficiency limit their large-scale breeding. We have used Duroc as a hybrid sire to improve TP. Our study found that TPs have higher intramuscular fat content and higher levels of monounsaturated fatty acids. Duroc × Tibetan crossbred pigs (DZs) not only retain the paternal high productivity but also inherit the superior meat quality of the maternal parent. Transcriptome analysis identified IL6, GPX1, GPX3, AOX1, ALDH7A1, PTGS2, NFKBIA, ADIPOQ and PPARG as being involved in affecting meat quality. Metabolomic analysis found that betaine, carnosine, L-carnitine, and lysophosphatidylcholine were important components that affect meat quality. Joint analysis further reveals that the expression of ATF4, DGKB, GNMT, and ADSL genes is closely related to arachidonic acid, lysophosphatidylcholine, betaines, and hypoxanthine, ultimately affecting the quality of the meat. By comprehensively analyzing the carcass and meat quality traits, genes and metabolites affecting meat quality traits, this study provides new evidence for improving pork quality and guiding breeding strategies.