# Multi-Omics Integration Identifies Key Pathways and Regulatory Genes Driving Marbling Formation and Meat Quality in Yunling Cattle

## TL;DR

This study identifies the molecular mechanisms behind marbling in Yunling cattle, revealing key genes and pathways that contribute to high-quality beef.

## Contribution

The study provides a multi-omics framework to uncover novel regulatory genes and metabolic pathways specific to Yunling cattle marbling.

## Key findings

- Yunling cattle show distinct lipid and amino acid profiles compared to Angus and Simmental breeds.
- Key genes like NDUFB1, COX7C, and ITGB3 are linked to marbling formation through co-expression network analysis.
- Energy metabolism and cell communication pathways are uniquely active in Yunling cattle, supporting fat deposition.

## Abstract

Marbling, the fat found inside muscle, is a key factor in determining beef quality, making the meat tender and flavorful. Yunling cattle, a breed from China, are known for their potential to produce excellent marbling, but the biological reasons behind this trait are not fully understood. This study investigated the muscle characteristics of Yunling cattle by comparing them with Angus and Simmental breeds. By analyzing gene activity, fat composition, and amino acid levels, we identified unique molecular patterns in Yunling cattle. We found that specific groups of genes work together with distinct fat molecules and amino acids to promote marbling formation. Specifically, Yunling cattle exhibit a unique energy metabolism and cell communication system that supports fat deposition. These results provide a scientific explanation for the superior meat quality of Yunling cattle. This knowledge is valuable for the beef industry as it helps breeders select the best animals, leading to genetic improvements and ensuring a consistent supply of high-quality, tasty beef for consumers.

Marbling, or intramuscular fat (IMF), is a primary determinant of high-quality beef, defining key sensory attributes and nutritional value. Yunling (YL) cattle, an indigenous breed from Yunnan, China, are renowned for their superior marbling, yet the underlying molecular mechanisms remain unclear. This study employed an integrated transcriptomic, lipidomic, and amino acid metabolomic approach to systematically compare the multi-omics profiles of the longissimus dorsi muscle among YL, Angus (AGS), and Simmental (XMTE) cattle. Transcriptome analysis identified 2053 and 2156 differentially expressed genes (DEGs) in XMTE vs. YL and AGS vs. YL, respectively. These DEGs were primarily enriched in the PI3K-Akt and MAPK signaling pathways, as well as oxidative phosphorylation. Lipidomic analysis revealed a distinct lipid profile in YL cattle, identifying 27 characteristic lipid molecules (e.g., SM(d20:0/24:1), DG(16:0/18:1(11Z)/0:0)) compared to XMTE and 17 differential lipids compared to AGS. The amino acid metabolome showed that Beta-Alanine and L-Aspartic acid levels in YL were 42.6% and 54.8% lower than in XMTE, respectively (p < 0.01), and levels of several functional amino acids were significantly reduced compared to AGS. Weighted Gene Co-expression Network Analysis (WGCNA) constructed a gene-metabolite network, identifying key modules strongly correlated with lipid and amino acid metabolism (|r| > 0.6). Within these modules, energy metabolism-related genes such as NDUFB1, COX7C, and IDH3B, along with signal transduction genes including ITGB3, PDGFRA, and FN1, were found to synergistically regulate marbling formation in YL cattle. This study systematically elucidates the molecular mechanisms underlying both marbling formation and the nutritional characteristics of meat in Yunling cattle. This provides a theoretical foundation for genetic improvement and offers potential molecular targets to enhance both marbling and overall meat quality in other indigenous cattle breeds worldwide.