# Integrating Transcriptomics and Metabolomics to Elucidate the Molecular Mechanisms Underlying Beef Quality Variations

## TL;DR

This study combines transcriptomics and metabolomics to understand the molecular basis of beef quality differences, identifying genes and metabolites that influence traits like flavor and tenderness.

## Contribution

The study integrates transcriptomic and metabolomic data to identify key genes and metabolites linked to beef quality traits, offering new insights for precision breeding.

## Key findings

- Significant differences in muscle fiber area, diameter, and density were observed between high- and low-quality beef samples.
- AMPD2, ACOX3, and glycolysis/gluconeogenesis pathway genes were identified as key regulators of beef flavor, fat deposition, and tenderness.
- Pearson correlation analysis revealed synergistic regulation between differentially expressed genes and metabolites in core metabolic pathways.

## Abstract

Elucidating the molecular mechanisms underlying beef quality differences is crucial for precision breeding of high-quality cattle. In this study, we first characterized the myofibrillar morphology of high-quality (H group) and low-quality (L group) beef samples using hematoxylin–eosin (HE) staining. Transcriptomic and metabolomic analyses were then conducted to reveal the molecular regulatory basis of quality variation. HE staining revealed highly significant differences in muscle fiber area and diameter between H and L groups (p < 0.01), along with significant differences in muscle fiber density (p < 0.05), but no significant differences in muscle fiber perimeter. Furthermore, by focusing on five core metabolic pathways shared across the transcriptome and metabolome datasets, 30 differentially expressed genes (DEGs) and 14 differentially accumulated metabolites (DAMs) were identified. Pearson correlation analysis revealed synergistic regulation between DEGs and DAMs: AMPD2 modulates umami flavor by regulating inosine accumulation via the purine metabolism pathway; ACOX3 promotes unsaturated fatty acid synthesis and intramuscular fat deposition through carbohydrate metabolism; genes in the glycolysis/gluconeogenesis pathway maintain post-slaughter muscle pH homeostasis, thereby influencing beef tenderness. Collectively, this study integrates morphological and molecular evidence to elucidate the multi-level basis of beef quality formation, providing key candidate genes, metabolites, and pathways for molecular breeding. These findings offer comprehensive theoretical and technical support for the sustainable development of the premium beef industry.