Integrative Analysis of Gene Networks Associated with Adipose and Muscle Traits in Hanwoo Steers

TL;DR

This study identifies gene networks in Hanwoo cattle that influence fat and muscle traits, offering insights to improve meat quality through better breeding.

Contribution

The study reveals tissue-specific gene co-expression modules and hub genes like AGPAT5 and ARPC5 that influence fat and muscle metabolism in Hanwoo cattle.

Findings

Yellow and blue modules were positively associated with back fat, while turquoise and green modules correlated negatively with abdominal fat.

ARPC5 was linked to lipid metabolism and energy storage, while AGPAT5 was associated with muscle cell structure and function.

Seven co-expression modules were identified, revealing distinct gene expression patterns between fat and muscle tissues.

Abstract

Hanwoo cattle are valued for their excellent meat quality and distinctive marbling; however, the genetic reasons behind the development of fat and muscle remain unclear. In this study, we analyzed gene expression in five tissues to understand how certain genes interact to shape these traits. We identified several groups of genes that were more active either in fat or in muscle. In fat tissue, many genes were related to lipid metabolism and tissue structure, whereas in muscle tissue, genes were primarily involved in energy production and mitochondrial function. Some genes, such as AGPAT5 and ARPC5, seemed to play key roles in linking these biological processes. These results give us a clearer picture of how gene networks contribute to the balance between fat and muscle in Hanwoo cattle. The findings may help improve breeding programs by enhancing marbling and reducing excess fat, ultimately supporting better beef quality and sustainable production.

This study aims to characterize tissue-specific expression patterns in Hanwoo steers by identifying co-expression modules, functional pathways, and hub genes related to fat and muscle traits using Weighted Gene Co-expression Network analysis (WGCNA). RNA-Seq data were generated from three muscle tissues (longissimus muscle, tenderloin, and rump) and two fat tissues (back fat and abdominal fat) collected from six 30-month-old Hanwoo steers. Quality control of raw sequencing reads was performed using FastQC, and trimmed reads were aligned to the bovine reference genome (ARS-UCD1.3) using HISAT2. We also identified a gene co-expression network via WGCNA using normalized gene expression values. Modules were defined based on topological overlap and correlated with tissue-specific expression patterns. Modules with a significant association (p < 0.05) were used for functional enrichment based on Gene Ontology (GO) and KEGG pathways, as well as Protein–Protein Interaction Network analysis. A total of seven co-expression modules were identified by WGCNA and labeled in distinct colors (yellow, blue, red, brown, turquoise, green, black). Among them, the yellow and blue modules were positively associated with back fat, while the turquoise and green modules showed a negative correlation with abdominal fat. Additionally, the turquoise or green module was positively correlated with longissimus and rump tissues, indicating distinct gene expression patterns between fat and muscle. This study identified key co-expression modules and hub genes associated with muscle and fat metabolism. Notably, ARPC5 (blue module) was involved in lipid metabolism and energy storage, whereas AGPAT5 (turquoise module) was linked to maintaining muscle cell structure and function. These findings reveal biological mechanisms for tissue-specific gene regulation, providing targets for enhancing meat quality in Hanwoo.

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