Comparative analysis of gene expression and allele-specific expression (ASE) in intramuscular and subcutaneous adipose tissues in beef cattle

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Agriculture, University of Zabol, Zabol, Iran.

2 Associate professor of Animal Breeding and Genetic, Department of Animal Science, University of Zabol, Zabol, Iran.

3 Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran.

4 Department of Animal Biosciences (HBIO), Center for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007 Uppsala, Sweden.

5 Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Poland.

Abstract

This study was conducted to investigate allele-specific expression (ASE) in two types of bovine adipose tissues—intramuscular adipose tissue (IMF) and subcutaneous adipose tissue (SCAT) in order to identify regulatory differences between these depots. Intramuscular fat is a key determinant of beef quality, contributing to tenderness, flavor, and juiciness, and unlike subcutaneous fat, it develops at later stages of animal growth. To achieve this objective, RNA-Seq data from eight tissue samples collected from the 9th to 11th rib region of crossbred Angus cattle were retrieved from the NCBI database (accession number PRJNA1053327) and processed using HISAT2, GATK, and VEP pipelines. The average read-mapping rate was 95%, and more than 580,000 genetic variants were identified. In IMF, among 214,613 ASE-informative SNPs, 890 significant ASE sites were detected, corresponding to 32 genes exhibiting clear allele-specific expression. In contrast, in SCAT, 1,094 significant ASE positions were identified among 305,996 ASE-informative SNPs, associated with 21 genes. Only one gene, SUGCT, was shared between the two tissues; this gene is involved in fatty acid metabolism and cellular energy regulation. Pathway enrichment analysis revealed that immune-related pathways such as JAK–STAT and Necroptosis were predominant in SCAT, whereas IMF was enriched for energy-related pathways, including Hippo signaling and Ubiquinone biosynthesis. The key regulatory genes IFNAR1 in SCAT and RB1 in IMF played major roles in immune regulation and adipocyte differentiation, respectively. Overall, the findings highlight fundamental biological differences between the two bovine fat depots: subcutaneous adipose tissue is more actively engaged in protective and immune-related functions,

Keywords

Main Subjects

Extended Abstract

Introduction

    Lipids constitute a diverse class of biomolecules that play essential roles in maintaining cellular structure and regulating metabolic processes across all cell types. Over the past several decades, long-chain fatty acids (FAs) have been recognized as key participants in a variety of biological functions, ranging from transcriptional regulation to physiological activities. Adipose tissue can be categorized according to its anatomical location into subcutaneous adipose tissue, visceral adipose tissue, bone marrow adipose tissue, intermuscular adipose tissue, and intramuscular adipose tissue. In cattle, intramuscular fat (IMF) differs from other white adipose depots not only in its anatomical position but also in its biological function and, importantly, its economic significance. Since IMF represents fat deposited within muscle fibers, it directly affects the energy balance and growth of muscle tissue. Moreover, the IMF contributes to the flavor, tenderness, and juiciness of beef, making it a “valuable” form of fat in the meat industry. The development of IMF in cattle accelerates after puberty and is modulated by multiple factors, including genetics, nutritional status, sex, and management practices, indicating that IMF deposition can be effectively targeted through selective interventions. In contrast, subcutaneous and other white adipose depots are often regarded as “waste” fat in the beef industry, as their accumulation consumes considerable dietary energy and they are typically undesirable to consumers due to health concerns associated with excessive fat intake, such as an increased risk of cardiovascular disease. This study aims to research and compare intramuscular (marbling) and subcutaneous adipose tissues to elucidate the molecular mechanisms regulating fat accumulation in different depots. Understanding the molecular basis of IMF development across distinct fat types provides valuable insights for improving meat quality and optimizing the utilization of cattle genetic and nutritional resources.

 

Method

In this study, RNA-Seq data from four intramuscular adipose tissue (IMF) samples and four subcutaneous adipose tissue (SCAT) samples of beef cattle (Bos taurus) (accession number PRJNA1053327) were used. Total RNA was extracted using the TRIzol reagent, and its quality was assessed with NanoDrop and Bioanalyzer instruments. RNA libraries were prepared with the Illumina TruSeq Stranded mRNA Kit and sequenced on the Illumina HiSeq 2500 platform using paired-end reads. Raw reads were processed and aligned using FastQC and HISAT2 on the Galaxy platform. Variant calling and allele-specific expression analysis were performed with GATK and Picard in a Linux environment, and gene annotation was carried out using VEP and the DAVID database.

 

Results

In this study, RNA-seq data from intramuscular adipose tissue (IMF) and subcutaneous adipose tissue (SCAT) of beef cattle were analyzed to investigate allele-specific expression (ASE) differences between the two fat depots. The sequencing data showed high quality, with over 95% of reads successfully mapped to the bovine reference genome. A total of 582999 variants were identified in IMF, of which 214613 exhibited ASE, and 890 SNPs showed statistically significant expression, corresponding to 32 genes. In SCAT, 1094 significant ASE SNPs were detected, associated with 21 genes. Only one gene, SUGCT, was shared between the two tissues, indicating its potential role in fatty acid metabolism and cellular energy regulation. Pathway enrichment analysis revealed distinct functional profiles between IMF and SCAT. Immune-related pathways such as JAK–STAT signaling and necroptosis predominated in SCAT, while IMF was enriched in pathways related to cellular growth and oxidative metabolism, including Hippo signaling and ubiquinone biosynthesis. The RB1 gene in IMF was identified as a regulator of adipocyte differentiation and lipid storage, whereas IFNAR1 in SCAT was linked to immune and metabolic responses. Enhanced activity of the ubiquinone pathway in IMF suggested higher mitochondrial energy metabolism, consistent with its role in maintaining muscle energy homeostasis. SCAT demonstrated a greater capacity for lipid accumulation than IMF. Overall, ASE patterns were found to be tissue-specific, reflecting distinct metabolic and regulatory mechanisms between fat depots. These findings provide valuable insights into cis-regulatory control of lipid metabolism and identify potential genomic markers for improving beef quality.

 

Conclusions

This study demonstrated that allele-specific expression (ASE) patterns differ markedly between intramuscular (IMF) and subcutaneous (SCAT) adipose tissues in beef cattle, reflecting distinct metabolic and regulatory functions. IMF showed enrichment in pathways related to mitochondrial activity and energy metabolism, whereas SCAT was primarily associated with immune and inflammatory signaling pathways. Key genes such as RB1 and IFNAR1 were identified as central regulators of adipocyte differentiation and immune modulation, respectively, while SUGCT emerged as the only shared gene, implicating its role in lipid and energy homeostasis. These findings highlight the tissue-specific nature of gene regulation in bovine adipose depots and suggest that cis-regulatory variation contributes to differences in fat deposition and meat quality. Overall, this research provides a foundational framework for future genomic studies aimed at improving beef quality through molecular and genetic selection strategies.

 

Author Contributions

     Methodology, H. N. S., G. R. D., M. H. B. and Z. R.; software, H. N. S., G. R. D. and Z. R.; formal analysis, H. N. S., G. R. D. and Z. R., writing—original draft preparation, H. N. S., G. R. D. and Z. R., writing—review and editing, H. N. S., G. R. D. and Z. R.; supervision, H. N. S., G. R. D., M. H. B., and Z. R., All authors have read and agreed to the published version of the manuscript.

 

Data Availability Statement

     Data available on NCBI by ID: PRJNA1053327.

 

Acknowledgements

The authors would like to thank all participants of the present study.

 

Ethical considerations

    The study was approved by the Ethics Committee of the University of Zabol (Ethical cod: IR-UOZ-4398). The authors avoided data fabrication, falsification, plagiarism, and misconduct.

 

Conflict of interest

    The author declares no conflict of interest.

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Iranian Journal of animal Science
Volume 57, Issue 2
July 2026
Pages 333-349

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History

  • Receive Date: 18 November 2025
  • Revise Date: 12 December 2025
  • Accept Date: 26 December 2025

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