پردیس کشاورزی و منابع طبیعی دانشگاه تهران Iranian Journal of animal Science 2008-4773 57 2 2026 06 22 Comparative analysis of gene expression and allele-specific expression (ASE) in intramuscular and subcutaneous adipose tissues in beef cattle Comparative analysis of gene expression and allele-specific expression (ASE) in intramuscular and subcutaneous adipose tissues in beef cattle 333 349 105367 10.22059/ijas.2025.406502.654106 FA Hamideh Noori Sadegh Department of Animal Science, Faculty of Agriculture, University of Zabol, Zabol, Iran. 0009-0006-2736-8413 Gholam Reza Dashab Associate professor of Animal Breeding and Genetic, Department of Animal Science, University of Zabol, Zabol, Iran. 0000-0003-2227-542X Zahra Roudbari Department of Animal Science, Faculty of Agriculture, University of Jiroft, Jiroft, Iran. 0000-0002-3357-3126 Mohammad Hossein Banabazi Department of Animal Biosciences (HBIO), Center for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), 75007 Uppsala, Sweden. 0000-0002-7873-8123 Tomas Sadkowski Department of Physiological Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences, Poland. 0000-0001-9175-7110 Journal Article 2025 11 18 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, 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, https://ijas.ut.ac.ir/article_105367_8f0d589ed73e3f42652b42b71aa63041.pdf