Transcriptome Analysis of Muscle Tissue from Three Anatomical Locations in Male and Female Kazakh Horses.

The Kazakh horse, a versatile breed, is renowned for stable genetic performance and strong tolerance to coarse feed. Sex is a key factor influencing skeletal muscle development. However, the mechanisms underlying sex-specific regulation of equine muscle growth remain obscure. This study employed transcriptomic analysis to investigate sex-associated molecular differences in skeletal muscle of Kazakh horses. The experimental cohort comprised four three-year-old Kazakh stallions and four three-year-old Kazakh mares. After slaughter, six groups of muscle samples were collected immediately, including the longissimus dorsi, rectus abdominis, and diaphragm muscles of both sexes, with four biological replicates per group. RNA-seq analysis revealed 361, 230, and 236 differentially expressed genes (DEGs) in the longissimus dorsi of stallion Kazakh horses (Mb) vs. the longissimus dorsi of mare Kazakh horses (Gb), the rectus abdominis of stallion Kazakh horses (Mf) vs. the rectus abdominis of mare Kazakh horses (Gf), and the diaphragm of stallion Kazakh horses (Mg) vs. the diaphragm of mare Kazakh horses (Gg), respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that DEGs such as , , , and were primarily enriched in muscle system processes (BP), contractile fibers (CC), and adenosine ribonucleotide binding (MF). Furthermore, these genes were significantly associated with pathways such as the Cytoskeleton in muscle cells and the Thyroid hormone signaling pathway. The data demonstrate pronounced sex-related differences in gene expression and muscle structure in Kazakh horses, likely mediated by cytoskeleton-associated genes. Notably, , , , and may act as key regulators of sex-specific muscle development. These findings provide molecular insights into the mechanisms underlying sexual dimorphism in equine muscle growth.