Transcriptome-Based Investigation of Muscle Tissues in Three Anatomical Regions of Kazakh Horses: A Comparative Study Across Sexes

The Kazakh horse is a local breed known for its dual purpose of providing both milk and meat, characterized by stable genetic properties and a tolerance for coarse feeding. The differences in skeletal muscle fiber types and metabolic characteristics between sexes are crucial factors influencing athletic performance; however, the regulatory mechanisms through which sex affects skeletal muscle development in horses remain unclear. In this study, we examined the longest back muscles, abdominal muscles, and diaphragm muscles of three-year-old Kazakh horses (4 males and 4 females) using histochemical staining combined with transcriptome sequencing to systematically analyze the effects of sex on the characteristics of skeletal muscle fibers and their underlying molecular mechanisms. Our results revealed 361 differentially expressed genes (DEGs) in the longest back muscles of different genders, with 230 DEGs and 236 DEGs identified in the respective muscle types. Notably, TPM1, MYL1, and MYH3 exhibited significant differences between male and female muscles. Gene Ontology (GO) functional annotation indicated that the DEGs were predominantly enriched in categories such as contractile fiber and cytoskeletal framework. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis demonstrated significant enrichment of DEGs in muscle cell cytoskeleton and other signaling pathways associated with muscle fiber contraction and energy metabolism. RT-qPCR validation confirmed the reliability of the transcriptome data. Our findings suggest that sex influences the characteristics of muscle fibers in Kazakh horses by regulating the expression of genes related to the skeletal muscle cell framework. TPM1, MYL1, and MYH3 may serve as core candidate genes for sex-specific regulation of skeletal muscle development. This study may provide a molecular foundation for understanding gender differences in equine athletic performance and holds significant reference value for optimizing horse breeding and training strategies.