Abstract
BACKGROUND: Studying the genetic characteristics and molecular mechanisms of immune regulation in horses is of great significance for protecting their genetic resources, improving breeding strategies, and enhancing their disease resistance, thereby ensuring their healthy performance in both sports and production. AIMS/OBJECTIVES: This study investigates the genetic characteristics and molecular mechanisms underlying immune regulation in Yili horses, comparing them with Thoroughbreds and Kazakh horses. METHODS: Blood samples from each breed were analyzed for physiological, biochemical, and immune indices alongside transcriptome sequencing to identify differentially expressed genes (DEGs). RESULTS: The results revealed significant differences in neutrophil counts, monocytes, red blood cell parameters, glucose levels, and immunoglobulins (IgA, IgG, IgM) among breeds. Yili horses exhibited intermediate values for most parameters, aligning more closely with Thoroughbreds. Transcriptomic analysis identified 3574 DEGs, enriched in immune-related pathways such as platelet activation, antigen processing, and cytokine signaling. Key genes, including TNFRSF14, IFIT3, and IL21R, correlated with immune traits, highlighting hybrid vigor in Yili horses. Functional enrichment underscored pathways like IL-17 signaling and NF-κB regulation, linking genetic differences to immune adaptability. CONCLUSIONS: These findings provide molecular insights into breed-specific immune traits, supporting strategies to enhance disease resilience in Yili horses while preserving their athletic performance. This study underscores the importance of integrating transcriptomic and phenotypic data for informed breeding practices in equine conservation and improvement.