Comparative Transcriptomic Analysis Between High- and Low-Growth-Rate Meat-Type Rabbits Reveals Key Pathways Associated with Muscle Development

Rabbit meat constitutes a high-protein, low-fat nutritional resource demonstrating rising consumption, particularly within the Asia-Pacific region. Consequently, muscle growth and developmental pattern in meat rabbits represent critical economic considerations. To elucidate the primary signaling pathways governing muscle development, we first performed comparative body weight analyses between two rabbit breeds exhibiting divergent growth rates: the fast-growing Checkered Giant (Ju) and slow-growing Sichuan Ma rabbit. Subsequent, post-natal qualities of thigh and <i>longissimus dorsi</i> muscle fiber were quantified across three developmental phases (28, 56, and 84 days post-natal). The results showed the body weight of Ju rabbit was significantly higher than that of Ma rabbit beyond 3 weeks post-natal (<i>p</i> < 0.05), while Ma rabbit exhibited larger muscle fiber areas in both tissues at 56 days (<i>p</i> < 0.05). The transcriptome analysis showed that 284 and 305 differentially expressed genes (DEGs) (|log2FC| > 1, padj < 0.05) were identified in thigh muscle and <i>longissimus dorsi</i> muscle, respectively. GO (Gene Ontology) analysis of DEGs indicated DEGs in the thigh muscle were enriched in these terms related to biological processes of muscle cell migration and smooth muscle cell migration, cellular components of sarcomere, myofibril, and actin filament bundle, while DEGs in <i>longissimus dorsi</i> muscle were enriched in these terms associated with biological processes of muscle cell migration, smooth muscle cell migration and muscle structure development, cellular component of actin cytoskeleton, contractile fiber, myofibril, myosin complex and molecular function of actin filament binding. Integrated GO, KEGG and PPI analyses of co-expressive DEGs implicated the HIF-1 signaling pathway and Glycolysis/Gluconeogenesis in muscular development. Different expression of energy metabolism hub-genes might be the primary reason for interbreed muscle developmental disparities.