Comparative transcriptome analysis reveals the patterns of gene expression in different venison cuts of sika deer (Cervus nippon)

Objective: Venison (deer meat) is increasingly favored by consumers for its safety, nutrition, flavor, and natural qualities. However, venison cuts in different regions of the carcass have different meat quality due to their distinct physiological function. To investigate the molecular basis of these variations, RNA-seq was used to compare gene expression pattern across different cuts of venison. Methods: In this study, we performed a transcriptomic analysis based on RNA-seq data of 72 cuts from 6 different body parts of sika deer (Cervus nippon, n = 12), with the aim of understanding the genetic factors affecting the differences in venison quality, providing important references for further deer breeding. Results: We identified 139,111 expressed genes, including 79 region-specific genes enriched in pathways crucial for meat texture, tenderness, and nutrition. Differential gene expression analysis revealed significant variations among venison cuts, especially between the longissimus dorsi and trapezius cuts, highlighting roles in metal ion transport, organic acid biosynthesis, and glycolysis/gluconeogenesis. Additionally, fatty acid metabolism genes showed stable expression, while muscle fiber structure genes varied, affecting tenderness and juiciness. Conclusion: Our findings provide insights into the genetic factors influencing venison quality, offering a foundation for future breeding strategies to enhance meat quality.