Single-nucleus transcriptome profiling of skeletal muscle in Diqing Tibetan pigs with distinct body sizes

The Diqing Tibetan pig (DQTP) is a local breed in China, renowned for its high adaptation to plateau climates. However, it has undergone less human selection compared to modern commercial pigs, resulting in smaller but a wide range of body sizes and meat production within its population. The cellular transcriptional variation in this breed related to muscle phenotypes remains unexplored. In this study, we performed single-nucleus transcriptome analysis to investigate the muscle cell profiles of 6-month-old pigs with differing body sizes. Cell clustering analysis indicated muscle cells can be categorized into myogenic lineages (myocytes and satellite cells), fibro-adipogenic progenitors (FAPs), endothelial and vascular-related cells (EVRCs), and immune cells (both myeloid and lymphoid). The composition of cell types reflected subtypes of myocytes and mitochondrial metabolism-related FAPs and endothelial cells, with significant differences observed among cell subtypes. We discovered some genes with cell subtype-specific differential expression levels, such as TECRL and MYOZ2 (slow-twitch muscle), and MYL1, AMPD, and FILIP1L (Myocyte-like FAPs). Additionally, ligand-receptor analysis identified significantly stronger cell interaction activities in larger DQTP pigs, suggesting a potential association with the observed the body size variation. The pathways involving COLLAGEN, LAMININ, and PTPRM, which are crucial for extracellular matrix organization and adhesion, were mostly enriched in interactions between FAPs and EVRCs. This work provides a comprehensive overview of muscle-resident cell profiles and identifies differences in cell type composition, cellular gene expression levels, and cell communication intensity in DQTP, which may enhance the understanding of the mechanisms underlying discrepancies in porcine muscle growth.