Single-Nucleus RNA Sequencing Reveals Cellular Transcriptome Features at Different Growth Stages in Porcine Skeletal Muscle

Porcine latissimus dorsi muscle (LDM) is a crucial source of pork products. Meat quality indicators, such as the proportion of muscle fibers and intramuscular fat (IMF) deposition, vary during the growth and development of pigs. Numerous studies have highlighted the heterogeneous nature of skeletal muscle, with phenotypic differences reflecting variations in cellular composition and transcriptional profiles. This study investigates the cellular-level transcriptional characteristics of LDM in large white pigs at two growth stages (170 days vs. 245 days) using single-nucleus RNA sequencing (snRNA-seq). We identified 56,072 cells across 12 clusters, including myofibers, fibro/adipogenic progenitor (FAP) cells, muscle satellite cells (MUSCs), and other resident cell types. The same cell types were present in the LDM at both growth stages, but their proportions and states differed. A higher proportion of FAPs was observed in the skeletal muscle of 245-day-old pigs. Additionally, these cells exhibited more active communication with other cell types compared to 170-day-old pigs. For instance, more interactions were found between FAPs and pericytes or endothelial cells in 245-day-old pigs, including collagen and integrin family signaling. Three subclasses of FAPs was identified, comprising FAPs_COL3A1⁺, FAPs_PDE4D⁺, and FAPs_EBF1⁺, while adipocytes were categorized into Ad_PDE4D⁺ and Ad_DGAT2⁺ subclasses. The proportions of these subclasses differed between the two age groups. We also constructed differentiation trajectories for FAPs and adipocytes, revealing that FAPs in 245-day-old pigs differentiated more toward fibrosis, a characteristic reminiscent of the high prevalence of skeletal muscle fibrosis in aging humans. Furthermore, the Ad_PDE4D⁺ adipocyte subclass, predominant in 245-day-old pigs, originated from FAPs_PDE4D⁺ expressing the same gene, while the Ad_DGAT2⁺ subclass stemmed from FAPs_EBF1⁺. In conclusion, our study elucidates transcriptional differences in skeletal muscle between two growth stages of pigs and provides insights into mechanisms relevant to pork meat quality and skeletal muscle diseases.