The genome variation and developmental transcriptome maps reveal genetic differentiation of skeletal muscle in pigs

Abstract

Natural and artificial directional selections have resulted in significantly genetic and phenotypic differences across breeds in domestic animals. However, the molecular regulation of skeletal muscle diversity remains largely unknown. Here, we conducted transcriptome profiling of skeletal muscle across 27 time points, and performed whole-genome re-sequencing in Landrace (lean-type) and Tongcheng (obese-type) pigs. The transcription activity decreased with development, and the high-resolution transcriptome precisely captured the characterizations of skeletal muscle with distinct biological events in four developmental phases: Embryonic, Fetal, Neonatal, and Adult. A divergence in the developmental timing and asynchronous development between the two breeds was observed; Landrace showed a developmental lag and stronger abilities of myoblast proliferation and cell migration, whereas Tongcheng had higher ATP synthase activity in postnatal periods. The miR-24-3p driven network targeting insulin signaling pathway regulated glucose metabolism. Notably, integrated analysis suggested SATB2 and XLOC_036765 contributed to skeletal muscle diversity via regulating the myoblast migration and proliferation, respectively. Overall, our results provide insights into the molecular regulation of skeletal muscle development and diversity in mammals.

The Landscape of Accessible Chromatin and Developmental Transcriptome Maps Reveal a Genetic Mechanism of Skeletal Muscle Development in Pigs

“…In addition, the number of differential genes between D0, D60, D120, and D180 was compared, and day 0 had the highest amount from the volcano plot ( Figure 2 C). In a previous study, transcriptome analysis and whole-genome resequencing of skeletal muscles from Landrace (lean) and Tongcheng (obese) pigs at 27 time points yielded similar results [ 49 ]. Time-series expression miner (STEM) analysis revealed differential gene expression profiles in the Landrace pigs.…”

Identification of the cuproptosis-related hub genes and therapeutic agents for sarcopenia

“…Previous studies have suggested that these genes were functionally enriched in processed related to metabolism and cell activities such as cellular respiration and oxidationreduction process (Yang et al, 2021). KEGG analysis showed that they were involved in biological processes related to mitochondrial functions in skeletal muscles, including central carbon metabolism, citrate cycle, glycolysis, and oxidative phosphorylation (Chae et al, 2018).…”

Integrative single-cell RNA-seq and ATAC-seq analysis of myogenic differentiation in pig

“…There are significant differences in skeletal muscle development between pig breeds differing in growth rate, muscle production, muscle fiber diameter, and meat quality [ 70 ]. In this study, the results of immunohistochemistry, scRNA, and scATAC analysis did not show significant differences between ZZ and DZ in early embryonic development, despite their considerable difference in meat production.…”