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

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. Author summaryCompared with the commercial breeds, Chinese local pig breeds have lower growth rates, higher fat content and better meat quality, because they have adapted to local environment and have not been strongly selected. These differences make them as exceptional resources to identify candidate markers for the improvement of meat production traits in pig breeding. In this study, we compared the genome and skeletal muscle transcriptome differences between Chinese local Tongcheng and commercial Landrace pigs, and uncovered the genetic regulation of coding and non-coding RNAs, such as SATB2 and XLOC_036765, in skeletal muscle development and diversity. This study enhances our understanding of the genetic basis of skeletal muscle development and diversity, and provide useful molecular markers for the genetic improvement meat production traits.