Comparative transcriptomic analysis of skeletal muscle tissue during prenatal stages in Tongcheng and Yorkshire pig using RNA-seq

Myogenesis is accompanied by a number of changes in gene expression in mammals, and the transcriptional events that underlie these processes have not been yet fully elucidated. In this study, RNA-seq was used to comprehensively compare the transcription profiles of skeletal muscle between Tongcheng (TC) and Yorkshire (YK) pigs at 40, 55, 63, 70, and 90 days of gestation. One thousand three hundred seventeen and 691 differentially expressed genes (DEGs) were detected in TC and YK, respectively, among which 321 DEGs were shown to be common in TC and YK. STEM (Time-series Expression Miner) analysis revealed different gene expression profiles between the two breeds. One thousand six hundred seventy-seven genes showed significant differential expression between TC and YK at the identical stages, while three genes were found to be common in all comparisons. A total of 3185 new putative transcripts were also predicted. Several gene expression profiles were further validated by qRT-PCR. Fifty-five dpc (days post coitum) was suggested to be the key stage to contribute developmental differences between TC and YK. PTEN, EP300, ENSSSCG00000004979 (Myosin 9A), CDK14, IRS1, PPP1CC, and some ribosomal proteins were suggested to be the key candidate genes for elucidating the developmental differences between the two breeds. In conclusion, we constructed comprehensive high-resolution gene expression maps of these two pig breeds, which not only provides an in-depth understanding of the dynamics of transcriptional regulation during myogenesis in this study, but also would facilitate the elucidation of molecular mechanisms underlying myogenesis in the future studies.