Integrated proteomics and transcriptomics analysis of dynamic changes in muscle fiber types in different regions of porcine skeletal muscle

Skeletal muscle serves as a valuable source of nutrition, with distinct muscle fiber types exhibiting different physicochemical properties that influence both meat quality and muscle function. Bama miniature pigs (BM) are recognized for their superior meat quality and their relevance as models for human medical research. Therefore, investigating the differences between slow and fast muscles at various developmental stages (from 57 days post-fertilization to 120 days postnatally) in BM is crucial for both the pork industry and biomedical studies. In this study, we employed a non-targeted data-independent acquisition (nDIA) -based proteomic approach for the first time to porcine embryonic skeletal muscle fibers. A total of 616 differentially expressed genes (DEGs) and 272 differentially abundant proteins (DAPs) were identified in the fast-twitch longissimus dorsi (LD) and slow-twitch semitendinosus (SD) muscles of BM. Domain enrichment analysis and in vitro experiments demonstrated that the NEK3 gene, containing the S_TKc domain, inhibits fast-twitch muscle fiber differentiation postnatally. Additionally, cross-species analysis showed upregulation of skeletal muscle development organ genes in pigs at postnatal day 28. In summary, our results provide both fundamental data and novel insights to further uncover the mechanisms underlying pig skeletal muscle development and muscle fiber transition.