Transcriptomic Insights into the Dynamic Regulatory Mechanisms of Longissimus Dorsi Muscle Development in Jinhua Pigs

Pigs are a major source of animal protein for humans and serve as valuable biomedical models. Compared to Western commercial pig breeds, Jinhua pigs are characterized by superior meat quality due to dynamic muscle development and fat deposition. However, studies investigating dynamic transcriptional regulation of swine meat quality traits across developmental stages remain limited. In this work, we collected longissimus dorsi muscle tissue from three Jinhua and three Landrace × Yorkshire pigs at 1, 90, and 180 days of age, respectively. We have uncovered differentially expressed genes and transcripts, alternative splicing events, and gene fusion events across development stages utilizing RNA sequencing data. CKM exhibited consistent breed-specific alternative splicing and gene fusion events across all three stages, representing a stable regulator of muscle development in Jinhua pigs. On the other hand, our findings highlight day 90 as a critical “window phase” for muscle development and meat quality differences between Jinhua and Landrace × Yorkshire pigs at this stage, exhibiting the greatest number of inter-breed differences in transcriptomic genetic regulation. Additionally, time series analysis revealed that genes with peak expression at day 90 were significantly enriched in pathways associated with muscle development and function. Finally, we identified PFKM, PRKAG3, and CKM as candidate genes with age-specific expression and post-transcriptional regulation that likely influence muscle development. This study advances understanding of transcriptional regulation in pig muscle with implications for meat quality improvement.