Integrated analysis of non-coding RNA and mRNA expression profiles of 2 pig breeds differing in muscle traits

Production of high-quality meat is important to satisfy the consumer and allow the pork industry to be competitive. It is evident that different muscle fiber types in different breeds greatly influence the pork quality, but the underlying molecular mechanism remains unclear. We used Ribo-Zero RNA-Seq and miRNA-Seq to examine global expressions of protein-coding transcripts and non-coding RNAs including miRNA, lncRNA, and circRNA in the longissimus dorsi of Landrace and Lantang pigs. Of the 22,469 identified coding transcripts, only 547 candidates were differentially expressed, including 461 upregulated and 86 downregulated transcripts in the Lantang pigs compared with Landrace. Gene ontology analysis of these differentially-expressed transcripts further revealed 17 genes involved in myogenesis. In addition, 5,566 lncRNA and 4,360 circRNA candidates were found to be differentially expressed. Of these, 3,976 lncRNAs and 1,401 circRNAs were upregulated in the Lantang library, while 1,590 lncRNAs and 2,959 circRNAs were downregulated. Of the differentially expressed circRNAs, 236 candidates were edited from 93 functional hosting-genes related to myogenesis. We found 96 showed upregulation and 140 showed downregulation. By analyzing Ribo-Zero RNA-Seq data in combination with matched miRNA profiles, we identified 68 sponge modulators participating in 26 miRNA-mediated ceRNA interactions, including 19 lncRNAs, 40 circRNAs, and 9 mRNAs. Our study uncovered a novel post-transcriptional regulation layer which could help in the understanding of the mechanisms that underlie porcine myofiber development in different breeds.