High-throughput Sequencing Analysis of miRNA Expression in Embryonic Chicken Breast Muscle

The embryonic period is a critical period for the development of muscle and adipose tissue in chickens. MicroRNAs (miRNAs) have been shown to play important roles in various biological processes, but little is known about miRNAs in chicken embryos. To investigate functional miRNAs regulating the meat quality of adult chickens, embryonic breast muscle tissues of Cobb broilers (CB) and rose-crowned chickens (RC) were collected and analyzed with high-throughput small RNA deep sequencing. The results showed that 842 known miRNAs and 598 novel miRNAs were identified from the four sequencing libraries, of which 592 were differentially expressed (DE) miRNAs (P<0.05). Taking Cobb broilers as a reference, 321 miRNAs were upregulated, and 271 miRNAs were downregulated. Real-time PCR confirmed that the trends in differentially expressed miRNAs were completely consistent with the sequencing results. We identified 120,666 target genes of the differentially expressed miRNAs, and functional enrichment analysis revealed that these genes were mainly involved in the Wnt signaling pathway, Adherens junction, Butirosin and neomycin biosynthesis and the Hedgehog signaling pathway. Furthermore, regulatory networks of interactions among miRNAs and their targets were constructed, and fatty acid binding protein 5 (FABP5) was confirmed as a target of miR-3532-5p by dual-luciferase assay. The results of this study enriched the relevant data on chicken muscle miRNA expression, and they laid a foundation for further analysis of the miRNA-mediated regulation of genes and the link between miRNA and chicken meat quality traits.