Identification of the Key microRNAs and miRNA-mRNA Interaction Networks during the Ovarian Development of Hens

SIMPLE SUMMARY: In this study, we analyzed the microRNA (miRNA) sequencing libraries of the hen ovary at four different developmental stages (15, 20, 30, and 68 W) and found 209 differently expressed (DE) miRNAs in the six comparisons of the four stages, which might be involved in ovarian growth and functions. In particular, five key miRNAs (gga-miR-2954, gga-miR-6634-5p, gga-miR-449b-5p, gga-miR-449c-3p, and gga-miR449c-5p) targeting 23 predicted genes were obtained in the interaction network and functional enrichment analysis through a combination of DE miRNAs and differentially expressed genes (DEGs), which might be involved in cell differentiation and proliferation, steroid hormone biosynthesis, and angiogenesis in ovarian development. Our findings can contribute to a better understanding of the role of functional miRNAs in ovarian development and the ovulatory cycle during the four developmental stages of hens. ABSTRACT: It is well-known that multiple functional miRNAs are found in mammals’ ovaries, which are linked not only to ovarian development, but also to maturation and apoptosis. However, there is still a lack of knowledge regarding the role of miRNAs in the hen ovary. In the present study, we analyzed the miRNA sequencing libraries of ovaries at the four different developmental stages of hens (15, 20, 30, and 68 W) and a total of 677 known miRNAs and 61 novel miRNAs were identified. In total, 209 of them were differently expressed miRNAs (DE miRNAs) obtained from comparisons of the four stages, including 84 upregulated and 125 downregulated DE miRNAs. Furthermore, the five key DE miRNAs gga-miR-2954, gga-miR-6634-5p, gga-miR-449b-5p, gga-miR-449c-3p, and gga-miR449c-5p were screened using an analysis of the miRNA-mRNA interaction network and functional enrichment annotated in seven significantly enriched pathways, such as endocytosis, lysine degradation, the biosynthesis of amino acids, and the MAPK signaling pathway, which may primarily participate in cell differentiation and proliferation, steroid hormone biosynthesis, and angiogenesis by targeting the related genes. For instance, gga-miR-449 family members were predicted to target 15 genes, including TGFB1, TPM1, TPM3, and CAMKB2, which were reported to regulate follicular growth, selection, and the ovulatory cycle. Taken together, our results illustrate the ovarian miRNA profiles of the four classic developmental stages of hens and highlight the significant role of miRNAs in ovarian development and functions. However, in-depth research needs to be carried out to validate the potential functional miRNAs found in this study.