Comprehensive analysis of mRNA and miRNA expression profiles in follicular development in quail

1. Ovarian follicle development is a key determinant of egg production in quail which is regulated by a dynamic and stage-specific genetic program. However, most follicle-related genes and miRNAs have not yet been identified in quail. 2. This study applied transcriptome sequencing to dissect mRNA and miRNA expression patterns in quail ovarian follicles at distinct developmental stages: the pre-selection (SYF), the post-selection (F5) and the pre-ovulatory follicles (F1) in egg-laying birds. Comparative analyses identified 362 differentially-expressed mRNAs and 13 miRNAs in the F1 vs. F5 comparison, 549 and 72 in the F5 vs. SYF comparison and 1833 and 55 in the F1 vs. SYF comparison, respectively. 3. Significant differentially-expressed mRNAs implicated in follicle development included VCAN, FGFR3, ALDH1A1, NR0B1,ZP2 and SMOC1. Other significant miRNAs were represented by ga-miR-460b-5p, gga-miR-1552-5p, gga-miR-125b-5p, gga-miR-135a-5p, gga-miR-122-5p, gga-miR-29b-3p and ggga-miR-138-1-3p. 4. Enrichment analyses using GO and KEGG databases highlighted the influence of the extracellular matrix (ECM), cell adhesion molecules (CAMs), TGF-β and calcium signalling pathways and the steroid synthesis pathway on follicular development. 5. Additionally, the miRNA-mRNA interaction network pinpointed the regulatory roles of specific differentially expressed miRNAs (DE miRNAs), including gga-miR-1306-5p, gga-miR-133a-3p, gga-miR-133c-3p, gga-miR-214, gga-miR-214b-5p and gga-miR-34a-5p.