High-throughput sequencing analysis identified microRNAs associated with egg production in ducks ovaries

Background: MicroRNAs (miRNAs) exist widely and are involved in multiple biological processes in ducks, whereas the regulatory mechanism of miRNAs in egg laying of ducks has remained unclear. This study aims to reveal key miRNAs involved in the regulation of egg production in duck ovaries. Methods: High-throughput sequencing was performed on four egg-type duck ovaries and four egg-meat-type duck ovaries at the start of the egg-laying stage. Quantitative reverse transcription PCR (qRT-PCR) validation was performed on differentially expressed miRNAs (DE miRNAs). Gene network of DEmiRNA-mRNA-pathway was constructed by Cytoscape. Results: A total of 251 know miRNAs and 1,972 novel miRNAs were obtained from whole clean reads. Among the known miRNAs, we identified 21 DEmiRNAs, including eight down-regulated and 13 up-regulated miRNAs in egg-type ducks compared with egg-meat-type ducks. Among the novel miRNAs, we identified 70 DEmiRNAs, including 58 down-regulated and 12 up-regulated in egg-type ducks compared with egg-meat-type ducks. The expression patterns of four miRNAs were verified by qRT-PCR. The DEmiRNAs were involved in the function of response to folic acid and the pathway of valine, leucine and isoleucine degradation. Specific target genes of DEmiRNAs enrichment was found in some egg-laying regulation pathways, such as dopaminergic synapse, ovarian steroidogenesis and oocyte meiosis. The DEmiRNA-mRNA-pathway network including three DEmiRNAs, nine mRNAs and 11 pathways. apl-miR-194-5p and apl-miR-215-5p may be potential key miRNAs in regulating egg laying. Conclusions: This study provided miRNAs profiles in ducks about egg laying and establish a theoretical basis for subsequent selection or modification of duck phenotypes at the molecular level.