High-throughput sequencing of pituitary and hypothalamic microRNA transcriptome associated with high rate of egg production

BACKGROUND: MicroRNAs exist widely in viruses, plants and animals. As endogenous small non-coding RNAs, miRNAs regulate a variety of biological processes. Tissue miRNA expression studies have discovered numerous functions for miRNAs in various tissues of chicken, but the regulation of miRNAs in chicken pituitary and hypothalamic development related to high and low egg-laying performance has remained unclear. RESULTS: In this study, using high-throughput sequencing technology, we sequenced two tissues (pituitary and hypothalamus) in 3 high- and 3 low-rate egg production Luhua chickens at the age of 300 days. By comparing low- and high-rate egg production chickens, 46 known miRNAs and 27 novel miRNAs were identified as differentially expressed (P < 0.05). Six differentially expressed known miRNAs, which are expressed in both tissues, were used in RT-qPCR validation and SNP detection. Among them, seven SNPs in two miRNA precursors (gga-miR-1684a and gga-miR-1434) were found that might enhance or reduce the production of the mature miRNAs. In addition, 124 and 30 reciprocally expressed miRNA-target pairs were identified by RNA-seq in pituitary and hypothalamic tissues, respectively and randomly selected candidate miRNA and miRNA-target pairs were validated by RT-qPCR in Jiuyuan black fowl. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation illustrated that a large number of egg laying-related pathways were enriched in the high-rate egg production chickens, including ovarian steroidogenesis and steroid hormone biosynthesis. CONCLUSIONS: These differentially expressed miRNAs and their predicted target genes, especially identified reciprocally expressed miRNA-target pairs, advance the study of miRNA function and egg production associated miRNA identification. The analysis of the miRNA-related SNPs and their effects provided insights into the effects of SNPs on miRNA biogenesis and function. The data generated in this study will further our understanding of miRNA regulation mechanisms in the chicken egg-laying process. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12864-017-3644-3) contains supplementary material, which is available to authorized users.