Comparative Analysis of Long Noncoding RNA and mRNA Expression Profiles in Ovarian Tissues of Tibetan Chickens and Roman Chickens During the Egg Laying Period

To explore the important long noncoding RNA (lncRNA) and its target genes in Tibetan chicken ovarian tissue, whole transcriptome sequencing technology and bioinformatics methods were used to analyze and predict lncRNA, differential expression of mRNA, and lncRNA between the two different breeds using DESeq2 software. The study predicted the Antisense and Cis regulatory target genes of differentially expressed lncRNA and performed functional annotation of GO, and analysis of the KEGG signaling pathway in these target genes. Quantitative fluorescence PCR was conducted in real time to validate the expression of important target genes. The results showed the discovery of 532 differentially expressed lncRNAs, 340 of which upregulated and 292 downregulated, as well as 2314 differentially expressed mRNAs, with 983 being upregulated and 1331 downregulated. The differentially expressed lncRNAs were found to regulate 48 differentially expressed mRNAs in the sense direction, and 14 in the antisense direction. Enrichment analysis on the intersection of target genes of differentially expressed lncRNAs and mRNAs showed enrichment mainly in KEGG signaling pathways such as TGF-beta signaling pathway (ko04350), organic selenium compound metabolism (ko00450), and oocyte meiosis (ko04114). The quantitative fluorescence PCR validation of important target genes such as CYP17A1, PTPN5, ACSL3, Nf2, CYP11A1 showed consistent results with RNA-seq results. This indicates the presence of lncRNA and mRNA with different expression levels and specific expression in the ovarian tissues of Tibetan and Roman chickens, and that genes such as CYP17A1, PTPN5, ACSL3, Nf2, and CYP11A1 may be key factors regulating the laying performance of Tibetan chickens