Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

Abstract

Background Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics. Results In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log2 (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data. Conclusions These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

Mechanisms of Oogenesis-Related Long Non-coding RNAs in Porcine Ovaries Treated With Recombinant Pig Follicle-Stimulating Hormone

“…In this study, gilts treated with rpFSH showed higher ovulation number and estrogen concentration, which might contribute to improving the litter size of pigs. Many researches have been reported that lncRNAs could regulated reproduction of pigs (10)(11)(12), but none of these studies have interpreted regulatory networks of lncRNAs for regulation of exogenous hormones on follicular formation in sow production. Therefore, in this study, we performed transcriptome analysis of ovaries in pigs treated with rpFSH by RNA sequencing.…”

“…In the last decade, a number of researches had reported that lncRNAs played important roles in the oogenesis and ovulation in ovaries among different species, including pigs, cattle, mice, and sheep ( 11 , 21 , 32 , 33 ). The present study is the first to report the transcriptome profiling of lncRNAs and mRNA in pig ovaries treated with rpFSH.…”

“…Follicular formation, ovulation, and luteal formation and regression all occur in the ovaries, and these processes take place repeatedly during mammalian reproduction and regulate reproduction (9). Previous reports have shown that long non-coding RNAs (lncRNAs) are involved in ovarian processes and regulate fertility (10)(11)(12).…”

“…The previous studies demonstrated that lncRNAs played an important role in the regulation of pigeon ovulation and sheep fertility ( 20 , 22 ). Hu et al ( 11 ) identified the ovarian lncRNAs associated with prolificacy of Large White sows during the follicular and luteal phases of the estrous cycle, and found that lncRNAs in ovaries significantly influenced fertility of pigs. Liu et al ( 12 ) identified the lncRNA and mRNA expression profiles for pig ovaries on days 0, 2, and 4 of the follicular periods in Duroc pigs, and found that lncRNA ENSSSCT00000034907 might play an important role in follicular development.…”

Whole Transcriptome Analysis: Implication to Estrous Cycle Regulation

“…However, the coalition analysis between each database is not reported in goat. An integrated analysis of lncRNA, miRNA, and mRNA in ovary at different phases of estrous cycle has been reported to explore the regulation networks in large white sows, and it reveals a novel insight in the regulation of pig fertility [28]. In this study, the databases of miRNA, circRNA, lncRNA, and mRNA in the ovary of Xinong Sannen goat in ES and DS were acquired and analyzed in combination.…”