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. 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. These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

中文翻译：

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对lncRNA，miRNA和mRNA的综合分析揭示了对大白母猪生育力调节的新见解。

改善母猪的繁殖力极为重要，因为它可以提高繁殖效率，从而为养猪者带来收益。个体动物的受精率存在很大差异，但潜在的分子机制仍不清楚。在这项研究中，通过使用不同类型的RNA库，我们调查了高（H）和低（L）大白猪发情周期的黄体期（L）和卵泡期（F）期间卵巢组织的完整转录组。并通过结合RNA测序（RNA-seq）和生物信息学对16个样品中的长非编码RNA（lncRNA），mRNA和微小RNA（miRNA）进行了全面分析。在卵巢组织中总共鉴定出24,447个lncRNA，27,370个mRNA和216个已知的miRNA。lncRNA的基因组特征 如长度分布和外显子数量，将进一步分析。我们选择阈值P <0.05和| log2（倍数变化）| ≥1可通过成对比较（LH与LL，FH与FL）获得差异表达的lncRNA，miRNA和mRNA。这些差异表达的RNA的生物信息学分析显示，多个显着富集的途径（P <0.05）与生殖过程密切相关，例如卵巢类固醇生成，溶酶体，类固醇生物合成以及雌激素和GnRH信号传导途径。此外，进行了与lncRNA及其下游mRNA靶点共享共同miRNA反应元件（MRE）的差异表达miRNA的生物信息学筛选。最后，我们构建了lncRNA–miRNA–mRNA调控网络。这些网络中的关键基因已通过逆转录实时定量PCR（RT-qRCR）进行了验证，这与RNA-Seq数据的结果一致。这些结果为猪的生育能力提供了进一步的见识，并有助于进一步研究这些基因的功能。