Shi Tianpei, Hu Wenping, Hou Haobin, Zhao Zhida, Shang Mingyu, Zhang Li
Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Genes (Basel). 2020 May 4;11(5):508. doi: 10.3390/genes11050508.
Long non-coding RNA (lncRNA) has been extensively studied in many livestock. However, compared with other livestock breeds, there is less research regarding donkey lncRNA function. It has been reported that lncRNA plays an important role in the timing control of development, aging, and death of livestock. Therefore, the study of donkey skeletal muscle lncRNA is of great significance for exploring donkey meat production performance. In this study, RNA-Seq was used to perform high-throughput sequencing of skeletal muscle (longissimus dorsi and gluteus) of two Dezhou donkey strains (SanFen and WuTou). The differentially expressed lncRNAs were screened between different strains and tissues. Then candidate genes for conjoint analysis were screened based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Finally, the accuracy of the sequencing data was verified by real-time quantitative polymerase chain reaction (RT-qPCR). Herein, we identified 3869 novel lncRNAs and 73 differentially expressed lncRNAs. Through the comparison between groups, the specific expression of lncRNAs were found in different strains and muscle tissues. Importantly, we constructed the lncRNA-miRNA-mRNA interaction network and found three important candidate lncRNAs (MSTRG.9787.1, MSTRG.3144.1, and MSTRG.9886.1) and four candidate genes (, , , and ). Analysis of the KEGG pathway indicates that the TGF-β signaling pathway plays a pivotal role in the growth and development of skeletal muscle in Dezhou donkey strains.
长链非编码RNA（lncRNA）已在许多家畜中得到广泛研究。然而，与其他家畜品种相比，关于驴lncRNA功能的研究较少。据报道，lncRNA在牲畜发育、衰老和死亡的时间控制中起着重要作用。因此，研究驴骨骼肌lncRNA对探索驴肉生产性能具有重要意义。在本研究中，利用RNA测序技术对两个德州驴品系（三分和乌头）的骨骼肌（背最长肌和臀肌）进行高通量测序。筛选不同品系和组织之间差异表达的lncRNAs。然后基于基因本体论（GO）和京都基因与基因组百科全书（KEGG）分析筛选用于联合分析的候选基因。最后，通过实时定量聚合酶链反应（RT-qPCR）验证测序数据的准确性。在此，我们鉴定出3869个新的lncRNAs和73个差异表达的lncRNAs。通过组间比较，发现lncRNAs在不同品系和肌肉组织中具有特异性表达。重要的是，我们构建了lncRNA- miRNA -mRNA相互作用网络，发现了三个重要的候选lncRNAs（MSTRG.9787.1、MSTRG.3144.1和MSTRG.9886.1）和四个候选基因（，，，和）。KEGG通路分析表明，TGF-β信号通路在德州驴品系骨骼肌的生长发育中起关键作用。
