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Long non-coding RNAs (lncRNAs) play a critical role in the development of muscles. However, the role of lncRNAs in regulating skeletal muscle development has not been studied systematically in the donkey. In this study, we performed the RNA sequencing for different stages of muscles in donkeys, and investigate their expression profile, which showed that 3215 mRNAs ( p -adjust &lt;0.05) and 471 lncRNAs ( p -value &lt;0.05) were significantly differently expressed (DE) verified by RT-qPCR. GO and KEGG enrichment analysis indicated that DE genes and target genes of DE lncRNAs were associated with muscle development in the donkey. We also found these four target genes ( DCN ,  ITM2A ,  MUSTN1 ,  ARRDC2 ) involved in skeletal muscle growth and development. Combined with transcriptome data, network, and RT-qPCR results showed that four co-expression networks of  DCN  and lnc-008278,  ITM2A  and lnc_017247,  MUSTN1  and lnc_030153, and  ARRDC2  and lnc_033914, which may play an important role in the formation and development of muscle in the donkey.

Identification of Dezhou donkey muscle development-related genes and long non-coding RNA based on differential expression analysis