Differential lncRNA analysis of skeletal muscles in Bama Xiang pig and Duroc pig based on transcriptome sequencing

【Objective】The aim of this study was to provide a theoretical basis for clarifying the regulatory mechanism of lncRNA on skeletal muscle growth and development， by conducting transcriptome sequencing on the longest dorsal muscle tissues of Bama Xiang pigs and Duroc pigs to identify differential expression of lncRNA and screening candidate genes related to skeletal muscle development. 【Method】Transcriptome sequencing was performed on the longest dorsal muscle tissues of 12 months-old Bama Xiang pigs and Duroc pigs. Using false discovery rate（FDR）<0.05 and |log₂ Fold Change|>1 as the standard， differentially expressed genes（DEGs） and differentially expressed lncRNA were screened， and real-time fluorescence quantitative PCR validation was performed， in order to predict differentially expressed lncRNA target genes and to perform GO functional annotation and KEGG signaling pathway enrichment analysis. The lncRNA with the greatest differential expression was selected to construct its interaction network with target genes. 【Result】The results showed that a total of 6316 DEGs and 675 differentially expressed lncRNA were identified in the dorsal muscles of Bama Xiang pigs and Duroc pigs. GO functional annotation analysis showed that differentially expressed lncRNA target genes mainly involved biological processes such as metabolism process， muscle tissue development， and skeletal muscle cell proliferation and differentiation. KEGG signaling pathway enrichment analysis showed that differentially expressed lncRNA target genes were significantly enriched in the Hippo and Wnt signaling pathways （P<0.05）， indicating that differentially expressed lncRNA was associated with proliferation， autophagy， and differentiation of skeletal muscle cells. Real time fluorescence quantitative PCR validation was performed on lncRNA-MSTRG.16703， which had the largest expression difference. It was found that its relative expression level in Bama Xiang pigs was extremely significantly higher than that in Duroc pigs （P<0.01）， which was consistent with the result of transcriptom sequencing. Analysis of the interaction network between lncRNA-MSTRG.16703 and target genes showed that the up-regulated target genes including QKI， MBNL1， and YBX2. QKI and MBNL1 were related to alternative splicing. 【Conclusion】The differentially expressed lncRNA found between Bama Xiang pig and Duroc pig is a candidate gene for regulating skeletal muscle development， its target genes mainly enrich on skeletal muscle development related signaling pathways such as Hippo and Wnt. The expression difference of lncRNA-MSTRG.16703 is the largest and up-regulates in Bama Xiang pigs. Its target gene plays an important regulatory role in the proliferation and differentiation of skeletal muscle cells and muscle fiber formation.