Transcriptome sequencing reveals candidate genes and signaling pathways for skeletal muscle development in Ningxiang pig

Abstract Background Ningxiang pig is resistant to roughage, delicious in meat quality and rich in polyunsaturated fatty acids. However, its growth rate is slow and its meat yield is low, so it is urgent to analyze the molecular mechanism of its muscle growth and development. Genes are important molecules involved in muscle growth and development. In this study, transcripts of difference tables of Ningxiang pig at two developmental stages (30 days and 150 days after birth) were identified by transcriptome sequencing, and the molecular mechanism of their regulation of muscle development was further explored. Result A total of 22,411 transcripts were identified by transcriptome sequencing, and 9,021 transcripts were obtained after screening with TPM ≥ 1. Differential expression analysis obtained 1,322 differentially expressed transcripts, 978 of which were up-regulated and 344 down-regulated. There were 1,125 known and 197 novel identified differentially expressed transcripts, 823 up-regulated and 302 down-regulated in known transcripts, and 155 up-regulated and 42 down-regulated in novel identified transcripts. RT-qPCR verification is consistent with sequencing results. After GO enrichment analysis of differentially expressed genes, 15 known genes (15 transcripts) and 6 new genes (8 transcripts) related to muscle were screened. KEGG enrichment found that muscle-related genes were significantly enriched in FoxO, MAPK, cAMP, IL-17 and PI3K-Akt signal pathways. The prediction of PPI and transcription factors of 15 known genes showed that there were significant interactions among 9 proteins (ATF3-EGR1-EGR2-FOS-HOMER1-KLF5, KLHL40-LMOD2-MYOZ2), and there were 8 transcription factors (KLF5, COPS2, FOXN2, EGR2, ATF3, EGR1, FOS, PAX7) among the 15 proteins. To sum up, 15 known genes and 6 novel identified genes related to muscle development in Ningxiang pigs were identified by transcriptome sequencing. These genes regulate muscle development via FoxO, MAPK, cAMP, IL-17 and PI3K-Akt signaling pathways, and there is a significant interaction between them, and they participate in gene expression regulation as transcription factors. Conclusion To sum up, 15 known genes and 6 novel identified genes related to muscle development in Ningxiang pigs were identified by transcriptome sequencing. These genes mainly regulate muscle development through FoxO, MAPK, cAMP, IL-17 and PI3K-Akt signaling pathways, and there is a significant interaction between them, and they participate in gene expression regulation as transcription factors. These results provide theoretical basis for the study of the mechanism of muscle development in Ningxiang pig.