Transcriptome Sequencing Reveals Candidate Genes and Signalling Pathways for Skeletal Muscle Development in Ningxiang Pig

ABSTRACT: Ningxiang pigs are resistant to roughage, have good meat quality, and are rich in polyunsaturated fatty acids. However, their growth rate is slow, and meat yield is low; therefore, it is necessary to analyse the molecular mechanisms of their muscle growth and development. Genes are important molecules that are involved in muscle growth and development. In this study, the transcripts of difference tables of Ningxiang pigs at two developmental stages (30 and 150 days after birth) were identified by transcriptome sequencing, and the molecular mechanism of their regulation of muscle development was further explored. A total of 22,411 transcripts were identified by transcriptome sequencing, and 9021 transcripts were obtained after screening with TPM > 1. Differential expression analysis revealed 1322 differentially expressed transcripts, 978 of which were up-regulated and 344 were downregulated. There were 1125 known and 197 novel identified differentially expressed transcripts, 823 upregulated and 302 downregulated known transcripts, and 155 upregulated and 42 downregulated novel transcripts. Quantitative PCR verification was consistent with the sequencing results. After gene ontology (GO) enrichment analysis of the differentially expressed genes, 15 known genes (15 transcripts) and six new genes (8 transcripts) related to muscle were screened. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that muscle-related genes were significantly enriched in the FoxO, MAPK, cAMP, IL-17, and PI3K-Akt signalling pathways. The prediction of PPI and transcription factors of 15 known genes showed that there were significant interactions among nine proteins (ATF3-EGR1-EGR2-FOS-HOMER1-KLF5 and KLHL40-LMOD2-MYOZ2) and eight transcription factors (KLF5, COPS2, FOXN2, EGR2, ATF3, EGR1, FOS, PAX7) among the 15 proteins. Furthermore, we elucidated the role of candidate gene HOMER1 in myoblast proliferation and differentiation. These results provide a theoretical basis for studying the mechanisms underlying muscle development in Ningxiang pigs.