Expression difference analysis of hub genes between high and low intramuscular fat content in longissimus dorsi of pigs

【Objective】To screen the hub genes of high intramuscular fat(IMF)deposition and to verify their expression,so as to provide a theoretical basis for revealing the molecular regulation mechanism of IMF deposition in pigs.【Method】Based on the transcriptome data of Berkshire pigs with high and low IMF in NCBI-GEO database,the differentially expressed genes(DEGs)were screened by DESeq2(|log₂Fold Change|≥1,FDR< 0.05),the functional enrichment of DEGs were analyzed by Metascape. Meanwhile,MCODE were used to identify the key genes of high IMF deposition,real-time fluorescence quantitative PCR(q RT-PCR)was used to verify the expression of hub genes in indigenous pigs(Kole)and foreign pigs(DLY pigs).【Result】7661 genes were identified from six libraries of Berkshire pigs with high and low IMF. The total expression of genes related to lipid metabolism in high IMF group was significantly higher than that in low IMF group(P<0.05,the same below). Additionally,the total number of DEGs in two groups was 133110were up-regulated(high expression in high IMF)and 23 were down-regulated(high expression in low IMF). The upregulated DEGs were mainly enriched in GO items such as collagen binding,extracellular matrix assembly,fatty acetylcoA biosynthesis,sterol metabolism and lipid metabolism regulation,and in signaling pathways such as fatty acetyl-coA biosynthesis,CHREBP activated metabolic genes and fatty acid metabolism. Meanwhile,the down-regulated genes were mainly enriched in GO items such as mitochondrial assembly,multi-multicellular biological processes,coenzyme binding and hypoxia response,and in signaling pathways such as TNFA signaling via NFKB,interleukin-4 and interleukin-13 signaling and signaling by interleukins. Five hub genes,SLC25A5,FN1,FASN,ACACA and PRKDC,were identified by MCODE analysis,and then SCD,FASN and ACACA were selected for expression verification. The results showed that the relative expression of these three genes were significantly higher in Kole pigs than that in DLY pigs(P<0.01),and it was further proved that SCD,FASN and ACACA were highly expressed in high IMF pigs.【Conclusion】SCD,FASN and ACACA genes that highly expressed in the high IMF group of Berkshire pigs are also significantly or extremely highly expressed in Kole pigs with the high IMF. Therefore,these three hub genes may be used as molecular markers for selecting and breeding pigs with high IMF,and provide technical support for studying the molecular regulation mechanism of IMF deposition.