高低肌内脂肪猪背最长肌关键基因表达差异分析

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

  • 摘要: 【目的】筛选出高肌内脂肪(Intramuscular fat,IMF)沉积的关键基因并进行表达验证,为揭示猪肌内脂肪沉积的分子调控机制提供理论依据。【方法】根据NCBI-GEO数据库中高、低肌内脂肪巴克夏群体的转录组数据,利用DESeq2进行差异表达基因筛选(|log2Fold Change|≥1,FDR<0.05),采用Metascape对差异表达基因进行功能富集分析,通过MCODE筛选及鉴定出高肌内脂沉积的关键基因,并采用实时荧光定量PCR在地方猪(柯乐猪)和外种猪(杜长大猪)上进行关键基因表达量验证。【结果】从高、低肌内脂肪巴克夏群体6个文库中共鉴定出7661个基因,高肌内脂肪群体样本的脂质代谢相关基因总表达量显著高于低肌内脂肪群体样本(P<0.05,下同),其中差异表达基因有133个110个上调(在高肌内脂肪群体高表达),23个下调(在低肌内脂肪群体高表达)。上调差异表达基因主要富集于胶原蛋白绑定、细胞外基质组装、脂肪酰辅酶A生物合成过程、固醇代谢过程和脂质代谢调控过程等GO功能条目,以及脂肪乙酰辅酶A生物合成、ChREBP激活代谢基因、脂肪酸代谢等信号通路上;下调基因主要富集于线粒体组装、多细胞生物学过程、辅酶绑定和缺氧反应等GO功能条目,以及基于NFKB的TNFA信号、白细胞介素4和白细胞介素13信号和干扰素信号等信号通路上。通过MCODE分析共筛选获得5个关键基因,分别是SLC25A5、FN1、FASN、ACACAPRKDC基因;挑选SCD、FASNACACA基因进行表达量验证,结果发现这3个基因的相对表达量均表现为柯乐猪高于杜长大猪,其差异达显著或极显著(P<0.01)水平,进一步佐证SCD、FASNACACA基因在高肌内脂肪猪群体中高表达。【结论】在巴克夏猪高肌内脂肪群体中高表达的SCD、FASNACACA基因,在高肌内脂肪的柯乐猪中也呈显著或极显著高表达,因此这3个关键基因有望作为筛选和培育高肌内脂肪猪品种的分子标记,同时为研究肌内脂肪沉积的分子调控机制提供技术支撑。

     

    Abstract: 【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.

     

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