摘要
为挖掘调控肌肉生长及骨骼肌纤维转化的关键基因,本研究利用差异分析、基因共表达网络分析和外显子选择信号分析的研究方法,通过对肌纤维类型差异明显的腓肠肌(G,n=18)和比目鱼肌(S,n=21)进行转录组测序分析。结果表明:1)共有1576个差异表达基因,其中腓肠肌与比目鱼肌相比有170个基因上调,1406个基因下调,富集分析发现主要富集在肌肉收缩、骨骼肌收缩、糖酵解过程、肌原纤维、肌钙蛋白复合体、AMPK信号通路和脂肪细胞脂解调节等通路中。2)基因共表达网络(WGCNA)分析显示,共被聚类为4个模块其中品红色、黑色、蓝色模块为显著模块。3)外显子选择信号分析(EWSS)发现26467个高质量的SNP,最后联合多种方法共筛选到6个候选基因CACNA2D2、PFKFB4、ATP2B2、PRUNE2、PRKG1和FAM13A。4)对候选基因进行qPCR检测,结果与RNA-Seq测序结果一致,将候选基因输入到STRING数据库以及OmicsNet中进行蛋白质及代谢物互作网络分析,发现与候选基因互作的蛋白质之间共同作用促成了一个共享功能。综上,本研究最终筛选到6个相关差异基因,其可能是调控肌肉生长脂质代谢以及骨骼肌纤维转化的关键基因,为骨骼肌纤维转化的调控机制研究提供了基础,并为探索改善牛肉品质的新靶点和潜在机制提供了新的研究视角。
The study was to explore the key genes regulating muscle growth and skeletal muscle fiber transformation.By differential expression analysis,gene co-expression network analysis(WGCNA),and exonbased selection signal analysis,transcriptome sequencing was performed on the gastrocnemius(G,n=18)and soleus(S,n=21)muscles with significant differences in muscle fiber types.The results showed that:1)There were 1576 differentially expressed genes,with 170 genes upregulated and 1406 genes downregulated in gastrocnemius compared to soleus muscle.Enrichment analysis revealed that these genes were mainly enriched in pathways such as muscle contraction,skeletal muscle contraction,glycolysis process,myofibrils,troponin complex,AMPK signaling pathway,and Regulation of lipolysis in adipocytes.2)Weighted gene co-expression network analysis showed that the genes were clustered into four modules,with the blue,black,and blue modules being significant modules.3)Exon wide selection signature(EWSS)identified 26467 high-quality SNPs,and ultimately combined multiple methods to screen for 6 candidate genes,including CACNA2D2,PFKFB4,ATP2B2,PRUNE2,PRKG1,and FAM13A.4)The candidate genes were validated by qPCR,and the results were consistent with the RNA-Seq data.Protein-protein and protein-metabolite interaction networks were constructed using the STRING database and OmicsNet,which revealed that the proteins that interact with the candidate genes work together contribute to shared biological processes.In conclusion,this study ultimately identified six key differentially expressed genes(DEGs)that are likely to regulate muscle growth,lipid metabolism,and skeletal muscle fiber-type transformation.These findings provide new insights into the molecular mechanisms underlying muscle fiber-type switching and offer potential targets for improving beef quality.
作者
李帅
霍晨曦
过亚强
娜日格拉
朱琳
娜日苏
石彩霞
谷明娟
张文广
LI Shuai;HUO Chenxi;GUO Yaqiang;NA Rigela;ZHU Lin;NA Risu;SHI Caixia;GU Mingjuan;ZHANG Wenguang(College of Animal Science and Technology,Inner Mongolia Agricultural University,Hohhot 010018,China;Inner Mongolia Engineering Research Centerof Genomic Big Data for Agriculture,Hohhot 010018,China;College of Life Sciences,Inner Mongolia Agricultural University,Hohhot 010018,China)
出处
《中国农业大学学报》
北大核心
2025年第8期107-119,共13页
Journal of China Agricultural University
基金
内蒙古自治区揭榜挂帅项目(2022JBGS0025)
内蒙古自治区重大专项(2021ZD0009-2)
内蒙古自治区科技计划(2023YFHH0058)
内蒙古农业大学高水平成果培育专项(CG202432)。
关键词
转录组
腓肠肌
比目鱼肌
肉质
肌纤维类型
transcriptome
gastrocnemius
soleus muscle
meat quality
muscle fiber types
