基于GEO数据库筛选与水牛肌内脂肪沉积相关的候选基因及生物信息学分析  

Screening of Key Genes Related to Intramuscular Fat Deposition in Buffaloes Based on GEO Database and Bioinformatics Analysis

作　　者：梁莎莎 于农淇 卢瑛 李厅厅 鄢胜飞 黄健[1] 谭正准[1] 黄荣春 李辉[1] 潘伟军 覃广胜[1] LIANG Shasha;YU Nongqi;LU Ying;LI Tingting;YAN Shengfei;HUANG Jian;TAN Zhengzhun;HUANG Rongchun;LI Hui;PAN Weijun;QIN Guangsheng(Key Laboratory of Buffalo Genetics,Breeding and Reproduction Technology,Guangxi Buffalo Research Institute,Chinese Academy of Agricultural Sciences,Nanning 530001,China)

机构地区：[1]中国农业科学院广西水牛研究所,广西水牛遗传繁育重点实验室,南宁530001

出　　处：《中国畜牧兽医》2023年第11期4359-4369,共11页China Animal Husbandry & Veterinary Medicine

基　　金：广西重大科技专项(桂科AA22068099-2、桂科AA22068099-9);广西人才基地项目(桂科AD19259009);广西自然基金项目(2022GXNSFAA035588);国家现代农业产业技术体系广西奶水牛产业创新团队项目(nycytxgxcxtd-2021-21-01)。

摘　　要：【目的】筛选与水牛肌内脂肪沉积相关的关键基因,为挖掘改善水牛肌内脂肪沉积的分子标记提供参考。【方法】通过GEO数据库下载GSE19586数据集,使用limma R语言程序包筛选广西水牛和青海牦牛36月龄背最长肌的差异表达基因(differentially expressed genes,DEGs),使用clusterProfiler R语言程序包分别对上调、下调的DEGs进行GO功能和KEGG通路富集分析,使用STRING在线软件对DEGs进行蛋白互作(PPI)网络分析,并使用Cytoscape 3.9.1软件对其结果进行可视化,筛选排名前二十的枢纽基因。【结果】本研究共筛选出254个DEGs,其中61个上调,193个下调。GO功能富集结果显示,上调DEGs主要富集于肌动蛋白-肌球蛋白细丝滑动、肌球蛋白复合体、肌球蛋白结合、甘油三酯代谢、酰基甘油代谢、中性脂代谢、细胞凋亡信号通路调控等过程;下调DEGs主要富集于短链脂肪酸代谢、不饱和脂肪酸代谢、细胞对酮的反应、细胞基质连接、脂蛋白合成及蛋白质的成熟、加工、聚合等过程。KEGG通路富集结果显示,上调DEGs主要参与代谢途径、脂肪细胞因子、胰岛素抵抗、磷酸腺苷活化蛋白激酶(AMPK)、甲状腺激素信号转导途径和碳水化合物消化吸收等信号通路;下调DEGs主要参与代谢途径、吞噬体、溶酶体、黏着斑和细胞凋亡等信号通路。PPI网络中共有116个节点和205条连线,其中上调蛋白26个,下调蛋白90个;筛选出的前20个枢纽基因分别为ACTB、PPARGC 1、NR3C 1、FOS、GOT 2、SERPINE 1、RAC 1、LEP、STAT 5 B、HPRT 1、DDC、FABP 1、HDAC 1、RHOA、EEF 1 A 1、PCK 1、SOD 2、PRKCB、GPX 1和CTGF。【结论】本研究共筛选出广西水牛和青海牦牛36月龄背最长肌DEGs 254个,挖掘到可能与水牛肌内脂肪沉积相关的候选基因MYH 3、GPX 1、LDLR、LEP和PCK 1,为寻找改善水牛肌内脂肪沉积的分子标记提供了理论基础。【Objective】This study was aimed to screen the key genes related to intramuscular fat(IMF)deposition,and provide reference for mining molecular markers to improve IMF deposition in buffaloes.【Method】The GSE19586 dataset was downloaded from GEO database,the differentially expressed genes(DEGs)of longissimus dorsi muscle in Guangxi buffaloes and Qinghai yaks at 36 months of age were screened using limma R package,the up-and down-regulated DEGs were enriched for GO function and KEGG pathway using clusterProfiler R package,respectively,and the protein-protein interaction(PPI)network of DEGs were analyzed using STRING online.The results were visualized by Cytoscape 3.9.1,and the top 20 pivotal genes in terms were screened.【Result】A total of 254 DEGs were screened in this study,including 61 up-regulated genes and 193 down-regulated genes.GO function enrichment analysis showed that up-regulated DEGs were mainly enriched in processes such as actin-myosin filament sliding,myosin complex,myosin binding,triglyceride metabolism,acylglycerol metabolism,neutral lipid metabolism,cell apoptosis signaling pathway regulation,etc.Down-regulated DEGs were mainly enriched in short-chain fatty acid metabolism,unsaturated fat metabolism,cell reaction to ketone,cell matrix connection,lipoprotein synthesis,protein maturation,processing,polymerization and other processes.KEGG pathway enrichment analysis showed that up-regulated DEGs were mainly involved in metabolic pathways,adipocytokines,insulin resistance,AMP-activated protein kinase(AMPK),thyroid hormone signaling pathways,carbohydrate digestion and absorption and other signal pathways.Down-regulated DEGs were mainly involved in metabolic pathway,phagosome,lysosome,adhesive spot,apoptosis and other signal pathways.There were 116 nodes and 205 links in PPI network,including 26 up-regulated proteins and 90 down-regulated proteins.The top 20 pivotal genes were ACTB,PPARGC 1,NR3C 1,FOS,GOT 2,SERPINE 1,RAC 1,LEP,STAT 5 B,HPRT 1,DDC,FABP 1,HDAC 1,RHOA,EEF 1 A 1,PCK 1,SOD 2,PRKCB,

关 键 词：水牛 肌内脂肪沉积 差异表达基因 蛋白互作 

分 类 号：Q78[生物学—分子生物学] S823.8[农业科学—畜牧学]