摘要
旨在运用加权基因共表达网络分析技术(weighted gene co-expression network analysis,WGCNA)筛选出荷斯坦奶牛(Bos taurus)肝脏组织中与泌乳时期及繁殖力相关的基因。本研究采用GEO数据库中的GSE62159数据集,该数据集分别包含高繁殖力(分泌到配种的平均时间间隔为85.6 d,n=24)和低繁殖力(分泌到配种的平均时间间隔为113.8 d,n=24)健康荷斯坦母牛在妊娠后期、泌乳初期和泌乳中期的肝脏组织转录组数据,使用R语言中的WGCNA包对该数据集进行共表达分析。将所得到的模块与不同泌乳时期以及不同繁殖力进行关联分析,得到目标模块,再依据连接度选择出排名前30的基因作为枢纽基因(Hub基因),对Hub基因进行功能富集分析,使用String网站构建出模块的蛋白互作网络(PPI),并使用Cytoscape软件筛选出Hub基因与蛋白互作分析(PPI)网络核心基因的交集,最终得到肝脏中与泌乳时期及繁殖力相关的目标基因。研究共得到14个模块,其中tan、greenyellow两个模块与泌乳时期相关,black模块与繁殖力相关。对hub基因进行富集分析后,发现肝脏中与泌乳早期相关基因功能主要包括:有物质的合成代谢途径、脂质脂蛋白的基因表达、蛋白质的合成到分泌等;与泌乳中期相关基因功能主要包括:疾病、机体的炎症反应、免疫反应以及急性期等;与繁殖力相关基因功能主要包括:胰岛素抵抗、子宫内膜癌以及癌症等。筛选到的12个肝脏中与泌乳早期相关的目标基因有RPN1、SEC 61A1、SEC 61B、SEC 61G、SSR1、SSR3、STT 3A、DAD1、DDOST、ERLEC1、HM 13和OSTC;6个与泌乳中期相关的目标基因有ITGAL、ITGB2、LAPTM5、PTPRC、C 3AR1和CTSS;4个与繁殖力相关的目标基因有:PDS 5A、ROCK1、AQR和LTN 1。本研究使用WGCNA、PPI、基因功能富集等生物信息学方法,鉴定得到荷斯坦奶牛肝脏中与泌乳时期、繁殖力相关的目标基因,并对目标基因进行了功能富集分
The purpose of this study was to use the weighted gene co-expression network analysis(WGCNA)to screen for genes related to lactation and reproductive performance in Holstein cow liver tissue.The study used the GSE62159 dataset from the GEO database was used and the co-expression analysis was performed using the WGCNA package in R.The dataset included transcriptome data of liver tissues from healthy Holstein cows with high reproductive performance(mean interval from parturition to insemination of 85.6 days,n=24)and low reproductive performance(mean interval from parturition to insemination of 113.8 days,n=24)during late pregnancy,early lactation,and mid-lactation.The obtained modules were associated with different lactation stages and different reproductive performance.The target module was identified,and the top 30 genes based on connectivity were selected as hub genes.Functional enrichment analysis was performed on hub genes,and a protein-protein interaction(PPI)network of the module was constructed using the String website.The intersection of hub genes and PPI network core genes was screened using Cytoscape software to obtain the target genes related to lactation and reproductive performance in the liver.A total of 14 modules were obtained,of which the tan and greenyellow modules were related to lactation stages,and the black module was related to reproductive performance.After performing functional enrichment analysis on hub genes,genes related to early lactation in the liver were mainly involved in pathways related to the synthesis of substances,gene expression of lipid lipoproteins,and protein synthesis and secretion.Genes related to mid-lactation were mainly involved in diseases,body inflammation,immune responses,and acute phases.Genes related to reproductive performance were mainly involved in insulin resistance,endometrial cancer,and cancer.Twelve target genes related to early lactation in the liver were screened,including RPN1,SEC 61A1,SEC 61B,SEC 61G,SSR1,SSR3,STT 3A,DAD1,DDOST,ERLEC1,HM 13,and OSTC.Six
作者
张志飞
唐雪颖
闵力
童雄
陈卫东
巨向红
李大刚
ZHANG Zhifei;TANG Xueying;MIN Li;TONG Xiong;CHEN Weidong;JU Xianghong;LI Dagang(Key Laboratory of Livestock Breeding and Nutrition Research,Institute of Animal Science,Guangdong Academy of Agricultural Sciences,Guangzhou 510000,China;College of Animal Science and Technology Coastal Agricultural Sciences,Guangdong Ocean University,Zhanjiang 524000,China)
出处
《畜牧兽医学报》
CAS
CSCD
北大核心
2024年第2期528-539,共12页
ACTA VETERINARIA ET ZOOTECHNICA SINICA
基金
岭南现代农业科学与技术广东省实验室河源分中心项目(DT20220021)
广东省现代农业产业技术体系创新团队项目(2023KJ114)
广州市农村科技特派员项目(20212100032)。
关键词
荷斯坦奶牛
肝脏
泌乳
繁殖性能
加权基因共表达网络分析
Holstein cows
liver
lactation
reproductive performance
weighted gene co-expression network analysis
