荷斯坦牛肌肉组织中与妊娠末期、泌乳期及繁殖力相关的基因共表达网络构建

【目的】筛选荷斯坦牛肌肉组织中与妊娠末期、泌乳期及繁殖力相关的关键目标基因，为进一步开展基因功能研究提供理论依据。【方法】选择 GEO 数据库中有关荷斯坦牛在妊娠末期、泌乳早期和泌乳中期肌肉基因表达及生育能力的数据集 GSE62159，采用加权基因共表达网络分析（Weighted gene co-expression network analysis，WGCNA）方法进行基因共表达分析，将获得的模块与妊娠末期、泌乳中期及繁殖力性状相关联，选择各模块中连接度处于前 30 的基因作为枢纽基因（Hub 基因），使用 String 网站对模块进行蛋白互作（Protein-protein interaction，PPI）网络分析，选择 PPI 网络中节点连接度值排名前 30 的基因作为核心基因，与 Hub 基因交集得到在肌肉中与不同生理时期及繁殖力相关的关键目标基因。【结果】研究共分析得到 13 个模块，其中 Green、Blue两个模块分别与妊娠末期、泌乳中期相关，Magenta 模块与繁殖力相关。对各目标模块内基因进行功能富集分析，富集结果显示肌肉组织中与妊娠末期相关的基因功能主要有物质代谢、能量代谢、蛋白质合成与分泌、机体对氧化应激的反应及神经退行性变等；与泌乳中期相关的基因功能有干细胞群维持、蛋白质合成与分泌、抗原加工与呈递及多种疾病发生等；与繁殖力相关的基因功能有血管形成、子宫内胚胎发育与肌动蛋白丝结合等。筛选到荷斯坦牛肌肉中与妊娠末期相关的关键基因有 3 个、与泌乳中期相关的关键基因有 1 个、与繁殖力相关的关键基因有 8 个。【结论】鉴定到荷斯坦牛肌肉组织中与妊娠末期相关的基因为 EIF5A、ACO2 和 EEF1G，与泌乳中期相关的基因为EIF4A2，与繁殖力相关的基因为 ITGB1、MYH9、TLN1、CAV1、COL4A1、COL4A2、FLNA 和 HSPG2。

Construction of Co-expressed Gene Network Associated with Late Pregnancy, Lactation Period and Fecundity Traits in Holstein Cattle Muscle Tissue

【Objective】The key target genes related to late pregnancy, lactation and fecundity in muscle tissue of Holstein cattle were screened, with a view to providing a theoretical basis for further study of gene function.【Method】The dataset GSE62159 from the GEO database on gene expression and fecundity in the muscle of Holstein cattles during late pregnancy, early lactation, and mid lactation were selected. The weighted gene co-expression network analysis (WGCNA) method was used for gene co- expression analysis, and the obtained modules were associated with late pregnancy, mid lactation and fecundity traits. The genes with connectivity in the top 30 of each module were selected as the Hub genes. The module was analyzed by protein-protein interaction (PPI) network with String website. The gene with the top 30 node connection degree value in PPI network was selected as the core gene, and intersected with Hub gene to obtain the key target genes related to different physiological periods and fecundity in the muscle.【Result】A total of 13 modules were obtained, of which the Green and Blue modules were related to late pregnancy and mid-lactation periods respectively, and the Magenta module was related to fecundity. The functional enrichment analysis of genes in each target module showed that the main functions of genes related to the late pregnancy were substance metabolism, energy metabolism, protein synthesis and secretion, body response to oxidative stress and neurodegeneration; the functions of genes related to mid-lactation included maintenance of stem cell population, protein synthesis and secretion, antigen processing and presentation and occurrence of many diseases; while those related to fecundity included angiogenesis, intrauterine embryonic development and actin filament binding, etc. Three key genes related to late pregnancy, one key gene related to mid-lactation and eight key genes related to fecundity were screened in the muscle of Holstein cattle.【Conclusion】The genes related to and late pregnancy in the muscle of Holstein cattle were identified as EIF5A, ACO2 and EEF1G, and the gene related to mid-lactation as EIF4A2, and the genes related to fecundity as ITGB1, MYH9, TLN1, CAV1, COL4A1, COL4A2, FLNA and HSPG2.