Ratio of Dietary Forage-to-concentrate Affect Liver and Mammary Tissue Transcriptome in Primiparous Holstein Dairy Cows

Biopsies of liver and mammary were collected at the end of a 9-week feeding to measure mRNA profiles using a 4×44K Bovine Agilent microarray chip. Data were analyzed with SAS JMP Genomics using ANOVA with a false discovery rate correction (FDR < 0.2). Dynamic Impact Approach (DIA), Database for Annotation, Visualization and Integrated Discovery (DAVID), and ClueGO were used for bioinformatic analysis of differently expressed genes (DEGs). Considering an FDR<0.2, there were 299 DEG affected in both liver and mammary, 139 DEGs affected in liver, and 120 DEG affected in mammary in CS vs. MF.

在9周饲养周期结束时采集肝脏与乳腺活检组织，采用4×44K牛源安捷伦（Agilent）微阵列芯片检测其mRNA（messenger RNA）表达谱。数据采用SAS JMP Genomics软件进行分析，以方差分析（ANOVA）结合错误发现率（false discovery rate, FDR）校正，校正阈值设定为FDR<0.2。采用动态影响分析法（Dynamic Impact Approach, DIA）、注释、可视化与集成发现数据库（Database for Annotation, Visualization and Integrated Discovery, DAVID）以及ClueGO对差异表达基因（differently expressed genes, DEGs）开展生物信息学分析。在CS与MF组间，以FDR<0.2为筛选标准，共鉴定出同时在肝脏与乳腺中发生差异表达的基因299个，仅在肝脏中发生差异表达的基因139个，仅在乳腺中发生差异表达的基因120个。