Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi

Affymetrix soybean genome arrays were used to identify genes differentially expressed in the immune resistance response at 6, 12, 24, and 48 hours after inoculation with Phakopsora pachyrhizi isolates TW72-1 or HW94-1 soybean + HW94-1 = resistant; soybean + TW72-1 = susceptible Keywords: time course Overall design: For each of 4 time points (6, 12, 24 and 48 hours post inoculation) a soybean PI200492 plant was inoculated with 2 treatments: HW94-1, or TW72-1. A mock inoculation was performed and sampled at time 0. There were three biological replicates of the entire experiment, for a total of 27 samples. During data analysis two samples failed the quality control metrics and were removed from the analysis, leaving 25 samples in the final data set.

本研究采用Affymetrix大豆基因组芯片（Affymetrix soybean genome arrays），旨在鉴定接种大豆锈病菌（Phakopsora pachyrhizi）菌株TW72-1或HW94-1后，不同时间点大豆免疫抗性响应过程中的差异表达基因，取样时间点设为接种后6、12、24及48小时。其中，大豆与HW94-1菌株组合表现为抗病；大豆与TW72-1菌株组合表现为感病。关键词：时间进程（time course）。整体实验设计：针对4个取样时间点（接种后6、12、24、48小时），以大豆PI200492植株分别进行两种处理接种：HW94-1菌株或TW72-1菌株；同时设置模拟接种（mock inoculation）对照组，并于接种后0小时取样。本实验共设置3次生物学重复（biological replicates），总计27份样本。数据分析阶段有2份样本未通过质量控制指标（quality control metrics）检测，被移除出分析流程，最终数据集共保留25份样本。