Insights into Transcriptional Regulatory Pathways on Systemic Communication under Flooding in Arabidopsis. Arabidopsis thaliana

We analyzed global transcriptional changes in both shoots and roots of root-flooded Arabidopsis seedlings by microarrays. We also interpreted the significance of the systemic communication between roots and shoots by functional classification of affected genes. We performed genetic analysis with an ethylene signaling mutant, ein2-5, to correlate systemic flooding responses with ethylene signaling. We identified a class of genes that were up- or downregulated in shoots, but not affected in roots, under hypoxic conditions. A comprehensive managing program of carbohydrate metabolism was observed, providing an example of how systemic communications might facilitate the survival of plants under flooding. A proportion of long-distance hypoxic regulation was altered in ein2-5. Overall design: Time course experiments (0.5, 1, 3, 6, and 12h for Columbia; 0.5, 3, and 6h for ein2-5). Tissues from root-flooded seedlings vs. Tissues from un-flooded seedlings. Biological replicates: 4 replicates for each time point, independently grown, treated, and harvested. One replicate per array. 2 of 4 replicates are dye-swapped.

本研究通过微阵列（microarray）技术，分析了根系淹水处理的拟南芥幼苗地上部分与根部的全转录组变化。同时通过对差异表达基因进行功能分类，解析了根与冠部之间系统性信号交流的生物学意义。本研究还利用乙烯信号通路（ethylene signaling）突变体ein2-5开展遗传分析，以明确淹水系统性响应与乙烯信号通路的相关性。本研究鉴定出一类在低氧（hypoxic）胁迫下仅在拟南芥地上部分出现上调或下调表达、根部无显著表达变化的基因。研究观察到一套完整的碳水化合物代谢调控网络，为系统性信号交流如何助力植物在淹水胁迫下存活提供了实例。在ein2-5突变体中，部分长距离低氧调控通路发生了改变。
整体实验设计：
时间梯度实验：哥伦比亚野生型（Columbia）处理时长为0.5、1、3、6和12小时；ein2-5突变体处理时长为0.5、3和6小时。
实验分组为根系淹水处理幼苗组织与未淹水处理对照幼苗组织。
生物学重复：每个时间点设置4次独立生物学重复（biological replicate），所有重复均为独立培养、处理并取材；每个芯片对应一次生物学重复，其中4次重复中有2次采用了染料互换（dye-swapped）实验设计。