Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods.
Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods.
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标准和改良栽培方法培育的拟南芥幼苗中根基因的表达
DOI：
10.3390/ijms18050951
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发表时间：
2017-05-03
影响因子：
5.6
通讯作者：
Wan Y
中科院分区：
文献类型：
--
作者：
Qu Y;Liu S;Bao W;Xue X;Ma Z;Yokawa K;Baluška F;Wan Y
在实验室用传统植物生长培养系统(TPG)生长的拟南芥幼苗的根被覆盖，以保持它们在黑暗中。这种新方法是基于暗室的，被称为改进的植物生长法(IPG)。我们测量了暗室中的光条件，发现在暗室更深的地方，最高的光强度显著降低。在暗室的底部和侧面，树根几乎完全被遮挡住了。利用高通量的RNA测序方法从根中提取总RNA，比较两种条件下幼苗根中的整体基因表达水平，鉴定出141个差异表达基因(DEG)。根据KEGG(京都基因和基因组百科全书)的丰富，在所有注释的途径中，黄酮和黄酮醇的生物合成途径以及类黄酮的生物合成途径受到的影响最大。令人惊讶的是，通过这种方法，没有已知的植物光感受器基因被鉴定为degs。考虑到IPG系统中光照强度的降低，我们收集了在TPG和IPG条件下生长的拟南芥根的4个切片(每片1.5 cm)，利用qRT-PCR技术分析了植物光受体和生长素极性转运蛋白CRY1、CRY2、PHYA、PHYB、PHOT1、PHOT2和UVR8在空间上的差异基因表达水平。利用这些结果，我们生成了这些基因在IPG和TPG条件下的空间相关表达模式的图谱。根中光相关基因的表达水平对光照高度敏感，为实验室培育拟南芥幼苗选择改良的培养方法提供了背景参考。
Roots of Arabidopsis thaliana seedlings grown in the laboratory using the traditional plant-growing culture system (TPG) were covered to maintain them in darkness. This new method is based on a dark chamber and is named the improved plant-growing method (IPG). We measured the light conditions in dark chambers, and found that the highest light intensity was dramatically reduced deeper in the dark chamber. In the bottom and side parts of dark chambers, roots were almost completely shaded. Using the high-throughput RNA sequencing method on the whole RNA extraction from roots, we compared the global gene expression levels in roots of seedlings from these two conditions and identified 141 differently expressed genes (DEGs) between them. According to the KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment, the flavone and flavonol biosynthesis and flavonoid biosynthesis pathways were most affected among all annotated pathways. Surprisingly, no genes of known plant photoreceptors were identified as DEGs by this method. Considering that the light intensity was decreased in the IPG system, we collected four sections (1.5 cm for each) of Arabidopsis roots grown in TPG and IPG conditions, and the spatial-related differential gene expression levels of plant photoreceptors and polar auxin transporters, including CRY1, CRY2, PHYA, PHYB, PHOT1, PHOT2, and UVR8 were analyzed by qRT-PCR. Using these results, we generated a map of the spatial-related expression patterns of these genes under IPG and TPG conditions. The expression levels of light-related genes in roots is highly sensitive to illumination and it provides a background reference for selecting an improved culture method for laboratory-maintained Arabidopsis seedlings.