Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
AbstractRoots 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. View Full-Text
- Supplementary File 1:
ZIP-Document (ZIP, 846 KB)
Scifeed alert for new publicationsNever miss any articles matching your research from any publisher
- Get alerts for new papers matching your research
- Find out the new papers from selected authors
- Updated daily for 49'000+ journals and 6000+ publishers
- Define your Scifeed now
Qu, Y.; Liu, S.; Bao, W.; Xue, X.; Ma, Z.; Yokawa, K.; Baluška, F.; Wan, Y. Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods. Int. J. Mol. Sci. 2017, 18, 951.
Qu Y, Liu S, Bao W, Xue X, Ma Z, Yokawa K, Baluška F, Wan Y. Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods. International Journal of Molecular Sciences. 2017; 18(5):951.Chicago/Turabian Style
Qu, Yanli; Liu, Shuai; Bao, Wenlong; Xue, Xian; Ma, Zhengwen; Yokawa, Ken; Baluška, František; Wan, Yinglang. 2017. "Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods." Int. J. Mol. Sci. 18, no. 5: 951.
Note that from the first issue of 2016, MDPI journals use article numbers instead of page numbers. See further details here.