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Int. J. Mol. Sci. 2017, 18(5), 951; doi:10.3390/ijms18050951

Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods

1
College of Biological Sciences and Biotechnology, Beijing Forestry University, 35 Qinghua East Road, Haidian District, Beijing 100083, China
2
College of Agriculture, Henan University of Science and Technology, Luoyang 471003, China
3
Department of Biological Sciences, Tokyo Metropolitan University, Tokyo 192-0397, Japan
4
Institute of Cellular and Molecular Botany, University of Bonn, D-53115 Bonn, Germany
These authors contributed equally to this work.
*
Author to whom correspondence should be addressed.
Academic Editors: Yikun He, Xuchu Wang and Shaojun Dai
Received: 31 March 2017 / Revised: 25 April 2017 / Accepted: 27 April 2017 / Published: 3 May 2017
(This article belongs to the Special Issue Selected Papers from the 6th National Plant Protein Research Congress)
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Abstract

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. View Full-Text
Keywords: Arabidopsis roots; improved plant-growing method; transcriptome; photoreceptors; spatial expression Arabidopsis roots; improved plant-growing method; transcriptome; photoreceptors; spatial expression
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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.

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