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

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 dar...

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Autores principales: Qu, Yanli, Liu, Shuai, Bao, Wenlong, Xue, Xian, Ma, Zhengwen, Yokawa, Ken, Baluška, František, Wan, Yinglang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454864/
https://www.ncbi.nlm.nih.gov/pubmed/28467358
http://dx.doi.org/10.3390/ijms18050951
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author Qu, Yanli
Liu, Shuai
Bao, Wenlong
Xue, Xian
Ma, Zhengwen
Yokawa, Ken
Baluška, František
Wan, Yinglang
author_facet Qu, Yanli
Liu, Shuai
Bao, Wenlong
Xue, Xian
Ma, Zhengwen
Yokawa, Ken
Baluška, František
Wan, Yinglang
author_sort Qu, Yanli
collection PubMed
description 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.
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spelling pubmed-54548642017-06-08 Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods Qu, Yanli Liu, Shuai Bao, Wenlong Xue, Xian Ma, Zhengwen Yokawa, Ken Baluška, František Wan, Yinglang Int J Mol Sci Article 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. MDPI 2017-05-03 /pmc/articles/PMC5454864/ /pubmed/28467358 http://dx.doi.org/10.3390/ijms18050951 Text en © 2017 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Qu, Yanli
Liu, Shuai
Bao, Wenlong
Xue, Xian
Ma, Zhengwen
Yokawa, Ken
Baluška, František
Wan, Yinglang
Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
title Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
title_full Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
title_fullStr Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
title_full_unstemmed Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
title_short Expression of Root Genes in Arabidopsis Seedlings Grown by Standard and Improved Growing Methods
title_sort expression of root genes in arabidopsis seedlings grown by standard and improved growing methods
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454864/
https://www.ncbi.nlm.nih.gov/pubmed/28467358
http://dx.doi.org/10.3390/ijms18050951
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