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

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.

Integrated Analysis of Transcriptomic and Proteomics Data Reveals the Induction Effects of Rotenoid Biosynthesis of Mirabilis himalaica Caused by UV-B Radiation

“…In addition, a few of studies have shown that UVR8 in cells was not fully determined by light and UV-B radiation [ 23 ]. For example, UVR8s were found in the roots of Arabidopsis and carrots, which participated in root growth and secondary metabolism [ 24 , 25 ]. In this study, the UVR8 (Unigene0003427) in the roots of M. himalaica was significantly upregulated in UV-B radiation compare with CK plants.…”

Arabidopsis Roots and Light: Complex Interactions

“…It penetrates the soil to several centimeters or is conducted by vascular tissues (Mo et al, 2015). Using an improved Petri dish culture system, in which shoots are illuminated but roots are grown in darkness, Qu et al (2017) compared the differential gene expression patterns between illuminated and shaded roots. The authors found that shading of Arabidopsis roots grown in Petri dishes affects the expression pattern of the main groups of plant photoreceptors in the roots, implying that light affects roots via photoreceptor-mediated signaling pathways (Qu et al, 2017).…”

“…Using an improved Petri dish culture system, in which shoots are illuminated but roots are grown in darkness, Qu et al (2017) compared the differential gene expression patterns between illuminated and shaded roots. The authors found that shading of Arabidopsis roots grown in Petri dishes affects the expression pattern of the main groups of plant photoreceptors in the roots, implying that light affects roots via photoreceptor-mediated signaling pathways (Qu et al, 2017). Therefore, several experimental systems with shaded roots were suggested to mimic natural growth conditions to improve the Petri dish-based Arabidopsis culture methods (Yokawa et al, 2011, Rellá n-Á lvarez et al, 2015Silva-Navas et al, 2015;Qu et al, 2017).…”

“…The authors found that shading of Arabidopsis roots grown in Petri dishes affects the expression pattern of the main groups of plant photoreceptors in the roots, implying that light affects roots via photoreceptor-mediated signaling pathways (Qu et al, 2017). Therefore, several experimental systems with shaded roots were suggested to mimic natural growth conditions to improve the Petri dish-based Arabidopsis culture methods (Yokawa et al, 2011, Rellá n-Á lvarez et al, 2015Silva-Navas et al, 2015;Qu et al, 2017). In this issue, Zheng et al (2019) report that light can also affect root growth by directly triggering nonenzymatic chemical reactions in the root apex apoplast when roots are grown in transparent Petri dishes under Pi deficiency.…”

“…In summary, direct and strong illumination on roots creates unwanted biochemical and physiological responses and chemical reactions in root cells and rhizosphere. Several simple and cheap experimental systems with shaded roots were suggested to mimic natural growth conditions to improve Petri dish-based Arabidopsis culture methods (Xu et al, 2013;Silva-Navas et al, 2015;Qu et al, 2017). The GLO-Roots system with a highresolution imaging platform can also provide shaded root growth conditions for accurate analysis (Rellá n-Á lvarez et al, 2015).…”