Root photomorphogenesis in laboratory-maintained Arabidopsis seedlings

Yokawa, Ken; Kagenishi, Tomoko; Baluška, Frantǐsek

doi:10.1016/j.tplants.2013.01.002

Cited by 61 publications

(60 citation statements)

References 20 publications

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“…Several groups have suggested that Arabidopsis seedlings should be cultured using agar plates with shaded/darkened root system providing more natural culture conditions [4,5,6,7,8,9,11,12,13,23,24]. We used the standard and improved laboratory culture systems and measured the light intensities under the dark border.…”

Section: Discussionmentioning

confidence: 99%

“…This is the current standard culture method for Arabidopsis seedlings in laboratories [2]. The transparent Petri dish condition allows easy observation of the growth and development of young seedlings but aberrant growth and other stressful side effects occur due to the exposure of roots to light [3,4,5,6,7,8,9,10,11]. This possibility has sometimes been overlooked.…”

Section: Introductionmentioning

confidence: 99%

“…Root shading affects the primary root length, density of lateral roots, and root hairs. Altered cellular events, such as stimulation of reactive oxygen species (ROS), pectins, auxin biosynthesis and polar auxin transport, cytokinin biosynthesis and signaling, as well as expression levels of related genes have been reported [4,5,6,7,8,9,10,11,24,25]. Researchers have investigated aspects of growth phenomena in Arabidopsis , and reported that tissue-specific expression of photoreceptors in roots affected the shape and development of root tissues [21].…”

Section: Introductionmentioning

confidence: 99%

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

Liu

Bao

et al. 2017

IJMS

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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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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Liu

Bao

et al. 2017

IJMS

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“…12,13 It is well known that ROS molecules in plant cells have many crucial physiological roles. ROS generated in the illuminated cells are likely to modulate cellular signaling resulting in the regulation of light-induced root escape growth.…”

Section: Light-activated Generation Of Reactive Oxygen Speciesmentioning

confidence: 99%

Light-dependent control of redox balance and auxin biosynthesis in plants

Yokawa

Koshiba

Baluška

2014

Plant Signaling & Behavior

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“…Illumination of the specimens by virtue of a thin excitation light sheet, in addition to minimizing cellular phototoxicity, is also essential to avoid excessive illumination during acquisition, which might affect normal development of plant roots [20][21][22] . Stages of seed germination and early plant development do not necessarily require light per se because these processes take place in the dark under natural physiological conditions.…”

Section: Limitations Of the Methodsmentioning

confidence: 99%

Preparation of plants for developmental and cellular imaging by light-sheet microscopy

et al. 2015

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Long-term fluorescence live-cell imaging experiments have long been limited by the effects of excitation-induced phototoxicity. The advent of light-sheet microscopy now allows users to overcome this limitation by restricting excitation to a narrow illumination plane. In addition, light-sheet imaging allows for high-speed image acquisition with uniform illumination of samples composed of multiple cell layers. The majority of studies conducted thus far have used custom-built platforms with specialized hardware and software, along with specific sample handling approaches. The first versatile commercially available light-sheet microscope, Lightsheet Z.1, offers a number of innovative solutions, but it requires specific strategies for sample handling during long-term imaging experiments. There are currently no standard procedures describing the preparation of plant specimens for imaging with the Lightsheet Z.1. Here we describe a detailed protocol to prepare plant specimens for light-sheet microscopy, in which Arabidopsis seeds or seedlings are placed in solid medium within glass capillaries or fluorinated ethylene propylene tubes. Preparation of plant material for imaging may be completed within one working day.

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Root photomorphogenesis in laboratory-maintained Arabidopsis seedlings

Cited by 61 publications

References 20 publications

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

Light-dependent control of redox balance and auxin biosynthesis in plants

Preparation of plants for developmental and cellular imaging by light-sheet microscopy

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