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Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana

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Title Uncovering the molecular signature underlying the light intensity-dependent root development in Arabidopsis thaliana
 
Creator Kumari, Sony
Yadav, Sandeep
Patra, Debadutta
Singh, Sharmila
Sarkar, Ananda K.
Panigrahi, Kishore C. S.
 
Subject Root
Light signaling
Intensity
Gene expression
Auxin
Hormone
 
Description Accepted date: 24 June 2019
Background
Root morphology is known to be affected by light quality, quantity and direction. Light signal is perceived at the shoot, translocated to roots through vasculature and further modulates the root development. Photoreceptors are differentially expressed in both shoot and root cells. The light irradiation to the root affects shoot morphology as well as whole plant development. The current work aims to understand the white light intensity dependent changes in root patterning and correlate that with the global gene expression profile.

Results
Different fluence of white light (WL) regulate overall root development via modulating the expression of a specific set of genes. Phytochrome A deficient Arabidopsis thaliana (phyA-211) showed shorter primary root compared to phytochrome B deficient (phyB-9) and wild type (WT) seedlings at a lower light intensity. However, at higher intensity, both mutants showed shorter primary root in comparison to WT. The lateral root number was observed to be lowest in phyA-211 at intensities of 38 and 75 μmol m − 2 s − 1. The number of adventitious roots was significantly lower in phyA-211 as compared to WT and phyB-9 under all light intensities tested. With the root phenotypic data, microarray was performed for four different intensities of WL light in WT. Here, we identified ~ 5243 differentially expressed genes (DEGs) under all light intensities. Gene ontology-based analysis indicated that different intensities of WL predominantly affect a subset of genes having catalytic activity and localized to the cytoplasm and membrane. Furthermore, when root is irradiated with different intensities of WL, several key genes involved in hormone, light signaling and clock-regulated pathways are differentially expressed.

Conclusion
Using genome wide microarray-based approach, we have identified candidate genes in Arabidopsis root that responded to the changes in light intensities. Alteration in expression of genes such as PIF4, COL9, EPR1, CIP1, ARF18, ARR6, SAUR9, TOC1 etc. which are involved in light, hormone and clock pathway was validated by qRT-PCR. This indicates their potential role in light intensity mediated root development.
We are thankful to Prof. Eberhard Schäfer, Albert Ludwigs University of
Freiburg, Germany for the seed lines. The authors would like to thank Durga
Prasad Biswal, NISER for few of the experimental strategies. The authors
would also like to thank Dr. Chandan Goswami, NISER for his critical
comments to improve the manuscript. We would also like to acknowledge
the CIF facility, NIPGR.
 
Date 2019-07-22T11:23:01Z
2019-07-22T11:23:01Z
2019
 
Type Article
 
Identifier BMC Genomics, 20(1): 596
1471-2164
http://223.31.159.10:8080/jspui/handle/123456789/963
https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-5933-5?optIn=false
https://doi.org/10.1186/s12864-019-5933-5
 
Language en_US
 
Format application/pdf
 
Publisher BioMed Central Ltd