Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress

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Abstract

Background

Rice ( Oryza sativa L.) is one of the most important crops cultivated in both tropical and temperate regions and is characterized by a low water-use efficiency and a high sensitivity to a water deficit, with yield reductions occurring at lower stress levels compared to most other crops. To identify genes and pathways involved in the tolerant response to dehydration, a powerful approach consists in the genome-wide analysis of stress-induced expression changes by comparing drought-tolerant and drought-sensitive genotypes.

Results

The physiological response to osmotic stress of 17 japonica rice genotypes was evaluated. A clear differentiation of the most tolerant and the most sensitive phenotypes was evident, especially after 24 and 48 h of treatment. Two genotypes, which were characterized by a contrasting response (tolerance/sensitivity) to the imposed stress, were selected. A parallel transcriptomic analysis was performed on roots and leaves of these two genotypes at 3 and 24 h of stress treatment. RNA-Sequencing data showed that the tolerant genotype Eurosis and the sensitive genotype Loto mainly differed in the early response to osmotic stress in roots. In particular, the tolerant genotype was characterized by a prompt regulation of genes related to chromatin, cytoskeleton and transmembrane transporters. Moreover, a differential expression of transcription factor-encoding genes, genes involved in hormone-mediate signalling and genes involved in the biosynthesis of lignin was observed between the two genotypes.

Conclusions

Our results provide a transcriptomic characterization of the osmotic stress response in rice and identify several genes that may be important players in the tolerant response.

Electronic supplementary material

The online version of this article (doi:10.1186/s12284-016-0098-1) contains supplementary material, which is available to authorized users.

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Most cited references 77

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Gene networks involved in drought stress response and tolerance.

Kazuo Shinozaki, Kazuko Yamaguchi-Shinozaki (2007)

Plants respond to survive under water-deficit conditions via a series of physiological, cellular, and molecular processes culminating in stress tolerance. Many drought-inducible genes with various functions have been identified by molecular and genomic analyses in Arabidopsis, rice, and other plants, including a number of transcription factors that regulate stress-inducible gene expression. The products of stress-inducible genes function both in the initial stress response and in establishing plant stress tolerance. In this short review, recent progress resulting from analysis of gene expression during the drought-stress response in plants as well as in elucidating the functions of genes implicated in the stress response and/or stress tolerance are summarized. A description is also provided of how various genes involved in stress tolerance were applied in genetic engineering of dehydration stress tolerance in transgenic Arabidopsis plants.

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Ethylene Biosynthesis and its Regulation in Higher Plants

S F Yang, N Hoffman (1984)

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NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis.

June M. Kwak, Izumi C. Mori, Zhen-Ming Pei … (2003)

Reactive oxygen species (ROS) have been proposed to function as second messengers in abscisic acid (ABA) signaling in guard cells. However, the question whether ROS production is indeed required for ABA signal transduction in vivo has not yet been addressed, and the molecular mechanisms mediating ROS production during ABA signaling remain unknown. Here, we report identification of two partially redundant Arabidopsis guard cell-expressed NADPH oxidase catalytic subunit genes, AtrbohD and AtrbohF, in which gene disruption impairs ABA signaling. atrbohD/F double mutations impair ABA-induced stomatal closing, ABA promotion of ROS production, ABA-induced cytosolic Ca(2+) increases and ABA- activation of plasma membrane Ca(2+)-permeable channels in guard cells. Exogenous H(2)O(2) rescues both Ca(2+) channel activation and stomatal closing in atrbohD/F. ABA inhibition of seed germination and root elongation are impaired in atrbohD/F, suggesting more general roles for ROS and NADPH oxidases in ABA signaling. These data provide direct molecular genetic and cell biological evidence that ROS are rate-limiting second messengers in ABA signaling, and that the AtrbohD and AtrbohF NADPH oxidases function in guard cell ABA signal transduction.

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Author and article information

Contributors

Elena Baldoni: +390250316534 , +390250316521 , elena.baldoni@unimi.it

Annamaria Genga: +390223699438 , +390223699411 , genga@ibba.cnr.it

Journal

Journal ID (nlm-ta): Rice (N Y)

Journal ID (iso-abbrev): Rice (N Y)

Title: Rice

Publisher: Springer US (New York )

ISSN (Print): 1939-8425

ISSN (Electronic): 1939-8433

Publication date (Electronic): 23 May 2016

Publication date PMC-release: 23 May 2016

Publication date Collection: 2016

Volume: 9

Electronic Location Identifier: 25

Affiliations

[ ]Institute of Agricultural Biology and Biotechnology - National Research Council, via Bassini 15, 20133 Milan, Italy

[ ]Dipartimento di Scienze Agrarie e Ambientali - Produzione, Territorio, Agroenergia, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy

[ ]Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria, Genomics Research Centre, Fiorenzuola d’Arda, Piacenza Italy

Article

Publisher ID: 98

DOI: 10.1186/s12284-016-0098-1

PMC ID: 4877341

PubMed ID: 27216147

SO-VID: 3990f200-0210-4882-aee1-d1fc3c00969a

License:

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

History

Date received : 13 January 2016

Date accepted : 14 May 2016

Funding

Funded by: AGER

Award ID: 2010-2369

Award Recipient : Annamaria Genga

Custom metadata

ScienceOpen disciplines: Agriculture

Keywords: hormones,lignin,oryza sativa,osmotic stress,rna-seq analysis,transcription factors

Data availability:

ScienceOpen disciplines: Agriculture

Keywords: hormones, lignin, oryza sativa, osmotic stress, rna-seq analysis, transcription factors

Comparative Leaf and Root Transcriptomic Analysis of two Rice Japonica Cultivars Reveals Major Differences in the Root Early Response to Osmotic Stress

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Landscape Agronomy

Most cited references 77

Gene networks involved in drought stress response and tolerance.

Ethylene Biosynthesis and its Regulation in Higher Plants

NADPH oxidase AtrbohD and AtrbohF genes function in ROS-dependent ABA signaling in Arabidopsis.

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