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Plant Physiol. 2018 Apr;176(4):3081-3102. doi: 10.1104/pp.17.00858. Epub 2018 Feb 23.

Time-Course Transcriptomics Analysis Reveals Key Responses of Submerged Deepwater Rice to Flooding.

Author information

1
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan anzu.minami0@gmail.com reuscher@agr.nagoya-u.ac.jp.
2
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan.
3
Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Aichi 464-8602, Japan.
4
Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan.
5
ERATO Higashiyama Live-Holonics Project, Nagoya University, Nagoya, Aichi 464-8602, Japan.
6
Institute of Transformative Bio-Molecules, Nagoya University, Nagoya Aichi 464-8601, Japan.
7
RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama 230-0045, Japan.
8
Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan.
9
Center for Information Biology, National Institute of Genetics, Mishima 411-8540, Japan.
10
Genetic Strains Research Center, National Institute of Genetics, Mishima 411-8540, Japan.

Abstract

Water submergence is an environmental factor that limits plant growth and survival. Deepwater rice (Oryza sativa) adapts to submergence by rapidly elongating its internodes and thereby maintaining its leaves above the water surface. We performed a comparative RNA sequencing transcriptome analysis of the shoot base region, including basal nodes, internodes, and shoot apices of seedlings at two developmental stages from two varieties with contrasting deepwater growth responses. A transcriptomic comparison between deepwater rice cv C9285 and nondeepwater rice cv Taichung 65 revealed both similar and differential expression patterns between the two genotypes during submergence. The expression of genes related to gibberellin biosynthesis, trehalose biosynthesis, anaerobic fermentation, cell wall modification, and transcription factors that include ethylene-responsive factors was significantly different between the varieties. Interestingly, in both varieties, the jasmonic acid content at the shoot base decreased during submergence, while exogenous jasmonic acid inhibited submergence-induced internode elongation in cv C9285, suggesting that jasmonic acid plays a role in the submergence response of rice. Furthermore, a targeted de novo transcript assembly revealed transcripts that were specific to cv C9285, including submergence-induced biotic stress-related genes. Our multifaceted transcriptome approach using the rice shoot base region illustrates a differential response to submergence between deepwater and nondeepwater rice. Jasmonic acid metabolism appears to participate in the submergence-mediated internode elongation response of deepwater rice.

PMID:
29475897
PMCID:
PMC5884608
[Available on 2019-04-01]
DOI:
10.1104/pp.17.00858

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