TY - JOUR
T1 - Time-course transcriptomics analysis reveals key responses of submerged deepwater rice to flooding
AU - Minami, Anzu
AU - Yano, Kenji
AU - Gamuyao, Rico
AU - Nagai, Keisuke
AU - Kuroha, Takeshi
AU - Ayano, Madoka
AU - Nakamori, Masanari
AU - Koike, Masaya
AU - Kondo, Yuma
AU - Niimi, Yoko
AU - Kuwata, Keiko
AU - Suzuki, Takamasa
AU - Higashiyama, Tetsuya
AU - Takebayashi, Yumiko
AU - Kojima, Mikiko
AU - Sakakibara, Hitoshi
AU - Toyoda, Atsushi
AU - Fujiyama, Asao
AU - Kurata, Nori
AU - Ashikari, Motoyuki
AU - Reuschera, Stefan
N1 - Funding Information:
We thank Dr. Ko Hirano for assisting with lignin quantification and Dr. M. Fujita for providing cv C9285 genomic sequencing data. Seeds of cv C9285 used in this study were distributed from the National Institute of Genetics supported by the National Bioresource Project, AMED, Japan.
Funding Information:
1 This work was supported by JST Core Research for Evolutional Science and Technology, a MEXT Grant-in-Aid for Scientific Research on Innovative Areas (22119007 and 17H06473) and JICA-JST SA-TREPS, by JSPS Grand-in Aid for Young Scientists (B) Grant Number 17K15136 to A.M., and by a JST ERATO Grant (JPMJER1004) to T.H.
Funding Information:
This work was supported by Japan Science and Technology AgencyJST Core Research for Evolutional Science and Technology, a MEXT Grant-in-Aid for Scientific Research on Innovative Areas (22119007and Japan Science and Technology AgencyJST17H06473) and
Publisher Copyright:
© 2018 American Society of Plant Biologists. All rights reserved.
PY - 2018/4
Y1 - 2018/4
N2 - 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.
AB - 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.
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U2 - 10.1104/pp.17.00858
DO - 10.1104/pp.17.00858
M3 - Article
C2 - 29475897
AN - SCOPUS:85045512133
SN - 0032-0889
VL - 176
SP - 3081
EP - 3102
JO - Plant Physiology
JF - Plant Physiology
IS - 4
ER -