Comparative Genome-Wide Transcriptional Analysis of Al-Responsive Genes Reveals Novel Al Tolerance Mechanisms in Rice

Tomokazu Tsutsui, Naoki Yamaji, Chao Feng Huang, Ritsuko Motoyama, Yoshiaki Nagamura, Jian Feng Ma

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 μM AlCl3 for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.

Original languageEnglish
Article numbere48197
JournalPLoS One
Volume7
Issue number10
DOIs
Publication statusPublished - Oct 26 2012

Fingerprint

Aluminum
aluminum
Genes
Genome
rice
genome
genes
Meristem
root tips
mutants
synthesis
Ephrin-A5
Oryza
Metabolites
Cell Wall
secondary metabolites
Crops
ethylene
assimilation (physiology)
small cereal grains

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Comparative Genome-Wide Transcriptional Analysis of Al-Responsive Genes Reveals Novel Al Tolerance Mechanisms in Rice. / Tsutsui, Tomokazu; Yamaji, Naoki; Huang, Chao Feng; Motoyama, Ritsuko; Nagamura, Yoshiaki; Ma, Jian Feng.

In: PLoS One, Vol. 7, No. 10, e48197, 26.10.2012.

Research output: Contribution to journalArticle

Tsutsui, Tomokazu ; Yamaji, Naoki ; Huang, Chao Feng ; Motoyama, Ritsuko ; Nagamura, Yoshiaki ; Ma, Jian Feng. / Comparative Genome-Wide Transcriptional Analysis of Al-Responsive Genes Reveals Novel Al Tolerance Mechanisms in Rice. In: PLoS One. 2012 ; Vol. 7, No. 10.
@article{eda2cac992dd4527ba00908bba0611f0,
title = "Comparative Genome-Wide Transcriptional Analysis of Al-Responsive Genes Reveals Novel Al Tolerance Mechanisms in Rice",
abstract = "Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 μM AlCl3 for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.",
author = "Tomokazu Tsutsui and Naoki Yamaji and Huang, {Chao Feng} and Ritsuko Motoyama and Yoshiaki Nagamura and Ma, {Jian Feng}",
year = "2012",
month = "10",
day = "26",
doi = "10.1371/journal.pone.0048197",
language = "English",
volume = "7",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "10",

}

TY - JOUR

T1 - Comparative Genome-Wide Transcriptional Analysis of Al-Responsive Genes Reveals Novel Al Tolerance Mechanisms in Rice

AU - Tsutsui, Tomokazu

AU - Yamaji, Naoki

AU - Huang, Chao Feng

AU - Motoyama, Ritsuko

AU - Nagamura, Yoshiaki

AU - Ma, Jian Feng

PY - 2012/10/26

Y1 - 2012/10/26

N2 - Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 μM AlCl3 for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.

AB - Rice (Oryza sativa) is the most aluminum (Al)-tolerant crop among small-grain cereals, but the mechanism underlying its high Al resistance is still not well understood. To understand the mechanisms underlying high Al-tolerance, we performed a comparative genome-wide transcriptional analysis by comparing expression profiling between the Al-tolerance cultivar (Koshihikari) and an Al-sensitive mutant star1 (SENSITIVE TO AL RHIZOTOXICITY 1) in both the root tips and the basal roots. Exposure to 20 μM AlCl3 for 6 h resulted in up-regulation (higher than 3-fold) of 213 and 2015 genes including 185 common genes in the root tips of wild-type and the mutant, respectively. On the other hand, in the basal root, genes up-regulated by Al were 126 and 2419 including 76 common genes in the wild-type and the mutant, respectively. These results indicate that Al-response genes are not only restricted to the root tips, but also in the basal root region. Analysis with genes up- or down-regulated only in the wild-type reveals that there are other mechanisms for Al-tolerance except for a known transcription factor ART1-regulated one in rice. These mechanisms are related to nitrogen assimilation, secondary metabolite synthesis, cell-wall synthesis and ethylene synthesis. Although the exact roles of these putative tolerance genes remain to be examined, our data provide a platform for further work on Al-tolerance in rice.

UR - http://www.scopus.com/inward/record.url?scp=84868100938&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84868100938&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0048197

DO - 10.1371/journal.pone.0048197

M3 - Article

C2 - 23110212

AN - SCOPUS:84868100938

VL - 7

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 10

M1 - e48197

ER -