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

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

doi:10.1371/journal.pone.0048197

Tomokazu Tsutsui, Chao Feng Huang + Show 5 more

Open Access

https://doi.org/10.1371/journal.pone.0048197

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Journal: PLoS ONE	Publication Date: Oct 26, 2012
Citations: 76	License type: CC BY 4.0

Affiliation: Okayama University, Institute of Agrobiological Sciences

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.

Highlights

Aluminum (Al) toxicity is a major factor limiting crop production on acid soils, which comprise approximately 40% of the world’s arable soils and up to 70% of potentially arable land [1]
ART1 is constitutively expressed in the roots and its expression is not induced by Al3+ treatment
By comparing transcriptional profiling between a wild-type rice and an Alsensitive rice mutant star1, we found that rice possesses novel mechanisms of Al-tolerance in addition to ART1-regulated mechanism in rice

Summary

Introduction

Aluminum (Al) toxicity is a major factor limiting crop production on acid soils, which comprise approximately 40% of the world’s arable soils and up to 70% of potentially arable land [1]. To extract genes related to Al-tolerance, we compared the transcriptional profiling between the wild-type rice and an Al-sensitive mutant, star1 [10]. The root elongation of the wild-type rice was hardly inhibited, whereas that of the mutant was inhibited by 75% (Figure 1), which make possible to extract genes possibly associated with Al-tolerance.

Results

Conclusion