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Plant and Cell Physiology Advance Access originally published online on April 15, 2008
Plant and Cell Physiology 2008 49(6):865-879; doi:10.1093/pcp/pcn061
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© The Author 2008. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

A Comprehensive Transcriptional Profiling of the WRKY Gene Family in Rice Under Various Abiotic and Phytohormone Treatments

Rengasamy Ramamoorthy1, Shu-Ye Jiang1, Nadimuthu Kumar, Prasanna Nori Venkatesh and Srinivasan Ramachandran*

Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, the National University of Singapore, Singapore 117604

*Corresponding author: E-mail, sri{at}tll.org.sg; Fax, +65-68727007.


  Abstract

WRKY transcription factors play important roles in the regulation of various biological processes. We have analyzed the publicly available rice genome sequence databases and predicted 103 genes encoding WRKY transcription factors. Among them, the majority of rice WRKY genes (77.7%) were located in duplicated regions; 45.6% of WRKY genes were fragmentally duplicated and 35% of them were tandemly duplicated. These results suggested that genome duplications might be regarded as a major mechanism for expansion of this family in the rice genome. Subsequently, we analyzed their expression profiles under normal and abiotic stress, as well as various hormone treatments. Under normal growth conditions, 65 WRKY genes were expressed differentially either in their transcript abundance or in their expression patterns. Under abiotic (cold, drought and salinity) stresses and various phytohormone treatments, 54 WRKY genes exhibited significant differences in their transcript abundance; among them three genes were expressed only in stressed conditions. Among the stress-inducible genes, 13 genes were regulated only by abiotic stresses, another set of 13 genes were responsive to only phytohormone treatments and the remaining 28 genes were regulated by both factors, suggesting an interaction between abiotic stress and hormone signaling. On the other hand, we have also surveyed the expression divergence of duplicated genes under normal or stressed conditions, and the results showed that high expression divergence has occurred not only among fragmentally but also among tandemly duplicated genes. These results suggested that the high expression divergence could be one of the mechanisms for the retention of these duplicated WRKY genes.

Keywords: Expression profile - Oryza sativa cv Nipponbare - Real-time PCR

Abbreviations: GA3, gibberellic acid; MeJA, methyl jasmonate; PEG, polyethylene glycol; RT–PCR, reverse transcription–PCR; SA, salicylic acid; TF, transcription factor.

1These authors contributed equally to this work.

(Received January 28, 2008; Accepted April 9, 2008)
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