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Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray

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Abstract

In this study, we constructed a 22k wheat oligo-DNA microarray. A total of 148,676 expressed sequence tags of common wheat were collected from the database of the Wheat Genomics Consortium of Japan. These were grouped into 34,064 contigs, which were then used to design an oligonucleotide DNA microarray. Following a multistep selection of the sense strand, 21,939 60-mer oligo-DNA probes were selected for attachment on the microarray slide. This 22k oligo-DNA microarray was used to examine the transcriptional response of wheat to salt stress. More than 95% of the probes gave reproducible hybridization signals when targeted with RNAs extracted from salt-treated wheat shoots and roots. With the microarray, we identified 1,811 genes whose expressions changed more than 2-fold in response to salt. These included genes known to mediate response to salt, as well as unknown genes, and they were classified into 12 major groups by hierarchical clustering. These gene expression patterns were also confirmed by real-time reverse transcription-PCR. Many of the genes with unknown function were clustered together with genes known to be involved in response to salt stress. Thus, analysis of gene expression patterns combined with gene ontology should help identify the function of the unknown genes. Also, functional analysis of these wheat genes should provide new insight into the response to salt stress. Finally, these results indicate that the 22k oligo-DNA microarray is a reliable method for monitoring global gene expression patterns in wheat.

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Acknowledgements

This work was supported by Grants-in-Aid for Scientific Research on Priority Areas (C) “Genome Science” (No. 13202055) and the National Bioresource Project of the Ministry of Education, Culture, Sports, Science, and Technology of Japan.

Data obtained from the present microarray experiments have been deposited to the public site: http://www.shigen.nig.ac.jp/wheat/komugi/array/.

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Authors and Affiliations

  1. Laboratory of Genetic Engineering, Kyoto Prefectural University, Shimogamo, Kyoto, 606-8522, Japan

    Kanako Kawaura & Yasunari Ogihara

  2. Kyoto Prefectural Institute of Agricultural Biotechnology, Kyoto, Japan

    Kanako Kawaura & Yasunari Ogihara

  3. Nagahama Institute of Bio-Science and Technology, Shiga, 526-0829, Japan

    Keiichi Mochida

  4. Genetic Informatics Laboratory, Center for Genetic Resource Information, National Institute of Genetics, Mishima, 411-8540, Japan

    Yukiko Yamazaki

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  1. Kanako Kawaura
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  4. Yasunari Ogihara
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Correspondence to Yasunari Ogihara.

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Kawaura, K., Mochida, K., Yamazaki, Y. et al. Transcriptome analysis of salinity stress responses in common wheat using a 22k oligo-DNA microarray. Funct Integr Genomics 6, 132–142 (2006). https://doi.org/10.1007/s10142-005-0010-3

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  • DOI: https://doi.org/10.1007/s10142-005-0010-3

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