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Genome-wide analysis for identification of salt-responsive genes in common wheat

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Abstract

To identify salt-responsive genes in wheat, global expression analysis of transcripts was carried out using oligo-DNA microarrays. Microarrays have been designed from approximately 32,000 unique wheat genes classified from a large number of expressed sequence tags (ESTs). Two-week-old seedlings of wheat were treated with 150 mM NaCl for 1, 6, and 24 h, and their roots and shoots were separately subjected to analyses. Consequently, 5,996 genes showed changes in expression of more than twofold and were classified into 12 groups according to correlations in expression patterns. These salt-responsive genes were assigned functions using the Gene Ontology (GO). Genes assigned to transcription factor, transcription-regulator activity, and DNA-binding functions were preferentially classified into early response groups. On the other hand, those assigned transferase and transporter activity were classified into late response groups. These data suggest that multiple signal transduction pathways in response to salinity exist in wheat. Transcription factors (TFs) which have been reported as participants in salt-tolerant pathway changed their expression levels in response to salt treatment. Among them, only a few TFs show high sequence homologies to genes in rice. These investigations suggest that salt-responsive genes identified by this study are candidates for salt-stress tolerance uniquely in wheat.

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Acknowledgements

This work was supported by Grant-in-Aid for Scientific Research on Priority Areas “Comparative Genomics” and the National Bioresource Project of the Ministry of Education, Culture, Sports, Science, and Technology of Japan. The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/), GSM198948, GSM198949, GSM198952, GSM198955, GSM198961, GSM198962, GSM198969, GSM198970, GSM198971, GSM198972, GSM-198973, GSM199012, GSM199013, GSM199014, GSM199015, GSM199016, GSM199017, GSM199018, GSM199019, GSM199020, GSM199021, GSM199022 and GSM199023.

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Authors and Affiliations

  1. Kihara Institute for Biological Research, Yokohama City University, Maioka-cho 641-12, Totsuka-ku, Yokohama, 244-0813, Japan

    Kanako Kawaura & Yasunari Ogihara

  2. RIKEN Plant Science Center, Suehiro-cho 1-7-22, Tsurumi-ku, Yokohama, 230–0045, Japan

    Keiichi Mochida

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  1. Kanako Kawaura
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Correspondence to Yasunari Ogihara.

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Table S1

Experimental design for microarray hybridizations. (doc 35 KB)

Table S2

Primer pairs using for qRT-PCR in wheat. (doc 30 KB)

Fig. S1

Validation of microarray data by qPCR. Vertical axis indicates log-transformed ratio of expression level. Solid black bar shows log-transformed ratio from qPCR, and gray bar shows log-transformed ratio from microarrays. Probe IDs and definitions are as follows: a w15334 dehydrin, b 23lib_15343 transcription factor AP2D23-like, c 23lib_11009 RAV1-like, d w9701 NAC domain containing protein, e w15821 alcohol dehydrogenase, f w14201 thiamine biosynthesis protein, g w13500 fructokinase, h w12804 chalcone synthase. Primer pairs using for qPCR are listed in Supplemental Table 2. (doc 240 KB)

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Kawaura, K., Mochida, K. & Ogihara, Y. Genome-wide analysis for identification of salt-responsive genes in common wheat. Funct Integr Genomics 8, 277–286 (2008). https://doi.org/10.1007/s10142-008-0076-9

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