Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice

Junshi Yazaki, Naoki Kishimoto, Yuko Nagata, Masahiro Ishikawa, Fumiko Fujii, Akiko Hashimoto, Kanako Shimbo, Zenpei Shimatani, Keiichi Kojima, Kouji Suzuki, Makoto Yamamoto, Sachiko Honda, Ayano Endo, Yumiko Yoshida, Yuki Sato, Keiko Takeuchi, Kazuko Toyoshima, Chikako Miyamoto, Jianzhong Wu, Takuji SasakiKatsumi Sakata, Kimiko Yamamoto, Koh Iba, Takahiro Oda, Yasuhiro Otomo, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi

Research output: Contribution to journalArticle

56 Citations (Scopus)

Abstract

We used an 8987-EST collection to construct a cDNA microarray system with various genomics information (full-length cDNA, expression profile, high accuracy genome sequence, phenotype, genetic map, and physical map) in rice. This array was used as a probe to hybridize target RNAs prepared from normally grown callus of rice and from callus treated for 6 hr or 3 days with the hormones abscisic acid (ABA) or gibberellin (GA). We identified 509 clones, including many clones that had never been annotated as ABA- or GA-responsive. These genes included not only ABA- or GA-responsive genes but also genes responsive to other physiological conditions such as pathogen infection, heat shock, and metal ion stress. Comparison of ABA- and GA-responsive genes revealed antagonistic regulation for these genes by both hormones except for one defense-related gene, thionin. The gene for thionin was up-regulated by both hormone treatments for 3 days. The upstream regions of all the genes that were regulated by both hormones had cis-elements for ABA and GA response. We performed a clustering analysis of genes regulated by both hormones and various expression profiles that showed three notable clusters (seed tissues, low temperature and sugar starvation, and thionin-gene related). A comparison of the cis-elements for hormone response genes between rice and Arabidopsis thaliana, we identified cis-elements for dehydration-stress response or for expression of amylase gene as Arabidopsis gene-specific or rice gene-specific, respectively.

Original languageEnglish
Pages (from-to)249-261
Number of pages13
JournalDNA Research
Volume10
Issue number6
DOIs
Publication statusPublished - Dec 1 2003

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Gibberellins
Abscisic Acid
Genomics
Genes
Thionins
Hormones
Bony Callus
Arabidopsis
Oryza
Clone Cells
Expressed Sequence Tags
Response Elements
Amylases
Starvation
Oligonucleotide Array Sequence Analysis
Dehydration
Cluster Analysis

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Yazaki, J., Kishimoto, N., Nagata, Y., Ishikawa, M., Fujii, F., Hashimoto, A., ... Kikuchi, S. (2003). Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice. DNA Research, 10(6), 249-261. https://doi.org/10.1093/dnares/10.6.249

Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice. / Yazaki, Junshi; Kishimoto, Naoki; Nagata, Yuko; Ishikawa, Masahiro; Fujii, Fumiko; Hashimoto, Akiko; Shimbo, Kanako; Shimatani, Zenpei; Kojima, Keiichi; Suzuki, Kouji; Yamamoto, Makoto; Honda, Sachiko; Endo, Ayano; Yoshida, Yumiko; Sato, Yuki; Takeuchi, Keiko; Toyoshima, Kazuko; Miyamoto, Chikako; Wu, Jianzhong; Sasaki, Takuji; Sakata, Katsumi; Yamamoto, Kimiko; Iba, Koh; Oda, Takahiro; Otomo, Yasuhiro; Murakami, Kazuo; Matsubara, Kenichi; Kawai, Jun; Carninci, Piero; Hayashizaki, Yoshihide; Kikuchi, Shoshi.

In: DNA Research, Vol. 10, No. 6, 01.12.2003, p. 249-261.

Research output: Contribution to journalArticle

Yazaki, J, Kishimoto, N, Nagata, Y, Ishikawa, M, Fujii, F, Hashimoto, A, Shimbo, K, Shimatani, Z, Kojima, K, Suzuki, K, Yamamoto, M, Honda, S, Endo, A, Yoshida, Y, Sato, Y, Takeuchi, K, Toyoshima, K, Miyamoto, C, Wu, J, Sasaki, T, Sakata, K, Yamamoto, K, Iba, K, Oda, T, Otomo, Y, Murakami, K, Matsubara, K, Kawai, J, Carninci, P, Hayashizaki, Y & Kikuchi, S 2003, 'Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice', DNA Research, vol. 10, no. 6, pp. 249-261. https://doi.org/10.1093/dnares/10.6.249
Yazaki J, Kishimoto N, Nagata Y, Ishikawa M, Fujii F, Hashimoto A et al. Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice. DNA Research. 2003 Dec 1;10(6):249-261. https://doi.org/10.1093/dnares/10.6.249
Yazaki, Junshi ; Kishimoto, Naoki ; Nagata, Yuko ; Ishikawa, Masahiro ; Fujii, Fumiko ; Hashimoto, Akiko ; Shimbo, Kanako ; Shimatani, Zenpei ; Kojima, Keiichi ; Suzuki, Kouji ; Yamamoto, Makoto ; Honda, Sachiko ; Endo, Ayano ; Yoshida, Yumiko ; Sato, Yuki ; Takeuchi, Keiko ; Toyoshima, Kazuko ; Miyamoto, Chikako ; Wu, Jianzhong ; Sasaki, Takuji ; Sakata, Katsumi ; Yamamoto, Kimiko ; Iba, Koh ; Oda, Takahiro ; Otomo, Yasuhiro ; Murakami, Kazuo ; Matsubara, Kenichi ; Kawai, Jun ; Carninci, Piero ; Hayashizaki, Yoshihide ; Kikuchi, Shoshi. / Genomics Approach to Abscisic Acid- and Gibberellin-responsive Genes in Rice. In: DNA Research. 2003 ; Vol. 10, No. 6. pp. 249-261.
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