Genomics approach to abscisic acid- and gibberellin-responsive genes in rice.
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.
Yazaki
Junshi
J
Department of Molecular Genetics, National Institute of Agrobiological Sciences, 2-1-2 Kannon-dai, Tsukuba, Ibaraki 305-8602, Japan.
Kishimoto
Naoki
N
Nagata
Yuko
Y
Ishikawa
Masahiro
M
Fujii
Fumiko
F
Hashimoto
Akiko
A
Shimbo
Kanako
K
Shimatani
Zenpei
Z
Kojima
Keiichi
K
Suzuki
Kouji
K
Yamamoto
Makoto
M
Honda
Sachiko
S
Endo
Ayano
A
Yoshida
Yumiko
Y
Sato
Yuki
Y
Takeuchi
Keiko
K
Toyoshima
Kazuko
K
Miyamoto
Chikako
C
Wu
Jianzhong
J
Sasaki
Takuji
T
Sakata
Katsumi
K
Yamamoto
Kimiko
K
Iba
Koh
K
Oda
Takahiro
T
Otomo
Yasuhiro
Y
Murakami
Kazuo
K
Matsubara
Kenichi
K
Kawai
Jun
J
Carninci
Piero
P
Hayashizaki
Yoshihide
Y
Kikuchi
Shoshi
S
D000040:Abscisic Acid / Q000494:pharmacology*; D002478:Cells, Cultured; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant / Q000187:drug effects* / Q000235:genetics; D017343:Genes, Plant; D005875:Gibberellins / Q000494:pharmacology*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000187:drug effects / Q000235:genetics*; D010937:Plant Growth Regulators / Q000494:pharmacology*; D020218:Response Elements / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
D005875:Gibberellins; D010937:Plant Growth Regulators; D014157:Transcription Factors; D000040:Abscisic Acid