Poster: Genomics Resources

Abs # 933: 22K Oligo-based microarray system for rice gene expression analysis

Presenter:	Kikuchi, Shoshi , skikuchi@nias.affrc.go.jp
Authors	Kikuchi, Shoshi  (B)   Shimatani, Zempei  (A)   Yazaki, Junshi  (B)   Kishimoto, Naoki  (B)   Hashimoto, Akiko  (A)   Nagata, Yuko  (A)   Kanako, Shimbo  (A)   Fujii, Fumiko  (B)   Taya, Toshiki  (C)   Tonouchi, Mio  (C)   Nelson, Charles  (C)   Nakagawa, Allen  (C)   Jun, Kawai  (D)   Carninci, Piero  (D)   Hayashizaki, Yoshihide  (D)   Ohtomo, Yasuhiro  (E)   Murakami, Kazuo  (E)   Matsubara, Kenichi  (E)   Kojima, Keiichi  (F)   Suzuki, Kohji  (F)
Affiliations:	(A): STAFF Institute (B): National Institute of Agrobiological Sciences (C): Agilent Technologies (D): RIKEN Institute (E): Foundation of Advancement of International Science (F): Hitachi Software Engineering

We have established a rice microarray system by comparing of a semi-unique set of 8987 EST clones (RMOS: http://cdna01.dna.affrc.go.jp/RMOS/index.html ) with our Rice Expression Database (RED: http://red.dna.affrc.go.jp/RED/). In this report, we have created a new custom microarray, developed by Agilent Technologies. This array contains in-situ synthesized 60-mer oligo nucleotide probes, which represent approximately 22,000 unique rice full-length transcripts collected and sequenced by the rice full-length cDNA project (KOME: http://cdna01.dna.affrc.go.jp/cDNA/ ). We have analyzed the effects of two phytohormones: 50uM of abscisic acid (ABA), and 50 uM of Gibberellin (GA3) on the gene expression in calli derived from mature seed. Reproducibility of the array data were checked by using the array's replicates, and a dye-swap methodology throughout the two-color microarray experiment. Based on the criterion of two-fold difference, it was found that 0.76~ 0.89% of all clones were up-regulated by ABA treatment: 70 % of which were commonly observed among four arrays. As a result, after each 72 hour hormone treatment, 111 clones were commonly up-regulated and 89 clones were commonly down-regulated by ABA. In addition, 207 clones were commonly up-regulated, and 96 clone were commonly down-regulated by GA3. ABA and GA3 are known to act antagonistically in plant cells. The observed ratios of ABA-treatment and GA3-treatment showed a statistically significant anti-correlation. Considering the annotation of the listed clones, and the real-time quantitative PCR data, it was determined that this array is an excellent tool for conducting genome-wide, gene expression analysis in rice