32. Microarray analysis of transcription patterns in rice: Comparison of differential expression among different tissues/organs

1) National Institute of Agrobiological Sciences, Kannondai, Tsukuba, Ibaraki 305-8602, Japan
2) STAFF-Institute, Ippaizuka, Tsukuba, Ibaraki 305-0854, Japan

We have investigated gene expression patterns at transcriptional level in rice different tissues/organs, using our first generation microarrays with 1265 cDNAs which were randomly selected from the independent cDNAs of rice. We isolated RNAs from rice tissues/organs described below (cv. 'Nipponbare'): [1] water-imbibed seeds (for 1 day at 30C in the dark) and

leaves from rice plants grown under green house condition (3 months after transplanting); [2] calli induced from scutellum of mature seeds and grown on MS medium containing 2,4-D (2 mg/l) for three weeks and young seedlings grown on MS medium without phytohormones for three weeks (30C, 24hrs-light condition); [3] panicles beginning to flower on the sampling day or began to flower on the day before sampling day and mature leaves from the same paddy fields; [4] heat-shocked and untreated seeds both of which were water-imbibed for three days at 30C in the dark. We have compared expression profiles about each pair of materials in these 4 combinations of the rice tissues/organs. For expression profiling by microarray, we used 1 micro g of poly(A)+ RNA from each material per slide of microarray. Methods on our micorarray analysis were as described by Yazaki et al. (1999). The quantified data for duplicated spots on each cDNA were averaged, then log2(ratio of between the averaged data about each pair of the 4 material combinations) was calculated to make the data have the normal distribution: that is, [1] log2(mature leaves/imbibed seeds); [2] log2(seedlings cultured in vitro/calli); [3] log2(mature leaves/panicles); [4] log2(heat-treated germinated seeds/untreated germinated seeds). These 4 sets of data were normalized with the medians for each data set. We judged an expression level of each cDNA to be significantly altered when its {log2 (ratio) - median} was larger than +2SD or smaller than -2SD. Figure 1 shows the genes having alternations in gene expression in each pair of the materials in the 4 combinations described above ([1] to [4]), with results of blast search; however it does not show the genes whose products are unknown. Genes showing alternations in gene expression in each pair of the materials are summarized as follows: [1]A: 19 genes were up-regulated in mature leaves (including 4 unknown genes), which contained photosynthesis-related proteins, protein-kinases, and thioredoxins; [1]B: 29 genes were up-regulated in imbibed seeds (incl. 6 unknown genes), which contained storage proteins, ADHs, and ribosomal proteins; [2]A: 22 genes were up-regulated in seedlings cultured in vitro (incl. 4 unknown genes), which contained cytochrome P450 monooxygenases, a fatty acid synthesis gene, photosynthesis-related proteins, PAL and ubiquitins; [2]B: 10 genes were up-regulated in calli (incl. 5 unknown genes), which contained an urate oxidase, a MADS box protein, a glycoprotein and an auxin transporter; [3]A: 19 genes were up-regulated in mature leaves (incl. 6 unknown genes), which contained thioredoixins, protein kinases, cytochrome P450 monooxygenases and a fatty acid synthesis gene; [3]B: 24 genes were up-regulated in flowering panicles (incl. 13 unknown genes), which contained pollen allergens, ADH, transcription factors, primary metabolism-related enzymes (sugar-metabolism, ATP-hydrolysis); [4] 32 genes were up-regulated in heat-treated seeds (incl. 19 unknown genes), which contained heat shock proteins/chaperones, a ribonucleoprotein, beta-expansin and protein kinases; on the contrary, no genes were up-regulated in untreated seeds. We reasonably detected up-regulation of many of these genes in each pair of the materials (e.g. photosynthesis-related proteins in [1]A and [2]A; heat shock proteins in [4]). We concluded that our cDNA microarray system is suitable for analysis on differential expression between different organs/tissues, also between stresstreated and untreated plants.


Yazaki, J., N. Kishimoto, K. Nakamura, F. Fujii, K. Shimbo, Y. Otsuka, J. Wu, K. Yamamoto, K. Sakata, T. Sasaki and S. Kikuchi, 1991. Embarking on rice functional genomics via cDNA microarray: use of 3’ UTR probes for specific gene expression anaysis. DNA Res. 7: 367-370.