Abstract
For the purpose of monitoring gene regulation in the seminal root of rice (Oryza sativa L.) under a low pH condition, we carried out gene expression profiling by cDNA microarray constructed from 1, 265 rice cDNA clones. Total RNA was isolated from the rice seminal root with or without low pH treatment (pH 3.5), and fluorescence labeled by reverse transcription before hybridization. In order to identify up-regulated genes under a low pH condition, principal component analysis (PCA) was applied to analyze the gene expression profiles. The first two components appear to represent (1) the variance of signal intensity specific for each gene and (2) the variance resulted from a low pH treatment. Genes corresponding to upper 2.5 % based on the score of the second principal component were assumed to be acid response genes. Several genes, suggested to be responsible for metabolic regulation of intracellular pH in plants, were apparently up-regulated after acid treatment. On the basis of the above results, we concluded that PCA was a suitable method for gene expression analysis by cDNA microarray.
