Comparison of gene expression between upland and lowland rice cultivars under water stress using cDNA microarray

To elucidate the differences in the regulation of water stress tolerance between two genotypes of rice, upland-rice (UR, resistant to water stress) and lowland-rice (LR, susceptible to water stress), we constructed subtracted cDNA libraries from polyethyleneglycol (PEG)-treated and non-treated rice seedlings (IRAT109, an upland-rice variety) by suppression subtractive hybridization (SSH), from which about 2,000 recombinant colonies were picked and amplified. Then, a cDNA microarray containing these expressed sequence tags (ESTs) was used to analyze the gene expression profiles in UR and LR in response to PEG treatment. Microarray data revealed that the majority of genes expressed in UR and LR are almost identical and Student’s t test showed that 13% of all the ESTs detected in leaves and 7% of that in roots expressed differentially in transcripts abundance between the two genotypes. After sequencing, it was found that 64 and 79 unique ESTs expressed at higher levels in UR and LR, respectively. Many of the ESTs that showed higher expression in UR upon PEG treatment represented genes for transcription factors, genes playing roles in detoxification or protection against oxidative stress, and genes that help in maintaining cell turgor. In contrast, some ESTs that showed higher expression in LR were genes functioning in the degradation of cellular components. Based on data from this study and previous reports, we suggest that overexpression of some genes that expressed at higher level in UR may improve water stress tolerance in LR and other plant species.