Genome-wide transcriptome analysis of rice genes responsive to chilling stress

Cho, H. Y., Hwang, S.-G., Kim, D. S. and Jang, C. S. 2012. Genome-wide transcriptome analysis of rice genes responsive to chilling stress. Can. J. Plant Sci. 92: 447–460. Low temperature is known to be one of the major challenges to rice production. We have selected chilling-tolerant TILLING of Donganbyeo, which showed significantly vigorous growth relative to wild-type plants under chilling stress conditions (10–12°C). We performed a comparative transcriptome analysis using a chilling-tolerant line and wild-type plant with the objective to evaluate genomic responses to chilling stress and to identify chilling inducible genes. Functional enrichment analysis results demonstrated that a large proportion of chilling-inducible genes were associated with certain biological pathways, e.g., monosaccharide catabolic processes, reflecting the energy requirements necessary for adaptation to sub-optimal temperatures in plants. Extremely low correlation coefficients in a range of −0.07 to 0.04 were detected between plant responses to chilling stress and different abiotic stress conditions such as drought, salt, cold, and heat; these results imply that plants might exploit strikingly different response mechanisms against stress conditions. The largest subnetwork, which was composed of 78 chilling-specific inducible genes, was found in the tolerant plants, but not in the wild-type plants, which probably implies the existence of a delicate and harmonious signaling pathway setup in the tolerant plants. Expression patterns of 20 chilling-responsive genes were assessed via abiotic stress treatments and phytohormone treatments. About 80% of the tested chilling-inducible genes were upregulated by exogenous abscisic acid (ABA) treatment. The results of this study may prove useful in elucidating the chilling-response pathway and in the development of chilling-tolerant rice varieties.