Open Access Highly Accessed Research article

RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions

Yuhya Wakasa1, Youko Oono2, Takayuki Yazawa23, Shimpei Hayashi1, Kenjirou Ozawa1, Hirokazu Handa2, Takashi Matsumoto2 and Fumio Takaiwa1*

Author Affiliations

1 Functional Transgenic Crops Research Unit, Genetically Modified Organism Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan

2 Agrogenomics Research Center, National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

3 Government and Public Corporation Information Systems, Hitachi Co., Ltd, 2-4-18 Toyo, Koto-ku, Tokyo 135-8633, Japan

For all author emails, please log on.

BMC Plant Biology 2014, 14:101  doi:10.1186/1471-2229-14-101

Published: 18 April 2014



The endoplasmic reticulum (ER) stress response is widely known to function in eukaryotes to maintain the homeostasis of the ER when unfolded or misfolded proteins are overloaded in the ER. To understand the molecular mechanisms of the ER stress response in rice (Oryza sativa L.), we previously analyzed the expression profile of stably transformed rice in which an ER stress sensor/transducer OsIRE1 was knocked-down, using the combination of preliminary microarray and quantitative RT-PCR. In this study, to obtain more detailed expression profiles of genes involved in the initial stages of the ER stress response in rice, we performed RNA sequencing of wild-type and transgenic rice plants produced by homologous recombination in which endogenous genomic OsIRE1 was replaced by missense alleles defective in ribonuclease activity.


At least 38,076 transcripts were investigated by RNA sequencing, 380 of which responded to ER stress at a statistically significant level (195 were upregulated and 185 were downregulated). Furthermore, we successfully identified 17 genes from the set of 380 ER stress-responsive genes that were not included in the probe set of the currently available microarray chip in rice. Notably, three of these 17 genes were non-annotated genes, even in the latest version of the Rice Annotation Project Data Base (RAP-DB, version IRGSP-1.0).


Therefore, RNA sequencing-mediated expression profiling provided valuable information about the ER stress response in rice plants and led to the discovery of new genes related to ER stress.

Gene targeting; ER stress response; Microarray; Oryza sativa L; RNA sequencing; Transcriptome