These authors contributed equally to this work.
A dynamic gene expression atlas covering the entire life cycle of rice
Article first published online: 9 DEC 2009
© 2010 The Authors. Journal compilation © 2010 Blackwell Publishing Ltd
The Plant Journal
Volume 61, Issue 5, pages 752–766, March 2010
How to Cite
Wang, L., Xie, W., Chen, Y., Tang, W., Yang, J., Ye, R., Liu, L., Lin, Y., Xu, C., Xiao, J. and Zhang, Q. (2010), A dynamic gene expression atlas covering the entire life cycle of rice. The Plant Journal, 61: 752–766. doi: 10.1111/j.1365-313X.2009.04100.x
- Issue published online: 22 FEB 2010
- Article first published online: 9 DEC 2009
- Received 3 October 2009; revised 14 November 2009; accepted 27 November 2009; published online 18 January 2010.
- Oryza sativa L.;
- expression profile;
- functional genomics;
- genome annotation;
Growth and development of a plant are controlled by programmed expression of suits of genes at the appropriate time, tissue and abundance. Although genomic resources have been developed rapidly in recent years in rice, a model plant for cereal genome research, data of gene expression profiling are still insufficient to relate the developmental processes to transcriptomes, leaving a large gap between the genome sequence and phenotype. In this study, we generated genome-wide expression data by hybridizing 190 Affymetrix GeneChip Rice Genome Arrays with RNA from 39 tissues collected throughout the life cycle of the rice plant from two varieties, Zhenshan 97 and Minghui 63. Analyses of the global transcriptomes revealed many interesting features of dynamic patterns of gene expression across the tissues and stages. In total, 38 793 probe sets were detected as expressed and 69% of the expressed transcripts showed significantly variable expression levels among tissues/organs. We found that similarity of transcriptomes among organs corresponded well to their developmental relatedness. About 5.2% of the expressed transcripts showed tissue-specific expression in one or both varieties and 22.7% of the transcripts exhibited constitutive expression including 19 genes with high and stable expression in all the tissues. This dataset provided a versatile resource for plant genomic research, which can be used for associating the transcriptomes to the developmental processes, understanding the regulatory network of these processes, tracing the expression profile of individual genes and identifying reference genes for quantitative expression analyses.