Genome-wide RNA expression profiling in rice

One of the most daunting challenges in the post-genomic era is to identify and characterize all the transcribed regions in a genome. In the past few years, significant progress has been made in transcriptome analysis of the rice genome via a number of new technologies. In this chapter, we review the recent advances in the large-scale expressed sequence tag (EST) sequencing, establishment of microarray systems using EST sequences, and new oligomicroarray systems based on the full-length cDNA sequences. New methods for a deep and comprehensive transcriptome analysis of the rice genome, such as serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS), and the whole genome tiling array system, are also discussed.