Microarray-based approaches to rice transcriptome analysis

The advent of rice genome sequences and subsequent annotation is having two marked, complementary effects on the relatively new discipline of plant transcriptomics. First, the rice genome contains approximately 60,000 annotated protein-coding loci that top other full sequenced genomes. Although masking protein related transposable elements considerably reduces this number, abundant rice- or cereal-specific genes exist. Second, the application of various transcriptome-profiling techniques in rice has generated a large number of putative transcripts that have yet to be incorporated into the genome annotation. The unprecedented complexity and impending completeness of the transcriptome data are simultaneously demanding and creating opportunities for new avenues of discovery using novel, high-throughput approaches. In this chapter, we review the recent advances in rice microarray systems and the application of these systems in deep and comprehensive transcriptome analysis.