High-throughput transcriptome analysis in rice from a genomic perspective

Abstract

The major goals of transcriptome analysis in rice (Oryza saliva L.) are to identify the transcribed regions in the rice genome and to understand the mechanisms of gene expression at the transcription level. Starting with the vast collection of complementary DNA (cDNA) clones (expressed sequence tags, ESTs) in the early 1990s, more than 580,000 full-length cDNA (FL-cDNA) clones were collected from japonica subspecies and more than 35,000 of their complete sequences were published; in contrast, no large-scale full-length cDNA collection is currently available for indica subspecies. Sequence information for ESTs and FL-cDNA clones has contributed to the global annotation of rice genes. Using cDNA clones and sequence information for the FL-cDNA clones, several kinds of microarray systems were established, along with databases storing the gene expression data from the microarray systems. Bioinformatics tools for the analysis of gene expression data and for data mining have also been developed. In this chapter, I will review and discuss the significant progress that has been achieved in rice transcriptome analysis.