Transcription analysis of rice chromosome 4 using a genomic fragment-based tiling microarray

Yuling Jiao¹, Peixin Jia², Thomas E. Royce³, Paul M. Harrison³, Shuliang Yu², Ligeng Ma¹, Ning Su¹, Ying Gao¹, Mark Gerstein³, Bin Han² and Xing Wang Deng¹

¹Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT; ²National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; ³Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT

The complete sequence of cultivated rice species Oryza sativa genome provides an unprecedented opportunity to study and improve our cereal crops. An essential step towards deciphering the biological information encoded in this nucleotide-level data is to obtain an accurate catalogue of genes and their respective expression patterns. Computational methods are still not sufficiently trained and informed for rice genome annotation, therefore there is a critical need for experimental validation. Here, we report the transcriptional activity of rice chromosome 4 using a genomic DNA fragment-based tiling microarray. Representative organ samples of rice and in vitro cultured cells were examined to catalogue the transcribed regions of rice chromosome 4, and to reveal organ- and developmental stage-specific transcription patterns. Our analysis revealed that 38% of all the genomic fragments with detected transcription lack any previous cDNA or EST support. Among them, about two-thirds also lack computational gene predictions. Further, a high percentage of rice genes that do not have homologues in the Arabidopsis genome are transcribed during rice development, supporting functional roles of that group of genes. Comparison of gene expression among the examined organ types revealed both common and organ-specific expressed genes in chromosome 4.