GSE30367
Transcriptome analysis of rice roots and tips in early development by massive parallel sequencing
Despite the major physiological dissimilarities between roots and their tips, differences in their gene expression profiles remain largely unexplored. In this research, the transcriptome of rice (Oryza sativa L. subsp. Japonica) mature root tissue and root tips was monitored using mRNA-Seq at 2 time points. Almost 50 million 76 bp reads were mapped onto the rice genome sequence, differential expression patterns between tissues and time points were investigated and at least 1,006 novel transcriptionally active regions (nTARs) were detected to be expressed in rice root tissue. More than 30,000 genes were found to be expressed in rice roots, among which 1,761 root-specific and 306 tip-specific transcripts. Mature root tissue appears to respond more strongly to external stimuli than tips, showing a higher expression of for instance auxin responsive and ABA-responsive genes, as well as the phenylpropanoid pathway and photosynthesis upon light. The root tip-specific transcripts are mainly involved in mitochondrial electron transport, organelle development, secondary metabolism, DNA replication and metabolism, translation, and cellular component organization. As roots developed, genes involved in electron transport, response to oxidative stress, protein phosphorylation and metabolic processes were activated. For some nTARs a potential role in root development can be put forward based on homology to genes involved in CLAVATA signaling, cell cycle regulators and hormone signaling. A subset of differentially expressed genes and novel transcripts was confirmed using (q)RT-PCR. These results uncover previously unrecognized tissue-specific expression profiles and provide an interesting starting point to study the different regulation of transcribed regions of these tissues. Overall design: 2 biological replicates of roots and 3 biological replicates of root tips were sampled at two time points (1 biological replicate contains pooled tissue from 6 plants)