E-MTAB-4465 - Transcription profiling by high throughput sequencing of four rice cultivars with variation in growth response to phosphate starvation

Released on 23 May 2014, last updated on 10 February 2016
Oryza sativa Indica Group, Oryza sativa Japonica Group
Samples (57)
Protocols (2)
Rice has developed several morphological and physiological strategies to adapt to phosphate starvation stress. In order to elucidate the molecular bases of response due to phosphate stress particularly the transcriptional profile of genotypes with variation in tolerance to phosphate starvation, we analyzed the gene expression profiles of 3 japonica rice cultivars and an indica cultivar with different levels of tolerance to phosphate starvation using the RNA-Seq method. We constructed a total of 48 libraries corresponding to root and shoot of the 4 cultivars for control (0 d) and −P treatment (22 d) with three biological replicates for root and shoot samples in each cultivar. Approximately 254 million sequenced tags were mapped onto the reference rice genome sequence (IRGSP1.0) and an average of about 5,000 transcripts in each genotype were found to be responsive to Pi-starvation. Comparative analysis of the responsive transcripts revealed an overall similarity in the transcriptome signatures resulting from phosphate starvation as well as distinct differences that distinguish the degree of tolerance among the 4 cultivars. We elucidated a set of core responsive transcripts commonly expressed in both root and shoot with different levels of expression reflecting variation as well genotype specificity in tolerance to Pi-starvation. De novo assembly of unmapped reads generated a large set of sequence assemblies that represent potential new transcripts that may be involved in tolerance to phosphate deficiency. Characterization of 88 assemblies unaligned in the reference genome revealed several dozen transcripts which correspond to plant ESTs. This study provides an overview of the diversity in response to P-starvation stress that can be used to identify the major genes for improving Pi acquisition and utilization in rice and other cereal crops. Note: Samples in DRA were assigned the same sample accession. This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original DRA sample accessions.
Experiment type
RNA-seq of coding RNA 
Diversity in the complexity of phosphate starvation transcriptomes among rice cultivars based on RNA-Seq profiles. Oono Y, Kawahara Y, Yazawa T, Kanamori H, Kuramata M, Yamagata H, Hosokawa S, Minami H, Ishikawa S, Wu J, Antonio B, Handa H, Itoh T, Matsumoto T. , PMID:23857470
Exp. designProtocolsVariablesProcessedSeq. reads
Investigation descriptionE-MTAB-4465.idf.txt
Sample and data relationshipE-MTAB-4465.sdrf.txt