Transcriptomics

Dataset Information

3

The response and recovery of Arabidopsis thaliana transcriptome to phosphate starvation [At35b_MR]


ABSTRACT: Background: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes the first genome-wide resource on the molecular dynamics underpinning the response and recovery in roots and shoots of Arabidopsis thaliana to phosphate-starvation. Results: Genome-wide profiling revealed minimal overlap between root and shoot transcriptomes suggesting two independent phosphate-starvation regulons. Novel gene expression patterns were detected for over 1000 candidates and were classified as either initial, persistent, or latent responders. Comparative analysis to AtGenExpress identified novel cohorts of genes co-regulated across multiple stimuli. The hormone ABA displayed a dominant role in regulating many phosphate-responsive candidates. Analysis of co-regulation enabled the determination of primary versus redundant members of closely related gene families with respect to phosphate-starvation. Thus, among others, we show that PHO1 acts in shoot, whereas PHO1;H1 is likely the primary regulator in root. Conclusion: Our results uncover a much larger, staged responses to phosphate-starvation than previously described. To our knowledge, this work describes the highest resolution of genome-wide data on plant nutrient stress to date. 2 tissues X 3 treatments X 3 biological replicates

OTHER RELATED OMICS DATASETS IN: E-GEOD-33790

ORGANISM(S): Arabidopsis thaliana  

SUBMITTER: Nam-Hai Chua   Matthew Hannah  Takatoshi Kiba1  Cameron R MacPherson  Vladimir B Bajic  Xiu-Jie Wang  Jun Liu  Jongchan Woo  Huan Wang 

PROVIDER: E-GEOD-33996 | ArrayExpress | 2012-06-17

SECONDARY ACCESSION(S): GSE33996PRJNA156451

REPOSITORIES: GEO, ArrayExpress

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Publications

The response and recovery of the Arabidopsis thaliana transcriptome to phosphate starvation.

Woo Jongchan J   MacPherson Cameron Ross CR   Liu Jun J   Wang Huan H   Kiba Takatoshi T   Kiba Takatoshi T   Hannah Matthew A MA   Wang Xiu-Jie XJ   Bajic Vladimir B VB   Chua Nam-Hai NH  

BMC plant biology 20120503


BACKGROUND: Over application of phosphate fertilizers in modern agriculture contaminates waterways and disrupts natural ecosystems. Nevertheless, this is a common practice among farmers, especially in developing countries as abundant fertilizers are believed to boost crop yields. The study of plant phosphate metabolism and its underlying genetic pathways is key to discovering methods of efficient fertilizer usage. The work presented here describes a genome-wide resource on the molecular dynamics  ...[more]

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