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Expression data from poplar roots under nitrogen limitation

ABSTRACT: We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation.

ORGANISM(S): Populus tremula x Populus alba Populus sp.

PROVIDER: GSE43162 | GEO | 2013/07/17

SECONDARY ACCESSION(S): PRJNA184760

REPOSITORIES: GEO

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Expression data from poplar roots under nitrogen limitation

Project description:We study the effect of nitrogen limitation on the growth and development of poplar roots. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by low nitrogen in the growth media. We report the effect of nitrogen limitation on the growth and development of poplar roots. Low nitrogen concentration led to increased root elongation followed by lateral root proliferation and finally increased root biomass. These morphological responses correlated with high and specific activation of genes encoding regulators of cell cycle and enzymes involved in cell wall biogenesis, growth and remodeling. Comparative analysis of poplar and Arabidopsis root transcriptomes under nitrogen deficiency indicated many similarities and diversification in the response in the two species. A reconstruction of genetic regulatory network (GRN) analysis revealed a sub-network centered on a PtaNAC1-like transcription factor. Consistent with the GRN predictions, root-specific upregulation of PtaNAC1 in transgenic poplar plants increased root biomass and led to significant changes in the expression of the connected genes specifically under low nitrogen. PtaNAC1 and its regulatory miR164 showed inverse expression profiles during response to LN, suggesting of a micro RNA mediated attenuation of PtaNAC1 transcript abundance in response to nitrogen deprivation. Poplar roots from low nitrogen treated and untreated from in vitro condition was selected for RNA extraction and hybridization on Affymetrix microarrays. Roots were sampled at 6, 12, 24, 48, 96 and 504h after transfer to control and low nitrogen media and RNA was extacted.

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Time-Dependent Transcriptome Profiling Reveals the Importance of Multiple Transcription Factors in Brachypodium Root Development

Project description:The goal of this study was to examine the transcriptional events occuring during stress-free Brachypodium distachyon root development via illumina paired-end RNA-seq. 4 time-points were chosen that capture the transition from rapid vegetative growth into slower reproductive growth. Abstract - Root systems are dynamic, adaptable organs that play critical roles in plant development. Roots, however, remain understudied and therefore present opportunities for trait improvement in food and bioenergy crops. A comprehensive growth stage-based root phenotyping integrated with molecular signatures is required to advance our understanding of root growth and development. Here we studied Brachypodium distachyon rooting process by monitoring root biomass, length, branching, root-to-shoot ratio and Carbon-to-Nitrogen ratio during time. To provide insight into gene regulation that accompanies root development and biomass accumulation, we generated comprehensive transcript profiles of Brachypodium whole-root system at four initial developmental stages that capture the transition from vegetative to reproductive growth. Our stringent data analysis revealed that multiple biological processes and various families of transcription factors (TFs) were differentially expressed during root development. In particular, the AUX/IAA, ERFs, WRKY, NAC, and MADS TF family members were upregulated, while ARFs and GRFs were downregulated in a time-dependent manner. Our results suggested particular TF families and biological processes including trehalose metabolism as important factors possibly involved in root biomass accumulation. We introduced several Brachypodium root biomass-promoting genes which can be employed by the genome editing approaches for improving biomass productivity in grasses.

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Gene expression signatures in Arabidopsis thaliana roots under sufficient nitrogen or mild nitrogen deficiency

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Project description:Expression data from poplar roots under nitrogen limitation

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The root-colonizing endophyte Piriformospora indica supports nitrogen-starved Arabidopsis seedlings with N metabolites

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