Drought-responsive changes in poplar roots
Ontology highlight
ABSTRACT:
ORGANISM(S): Populus nigra Populus tremula x Populus alba Populus trichocarpa x Populus deltoides Populus euphratica
PROVIDER: GSE30266 | GEO | 2011/06/29
SECONDARY ACCESSION(S): PRJNA143727
REPOSITORIES: GEO
Similar Datasets
Project description:Drought-treated and corresponding control root tissue of poplar was subjected to array analyses Two-condition experiment, control (K) vs. Drought-stressed (S) leaves. Biological replicates: 3 control (1-3), drought-exposed (1-3), independently grown and harvested. One swap replicate per array.
2011-06-29 | E-GEOD-30266 | biostudies-arrayexpress
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.
2013-07-17 | GSE43162 | GEO
Project description:Drought avoidance mechanism is one of the component mechanisms contributing for drought tolerance in which roots serves as the master keys, but poorly understood. Comparative analysis of drought stress responsive root transcriptome between drought-tolerant Nootripathu and drought-susceptible IR20 In this study, we used microarrays to dissect out drought responsive changes in roots of two contrasting rice genotypes viz., IR 20 (a shallow rooted lowland indica genotype) and Nootripathu (a deep rooted upland indica genotype) at molecular level.
2018-04-01 | GSE92883 | GEO
Project description:Drought is one of the major factor that limits crop production and reduces yield. To understand the early response of plants under nearly natural conditions, pepper plants were grown in a greenhouse and drought stressed by withholding water for one week. Plants adapted to the decreasing water content of the substrate by adjustment of their osmotic potential in roots by accumulation of raffinose, glucose, galactinol and proline. In contrast in leaves levels of fructose, sucrose and also galactinol increased. Due to the water deficit cadaverine, putrescine, spermidine and spermine accumulated in leaves whereas the concentration of polyamines was reduced in roots. These polyamines are suggested to rather act as stress protectants than for osmotic adjustment. To understand the molecular basis of the response to this early drought stress better, four suppression subtractive hybridisation libraries from leaves and roots were constructed. Microarray technique was used to identify differentially expressed genes. A total of 109 unique ESTs were detected. The diversity of the putative functions of all identified genes confirms the complexity of the plant response to drought stress. Keywords: Transcription profiling
2009-10-28 | GSE18627 | GEO
Project description:Illumina technology was used to generate mRNA profiles of galls from root-knot nematodes infected and corresponding uninfected roots from Poplar CAD and WT lines. RNA was extracted from 3 replicates.TruSeq mRNA Stranded libraries were constructed and after pooling and normalization of libraries, sequencing was done on a NextSeq500 Sequencing System. Raw reads were trimmed for quality and mapped to the substituted genome sequence of P. tremula x P. alba 717-1B4 using CLC Genomics Workbench v9.5.2 and the primary transcripts only.
2019-01-15 | GSE112673 | GEO
Project description:Drought is one of the major factor that limits crop production and reduces yield. To understand the early response of plants under nearly natural conditions, pepper plants were grown in a greenhouse and drought stressed by withholding water for one week. Plants adapted to the decreasing water content of the substrate by adjustment of their osmotic potential in roots by accumulation of raffinose, glucose, galactinol and proline. In contrast in leaves levels of fructose, sucrose and also galactinol increased. Due to the water deficit cadaverine, putrescine, spermidine and spermine accumulated in leaves whereas the concentration of polyamines was reduced in roots. These polyamines are suggested to rather act as stress protectants than for osmotic adjustment. To understand the molecular basis of the response to this early drought stress better, four suppression subtractive hybridisation libraries from leaves and roots were constructed. Microarray technique was used to identify differentially expressed genes. A total of 109 unique ESTs were detected. The diversity of the putative functions of all identified genes confirms the complexity of the plant response to drought stress. Keywords: Transcription profiling Two-condition experiment in roots and leaves, control leaves (CL) vs. drought-stressed leaves (DL) and control roots (CR) vs. drought-stressed roots (DR). Biological replicates: 4 control (1-4), drought-stressed (1-4), independently grown and harvested. One swap replicate per array.
2010-06-20 | E-GEOD-18627 | biostudies-arrayexpress
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.
2013-07-17 | E-GEOD-43162 | biostudies-arrayexpress
Project description:In this study we employ a strand-specific RNA-seq appoach and stranded gene expression analysis tools to identify drought responsive antisense gene loci and sense-antisense gene pairs in Populus. we generated and sequenced 28 strand-specific cDNA libraries derived from either leaf or root tissues of Populus trichocarpa plants associaed with both short-term drought (24 hours of water stress of 40% of field capacity) and long-term drought ( 25 days of water stress of 40% of field capacity) . We mapped over 71 billion nucleotides to Populus genome. Our data demonstrates that with the current sequence depth ~ 19 % of Populus genome undergoes antisense transcription subjected to drought regulation. All in all we have identified that in root tissues 524 differentially expressed antisense genes and 247 drought-responsive SA gene pairs which are significantly regulated by drought (padj <0.05). Taken all data from both drought treatments, we have identified 1185 unique drought-responsive antisense gene loci and 606 drought-responsive SA gene pairs (padj <0.05).
2019-01-06 | GSE97463 | GEO
Project description:Drought is one of the most important environmental fluctuations affecting tree growth and survival. Therefore, understanding of physiological and transcriptomic responses of trees to this stress factor will make important contributions to forest health and productivity. Here, we report comparative physiological and microarray based transcriptome analysis between drought resistant (N.62.191) and drought-sensitive (N.03.368.A) black poplar genotypes under well-watered (WWP), moderate drought (MD), severe drought (SD) and post drought re-watering (PDR) conditions. In the study, sensitive genotype exhibited a drought escape strategy with lower leaf water potential, higher reactive oxygen production, complete leaf abscission and subsequent terminal shoot necrosis under drought stress. On the other hand, resistant genotype had a dehydration tolerance indicating highly delayed leaf abscission under drought and fast growing capacity during re-watering conditions. Gene ontology enrichment analysis attributed drought susceptibility of black poplar to significant up-regulation of genes functional in transcription regulation (AP2/ERF, NAC and WRKY), cell wall modification (Expansins), fatty acid metabolism (enoyl-ACP reductase, lipid transport protein particle), protein degradation (endopeptidases), ethylene synthesis (1-aminocyclopropane-1-carboxylate) and riboflavin synthesis (GTP cyclohydrolase II) under drought stress. Transcriptomic comparison indicated significant down-regulation of photosynthesis, electron transport and carbohydrate metabolism related genes under drought stress in sensitive genotype. Although, similar reduction in carbohydrate metabolism was also recorded for resistant genotype, genes related with photosynthesis and electron transport systems were not down regulated even under SD for this genotype. Resistant genotype specific up-regulation of small heat shock proteins (sHSP) and bark storage proteins revealed importance of protein protection and nitrogen remobilization under drought stress, respectively. This is the first study associating BSP production to delayed leaf abscission and drought tolerance in trees.
2017-02-28 | GSE76322 | GEO
Project description:Episodic drought stress negatively impacts the health of long-lived trees. Understanding the genetic and molecular mechanisms that underpin response to drought stress is requisite for selecting or enhancing climate change resilience. Here we aim to establish standardized drought stress protocols for transcriptome studies in poplar trees, to determine how hybrid poplars respond to prolonged and uniform exposure to drought; to determine if the responses to moderate and more severe growth-limiting drought stresses were qualitatively or quantitatively different; and, to determine how response to drought changes throughout the day. We established hybrid poplar trees (Populus x ’Okanese’) from unrooted stem cutting with abundant soil moisture for six weeks. We then withheld water to establish three soil water contents reflecting well-watered, moderate, and severe growth-limiting drought conditions. Plants were rewatered as needed for three weeks to maintain the soil water conditions. The mild and severe drought treatments elicited distinct changes in growth and development, photosynthetic rates and global transcriptomic changes. Notably, the time of day of sampling was strongest signal in the transcriptome data and it quantitatively and qualitatively affected drought responsive changes in gene expression. These analyses emphasize the complex nature of drought regulation in long-lived trees.
2021-12-20 | GSE191155 | GEO