Genotype and time of day shape the Populus drought response
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA116527 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important hybrid Populus clones (P. deltoides · P. nigra, DN34, and P. nigra · P. maximowiczii, NM6) was characterized over a diurnal period using a 4 · 2 · 2 completely randomized factorial ANOVA experimental design (four time points, two genotypes, and two treatment conditions) using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus.
2009-12-31 | GSE15242 | GEO
Project description:As exposure to episodic drought can impinge significantly on forest health and the establishment of productive tree plantations, there is great interest in understanding the mechanisms of drought response in trees. The ecologically dominant and economically important genus Populus, with its sequenced genome, provides an ideal opportunity to examine transcriptome level changes in trees in response to a drought stimulus. The transcriptome level drought response of two commercially important hybrid Populus clones (P. deltoides · P. nigra, DN34, and P. nigra · P. maximowiczii, NM6) was characterized over a diurnal period using a 4 · 2 · 2 completely randomized factorial ANOVA experimental design (four time points, two genotypes, and two treatment conditions) using Affymetrix Poplar GeneChip microarrays. Notably, the specific genes that exhibited changes in transcript abundance in response to drought differed between the genotypes and/or the time of day that they exhibited their greatest differences. This study emphasizes the fact that it is not possible to draw simple, generalized conclusions about the drought response of the genus Populus on the basis of one species, nor on the basis of results collected at a single time point. The data derived from our studies provide insights into the variety of genetic mechanisms underpinning the Populus drought response, and provide candidates for future experiments aimed at understanding this response across this economically and ecologically important genus. 48 arrays total. 2 genotypes (DN34, NM6), 4 time points (midnight, pre-dawn, mid-day, late day), 2 water regimes (well-watered, water-limited). 3 biological replicates per treatment.
2009-12-31 | E-GEOD-15242 | biostudies-arrayexpress
Project description:Under natural conditions, plants experience episodes of drought for periods of days or longer. Plants respond to drought stress by reconfiguring their transcriptome activity. Transcriptome changes in response to drought are dynamic, and are likely to be shaped by mitigating factors such as diel signals. To gain insights into the dynamics of transcriptome reconfiguration in response to gradual soil drying, the drought-induced transcriptomes of Arabidopsis thaliana were examined at four time points over a single diel period – midday, late day, midnight, and pre-dawn. A core set of genes was identified that was responsive to drought, independent of the time of day at which they were measured. Strikingly, the magnitude of the drought-induced changes for these genes varied in a time-of-day-dependent manner. An additional set of time-of-day-specific drought-responsive genes were also identified. The diurnal patterns of transcript accumulation for these genes was strongly influenced by drought stress. This study indicates that analysis of a single time point would miss suites of drought-responsive genes that are revealed through assessment of the dynamics of diurnal changes, emphasizing the value of characterizing multiple time-of-day-specific drought transcriptomes.
2010-07-01 | GSE19700 | GEO
Project description:Under natural conditions, plants experience episodes of drought for periods of days or longer. Plants respond to drought stress by reconfiguring their transcriptome activity. Transcriptome changes in response to drought are dynamic, and are likely to be shaped by mitigating factors such as diel signals. To gain insights into the dynamics of transcriptome reconfiguration in response to gradual soil drying, the drought-induced transcriptomes of Arabidopsis thaliana were examined at four time points over a single diel period â midday, late day, midnight, and pre-dawn. A core set of genes was identified that was responsive to drought, independent of the time of day at which they were measured. Strikingly, the magnitude of the drought-induced changes for these genes varied in a time-of-day-dependent manner. An additional set of time-of-day-specific drought-responsive genes were also identified. The diurnal patterns of transcript accumulation for these genes was strongly influenced by drought stress. This study indicates that analysis of a single time point would miss suites of drought-responsive genes that are revealed through assessment of the dynamics of diurnal changes, emphasizing the value of characterizing multiple time-of-day-specific drought transcriptomes. 24 arrays total. 4 time points (midday, late day, midnight, pre-dawn). 2 water regimes (well-watered, water-limited). 3 biological replicates per treatment.
2010-07-30 | E-GEOD-19700 | biostudies-arrayexpress
Project description:Sorghum is one of the four major C4 crops that are considered to be tolerant to environmental extremes. Sorghum shows distinct growth responses to temperature stress depending on the sensitivity of the genetic background. About half of the transcripts in sorghum exhibit diurnal rhythmic expressions emphasizing significant coordination with the environment. However, an understanding of how molecular dynamics contribute to genotype-specific stress responses in the context of the time of day is not known. We examined whether temperature stress and the time of day impact the gene expression dynamics in cold-sensitive and tolerant and heat-sensitive and tolerant sorghum genotypes. We found that time of day is highly influencing the temperature stress responses, which can be explained by the rhythmic expression of most thermo-responsive genes. This effect is more pronounced in thermo-tolerant genotypes, suggesting a stronger regulation of gene expression by the time of day and/or by the circadian clock. Genotypic differences were mostly observed on average gene expression levels, but we identified groups of genes regulated by temperature stress in a time-of-day and genotype-specific manner. These include transcriptional regulators and several members of the Ca2+-binding EF-hand protein family. We speculate that expression variation of these genes between genotypes may be responsible for contrasting sensitivities to temperature stress in tolerant vs susceptible sorghum varieties. These findings offer a new opportunity to selectively target specific genes in efforts to develop climate-resilient crops based on their time of day and genotype variation responses to temperature stress.
2023-12-04 | GSE225632 | 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
Project description:Drought stress is a major environmental factor limiting crop productivity. Arbuscular mycorrhizal fungi (AMF), as beneficial soil microbes, can improve plant growth and stress resilience; however, the effectiveness of this symbiosis is often influenced by the host plant's genetic background. In this study, we investigated the interaction between AM symbiosis and drought tolerance in two foxtail millet (Setaria italica) genotypes with contrasting drought responses: the drought-tolerant ISE42 and the drought-sensitive TT8. Following a 14-day drought treatment, both genotypes exhibited wilting, but only AMF-colonized ISE42 plants recovered upon rewatering. Transcriptomic analysis revealed that AM symbiosis significantly enhanced the expression of genes involved in nitrogen transport, assimilation, lignin metabolism, and cellulose biosynthesis in ISE42, but not in TT8. These molecular changes suggest improved nutrient uptake and cell wall reinforcement as key mechanisms underlying enhanced drought tolerance. Additionally, stress hormone signaling pathways were downregulated in colonized ISE42 roots, indicating possible alleviation of drought-induced stress through AM symbiosis. Our results demonstrate genotype-specific effects of AMF on drought tolerance and highlight the importance of considering host genetic variation in the application of AMF for crop improvement.
2025-09-02 | GSE306689 | GEO
Project description:Time of day determines Arabidopsis transcriptome and growth dynamics under mild drought
| PRJEB10930 | ENA
Project description:Time of day and genotype sensitivity adjust molecular responses to temperature stress in Sorghum
| PRJNA936856 | ENA
Project description:RNA sequencing on the third true Arabidopsis leaves of plants exposed to mild drought stress from 12 days after stratification onwards. Samples were harvested at 4AM, 12PM and 8PM on day 14, and at 4AM on day 15.
2017-07-03 | E-MTAB-3908 | biostudies-arrayexpress