Ontology highlight
ABSTRACT:
PROVIDER: PRJNA552799 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9645570.fastq.gz | Fastqsanger.gz | |||
| SRR9645571.fastq.gz | Fastqsanger.gz | |||
| SRR9645566.fastq.gz | Fastqsanger.gz | |||
| SRR9645567.fastq.gz | Fastqsanger.gz | |||
| SRR9645568.fastq.gz | Fastqsanger.gz |
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Project description:Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically-identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally-propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome-level drought responses of three economically important hybrid genotypes: DN34 (Populus deltoides x P. nigra); Walker (P. deltoides var. occidentalis x (P. laurifolia x P. nigra)); and, Okanese (‘Walker’ x (P. laurifolia x P. nigra)) derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, where the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenetic basis for the clone-history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for both the industrial application of Populus trees, and the evolution and persistence of these important tree species.
2011-05-01 | GSE27693 | GEO
Project description:Just as animal monozygotic twins can experience different environmental conditions by being reared apart, individual genetically-identical trees of the genus Populus can also be exposed to contrasting environmental conditions by being grown in different locations. As such, clonally-propagated Populus trees provide an opportunity to interrogate the impact of individual environmental history on current response to environmental stimuli. To test the hypothesis that current responses to an environmental stimulus, drought, are contingent on environmental history, the transcriptome-level drought responses of three economically important hybrid genotypes: DN34 (Populus deltoides x P. nigra); Walker (P. deltoides var. occidentalis x (P. laurifolia x P. nigra)); and, Okanese (‘Walker’ x (P. laurifolia x P. nigra)) derived from two different locations were compared. Strikingly, differences in transcript abundance patterns in response to drought were based on differences in geographic origin of clones for two of the three genotypes. This observation was most pronounced for the genotypes with the longest time since establishment and last common propagation. Differences in genome-wide DNA methylation paralleled the transcriptome level trends, where the clones with the most divergent transcriptomes and clone history had the most marked differences in the extent of total DNA methylation, suggesting an epigenetic basis for the clone-history-dependent transcriptome divergence. The data provide insights into the interplay between genotype and environment in the ecologically and economically important Populus genus, with implications for both the industrial application of Populus trees, and the evolution and persistence of these important tree species. 72 arrays total. 2 time points. 2 water regimes. 3 biological replicates per treatment
2011-05-01 | E-GEOD-27693 | biostudies-arrayexpress
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:Although utilization of heterosis has largely improved the yield of many crops worldwide, the underlying molecular mechanism of heterosis, particularly for allopolyploids, remains unclear. Here, we compared epigenome and transcriptome data of an elite hybrid and its parental lines in three assessed tissues (seedling, flower bud, and silique) to explore their contribution to heterosis in allopolyploid B. napus. Transcriptome analysis illustrated that a small proportion of non-additive genes in the hybrid compared with its parents, as well as parental expression level dominance, might have a significant effect on heterosis. We identified histone modification (H3K4me3 and H3K27me3) variation between the parents and hybrid, most of which resulted from the differences between parents. H3K4me3 variations were positively correlated with gene expression differences among the hybrid and its parents. Furthermore, H3K4me3 and H3K27me3 were rather stable in hybridization and were mainly inherited additively in the B. napus hybrid. Together, our data revealed that transcriptome reprogramming and histone modification remodeling in the hybrid could serve as valuable resources for better understanding heterosis in allopolyploid crops.
2023-07-18 | GSE218592 | 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:Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses.
2010-12-31 | GSE21171 | GEO
Project description:We used two hybrid combinations and their 4 parents as materials. One week after topping the tobacco plant, samples were taken, including three tissues: root, stalk, and leaf. The RNA of these samples was extracted, and transcriptome sequencing analysis was carried out to explore the transcriptional profile differences between hybrids and their parents, and to analyze the gene differential expression between different tissues.
2023-06-09 | GSE233199 | GEO
Project description:Heterosis is a phenomenon that hybrids exhibit superior performance relative to the parental phenotypes. However, most studies focused on aboveground agronomic traits. Thus, systematic investigation on root heterosis, particularly at reproductive stage in rice is needed to be carried out. The recent advent of RNA sequencing technology (RNA-Seq) provides an opportunity to conduct in-depth transcript profiling for heterosis study.Using the Illumina HiSeq 2000 platform, the root transcriptome of a super-hybrid rice Xieyou9308 and its parents were analyzed at tillering and heading stages. Totally, 829 and 4186 differentially expressed genes between the hybrid and its parents (DGHP) were detected at tillering stage and heading stage, respectively. In this study, the DGHP were significantly enriched in pathways such as carbohydrate metabolism and plant hormones signal transduction at heading stage, and most of the key genes involved in the two pathways were up-regulated in the hybrid. Several significant DGHP that could be mapped to QTLs for yield and root traits were also involved in carbohydrate metabolism and plant hormones signal transduction pathways. The candidate transcripts may underlie the heterosis and significantly contribute to root development and yield production. Root mRNA profiles of a super-hybrid rice Xieyou 9308 and its parents at tillering and heading stages were generated by deep sequencing, in duplicate, on Illumina Hiseq 2000 platform.
2013-08-19 | E-GEOD-41797 | biostudies-arrayexpress
Project description:Drought is a major limitation to the growth and productivity of trees in the ecologically and economically important genus Populus. The ability of Populus trees to contend with drought is a function of the responsiveness of their genome to this environmental insult, involving reconfiguration of the transcriptome to appropriately remodel growth, development and metabolism. The Populus drought transcriptome is shaped by interspecific genotypic variation, but the extent to which intraspecific variation shapes the drought transcriptome has not yet been examined. Here we test hypotheses aimed at examining the extent of intraspecific variation in the drought transcriptome. Transcriptome remodeling in response to water-deficit conditions was examined in six different Populus balsamifera L. genotypes using Affymetrix GeneChip technology. There were significant differences in the transcriptomes of the genotypes in response to water-deficit conditions; however, a common species-level response could also be identified across all individuals. Genotypes that had more similar drought-responsive transcriptomes also had fewer genotypic differences, as determined by microarray-derived single feature polymorphism (SFP) analysis, suggesting that responses may be conserved across individuals that share a greater degree of genotypic similarity. This work highlights the fact that a core species-level response can be defined; however, the underpinning genotype-derived complexities of the drought response in Populus must be taken into consideration when defining both species- and genus-level responses. 72 arrays total. 6 genotypes, 2 time points. 2 water regimes. 3 biological replicates per treatment
2010-12-31 | E-GEOD-21171 | biostudies-arrayexpress
Project description:Here we applied a novel approach to isolate nuclei from complex plant tissues (https://doi.org/10.1371/journal.pone.0251149), to dissect the transcriptome profiling of the hybrid poplar (Populus tremula × alba) vegetative shoot apex at single-cell resolution.
2022-10-04 | GSE190649 | GEO