Arabidopsis thaliana
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: E-GEOD-43560
PROVIDER: PRJNA186735 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Allele-specific expression in A. thaliana hybrids grown under control and drought stress conditions
2019-05-14 | E-GEOD-43560 | ExpressionAtlas
Project description:We estimate Allele-specific expression in F1 hybrids between Col-0 and Cvi-0 accessions grown under well watered and drought stress conditions. We found that ~90% of the genes showed similar ASE under both stresses. Trans-effects were less robust across environments, however its effect was milder compared to cis-variation.
2015-06-25 | GSE43560 | GEO
Project description:We estimate Allele-specific expression in F1 hybrids between Col-0 and Cvi-0 accessions grown under well watered and drought stress conditions. We found that ~90% of the genes showed similar ASE under both stresses. Trans-effects were less robust across environments, however its effect was milder compared to cis-variation. Assessment of ASE in different environments
2015-06-25 | E-GEOD-43560 | biostudies-arrayexpress
Project description:The evolution of maize yields under drought is of particular concern in the context of climate change and human population growth. To better understand the mechanisms associated with the genetic polymorphisms underlying the variations of traits related to drought tolerance, we used a systems genetics approach integrating high-throughput phenotypic, proteomics and genomics data acquired on 254 maize hybrids grown under two watering conditions. We show that the genetic architecture of protein abundances depends on protein function and that water deficit strongly remodeled the proteome and induced a reprogramming of the genetic control of the abundances of proteins involved in drought and stress response. These findings bring several lines of evidence supporting candidate genes at many loci and provide novel insight into the molecular mechanisms of drought tolerance.
2020-06-16 | MSV000085594 | MassIVE
Project description:au13-08_atpplaii-alpha - transcriptional profilling of arabidopsis plants. Understanding the physiological role of pPLAIIα; under control and drought stress conditions. Study on empty vector, overexpressor and antisense A. thaliana lines.
2016-06-01 | GSE58219 | GEO
Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
2020-11-04 | GSE153030 | GEO
Project description:Pearl millet [Pennisetum glaucum (L.) R.Br] is the fifth most important cereal crop next to rice, wheat, maize, and sorghum. It is cultivated especially by small holder farmers in arid and semi-arid regions because of its drought resistance. However, the molecular mechanisms during drought stress in Pennisetum remain elusive. In the present study we have used a shotgun proteomics approach (GEL-LC-Orbitrap-MS) for identification and quantification of proteins from different tissues (root, seed and leaf) under drought and control conditions. Plants were grown in a tube system to survey root growth under drought stress. The water content was measured in the upper and the lower part of the tube using soil moisture sensors. Under drought stress root elongation was observed. Measurement of stomatal conductance showed a clear response to drought stress. For proteomics measurements root, leaf and seed tissues were harvested. In total 2281 proteins were identified, 1095 in root, 1299 in seed, and 1208 in leaf in both stress and control conditions.
2023-08-23 | PXD002923 | Pride
Project description:Purpose: In this study we investigated the role of JASMONATE RESISTANT 1 (JAR1) and JAR1 mediated JA-Ile formation in drought stress tolerance in Arabidopsis thaliana. Methods: Global transcriptional changes in a newly generated over-expression line (JAR1-OE; 35S::JAR1-1-YFP)), a T-DNA insertion line in the JAR1 locus (jar1-11;SALK_034543), and wild-type Col-0 were investigated by RNA-seq analyses of rosette leaves from 32 day-old plant that were either well-watered (control) or not watered after day 18 (drought). Plants were grown on soil under long-day conditions Results: Under control conditions, using a stringent cut-off (DESeq, adjusted to FDR < 0.01 and LogFC ≥ 1), we found only four differentially expressed genes (DEGs) between jar1-11 and Col-0, all of them downregulated. By contrast, we found 339 DEGs between JAR1-OE and Col-0, of which 134 were downregulated and 205 were upregulated. A comparison of the RNA-seq data from Col-0 between control and drought conditions revealed 3401 DEGs, of which 2023 were down- and 1378 upregulated. By comparison, jar1-11 plants, which were most heavily affected by drought stress, showed a much higher number (6139 in total; 2616 up- and 3523 down-regulated) of DEGs, while the more drought-tolerant JAR1-OE line displayed a lower number (2025 in total; 971 up- and 1054 down-regulated) of DEGs. 2411 DEGs were found between Col-0 and jar1-11 under drought among which 966 genes showed a higher and 1445 genes a lower expression level in jar1-11. On the other hand, out of 998 DEGs found between Col-0 and JAR1-OE under drought, 737 genes showed a higher and 261 genes a lower expression level in JAR1-OE. Moreover, we found 391 DEGs counter-regulated between jar1-11 and JAR1-OE. Conclusion:RNA-seq analysis and additional experiments of plants under control and drought stress conditions provided insight into the molecular reprogramming caused by the alteration in JA-Ile content.
2022-07-25 | GSE196602 | GEO
Project description:We generated F1 hybrids of each of the sister species A. halleri and A. lyrata with their outgroup relative of A. thaliana and monitored allele-specific levels of expression in standard growth conditions, in response to dehydration or cold exposure. This data allowed us to map the genome-wide distribution of cis-regulatory mutations active in three distinct environments reflecting divergent adaptations of the two species. Because the sister species were both crossed to an outgroup species, it was possible to assign a phylogenetic origin to cis-acting mutations. Cis-acting mutations observed in only one of the two hybrids were likely to be derived, whereas those observed in both hybrids either predate predated the split between the two species or arose along the A. thaliana lineage. By contrasting the distribution of cis-regulatory mutations derived in the A. halleri to those derived on the A. lyrata lineage, we could establish relative rates of cis-acting evolution across polygenic molecular functions and detect lineage-specific polygenic adaptation to environmental challenges. A.thalianaxA.lyrata under cold, dehydration and standard conditions, 3 biological replicates; A.thalianaxA.halleri under cold, dehydration and standard conditions, 3 biological replicates; toal 18 RNA-seq samples
2016-06-01 | E-GEOD-80462 | biostudies-arrayexpress
Project description:Hybrid plants and animals grow larger and more vigorously than the parents, a common phenomenon known as hybrid vigor or heterosis. Heterosis often correlates with the genetic distance between hybridizing parents, but the mechanism for this is largely unknown. We found that genetic distance was correlated with natural variation of stress responses under the control of the circadian clock. CIRCADIAN-CLOCK-ASSOCIATED1 (CCA1) and LATE-ELONGATED-HYPOCOTYL (LHY) or CCA1 alone mediate expression amplitudes and periods of these stress-responsive genes in stress and non-stress conditions. In Arabidopsis thaliana intraspecific hybrids, genome-wide expression of many biotic and abiotic stress-responsive genes was diurnally repressed to promote biomass heterosis, which is associated with several biomass quantitative trait loci (QTLs). Expression differences in four selected stress-responsive genes among ten ecotypes could be used to predict heterosis in their hybrids. Parent plants with larger expression differences between stress-responsive genes produced higher-vigor hybrids, while those with smaller differences produced lower-vigor hybrids. Stress-responsive genes were epigenetically repressed in the hybrids under normal conditions but induced during times of stress at certain times of the day, balancing the tradeoff between stress responses and growth. Consistently, repressing the stress genes in diploids increased growth vigor. We demonstrate how hybrids manipulate diurnal stress-responsive gene expression to enhance growth vigor. Both circadian and epigenetic regulation play key roles in the altered expression of stress-responsive genes in hybrids. Our findings provide a conceptual advance and mechanistic understanding of heterosis, as well as selection criteria for parents to be effectively used for producing high-yield hybrids. Examination of gene expression in Arabidopsis thaliana F1 hybrids between Col and C24 and 3 time points using mRNA-seq
2015-05-31 | E-GEOD-51578 | biostudies-arrayexpress