Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA97693 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Production of morphologically and physiologically variable seeds is an important strategy that helps plants to survive in unpredictable natural conditions. However, the model plant Arabidopsis thaliana and most agronomically essential crops yield visually homogenous seeds. Using automated phenotype analysis, we observed that in Arabidopsis small seeds tend to have higher primary and secondary dormancy levels when compared to large ones. Transcriptomic analysis revealed distinct gene expression profiles between large and small seeds. Large seeds had higher expression of translation-related genes implicated in germination competence. In contrast, small seeds showed elevated expression of many positive regulators of dormancy, including a key regulator of this process – the DOG1 gene. Differences in DOG1 expression were associated with differential production of its alternative cleavage and polyadenylation isoforms where in small seeds proximal poly(A) site is selected resulting in a short mRNA isoform. Furthermore, single-seed RNA-seq analysis demonstrated that large seeds resemble DOG1 knockout mutant seeds. Finally, on the single seed level, the expression of genes affected by seed size was correlated with the expression of genes positioning seeds on the path towards germination. Our results demonstrate an unexpected link between seed size and dormancy phenotypes in a species producing highly homogenous seed pools, suggesting that the correlation between seed morphology and physiology is more widespread than initially assumed.
2023-10-16 | GSE203310 | GEO
Project description:The identification of novel genes involved in seed dormancy and after-ripening in Arabidopsis thaliana
| PRJNA354607 | ENA
Project description:Interplay Between Active Chromatin Marks and RNA-directed DNA Methylation in Arabidopsis thaliana
| PRJNA213000 | ENA
Project description:Nitrate control of Arabidopsis seed dormancy
| PRJNA100099 | ENA
Project description:The SWI/SNF chromatin remodeling complex is involved in various aspects of plant development and stress responses. In this study, we investigated the role of BRM, a core subunit of the SWI/SNF complex, in seed physiological quality in Arabidopsis thaliana. We found that brm-3 seeds exhibited enlarged size, reduced yield, increased longevity, and enhanced secondary dormancy, but no change in primary dormancy or salt tolerance. We also showed that some of these phenotypes were dependent on DOG1, a key regulator of seed dormancy, as they were reversed in the brm-3xdog1-4 double mutant. Transcriptomic and metabolomic analyses revealed that BRM and DOG1 synergisticly modulate the expression of majority genes and metabolites. In contrast some of the transcriptomic and metabolomic changes including glutathione were depended on DOG1. Moreover, we demonstrated that BRM controls secondary dormancy directly through DOG1 by binding to and remodeling its 3’ region, where an antisense promoter of DOG1 is located. Our results suggest that BRM and DOG1 cooperate to control seed physiological quality by fine-tuning the chromatin state and metabolic status of seeds. This study provides new insights into the molecular mechanisms of seed dormancy and longevity, and the interplay between chromatin remodelling at DOG1 locus.
2025-01-02 | GSE251921 | GEO
Project description:Interaction between gibberellins and brassinosteroids during etiolated growth in Arabidopsis.
| PRJNA146625 | ENA
Project description:Plants that exhibit secondary growth, such as trees, are a prominent feature of terrestrial ecosystems. Furthermore, secondary growth itself, particularly wood, has huge economic value. Despite the importance of secondary growth from both basic and applied science perspectives, little is known about the molecular mechanisms that underpin this facet of plant development. The proposed microarray experiments are designed to expand our knowledge of the regulation of secondary growth by combining the power of Arabidopsis genetics with complete transcriptome analysis. It is now well established that Arabidopsis can be grown under conditions that induce secondary growth in the hypocotyl, albeit small, wood. We have grown 8500 Arabidopsis plants of different genotypes under these conditions and will extract RNA from the developing vascular cambia of these plants to subject them to complete transcriptome analysis.The mutants that we have chosen for these analyses are all related to each other on the basis of the fact that they impact dormancy in either seeds or shoots (abi1, aba1, max4, axr1, AtMYB61 knockout, AtMYB50 knockout). The mutants themselves are the core group of mutants that are the focus of a three laboratory consortium, funded under the BBSRC Exploiting Genomics Initiative, to investigate the molecular basis of meristem dormancy in Arabidopsis. The other partners in the consortium are Dr. Ottoline Leyser (York) and Dr. Michael Holdsworth (IACR). While the Leyser and Holdsworth groups have investigated the impact of these mutations on transcriptome activity in shoot meristems and seeds respectively, our work focuses on the vascular cambium. Thus, this work will not only provide insights into the regulation of cambial function, but, when compared with the existing datasets from the Leyser and Holdworth labs, the work should also provide insights into the relationship between dormancy-impacted phenomena in different meristematic regions. Beyond this, the specific work on the cambium-specific regulation of genes in the MYB61KO will provide even greater insights into the functioning of this important resource allocation regulator, as it will build on a significant complete transcriptome dataset that is already available through GARNet. In total, the proposed analyses will generate important new data that builds on existing datasets, to provide an even more comprehensive understanding of gene function, and genetic networks, in an important biological and applied context. Please note that the sample numbers that we have provided below are meant to be the 'base' number for each biological condition (mutant, etc.), and that there will be independent TRIPLICATE biological replicates produced for each condition. (ie. A-1 to A-12). Experiment Overall Design: Number of plants pooled:200-400 per RNA sample
2008-06-14 | E-GEOD-6151 | biostudies-arrayexpress
Project description:Brassinosteroids (BRs) are endogenous plant hormones and essential for normal plant growth and development. MicroRNAs (miRNAs) of Arabidopsis thaliana are involved in mediating cell proliferation in leaves, stress tolerance, and root development. The specifics of BRs mechanisms involving miRNAs are unknown. To explore the role of miRNAs in BR-mediated pathways, we analyzed differences in miRNA profiles between control (mock solution) and 24-epibrassinolide (EBR) treatments from customized miRNA microarrays.
2016-03-25 | GSE46377 | GEO
Project description:Plants that exhibit secondary growth, such as trees, are a prominent feature of terrestrial ecosystems. Furthermore, secondary growth itself, particularly wood, has huge economic value. Despite the importance of secondary growth from both basic and applied science perspectives, little is known about the molecular mechanisms that underpin this facet of plant development. The proposed microarray experiments are designed to expand our knowledge of the regulation of secondary growth by combining the power of Arabidopsis genetics with complete transcriptome analysis. It is now well established that Arabidopsis can be grown under conditions that induce secondary growth in the hypocotyl, albeit small, wood. We have grown 8500 Arabidopsis plants of different genotypes under these conditions and will extract RNA from the developing vascular cambia of these plants to subject them to complete transcriptome analysis.The mutants that we have chosen for these analyses are all related to each other on the basis of the fact that they impact dormancy in either seeds or shoots (abi1, aba1, max4, axr1, AtMYB61 knockout, AtMYB50 knockout). The mutants themselves are the core group of mutants that are the focus of a three laboratory consortium, funded under the BBSRC Exploiting Genomics Initiative, to investigate the molecular basis of meristem dormancy in Arabidopsis. The other partners in the consortium are Dr. Ottoline Leyser (York) and Dr. Michael Holdsworth (IACR). While the Leyser and Holdsworth groups have investigated the impact of these mutations on transcriptome activity in shoot meristems and seeds respectively, our work focuses on the vascular cambium. Thus, this work will not only provide insights into the regulation of cambial function, but, when compared with the existing datasets from the Leyser and Holdworth labs, the work should also provide insights into the relationship between dormancy-impacted phenomena in different meristematic regions. Beyond this, the specific work on the cambium-specific regulation of genes in the MYB61KO will provide even greater insights into the functioning of this important resource allocation regulator, as it will build on a significant complete transcriptome dataset that is already available through GARNet. In total, the proposed analyses will generate important new data that builds on existing datasets, to provide an even more comprehensive understanding of gene function, and genetic networks, in an important biological and applied context. Please note that the sample numbers that we have provided below are meant to be the 'base' number for each biological condition (mutant, etc.), and that there will be independent TRIPLICATE biological replicates produced for each condition. (ie. A-1 to A-12). Keywords: strain_or_line_design; ecotype_analysis; mutant; insertion_mutant; gene_knock_out; tissue_organ_specificity;
2007-01-22 | GSE6151 | GEO
Project description:Identification of genes involved in secondary cell wall development in the hypocotyls of short day grown Arabidopsis
| PRJNA97697 | ENA