Arabidopsis thaliana
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA356875 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:As multicellular organisms, plants must integrate responses to environmental cues across different cell types and also over time. Nitrate is the major source of available Nitrogen for plants, and a limiting factor for plant growth and productivity. Plant root s are highly impacted by nitrate availability, modifying their architecture to optimize nitrate uptake from soils. In order to understand how this functional response is dynamically orchestrated across different cell types of the root, space and time must be addressed within the same experimental setup. We performed a transcriptomic analysis in five major root cell types of Arabidopsis plants in response to nitrate treatments considering short and long time exposure to this macronutrient. We found nitrate treatment triggers a dynamic reprogramming of root cell gene expression that follows a spatial pattern over time consistent with an early regulation of nitrate transport and assimilation in external layers of the root and a later regulation of hormonal and developmental processes in more internal layers of the root.
2022-01-01 | E-MTAB-9519 | biostudies-arrayexpress
Project description:Adaptation of Root Architecture to Abiotic Stress
| PRJNA106301 | ENA
Project description:Lateral root organogenesis plays an essential role in defining plant root system architecture. In Arabidopsis, the AP2-family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify downstream targets of PUCHI, we engineered a transgenic line with inducible PUCHI activity by expressing a fusion protein of PUCHI and rat glucocorticoid receptor (GR) under the control of its own regulatory region (gPUCHI-GR) in the puchi-1 mutant.
2019-06-12 | GSE128721 | GEO
Project description:Plants function as an integrated system of interconnected organs, with shoots and roots mutually influencing each other. Brassinosteroid (BR) signaling is essential for whole-plant growth, yet the relative importance of shoot versus root BR function in shaping root system architecture (RSA) remains unclear. Here, we directly tackle this question using micro-grafts between wild-type and BR-null mutants in both Arabidopsis and tomato, assisted by phenotyping, transcriptomics, metabolic profiling, transmission electron microscopy, and modeling approaches. These analyses demonstrate that shoot BR, by determining root carbon availability, allows for a full rescue of mutant root biomass, while loss of shoot BR attenuates root growth. In parallel, root BR dictates the spatial distribution of carbon along the root, through local regulation of growth anisotropy and cell wall thickness, shaping root morphology. A newly developed “grow and branch” simulation model demonstrates that these shoot- and root-derived BR effects are sufficient to explain and predict root growth dynamics and branching phenotype in wild-type, BR-deficient mutants, and micro-graft combinations. Our interdisciplinary approach, applied to two plant species and integrating shoot and root hormonal functions, provides a new understanding of how RSA is modulated at various scales.
2025-03-27 | GSE274161 | GEO
Project description:The interactions between co-cultivated plant cultivars are increasingly recognized as influencing their susceptibility to pathogens in mixtures. However, the underlying mechanisms remain largely unexplored. Using a model of durum wheat cultivar mixtures where susceptibility to Septoria foliar disease is increased, we combined aerial and root phenotyping with transcriptional analyses and untargeted metabolomics to elucidate the potential signaling cascade driving this modulation of susceptibility. We observed contrasting root architectures between cultivars in mixture. Molecular analysis showed a delayed induction of defense-related genes and metabolites following pathogen inoculation in plants grown in mixture compared to pure stand. The findings suggest that root architecture potentially triggers a competitive response that could delay the induction of defense responses following pathogen inoculation. Altogether, these results point to a possible interplay between root architecture, resource competition, plant metabolism, and defense modulation in shaping plant-pathogen interactions within varietal mixtures.
2025-12-10 | MSV000100172 | MassIVE
Project description:Transcription factors may orchestrate the health benefits of intermittent fasting through directing the expression of genome. Here, we find intermittent fasting can spin the spatiotemporal profile of transcription factors, and provide an atlas of transcription factors in biological space, time and feeding regimen.
2022-10-27 | GSE154797 | GEO
Project description:Shaping the Arabidopsis Root Microbiome via Effector- and Damage-Triggered Immunity (PRJCA043020)
| PRJDB38892 | ENA
Project description:The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. To further explore the specificity of naxillin for lateral root development, we compared the early effects of naxillin at the transcriptome level with NAA (1-Naphthaleneacetic acid) in roots of 3-day-old seedlings after 2-h and 6-h treatment. Arabidopsis thaliana (L). Heynh., Col-0 seeds were germinated vertically on solid medium derived from standard MS medium supplemented with 10 μM NPA (1-N-Naphthylphthalamic acid). Three days after germination, plants were transferred to 10 μM NAA (1-Naphthaleneacetic acid) or 50 μM naxillin for 2 and 6 hours. Plants were sampled before (Roots at T0, NPA) or after treatment (Roots at T1 and T2). RNA isolation was performed on 500 root sections (only root without meristems) for each sample. All sampling points were performed in three independent experiments.
2012-12-18 | E-GEOD-42896 | biostudies-arrayexpress
Project description:To optimize access to nitrogen under limiting conditions, root systems must continuously sense and respond to local or temporal fluctuations in nitrogen availability. In Arabidopsis thaliana and several other species, external N levels that induce only mild deficiency stimulate the emergence of lateral roots and especially the elongation of primary and lateral roots. However, the identity of the genes involved in this coordination remains still largely elusive. In order to identify novel genes and mechanisms underlying nitrogen-dependent root morphological changes, we investigated time-dependent changes in the root transcriptome of Arabidopsis thaliana plants grown under sufficient nitrogen or under conditions that induced mild nitrogen deficiency.
2023-09-12 | GSE216293 | GEO
Project description:The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. To further explore the specificity of naxillin for lateral root development, we compared the early effects of naxillin at the transcriptome level with NAA (1-Naphthaleneacetic acid) in roots of 3-day-old seedlings after 2-h and 6-h treatment.
2012-12-18 | GSE42896 | GEO