Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq analysis of different parts of Quercus robur seedling root

ABSTRACT: As an adaptive response to the environment, oaks have evolved long taproots that increase their ability to acquire water. Taproots penetrate deeper layers of soil and send out absorptive roots that can then uptake water from these layers. This ability enables taproots to supply trees with water better. Unfortunately, the applied agrotechnical procedures during seedlings production in container nurseries damage the oaks' taproot, leading to changes in the root system structure. That changes may make the seedlings more responsive to chronic or periodic episodes of severe drought. In turn, seedlings that containers do not restrict roots growth, i.e. grown in rhizotron, may elongate because they are not subjected to air-pruning. Despite their significant role, little is known about the internal factors (specific genes) and their interactions that regulate taproot elongation in oaks seedlings. Thus, our study aimed to determine the potential genes regulating growth, cessation and physiology of taproot and check whether there is a difference in the expression level of the genes involved in root development. For this purpose, we performed next-generation sequencing (NGS), taproots and lateral roots, which allowed us to obtain a complete picture of the transcriptomes. Our findings of taproot growth regulations can be used to improve trees production in forest nurseries.

ORGANISM(S): Quercus robur

PROVIDER: GSE181860 | GEO | 2022/11/23

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge (1dpi)

Project description:Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge with a pathogenic, saprophytic or symbiotic fungus. Seedlings of P. sylvestris (19 days post germination) were transferred to wet, sterile filter paper on Petri-plates. Thereafter, the roots of the seedlings were inoculated with the mycelial homogenate of either Heterobasidion annosum (FP5, P-type) a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees or Laccaria bicolor, an obligate ectomycorrhizal symbiont or Trichoderma aureoviride- an obligate saprotroph. Thereafter, incubated for 30 minutes, during which time some hyphae adhered to the roots. The inoculated seedlings (ten) were then transferred to another wet sterile filter paper placed on 1% water agar in Petri dishes. A second set of moist sterile filter paper was laid over the roots. The region of the Petri-dish containing the roots was covered with aluminium foil and the edges of the plate sealed with parafilm. The seedlings were then incubated for 24 hr under a photoperiod of 16h light at 20 ºC. Control seedlings were ‘inoculated’ with sterile distilled water. Keywords: other

2004-12-21 | GSE2089 | GEO

Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge (1dpi)

Project description:Comparative transcriptome analysis of early interaction events in Scots pine root tissues following challenge with a pathogenic, saprophytic or symbiotic fungus. Seedlings of P. sylvestris (19 days post germination) were transferred to wet, sterile filter paper on Petri-plates. Thereafter, the roots of the seedlings were inoculated with the mycelial homogenate of either Heterobasidion annosum (FP5, P-type) a pathogenic root rot fungus which attacks Norway spruce, Scots pine and broad leaf trees or Laccaria bicolor, an obligate ectomycorrhizal symbiont or Trichoderma aureoviride- an obligate saprotroph. Thereafter, incubated for 30 minutes, during which time some hyphae adhered to the roots. The inoculated seedlings (ten) were then transferred to another wet sterile filter paper placed on 1% water agar in Petri dishes. A second set of moist sterile filter paper was laid over the roots. The region of the Petri-dish containing the roots was covered with aluminium foil and the edges of the plate sealed with parafilm. The seedlings were then incubated for 24 hr under a photoperiod of 16h light at 20 ÂºC. Control seedlings were âinoculatedâ with sterile distilled water.

2010-05-27 | E-GEOD-2089 | biostudies-arrayexpress

Effect of high temperature on Arabidopsis thaliana root tips

Project description:Plant roots located in the upper soil layers are prone to experience high temperatures. To gain insight into the effect of high temperature on root development and functioning, we exposed five-day-old Arabidopsis thaliana seedlings grown on agar plates to 30 °C for 48 hours, and compared the gene expression profile in the root tip with that from seedlings that remained at 22 °C.

2024-02-07 | GSE254973 | GEO

Proteomic profile of Pinus pinaster roots under ammonium nutrition

Project description:Ammonium nutrition was studied at short times (24 hours) in roots from one month-old seedlings of maritime pine. Control seedlings were irrigated with 80 mL of water (C) and the experimental seedlings with 80 mL of 3 mM NH4Cl. Root samples were collected at 24 hours post-irrigation and immediately frozen in liquid N. This experiment was carried out three independent times.

2023-03-11 | PXD025331 | Pride

2-DE proteomics analysis of drought treated seedlings of Quercus ilex

Project description:Applying a gel-based proteomic approach, the dynamic changes in root proteins of drought treated Quercus ilex subsp. Ballota [Desf.] Samp. seedlings were followed. Water stress was applied on 20 day-old holm oak plantlets by water limitation for a period of 10 and 20 days, each followed by 10 days of recovery. Root proteins were extracted using trichloroacetate/acetone/phenol protocol and subjected to two-dimensional electrophoresis. Coomassie colloidal stained gel images were analysed and spot intensity data subjected to multivariate statistical analysis. Selected consistent spots in the three biological replicas, presenting significant changes under stress, were subjected to MALDI-TOF mass spectrometry (peptide mass fingerprinting and MS/MS). For protein identification, combined search was performed with MASCOT search engine over NCBInr Viridiplantae and Uniprot databases. Taxonomy Holm oak (Quercus ilex subsp. Ballota [Desf.] Samp.). Dentro de Q. ilex hay dos subespecies, ilex ilex e ilex Ballota.

2015-09-09 | PXD002484 | Pride

Overexpression of OsERF106MZ promotes root growth in rice seedlings by relieving the ABA-mediated inhibition of root growth

Project description:Background: Roots are essential for plant growth and serve a variety of functions, such as anchoring the plant to the ground and absorbing water and nutrients. OsERF106MZ is a salinity-induced gene that is expressed in germinating seeds and the roots of rice seedlings. However, the roles of OsERF106MZ in root growth remain poorly understood. Results: Histochemical staining of GUS (β-glucuronidase) activity in transgenic rice seedlings harboring OsERF106MZp::GUS indicated that OsERF106MZ is mainly expressed in the exodermis, sclerenchyma layer, and vascular system of roots. Overexpression of OsERF106MZ in rice seedlings leads to an increase in the length of primary roots (PRs). The expression of the ABA (abscisic acid) biosynthetic gene, OsAO3, is downregulated in OsERF106MZ-overexpressing roots under normal conditions, while the expression of OsNPC3, an AtNPC4 homolog involved in ABA sensitivity, is reduced in OsERF106MZ-overexpressin roots under both normal and NaCl-treated conditions. Under normal conditions, OsERF106MZ-overexpressing roots have a significantly low level of ABA; moreover, exogenous application of 1.0 µM ABA can suppress the OsERF106MZ-mediated promotion of root growth. Meanwhile, OsERF106MZ-overexpressing roots display less sensitivity to the ABA-mediated inhibition of root growth, when they are treated with ABA at 5.0 µM under normal conditions or exposed to NaCl-treated conditions. Chromatin immunoprecipitation (ChIP)-qPCR and luciferase (LUC) reporter assays showed that OsERF106MZ can bind directly to the sequence containing the GCC-box in the promoter region of OsAO3 gene and repress its expression. Conclusion: OsERF106MZ may play a role in maintaining root growth for resource uptake when rice seeds are sprouted under salinity stress, which is arrived at by alleviating the ABA-mediated inhibition of root growth.

2023-03-22 | GSE213466 | GEO

Zea mays Transcriptome or Gene expression

Project description:In this study a transcriptomic approach (RNA-sequencing) was utilized to elucidate molecular responses of maize (Zea mays L.) primary roots of the inbred line B73 to water deficit to gain a better understanding of the mechanisms underlying drought tolerance. Kernels of the maize inbred line B73 were germinated in paper rolls soaked with distilled water until seedlings had a primary root length of 2 to 4 cm. For mild and severe water deficit conditions, seedlings were transferred to PEG8000 solution with water potentials of -0.2 MPa and -0.8 MPa, respectively. Water deficit treatment was applied for 6 h and 24 h. Each treatment was performed in four biological replicates each consisting of 10 roots.

2014-05-03 | E-MTAB-4325 | biostudies-arrayexpress

Interactions between root knot nematodes and potato

Project description:Plant-parasitic nematodes and especially the root-knot nematodes are ubiquitous pathogens. Eggs of root-knot nematodes (Meloidogyne javanica) were extracted from greenhouse cultures and second-stage juveniles (J2) were hatched in tap, sterile water on 30 µm sieves. Solanum tubersum cv. Desiree explants, i.e., stem including an axillary bud, were sectioned, under sterile conditions from in vitro growing seedlings and transferred to Magenta boxes containing Gamborg's media. Seedlings, 4 weeks post transferring to Gamborg's media were planted in pots containing autoclaved quartz sand. Three weeks later the plants were infected with 3000 M. javanica infective juveniles, applied to the soil in tap, sterile water. Control uninfected plants were mock-inoculated with tap, sterile water. Roots from 6 infected and 6 mock-inoculated plants were collected at a series of time points, including 5, 10 and 15 days post nematode infection/mock inoculation. Roots were observed under the microscope, and nematode feeding sites were selectively dissected, from young lateral roots. To control for the effect of tissue sectioning on gene expression, young lateral roots of the mock inoculated roots were dissected similarly to the infected roots, and collected. Dissected roots were snapped-freeze in liquid nitrogen and immediately stored in -80 C freezer. Total RNA was extracted using Qiagen RNAEasy kit. The experiment for each time point was duplicated, each duplicate derived from independent biological repeat. All RNA samples were amplified using the Ambion kit Message Amp catalog no. 1750, using as starting material 2.5 to 5 µg of total RNA. Keywords: Reference design

2007-09-01 | GSE8209 | GEO

SAGE analysis of maize root segments

Project description:Dark-grown maize seedlings with primary roots 12-20 mm in length were transplanted to high (-0.03 MPa) water potential vermiculite. About 1,000 roots were collected. Each root was divided into 4 segments (distances are from the junction of the root apex and root cap): segment 1, 0-3 mm plus the root cap; segment 2, 3-7 mm; segment 3, 7-12 mm; segment 4, 12-20 mm. Details of the conditions and nutrient modifications have been described before (Sharp et al., 1988; Spollen et al, 2000). From each segment, 250 mg of material was used and RNA was isolated form the combined sample containing all four segments. RNA was isolated using the RNeasy Maxi Kit (Qiagen). RNA integrity was verified by denaturing agarose gel electorphoresis and spectrophotometry.

2010-12-01 | GSE25761 | GEO

Fine root gene expression of Norway spruce cuttings

Project description:We investigated root associated fungi in young Norway spruce (Picea abies) cuttings rooted from slow- and fast-growing trees showing variable growth rate in long-term field experiments and compared their roots’ gene expression patterns five and 18 months after adventitious root initiation. Gene expression patterns of adventitious roots could not be systematically linked with the growth phenotype at the initiation of root formation, and thus fundamental differences in the receptiveness of fungal symbionts could not be assumed.

2023-11-02 | GSE246281 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data