Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Genotype variation in rice (Oryza sativa L.) tolerance to Fe toxicity might be linked to root cell wall lignification

ABSTRACT: Iron (Fe) is an essential element to plants, but can be harmful if accumulated to toxic concentrations. Fe toxicity can be a major nutritional disorder in rice (Oryza sativa) when cultivated under waterlogged conditions, as a result of excessive Fe solubilization of in the soil. However, little is known about the basis of Fe toxicity and tolerance at both physiological and molecular level. Here we aim at understand the genotypic differences in two rice cultivars with contrasting phenotypes under Fe toxicity.

ORGANISM(S): Oryza sativa Oryza sativa Indica Group

PROVIDER: GSE131287 | GEO | 2019/05/16

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Introgression of genes and mechanisms conferring tolerance to iron toxicity from wild rice species Oryza meridionalis into domesticated rice Oryza sativa

Project description:Iron toxicity is one of the most common mineral disorders affecting Oryza sativa production in flooded lowland fields. Efforts have been made to develop new rice varieties tolerant to Fe toxicity (+Fe). Oryza meridionalis is an endemic from Northern Australia and grows in regions with Fe rich soils, which may provide Fe tolerance genes and mechanisms that can be used for adaptive breeding. Aiming to understand tolerance mechanisms in rice, we screened a population of interspecific introgression lines (IL) from a cross between O. sativa and O. meridionalis for the identification of QTLs contributing to Fe excess tolerance. Six putative QTLs were identified. A line carrying one introgression from O. meridionalis on chromosome 9 associated with one QTL for leaf bronzing score was identified as tolerant in terms of lipid peroxidation and electrolyte leakage despite presenting very high shoot Fe concentrations. Further physiological, biochemical, ionomic and transcriptomic analyses showed that the IL tolerance could be partly explained by Fe partitioning between the leaf sheath and culm. After the in silico construction of an interspecific hybrid genome to map the sequences from transcriptomic analysis, we identified 47 and 27 genes from O. meridionalis up and down-regulated, respectively, by Fe treatment on the tolerant IL. Among possible genes associated with shoot-based tolerance, we identified metallothionein-like proteins, genes from glutathione S-transferase family and transporters from ABC and Major Facilitator Superfamily. This is the first work to demonstrate that introgressions of O. meridionalis in O. sativa genome confer increased tolerance to +Fe

2021-10-08 | GSE151559 | GEO

Rice plants (Oryza sativa var. japonica): WT vs. MIT knockdown plant

2011-04-07 | GSE28428 | GEO

Silicon effect on suberization and lignification in roots of rice (Oryza sativa)

Project description:This study was performed to study the effect of silicon (Si) nutrition on suberization and lignification in roots of rice. Besides physiological and histochemical examinations of the roots, transcription of candidate genes related to synthesis of suberin and lignin was investigated using microarray analysis. 14 days old rice seedlings (Oryza sativa, cv. Selenio) were cultivated for 28 days in non-aerated nutrient solution (mM: 1.43 NH4NO3, 0.32 NaH2PO4 x H2O, 0.51 K2SO4, 1 CaCl2 x 2 H2O, 1.6 MgSO4 x 7 H2O; µM: 1.82 MnSO4, 0.03 (NH4)6Mo7O24, 9 H3BO3, 0.3 ZnSO4 x 7 H2O and 0.15 CuSO4). The pH-value was adjusted to 6.0 by addition of 10 % (v/v) H2SO4 and 0.75 M KOH.Plants were supplied with Si in form of K2SiO3 at concentrations 0 ppm Si (control) and 50 ppm Si (1.78 mM) and potassium in the control treatment was balanced with K2SO4 supply. The plants were grown in a growth chamber (photoperiod: 14 h light, 10 h dark; temperature 25°C day / 20°C night; relative humidity 75 %; light intensity 220 µmol m2 s-1). Adventitious roots were harvested at 0-2 cm and 4-6 cm distance from the root tip and frozen immediately in liquid nitrogen. For RNA isolation, roots were ground under liquid nitrogen and total RNA was isolated using TRIsure® Reagent (Bioline, Luckenwalde, Germany) following the instructions of the manufacturer. To examine transcription of genes related to suberin and lignin synthesis, a self developed microarray containing amongst others ABC transporter, aclytransferases, ß-ketoacyl-CoA synthases and peroxidases was used .

2010-10-10 | GSE23723 | GEO

Oryza sativa Transcriptome or Gene expression

Project description:In this study, we used RNA-Seq to understand the mechanisms of Cd toxicity, cellular detoxification and protection pathways in response to Cd in rice roots. To gain additional insight into the rice transcriptomic response to environmental Cd stress, 15-day-old rice seedlings were treated with 10 or 100 Î¼M solutions of Cd2+, or without Cd (control), for 24 h, at which point root samples were harvested and labeled as Cd+, Cd++, and control, respectively. These samples were used for 101 bp paired-end (PE) deep sequencing on an Illumina HiSeq 2500 platform.

2015-06-08 | E-MTAB-4445 | biostudies-arrayexpress

Comparative transcriptomic analysis of iron deficiency response in roots of Oryza sativa and O. rufipogon

Project description:Iron (Fe) is an essential micronutrient for almost all organisms. However, Fe is frequently inaccessible to plants. To acquire insoluble Fe from soil, rice (Oryza sativa L.) plants employ a Combined Strategy, which is composed by all features of Strategy II, common to all Poaceae species, and some features of the Strategy I from non-Poaceae. To understand the evolution of Fe uptake mechanisms, we analyzed the root transcriptomic response to Fe deficiency in two species from the Oryza genus: O. sativa and its wild progenitor O. rufipogon. A total of 622 and 2,017 genes were found to be differentially expressed in O. sativa and O. rufipogon, respectively. Among the genes regulated in both species, we found the Fe transporters associated with Strategy I, such as IRT1, IRT2 and NRAMP1; and genes associated with Strategy II, such as YSL15 and IRO2.

2019-11-19 | GSE131238 | GEO

Rice plants (Oryza sativa var. japonica): WT vs. MIT knockdown plant

Project description:Transcriptional profiling of MIT knockdown plants. MIT is a mitochondrial Fe transporter essential for rice growth and development. The goal was to determine the effects of MIT on global rice gene expression. Control condition experiment, root or shoot of WT vs. MIT knockdown plant. Two replicates each comparison, including a dye swap.

2011-04-07 | E-GEOD-28428 | biostudies-arrayexpress

Genotype variation in rice (Oryza sativa L.) tolerance to Fe toxicity might be linked to root cell wall lignification

Project description:Genotype variation in rice (Oryza sativa L.) tolerance to Fe toxicity might be linked to root cell wall lignification

| PRJNA543122 | ENA

Genotype Variation in Rice (Oryza sativa L.) Tolerance to Fe Toxicity Might Be Linked to Root Cell Wall Lignification.

Project description: Not available

| S-EPMC6581717 | biostudies-literature

Silicon enhances suberization and lignification in roots of rice (Oryza sativa).

Project description: Not available

| S-EPMC3060683 | biostudies-literature

Oryza sativa-Magnaporthe grisea interaction

Project description:5 leaves old rice plantlets were infected with Magnaporthe grisea spores and zero, two hours and twenty four houres after infection samples were collected

2014-01-31 | GSE50454 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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