Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Affy_root-dvt-nitrogen_medicago: Genetic determinism of root development in Medicago truncatula

ABSTRACT: affy_root-dvt-nitrogen_medicago. The biological question is the study of root development adaptation to external nitrogen availability. One of the typical responses to low N provision consists of an increased root branching which promotes soil exploration. In order to differentiate between genes specifically involved in nitrate response and genes of root development, we had performed experiments on both a wild type and a mutant affected in root architecture, both supplied with two different levels of nitrate. Global gene expression profiling of root cells using microarray analysis will be conducted to identify genes expressed during root branching. First, analysing the differential gene expression between the wild type and the mutant both at low and high level of nitrate, we will identify genes of root development but also genes specifically involved in nitrate response. Then, additional comparisons will concern the modifications of wild type and mutant gene expression between the two levels of nitrate. These genes will be compared to those found to be expressed in the wild type roots under submitted to various nitrogen sources (Ruffel et al., 2008). All together these results will allow us to determine which genes, among the firstly underlined, are specifically involved in root development. The kinetics of expression in different tissues of the most relevant of these genes will be further analysed by qRT-PCR. Three successive experiments in growth chamber were performed on two different genotypes of Medicago truncatula. Each experiment constituted a biological replicate. For each of them, after 4 days of seed cold-treatment followed by 4 days of germination, individual plantlets were transferred onto hydroponic culture tanks containing vigorously aerated nutrient solution. Each tank contained 6 plantlets of J5 and 6 plantlets of the mutant. On one shelf of the growth chamber, nutrient solution in the tanks was supplemented by 1mM of KNO3; on the other shelf, the level of KNO3 in the solution was of 10mM. Nutrient solution was renewed every week. Roots of the two genotypes were harvested separately but at the same time, 10 days after the plantlets transfer onto hydroponic culture tanks. Experiment Overall Design: 12 arrays - Medicago. Experiment Overall Design: WT and mutant (tr185) under 1mM or 10mM KNO3. Three biological replicates each genotype/condition.

ORGANISM(S): Medicago truncatula

SUBMITTER: sandrine balzergue

PROVIDER: E-GEOD-18318 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:affy_root-dvt-nitrogen_medicago. The biological question is the study of root development adaptation to external nitrogen availability. One of the typical responses to low N provision consists of an increased root branching which promotes soil exploration. In order to differentiate between genes specifically involved in nitrate response and genes of root development, we had performed experiments on both a wild type and a mutant affected in root architecture, both supplied with two different levels of nitrate. Global gene expression profiling of root cells using microarray analysis will be conducted to identify genes expressed during root branching. First, analysing the differential gene expression between the wild type and the mutant both at low and high level of nitrate, we will identify genes of root development but also genes specifically involved in nitrate response. Then, additional comparisons will concern the modifications of wild type and mutant gene expression between the two levels of nitrate. These genes will be compared to those found to be expressed in the wild type roots under submitted to various nitrogen sources (Ruffel et al., 2008). All together these results will allow us to determine which genes, among the firstly underlined, are specifically involved in root development. The kinetics of expression in different tissues of the most relevant of these genes will be further analysed by qRT-PCR. Three successive experiments in growth chamber were performed on two different genotypes of Medicago truncatula. Each experiment constituted a biological replicate. For each of them, after 4 days of seed cold-treatment followed by 4 days of germination, individual plantlets were transferred onto hydroponic culture tanks containing vigorously aerated nutrient solution. Each tank contained 6 plantlets of J5 and 6 plantlets of the mutant. On one shelf of the growth chamber, nutrient solution in the tanks was supplemented by 1mM of KNO3; on the other shelf, the level of KNO3 in the solution was of 10mM. Nutrient solution was renewed every week. Roots of the two genotypes were harvested separately but at the same time, 10 days after the plantlets transfer onto hydroponic culture tanks. Keywords: dose response, wt vs mutant comparison

Project description:Arable soils are extremely heterogeneous in spatial nutrient distribution. It is well documented that lateral roots (LRs) proliferate in nitrate-rich patch. Yet less information is available as to which genes are involved in this process, in particular in cereals. To understand the molecular mechanism for local nitrate induced LR growth in maize (Zea mays L.), we analyzed the gene expression profiling in maize root in early response (1 hour) to local nitrate stimulation by using Maize Oligonucleotide Array (http://www.maizearray.org) and a split-root system. Selected differentially expressed genes were further confirmed by semi-quantitative RT-PCR. The results showed that reception and/or transduction of local NO3- signal involve some important protein kinases and protein phosphatases (histidine kinases, serine/threonine kinases, protein phosphatase 2A etc.) and transcription factors (F-box, Zinc finger, Myb and bZIP transcription factors and response regulator). Increasing expression of genes encoding auxin response factor 7b, ethylene receptor, and cytokinin oxidase suggests strong interaction among hormonal pathways and local NO3- signaling pathways. Genes involving NO3- uptake and assimilation (NRT2.1, NR, etc.), sugar transport (a sugar transporter) and utilization (a sucrose synthase) were enhanced in the N-fed root. Furthermore, local NO3- induces rapid expression of genes related to cell division and expansion such as alpha-expansin, celluose synthase, kinesin, plasma membrane and tonoplast aquaporins. Based on the differentially expressed genes, a putative model which combines both the 'NO3- signal' and 'metabolic sink' theories is proposed to explain the molecular mechanism controlling local nitrate induced LR elongation in maize. plants were pre-cultured in solution containing 0.5 mmol L-1 NO3- for 6 days and then transferred to N-free solution to grow for another 2 days. Then these plants were transferred to a two-compartment split-root system with only half root supplied with 1.0 mmol L-1 NO3-. Supply of Ca2+ in the N-free half was compensated by adding 1.0 mmol L-1 CaCl2. One hour after the local nitrate treatment, root segments (15cm from root tip to lateral root elongation zone) were sampled for RNA extraction. Two biological replicates were performed for each treatment.

Dataset Information

Affy_root-dvt-nitrogen_medicago: Genetic determinism of root development in Medicago truncatula

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets