Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar

ABSTRACT: Paired-end RNA-Seq libraries were constructed for three root sections of the roots of barley cv. Clipper, and landrace Sahara, grown under control and salt-treated (100 mM NaCl) conditions on agar plates in quadruplicate. Experiments were conducted in a temperature-controlled growth cabinet at 17 C in the dark. After three days of germination, seminal roots were dissected according to the following steps: A 1.5 mm long section marked Zone 1 (meristematic zone) was taken from the root tip. A second section (Zone 2) was dissected from the elongation zone up to a third section, Zone 3 (maturation zone), which was excised at the point of visible root hair elongation up to 34 of the entire root. Four biological replicates were generated for each sample in four separate experiments totaling 48 samples. All RNA-seq libraries were constructed and paired-end sequenced (100 bp) on an Illumina HiSeq 2000 system at the Australian Genome Research Facility (Melbourne, Australia).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Hordeum vulgare

SUBMITTER: Andrew Cassin

PROVIDER: E-MTAB-4634 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Publications

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure.

Hill Camilla Beate CB Cassin Andrew A Keeble-Gagnère Gabriel G Doblin Monika S MS Bacic Antony A Roessner Ute U

Scientific reports 20160816

Plant roots are the first organs sensing and responding to salinity stress, manifested differentially between different root types, and also at the individual tissue and cellular level. High genetic diversity and the current lack of an assembled map-based sequence of the barley genome severely limit barley research potential. We used over 580 and 600 million paired-end reads, respectively, to create two de novo assemblies of a barley landrace (Sahara) and a malting cultivar (Clipper) with known ...[more]

PMID: 27527578

Similar Datasets

Project description:Switchgrass plants were grown in a Sandwich tube system to induce gradual drought stress by withholding watering. After 29 days, leaf photosynthetic rate decreased significantly, compared to the control plants which were watered regularly. The drought-treated plants recovered to the same leaf water content after three days of re-watering. Root tip (1cm basal fragment, designated as RT1 hereafter) and the elongation/maturation zone (the next upper 1 cm tissue, designated as RT2 hereafter) tissues were collected at the 29th day of drought stress treatment, (named SDT for severe drought treated), one (D1W) and three days (D3W) of re-watering. The tandem mass tags mass spectrometry-based quantitative proteomics analysis was performed to identify the proteomes, and drought-induced differentially expressed proteins (DEPs). From RT1 tissues, 6,156, 7,687 and 7,699 proteins were quantified, and 296, 535 and 384 DEPs were identified in the SDT, D1W and D3W samples, respectively. From RT2 tissues, 7,382, 7,255 and 6,883 proteins were quantified, and 393, 587 and 321 proteins DEPs were identified in the SDT, D1W and D3W samples. Between RT1 and RT2 tissues, very few DEPs overlapped at SDT, but the number of such proteins increased during the recovery phase. A large number of hydrophilic proteins and stress-responsive proteins were induced during SDT and remained at a higher level during the recovery stages. A large number of DEPs in RT1 tissues maintained the same expression pattern throughout drought treatment and the recovery phases. The DEPs in RT1 tissues were classified in cell proliferation, mitotic cell division, and chromatin modification, and those in RT2 were placed in cell wall remodeling and cell expansion processes. This study provided information pertaining to root zone-specific proteome changes during drought and recover phases, which will allow us to choose the proteins (genes) as better defined targets for developing drought tolerant plants.

Project description:Low phosphate concentrations are frequently a constraint for maize growth and development, and therefore, enormous quantities of phosphate fertilizer are expended in maize cultivation, which increases the cost of planting. Low phosphate stress not only increases root biomass but can also cause significant changes in root morphology. Low phosphate availability has been found to favor lateral root growth over primary root growth by dramatically reducing primary root length and increasing lateral root elongation and lateral root density in Arabdopsis. While in our assay when inbred line Q319 subjected to phosphate starvation, The numbers of lateral roots and lateral root primordia were decreased after 6 days of culture in a low phosphate solution (LP) compared to plants grown under normal conditions (sufficient phosphate, SP), and these differences were increased associated with the stress caused by phosphate starvation. However, the growth of primary roots appeared not to be sensitive to low phosphate levels. This is very different to Arabidopsis. To elucidate how low phosphate levels regulate root modifications, especially lateral root development, a transcriptomic analysis of the 1.0-1.5 cm lateral root primordium zone (LRZ) of maize Q319 treated after 2 and 8 days by low phosphate was completed respectively. The present work utilized an Arizona Maize Oligonucleotide array 46K version slides, which contained 46,000 maize 70-mer oligonucleotides designated by TIGR ID, and the sequence information is available at the website of the Maize Oligonucleotide Array Project as the search item representing the >30,000 identifiable unique maize genes (details at http://www.maizearray.org). Keywords: low phosphate, Lateral Root Primordium Zone, maize Two-condition experiment, low phosphate treated lateral root primordium zone of maize root vs. normal cultrued lateral root primordium zone. Biological replicates: 9 control, 9 treated, independently grown and harvested. One replicate per array.

Project description:Background; Heterodera schachtii is an economically important plant parasitic nematode that forms a syncytium from a cell superficial to the formed vascular bundle by progressive recruitment of other cells into the structure. The pattern of plant gene expression changes dramatically inside the syncytium. The pathogen probably plays a major role in defining the plant response by choice of initial plant cell during precise behaviour in planta and/or by the secretions it releases. The modified plant cells enable a high feeding rate by the female nematode so enhancing its rate of development and subsequent daily egg production. Arabidopsis is widely used as a model plant to characterise molecular responses to nematodes (e.g. Sijmons et al., 1991 Plant J. 1:245-254.). A complete overview of the changes in plant gene expression when sedentary nematodes establish has not yet been gained using Arabidopsis or any other host plant. Experimental Approaches; Our initial studies will focus on the H. schachtii/Arabidopsis interaction. To assure reliable microarray screening care has been taken to minimise extraneous differences between samples (see "Growth conditions" section). At 21 days (Growth stage 3.2-3.5 Boyes et al., 2001 Plant Cell 13:1499-1510) Arabidopsis plants were challenged with rigorously sterilised, infective nematodes of H. schachtii as before (Urwin et al., (1997) Plant Journal 12: 455-461.). 35 sterile J2s were pipetted onto small ~0.5mm2 squares of sterile GF/A filter paper. The GF/A paper was left in direct contact with the zone of elongation on 3 lateral roots per plant for 48 hours. Control plants were mock inoculated with sterile water. Sections of root containing syncytia have been excised from the thin and transparent roots of Arabidopsis and collected into RNAlater solution (Ambion) at 21 days post infection (Growth Stage 6.1 Boyes et al. 2001). The female nematode has been removed with watch-maker's forceps. Equivalent sections of root have been harvested from non-infected plants. Material has been collected from c. 1000 plants for each of the two samples and the uninfected material serves as an internal control. Total RNA has been prepared from the reference and test root material using an RNeasy plant RNA preparation kit (Qiagen) according to methods required by GARNET.Some questions on the form are omitted as we are not using mutant or transgenic lines. This is our first application. Experimenter name = Peter Edward Urwin; Experimenter phone = 0113 343 3035/2909; Experimenter fax = 0113 343 3144; Experimenter address = Centre for Plant Science; Experimenter address = University of Leeds; Experimenter address = Leeds; Experimenter zip/postal_code = LS2 9JT; Experimenter country = UK Experiment Overall Design: 2 samples were used in this experiment

Dataset Information

A study of transcriptome response to salt treatment across three zones of the root in a barley landrace and malting cultivar

Publications

De novo transcriptome assembly and analysis of differentially expressed genes of two barley genotypes reveal root-zone-specific responses to salt exposure.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure