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Transcriptome profiling and expression analyses of genes critical to wheat adaptation to low temperature

ABSTRACT: Understanding the mechanism of low temperature (LT) adaptation is crucial to the development of cold-tolerant crops. To identify the genes involved in the development of LT tolerance in the crown of hexaploid wheat we examined the global changes in genes expression during cold-treatment using the Affymetrix Wheat Genome Chip. Time-series experiment with 4 genotypes x 8 time-points X 3 biological replicates in random block design; 96 hybridizations

ORGANISM(S): Triticum aestivum

SUBMITTER: Debbie Laudencia-Chingcuanco

PROVIDER: E-GEOD-23889 | ArrayExpress | 2011-10-04

SECONDARY ACCESSION(S): GSE23889PRJNA130457

REPOSITORIES: GEO, ArrayExpress

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Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.).

Laudencia-Chingcuanco Debbie D Ganeshan Seedhabadee S You Frank F Fowler Brian B Chibbar Ravindra R Anderson Olin O

BMC genomics 20110607

To identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar)) cultivars, wherein the locus for the vernalization gene Vrn-A1 was swapped between the parental ...[more]

PMID: 21649926

Similar Datasets

Transcriptome profiling and expression analyses of genes critical to wheat adaptation to low temperature

Project description:Understanding the mechanism of low temperature (LT) adaptation is crucial to the development of cold-tolerant crops. To identify the genes involved in the development of LT tolerance in the crown of hexaploid wheat we examined the global changes in genes expression during cold-treatment using the Affymetrix Wheat Genome Chip. Overall design: Time-series experiment with 4 genotypes x 8 time-points X 3 biological replicates in random block design; 96 hybridizations

2011-10-05 | GSE23889 | GEO

Gene expression profiles during long-term low-temperature treatment and cold acclimation in synthetic wheat hexaploids

Project description:We conducted microarray analysis to study comprehensive changes of gene expression profile under long-term low-temperature (LT) treatment and to identify other LT-responsive genes related with cold acclimation in seedling leaves and crown tissues (shoots containing apical meristems) of a synthetic hexaploid wheat line. The microarray analysis revealed marked up-regulation of a number of Cor/Lea genes and fructan biosynthesis-related genes under the long-term LT treatment. For validation of the microarray data, we selected four synthetic wheat lines, which contained the A and B genomes from a tetraploid wheat cultivar Langdon and the diverse D genomes originating from the different Ae. tauschii accessions, with distinct levels of freezing tolerance after cold acclimation. Quantitative RT-PCR analyses showed that the transcription accumulated levels of the Cor/Lea, CBF, and fructan biosynthesis-related genes were higher in more freezing-tolerant lines than those in the sensitive lines. The fructan biosynthesis pathway would be associated with cold acclimation to develop wheat freezing tolerance and related with diversity of the freezing tolerance level in addition to the CBF-mediated Cor/Lea expression pathway. Expression patterns were compared between a synthetic wheat line which treated 24℃ and 4℃. Total RNA samples were respectively isolated from leaves and crown tissues of the synthetic line grown at normal temperature for 3 weeks and then at 4°C for 12 and 6 weeks. Two independent experiments were conducted in each exprement.

2014-10-10 | E-GEOD-61621 | ArrayExpress

Proteomic analysis of the apoplast reveals a differential cold acclimation response among winter wheat crown tissues

Project description:The crown is the critical region for survival of winter wheat exposed to low temperature stresses. When wheat is exposed to non-freezing low temperatures, they can increase their freezing tolerance (cold acclimation, ACC). Changes within the apoplast are thought to be crucial for acquisition of freezing tolerance. However, how individual tissues within the ccrown, namely the shoot apical meristem (SAM, responsible for new shoot growth) and vascular transition zone (VTZ, located at the base of the crown)enhance tolerance to freezing has not yet been characterized. In the present study, we conducted shotgun proteomic analysis of the apoplast fluid to investigate ACC-induced proteins in the SAM and VTZ.

2018-10-23 | PXD007796 | Pride

RNA-seq of developing starchy endosperm of Triticum aestivum at five stages during grain fill

Project description:Transcriptome of starchy endosperm of hexaploid wheat var. Cadenza at 5 stages during grain-fill. This provides a reference set of all genes which are expressed in this single cell type during development which is of huge importance for human nutrition and for industrial uses of wheat grain. Here we focus on genes in glycosyl transferase and glycosyl hydrolase families which are responsible for the non-starch polysaccharide composition of wheat flour.

2011-11-08 | E-MTAB-861 | ArrayExpress

Comparative (phospho)proteomic profiling of wheat shoots from different cultivars

Project description:Wheat is a cereal grain and one of the world’s major food crops. Recent advances in wheat genome sequencing are by now facilitating genomic and proteomic analyses of this crop. However, little is known about the protein levels of hexaploid versus tetraploid wheat cultivars, and knowledge on phosphorylated proteins still limited. Using our recently established (phospho)proteomic workflow, we performed a parallel analysis of the proteome and phosphoproteome on seedling leaves from two hexaploid wheat cultivars (Pavon 76 and USU-Apogee) and a tetraploid wheat (Senatore Cappelli). This revealed that a large portion of proteins and phosphosites can be quantified in all cultivars. Our shotgun proteomics data revealed a high similarity between hexaploid and tetraploid varieties with respect to protein abundance. However, we could identify a set of proteins that were differentially abundant between hexaploid and tetraploid cultivars. In addition, already at seedling stage, a small set of proteins were differential between the small (USU-Apogee) and larger hexaploid wheat cultivar (Pavon 76), which could potentially act as growth predictors. Finally, the phosphosites identified in this study can be retrieved from the in-house developed plant PTM-Viewer (bioinformatics.psb.ugent.be/webtools/ptm_viewer/), making this the first repository for phosphorylated wheat proteins. This paves the way for further in depth, quantitative (phospho)proteome-wide differential analyses upon a specific trigger or environmental change.

2017-04-03 | PXD005437 | Pride

Expression profiling of grass-clump dwarf in syntheitic hexaploids from triploid hybrids crossed between tetraploid wheat and Aegilops umbellulata.

Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in a grass-clump dwarf line, which is a synthetic hexaploid line from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon) and a diploid wheat relative Aegilops umbellulata (KU-4052). Up-regulation of metabolic and catabolic processes-related genes for cell wall-associated molecules was observed, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf line. Unusual expression of the branching-related SPLs and flowering time regulation-related MADS-box genes could explain the grass-clump dwarf phenotype. Overall design: Expression patterns were compared between the two synthetic hexaploid lines showing the wild-type phenotype (as a reference) and grass-clump dwarf. Total RNA samples were isolated from crown tissues of the plants grown at 24°C under long day (18-h light and 6-h dark) condition for 50 days. Two independent experiments were conducted in each exprement.

| GSE93969 | GEO

Transcription profiling of wheat response to infection by Fusarium pseudograminearum

Project description:Crown rot of wheat, caused by Fusarium pseudograminearum and other Fusarium species is an important disease globally. To understand the host response to challenge by Fp, we examined gene exression changes in the stem base of the wheat variety Kennedy, following inoculation with macroconidia using the Affymetrix GeneChip Wheat Genome Array. Induced genes included mainly those with defensive functions such as genes encoding anti-microbial proteins as well as oxidative stress-related proteins, signalling molecules, and proteins involved in both primary and secondary metabolism. This study is the first comprehensive analysis of the wheat transcriptome during crown rot infection and provides new insights into the host processes involved in plant defence against this pathogen. Experiment Overall Design: There are six samples, three F. pseudograminearum inoculated samples and three mock inoculated samples. Each sample consists of 2cm of stem base from approximately 20 plants.

2009-01-14 | E-GEOD-13660 | ArrayExpress

Triticum aestivum Transcriptome or Gene expression

Project description:Two azide mutagenized lines Freeze Resistance (FR, 75% survival) and Freeze Susceptible (FS, 30% survival) were compared with and without 4°C ± 1.5 cold acclimation of crown tissue to identify genes responsible for the difference in freeze resistance. Keywords: Wheat cold acclimation, stress response, cold, low temperature Overall design: Experiment design (8 hybridizations): Genotype: SD16029 (FR) or SD16169 (FS) Temperature: 25°C or 4°C

| GSE14697 | GEO

Expression profiling of grass-clump dwarf in synthetic hexaploids from triploid hybrids crossed between tetraploid wheat and Aegilops tauschii

Project description:We have employed whole genome microarray expression profiling as a discovery platform to identify genes to alter the transcript accumulation levels in grass-clump dwarf lines, which are synthetic hexaploid lines from triploid hybrids crossed between tetraploid wheat (Triticum turgidum ssp. durum cv. Langdon or T. turgidum ssp. carthlicum) and diploid wheat progenitor Aegilops tauschii (KU2025). No up-regulation of defense-related genes was observed under the normal temperature, and down-regulation of wheat APETALA1-like MADS-box genes, considered to act as flowering promoters, was found in the grass-clump dwarf lines. Together with small RNA sequencing analysis of the grass-clump dwarf line, unusual expression of the miR156/SPLs module could explain the grass-clump dwarf phenotype. Expression patterns were compared between the three synthetic hexaploid lines showing the wild-type phenotype (as a reference) and grass-clump dwarf. Total RNA samples were isolated from crown tissues of the plants grown at 24°C under long day (18-h light and 6-h dark) condition for 8 weeks. Two independent experiments were conducted in each exprement.

2016-03-02 | E-GEOD-78784 | ArrayExpress

Freeze resistance basis of winter wheat mutant lines

Project description:Two azide mutagenized lines Freeze Resistance (FR, 75% survival) and Freeze Susceptible (FS, 30% survival) were compared with and without 4°C ± 1.5 cold acclimation of crown tissue to identify genes responsible for the difference in freeze resistance. Keywords: Wheat cold acclimation, stress response, cold, low temperature Experiment design (8 hybridizations): Genotype: SD16029 (FR) or SD16169 (FS) Temperature: 25°C or 4°C

2013-07-01 | E-GEOD-14697 | ArrayExpress

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