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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.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE23889 | GEO | 2011/10/05

SECONDARY ACCESSION(S): PRJNA130457

REPOSITORIES: GEO

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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. Time-series experiment with 4 genotypes x 8 time-points X 3 biological replicates in random block design; 96 hybridizations

2011-10-04 | E-GEOD-23889 | biostudies-arrayexpress

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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.

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

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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

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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.

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Project description:Wheat is one of the most significant crops in terms of human consumption in the world. In a climate change scenario, extreme weather event such as heatwaves will be more frequent especially during the grain-filling (GF) stage and could affect grain weight and quality of crops. Molecular mechanisms underlying the response to short heat stress (HS) have been widely reported for the hexaploid wheat (Triticum aestivum) but the regulatory heat stress mechanisms in tetraploid durum wheat (Triticum turgidum ssp. durum) remain partially understood. In this work, we performed a transcriptomic analysis of durum wheat grains to HS during early GF to identify key HS response genes and their predicted regulatory networks under glasshouse conditions.

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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 24Â°C under long day (18-h light and 6-h dark) condition for 8 weeks. Two independent experiments were conducted in each exprement.

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