Triticum aestivum
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ABSTRACT:
PROVIDER: PRJNA275199 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:The study was conducted in order to find out the differential change in the transcript of tolerant and susceptible wheat cultivar under heat stress and to decipher the mechanism of thermotolerance in wheat by identifying novel genes and transcription factors involved in the pathways. Wheat cultivar HD2985 (thermotolerant) and HD2329 (thermosusceptible) were exposed to heat stress of 42 degree for 4h at pollination stage and samples were collected from both control and heat shock treated plants for further characterization.
2012-08-31 | E-MTAB-4370 | biostudies-arrayexpress
Project description:To better understand the regulatory mechanisms of water stress response in wheat, the transcript profiles in roots of two wheat genotypes, namely, drought tolerant 'Luohan No.2' (LH) and drought susceptible 'Chinese Spring' (CS) under water-stress were comparatively analyzed by using the Affymetrix wheat GeneChip®. A total of 3831 transcripts displayed 2-fold or more expression changes, 1593 transcripts were induced compared with 2238 transcripts were repressed, in LH under water-stress; Relatively fewer transcripts were drought responsive in CS, 1404 transcripts were induced and 1493 were repressed. Comparatively, 569 transcripts were commonly induced and 424 transcripts commonly repressed in LH and CS under water-stress. 689 transcripts (757 probe sets) identified from LH and 537 transcripts (575 probe sets) from CS were annotated and classified into 10 functional categories, and 74 transcripts derived from 80 probe sets displayed the change ratios no less than 16 in LH or CS. Several kinds of candidate genes were differentially expressed between the LH and CS, which could be responsible for the difference in drought tolerance of the two genotypes.
2012-01-01 | GSE30872 | GEO
Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity.
2014-08-20 | GSE53487 | GEO
Project description:Alteration in gene expression accompanying initial stages of allopolyploidy is a prominent feature in plants, but its spectrum and model are highly idiosyncratic. We used multi-colour GISH to identify individuals from two nascent allohexaploid wheat lines between Triticum turgidum and Aegilops tauschii, which had a transgenerationally stable chromosomal constitution mimicking that of common wheat. We performed genomewide analysis of gene expression for these plants along with their parental species using the Affymetrix GeneChip Wheat Genome-Array. Comparison with parental species coupled with inclusion of empirical mid-parent values (MPVs) revealed two patterns of alteration in gene expression in the allohexaploid lines: parental dominance expression and nonadditive expression. Genes involved in each altered pattern could be classified into three distinct groups, stochastic, heritable and persistent, based on their transgenerational heritability and inter-line conservation. Whereas both altered patterns of gene expression showed a propensity of inheritance, identity of the involved genes is stochastic, consistent with the involvement of diverse Gene Ontology (GO) terms. Nonetheless, those genes showing nonadditive expression exhibited a significant enrichment for vesicle-function. Our results suggest global alteration in gene expression conditioned by nascent allopolyploidy likely play functional roles in stabilization and establishment of the newly formed plants, and consequential to evolution.
2012-05-01 | GSE29882 | GEO
Project description:Allopolyploidy, entailing whole genome duplication (WGD) of merged divergent genomes of different species, often instigates transcriptome shock, whereby both total gene expression level and homeolog expression partitioning can be disrupted and remodeled. Little is known about the extent to which the parental expression-conserved genes will be disrupted/remodeled by allopolyploidization, nor the evolutionary relevancy of shock-induced expression repatterning. Here, by microarray-based gene expression profiling and gene-specific cDNA-pyrosequencing, we assessed transgenerational transcriptome shock in a synthetic allotetraploid wheat (AT2) with karyotype and basic morphology mimicking those of natural tetraploid wheat, Triticum turgidum. We show that the transcriptome shock in AT2 is exceptionally strong that it disrupted intrinsically conserved parental gene expression, and resulted in extensive expression nonadditivity in the newly formed allotetraploid plants. At total expression level, a substantial proportion of shock-induced novel expression, especially over-transgressive expression, was rapidly stabilized already in early generations of AT2. Extensive remodeling of homeolog expression occurred in AT2, including those genes that showed additive total expression, and which generated subgenome expression dominance, a pattern that mirrors T. turgidum. Thus, the shock-induced new patterns of gene expression at both the total expression level and subgenome homeolog partitioning showed evidence of evolutionary persistence. Complex relationships between homeolog expression remodeling and nonadditive total expression were observed in a tissue-specific manner.
2016-02-12 | GSE65844 | GEO
Project description:Background: MicroRNAs regulate various biological processes in plants. Considerable data are available on miRNAs involved in the development of rice, maize and barley. In contrast, little is known about miRNAs and their functions in the development of wheat. In this study, five small RNA (sRNA) libraries from wheat seedlings, flag leaves, and developing seeds were developed and sequenced to identify miRNAs and understand their functions in wheat development. Results: Twenty-four known miRNAs belonging to 15 miRNA families were identified from 18 MIRNA loci in wheat in the present study, including 15 (9 MIRNA loci) first identified in wheat, 13 miRNA families (16 MIRNA loci) being highly conserved and 2 (2 MIRNAs loci) moderately conserved. In addition, fifty-five novel miRNAs were also identified. The potential target genes for 15 known miRNAs and 37 novel miRNAs were predicted using strict criteria, and these target genes are involved in a wide range of biological functions. Four of the 15 known miRNA families and 22 of the 55 novel miRNAs were preferentially expressed in the developing seeds with logarithm of the fold change of 1.0～7.6, and half of them were seed-specific, suggesting that they participate in regulating wheat seed development and metabolism. From 5 days post-anthesis to 20 days post-anthesis, miR164 and miR160 increased in abundance in developing seeds, whereas miR169 decreased, suggesting their coordinating functions in the different developmental stages of wheat seed. Moreover, eight known miRNA families and 28 novel miRNAs exhibited tissue-biased expression in wheat flag leaves, with the logarithm of the fold changes of 0.5～5.2. The putative targets of these tissue-preferential miRNAs were involved in various metabolism and biological processes, suggesting complexity of the regulatory networks in different tissues. Our data also suggested that wheat flag leaves have more complicated regulatory networks of miRNAs than developing seeds. Conclusions: Our work identified and characterised wheat miRNAs, their targets and expression patterns. This study is the first to elucidate the regulatory networks of miRNAs involved in wheat flag leaves and developing seeds, and provided a foundation for future studies on specific functions of these miRNAs.
2017-01-01 | GSE50524 | GEO
Project description:Allopolyploidy, entailing whole genome duplication (WGD) of merged divergent genomes of different species, often instigates transcriptome shock, whereby both total gene expression level and homeolog expression partitioning can be disrupted and remodeled. Little is known about the extent to which the parental expression-conserved genes will be disrupted/remodeled by allopolyploidization, nor the evolutionary relevancy of shock-induced expression repatterning. Here, by microarray-based gene expression profiling and gene-specific cDNA-pyrosequencing, we assessed transgenerational transcriptome shock in a synthetic allotetraploid wheat (AT2) with karyotype and basic morphology mimicking those of natural tetraploid wheat, Triticum turgidum. We show that the transcriptome shock in AT2 is exceptionally strong that it disrupted intrinsically conserved parental gene expression, and resulted in extensive expression nonadditivity in the newly formed allotetraploid plants. At total expression level, a substantial proportion of shock-induced novel expression, especially over-transgressive expression, was rapidly stabilized already in early generations of AT2. Extensive remodeling of homeolog expression occurred in AT2, including those genes that showed additive total expression, and which generated subgenome expression dominance, a pattern that mirrors T. turgidum. Thus, the shock-induced new patterns of gene expression at both the total expression level and subgenome homeolog partitioning showed evidence of evolutionary persistence. Complex relationships between homeolog expression remodeling and nonadditive total expression were observed in a tissue-specific manner. We have 9 samples including two tissues, leaf and young-inflorescence, respectively. Each sample has three replicates. So we overall have 54 samples.
2016-02-12 | E-GEOD-65844 | biostudies-arrayexpress
Project description:We used isobaric tags for relative and absolute quantitation (iTRAQ) to perform a quantitative proteomic analysis of immature spikes harvested from tetraploid near-isogenic lines of wheat with normal spikelete (NSs), FRSs, and RSs and investigated the molecular mechanisms of lateral meristem differentiation and development. This work provides valuable insight into the underlying functions of the lateral meristem and how it can produce differences in the branching of tetraploid wheat spikes.
2018-10-19 | PXD008910 | Pride
Project description:wheat expression level polymorphism study parental genotypes 2 biological reps
| PRJNA95877 | ENA
Project description:Purpose: To identify abiotic stress responsive and tissue specific miRNAs at genome wide level in wheat (Triticum aestivum) Results: Small RNA libraries were constructed from four tissues (root, shoot, mature leaf and spikelets) and three stress treatments of wheat seedlings (control, high temperature, salinity and water-deficit). A total of 59.5 million reads were obtained by high throughput sequencing of eight wheat libraries, of which 32.5 million reads were found to be unique. Using UEA sRNA workbench we identified 47 conserved miRNAs belonging to 20 families, 1030 candidate novel and 51 true novel miRNAs. Several of these miRNAs displayed tissue specific expression whereas few were found to be responsive to abiotic stress treatments. Target genes were predicted for miRNAs identified in this study and their grouping into functional categories revealed that the putative targets were involved in diverse biological processes. RLM-RACE of predicted targets of three conserved miRNAs (miR156, miR160 and miR164) confirmed their mRNA cleavage, thus indicating their regulation at post-transcriptional level by corresponding miRNAs. Expression profiling of confirmed target genes of these miRNAs was also performed. Conclusions: This is the first comprehensive study on profiling of miRNAs in a variety of tissues and in response to several abiotic stresses in wheat. Our findings provide valuable resource for better understanding on the role of miRNAs in stress tolerance as well as plant development. Additionally, this information could be utilized for designing wheat plants for enhanced abiotic stress tolerance and higher productivity. Total eight (three stress, one control and four tissue specific small RNA libraries were pepared and sequenced independently [wheat control (WC), wheat high temperature stressed (WHTS), wheat salinity stressed (WSS) and wheat drought stressed (WDS), wheat shoot(WSH), wheat leaf (WLF), wheat flower(WFL), wheat root(WRT)] on Illumina GAIIx
2014-08-20 | E-GEOD-53487 | biostudies-arrayexpress