Triticum aestivum
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA383333 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR5460930.fastq.gz | Fastqsanger.gz | |||
| SRR5460941.fastq.gz | Fastqsanger.gz | |||
| SRR5460972.fastq.gz | Fastqsanger.gz | |||
| SRR5461176.fastq.gz | Fastqsanger.gz | |||
| SRR5460967.fastq.gz | Fastqsanger.gz |
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Project description:We collected infected wheat leaf material at up to nine time points per Z. tritici isolate and conducted confocal microscopy analyses to select samples for RNA extraction and transcriptome sequencing based on the morphological infection stage. Thereby, we generated stage-specific RNA-seq datasets corresponding to the four core infection stages allowing us to compare the isolate-specific expression profiles at the same developmental stage of infection. Our final dataset comprises four stage-specific transcriptomes per isolate with two biological replicates per sample. Comparative transcriptome analyses reveal that the expression phenotypes of the three isolates differ significantly.
2018-04-25 | GSE106136 | GEO
Project description:Wheat is the staple food of over 35% of the world’s population, accounts for 20% of all human calories, and its yield and quality improvement is a focus in the effort to meet new demands from population growth and changing diets. As the complexity of the wheat genome is unravelled, determining how it is used to build the protein machinery of wheat plants is a key next step in explaining detailed aspects of wheat growth and development. The specific functions of wheat organs during vegetative development and the role of metabolism, protein degradation and remobilisation in driving grain production are the foundations of crop performance and have recently become accessible through studies of the wheat proteome. With the aim of creating a resource complementary to current genome sequencing and assembly projects and to aid researchers in the specific analysis and measurement of wheat proteins of interest, we present a large scale, publicly accessible database of identified peptides and proteins derived from the proteome mapping of Triticum aestivum. This current dataset consists of twenty four organ and developmental samples in an online interactive resource allowing the selection, comparison and retrieval of proteomic data with rich biochemical annotation derived from multiple sources. Tissue specific sub-proteomes and ubiquitously expressed markers of the wheat proteome are identified alongside hierarchical assessment of protein functional classes and their presence in different tissues. The impact of wheat’s polyploid genome on proteome analysis and the effect on defining gene specific and protein family relationships is accounted for in the organisation of the data. The dataset will serve as a vehicle to build, refine and deposit confirmed targeted proteomic assays for wheat proteins and protein families to assess function.
2016-11-17 | PXD004720 | Pride
Project description:The biological functions of circadian clock on growth and development have been well elucidated in model plants, while its regulatory roles in crop species, especially the roles on yield-related traits are poorly understood. Here, we characterize the core clock gene CCA1 homoeologs in wheat and studied their biological functions in seedling growth and spike development. TaCCA1 homoeologs exhibit typical diurnal expression patterns which are positively regulated by rhythmic histone modifications (H3K4me3, H3K9ac and H3k36me3). TaCCA1s are preferentially located in the nucleus and tend to form both homo- and heterodimers. TaCCA1 overexpression (TaCCA1-OE) transgenic wheat plants show disrupted circadian rhythmicity coupling with reduced chlorophyll and starch content, as well as biomass at seedling stage, also decreased spike length, grain number per spike and grain size at the ripening stage. Further studies using DNA affinity purification followed by deep sequencing (DAP-seq) indicates that TaCCA1 preferentially binds to sequences similar to “evening elements” (EE) motif in the wheat genome, particularly genes associated with photosynthesis, carbon utilization and auxin homeostasis, and decreased transcriptional levels of these target genes are observed in TaCCA1-OE transgenic wheat plants. Collectively, our study provides novel insights into a circadian-mediated mechanism of gene regulation to coordinate photo synthetic and metabolic activities in wheat, which is important for optimal plant growth and crop yield formation.
2022-06-29 | GSE200426 | 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:Agrobacterium-mediated plant transformation is an extremely complex and evolved process involving genetic determinants of both the bacteria and the host plant cells. However, the mechanism of the determinants remains obscure, especially in some cereal crops such as wheat, which is recalcitrant for Agrobacterium-mediated transformation. In this study, differentially expressed genes (DEGs) were analyzed in wheat callus cells co-cultured with Agrobacterium by using RNA sequencing (RNA-seq). Note: All samples in SRA were assigned the same sample accession (SRS417803). This is incorrect as there are different samples, hence “Source Name” was replaced with new values. Comment[ENA_SAMPLE] contains the original SRA sample accessions.
2013-05-07 | E-MTAB-4272 | biostudies-arrayexpress
Project description:The pistillody mutant wheat (Triticum aestivum L.) plant HTS-1 exhibits homeotic transformation of stamens into pistils or pistil-like structures. Unlike common wheat varieties, HTS-1 produces three to six pistils per floret, potentially increasing the yield. Thus, HTS-1 is highly valuable in the study of floral development in wheat. In this study, we conducted RNA sequencing of the transcriptomes of the pistillody stamen (PS) and the pistil (P) from HTS-1 plants, and the stamen (S) from the non-pistillody control variety Chinese Spring TP to gain insights into pistil and stamen development in wheat.
2014-03-14 | E-MTAB-4469 | biostudies-arrayexpress
Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived Triticum aestivum transcriptome (RNA-seq) profiling methods and to evaluate genotypes associated with resistance against the Wheat dwarf virus. Methods: Triticum aestivum mRNA profiles of genotypes associated with resistance against the Wheat dwarf virus were generated by deep sequencing, in four replicates, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays. Conclusions: Our study represents the first detailed analysis of Triticum aestivum transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA and miRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
2023-04-04 | GSE192518 | 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: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