Ontology highlight
ABSTRACT:
PROVIDER: PRJNA863398 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR20705522.fastq.gz | Fastqsanger.gz | |||
| SRR20705523.fastq.gz | Fastqsanger.gz | |||
| SRR20705524.fastq.gz | Fastqsanger.gz | |||
| SRR20705525.fastq.gz | Fastqsanger.gz | |||
| SRR20705526.fastq.gz | Fastqsanger.gz |
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Project description:Root traits are significant targets for breeding stress-resilient and high-yielding wheat genotypes under climatic fluctuations. However, root transcriptome analysis is usually obscured due to challenges in root research. We performed transcriptome analysis of thirty bread wheat cultivars using RNA-seq to investigate the diversity and expression of root system architecture (RSA) related transcripts. We examined the expression patterns of these transcripts in both root and leaf tissues and found that various transcripts are root-specific which could be manipulated for desirable root traits.The presented RNA-seq datasets provide valueable source for identification of genes involved in various biological processes under varying climatic conditions.
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Project description:In this study, we used dual RNA-sequencing to profile FHB-resistant AC Emerson, FHB-moderately AC Morley, and FHB-susceptible CDC Falcon winter wheat cultivars prior to and in response to Fusarium graminearum at 7 days post inoculation. Differential expression analyses revealed distinct defense responses between resistant and susceptible wheat cultivars including increased mechanical defense through lignin biosynthesis and increased deoxynivalenol (DON) detoxification through UDP-glycosyltransferase activity in resistant cultivars. Further, differential expression analysis in F. graminearum challenging these distinct cultivars revealed changes genes involved in trichothecene mycotoxin biosynthesis.
2024-01-24 | GSE233409 | GEO
Project description:Waxy starch has an important influence on bread dough and the qualities of breads. Generally, grain weight and yield in waxy wheat (Triticum aestivum L.) are significantly lower than in bread wheat. In this study, we performed the first proteomic and phosphoproteomic analyses of starch granule-binding proteins by comparing the waxy wheat cultivar Shannong 119 and the bread wheat cultivar Nongda 5181. The waxy and non-waxy wheats had similar starch granule morphological features and developmental patterns, and similar amylopectin quality in the grain. These results indicate that reduced amylose content does not affect amylopectin synthesis, but it causes significant reduction of total starch biosynthesis, grain size, weight and yield. Two-dimensional differential in-gel electrophoresis identified 40 differentially expressed protein (DEP) spots in waxy and non-waxy wheats, which belonged mainly to starch synthase (SS) I, SS IIa and granule-bound SS I. Most DEPs involved in amylopectin synthesis showed a similar expression pattern during grain development, suggesting relatively independent amylose and amylopectin synthesis pathways. Phosphoproteome analysis of starch granule-binding proteins, using TiO2 microcolumns and LC-MS/MS, showed that the total number of phosphoproteins and their phosphorylation levels in ND5181 were significantly higher than in SN119, but proteins controlling amylopectin synthesis had similar phosphorylation levels. Dynamic transcriptional expression profiling of starch biosynthesis-related genes indicated similar transcriptional expression profiles in both cultivars. Our results revealed that phosphorylation modifications played critical roles in amylose and amylopectin biosynthesis, but the lack of amylose did not affect the expression and phosphorylation of the starch granule-binding proteins involved in amylopectin biosynthesis.
2017-10-30 | PXD002805 | Pride
Project description:Bread wheat is the major staple food of the world with a complex hexaploidy genome. The precise spatiotemporal gene expression is orchestrated by enhancers, which lack general sequence features and thus are difficult to be located, especially in large genomes. Epigenomic architecture, including chromatin openness and active chromatin marks, has been widely used to characterize enhancers. However, an active chromatin environment does not necessarily mean an active enhancer. Recently, enhancer RNAs (eRNAs), the hallmark for active enhancers, have been detected by nascent RNA sequencing in both Drosophila and mammalian. In order to answer whether plant enhancers could be transcribed, we investigated the transcriptome of bread wheat via two nascent RNA sequencing methods, GRO-seq and pNET-seq combining with epigenome profiling. Our study demonstrates the presence and wide distribution of transcription at intergenic enhancers, which accurately reflects high enhancer activity, shedding light on the complex gene expression regulation across subgenomes in bread wheat.
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Project description:Bread wheat (Triticum aestivum L.) is one of the most valuable cereal crops for the human consumption. Its grain storage proteins greatly impact bread quality, though may cause food intolerances or allergies in susceptible individuals. Consequently, the investigation of a proteome polymorphism among wheat varieties is important to spot the genotypes, which would be promising donors for the breeding of hypoallergenic cereals. Herein, we discovered diversity of grain proteins in three Ukrainian wheat cultivars: ‘Sotnytsia’, ‘Panna’ (both modern selection) and ‘Ukrainka’ (old landrace). Firstly, proteins were isolated with a SDS-containing buffer that allowed extraction of various groups of storage proteins (glutenins, gliadins, globulins and albumins). Secondly, the proteome was profiled by the two-dimensional gel electrophoresis, revealing 810 clearly-separated gel spots. Software-assisted analysis of gel images, showed 66 differentially abundant proteins. Using multi-enzymatic digestion, followed by the tandem mass spectrometry, we identified 49 differentially accumulated proteins. Parallel ultrahigh-performance liquid chromatography profiling and direct mass spectrometry quantification complemented the results. With this approach we quantified 127 proteins, 12 being differentially abundant. Principal component analysis confirmed genotype as a major source of variation in both cases. Non-gluten fraction was the most diverse among investigated bread wheat cultivars. Information from public databases of clinically relevant plant proteins highlighted variable groups of wheat allergens/toxins. Data suggested that one of the modern cultivars contained less health affecting proteins in grain. Finally, we proposed set of genetic landmarks for the development of DNA marker system, which will enable fast and efficient assessment of medical safety of multiple wheat genotypes to facilitate breeding programs.
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Project description:The goals of this study are to compare transcriptome profiling (RNA-seq) between two wheat cultivars with different antioxidant actvity and to clarify the differences of these two wheat cultivars.
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Project description:Introgression of a high molecular weight glutenin subunit (HMW-GS) gene, 1Ay21*, into commercial wheat cultivars increased overall grain protein content and bread-making quality by unknown mechanisms. As well as increased abundance of 1Ay HMW-GS, 115 differentially expressed proteins (DEPs) were discovered between three cultivars and corresponding introgressed near-isogenic lines (NILs). Functional category analysis showed that the DEPs were predominantly other storage proteins, and proteins involved in protein synthesis, protein folding, protein degradation, stress response and grain development. Nearly half the genes encoding the DEPs showed strong co-expression patterns during grain development. Promoters of these genes are enriched in elements associated with transcription initiation and light response, indicating a potential connection between these cis-elements and grain protein accumulation. A model of how this HMW-GS enhances the abundance of machinery for protein synthesis and maturation during grain filling is proposed. This analysis not only provides insights into how introgression of the 1Ay21* improves grain protein content, but also directs selection of protein candidates for future wheat quality breeding programmes.
2021-05-30 | PXD021706 | Pride
Project description:Intervention type:DRUG. Intervention1:Huaier, Dose form:GRANULES, Route of administration:ORAL, intended dose regimen:20 to 60/day by either bulk or split for 3 months to extended term if necessary. Control intervention1:None.
Primary outcome(s): For mRNA libraries, focus on mRNA studies. Data analysis includes sequencing data processing and basic sequencing data quality control, prediction of new transcripts, differential expression analysis of genes. Gene Ontology (GO) and the KEGG pathway database are used for annotation and enrichment analysis of up-regulated genes and down-regulated genes.
For small RNA libraries, data analysis includes sequencing data process and sequencing data process QC, small RNA distribution across the genome, rRNA, tRNA, alignment with snRNA and snoRNA, construction of known miRNA expression pattern, prediction New miRNA and Study of their secondary structure Based on the expression pattern of miRNA, we perform not only GO / KEGG annotation and enrichment, but also different expression analysis.. Timepoint:RNA sequencing of 240 blood samples of 80 cases and its analysis, scheduled from June 30, 2022..
| 2612481 | ecrin-mdr-crc
Project description:The small RNA transcriptomes of bread wheat (Triticum aestivum L.) and its emerging model (Brachypodium distachyon (L.) Beauv) were obtained by using deep sequencing technology. Small RNA compositions were analyzed in these two species. In addition to 70 conserved microRNAs (miRNA) from 25 families, 23 novel wheat miRNAs were identified. For Brachypodium, 12 putative miRNAs were predicted from a limited number of ESTs, of which one was a potential novel miRNA. Also, 94 conserved miRNAs from 28 families were identified in this species. Expression validation was performed for several novel wheat miRNAs. RNA ligase-mediated 5' RACE experiments demonstrated their capability to cleave predicted target genes including three disease resistant gene analogs. Differential expression of miRNAs was observed between Brachypodium vegetative and reproductive tissues, suggesting their different roles at the two growth stages. Our work significantly increases the novel miRNA numbers in wheat and provides the first set of small RNAs in Brachypodium distachyon. Keywords: Small RNA
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