Ontology highlight
ABSTRACT:
PROVIDER: PRJNA543396 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9077110.fastq.gz | Fastqsanger.gz | |||
| SRR9077103.fastq.gz | Fastqsanger.gz | |||
| SRR9077104.fastq.gz | Fastqsanger.gz | |||
| SRR9077105.fastq.gz | Fastqsanger.gz | |||
| SRR9077106.fastq.gz | Fastqsanger.gz |
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Project description:Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. Yield loss in durum wheat can be exacerbated due to minimal rainfall in the early reproductive stages of development during Spring in Australia. This study describes genotypic differences in the miRNAome between water deficit tolerant/sensitive durum, using flag leaf and developing head tissue, and more specifically identifies miRNAs associated with water deficit stress. Results: Small RNA libraries (96 in total) were constructed from flag leaf and developing head tissues of four durum genotypes (Tamaroi, Yawa, EGA Bellaroi, Tjilkuri), with or without water deficit stress. Illumina sequencing and subsequent analysis detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins. Statistical analysis of the abundance of sequencing reads revealed 66 conserved miRNAs and five novel miRNA hairpins showing differential expression under water deficit stress. During stress, several conserved and novel miRNAs showed unambiguous inverted regulatory profiles between the durum genotypes studied. Several miRNAs were also identified to have different abundance in the flag leaf compared to the developing head regardless of treatment. Predicted mRNA targets from four novel durum miRNAs were characterised using Gene Ontology (GO) which revealed functions common to stress responses and plant development. Conclusion: For the first time, we present a comprehensive study of the miRNA transcriptome of flag leaf and developing head tissues in different durum genotypes under water deficit stress. The identification of differentially expressed miRNAs provides molecular evidence that miRNAs are potential determinants of water stress tolerance in durum wheat. GO analysis of predicted targets contributes to the understanding of genotype-specific physiological responses leading to stress tolerance capacity. Further functional analysis of specific stress responsive miRNAs identified, and their interaction with mRNA targets is ongoing and will assist in developing future durum wheat varieties with enhanced water deficit stress tolerance.
2015-10-01 | GSE69339 | GEO
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.
2021-10-26 | GSE186472 | GEO
Project description:Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.
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Project description:Water deficiency and heat stress can severely limit crop production and quality. Stress imposed on the parents during reproduction could have transgenerational effects on their progeny. Seeds with different origins can vary significantly in germination time-course and early growth. Here, we investigated how water-deficit and heat stress on parental durum wheat plants affected seedling establishment of the subsequent generation. One stress-tolerant and one stress-sensitive Australian durum genotype were used. Seeds were collected from parents with or without exposure to stress during reproduction. Generally stress on the previous generation negatively affected seed germination and seedling vigour, but to a lesser extent in the tolerant variety. Small RNA sequencing utilising the new durum genome assembly has revealed significant differences in microRNA (miRNA) expression in the two genotypes. A bioinformatics approach was used to identify multiple miRNA targets which have critical molecular functions in stress adaptation and plant development and could therefore contribute to the phenotypic differences observed. Our data provides the first confirmation of the transgenerational effects of reproductive-stage stress on germination and seedling establishment in durum wheat. New insights gained on the epigenetic level indicate that durum miRNAs could be key factors in optimising seed vigour for superior breeding germplasm and/or varieties.
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Project description:Chromium (Cr) is a highly toxic heavy metal for both mono and dicot plants, causing severe cellular damage and disturbances in plant growth, development, and reproduction. Its phytotoxicity results in serious changes in plant physiology, gene expression, and at a transgenerational level in genomic DNA methylation. Herein, transcriptional responses of durum wheat (Triticum turgidum L.) to continuous and basal Cr stress were explored in roots and leaves by RNAseq analysis. Plants cultivated in a hydroponic system supplemented with 2.5 and 10 µM Cr were compared with control plants through transcriptomic analysis after 50 days and for the biomass accumulation and seed yield after senescence.
2024-08-26 | E-MTAB-13952 | biostudies-arrayexpress
Project description:Durum wheat is an important cereal crop grown mainly in semi-arid environments (e.g. Mediterranean regions) characterized by water scarcity and high temperatures often occurring at the same time. This work reports on a transcriptomic analysis carried out on two durum wheat cultivars (Cappelli and Ofanto) characterized by different water use efficiency (WUE), grown to booting stage and subjected to a combination of drought and heat stresses, a situation similar to the experience of a crop grown in Mediterranean environments and exposed to a terminal heat/drought stress. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, alessio. The equivalent experiment is TA47 at PLEXdb.]
2016-03-22 | GSE45563 | GEO
Project description:Durum wheat (Triticum turgidum subsp. durum) is widely grown for pasta production, and more recently, is gaining additional interest due to its resilience to warm, dry climates and its use as an experimental model for wheat research. To enable further research into endosperm development and storage reserve synthesis, we generated a high-quality transcriptomics dataset from developing endosperms of durum variety Kronos, to complement the extensive mutant resources available for this variety. Endosperms were dissected from grains harvested at eight timepoints during grain development (6 to 30 days post anthesis (dpa)), then RNA sequencing was used to profile the transcriptome at each stage. The largest changes in gene expression profile were observed between the earlier timepoints, prior to 15 dpa. We detected a total of 29,925 genes that were significantly differentially expressed between at least two timepoints, and clustering analysis revealed nine distinct expression patterns. Overall, we provide a valuable resource for studying endosperm development in this increasingly important crop species.
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Project description:A three-stage continuous fermentative system was developed to simulate and control physicochemical factors of the gut biology. Inoculation was of each reactor was performed from a human fecal sample which was initially amplified with a batch procedure. Samples from the initial feces, the batch and from the bioreactors media were collected to extract bacterial DNA. 16S PCR amplification was performed to assess the microbial diversity at the family level using the HuGChip. Amplified DNA was purified and labelled with either Cy3 or Cy5 dye and hybridized on the microarray. A 5 chip study was realized, each corresponding to hybridization with 250ng of labelled 16S rRNA gene amplicons from either the initial stool, the batch inoculum or fermentative medium different compartments of the simulated colon (Proximal, Transversal and Distal). Each probe (4441) was synthetized in three replicates.
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Project description:Cereal cyst nematode (Heterodera avenae) can be attracted by wheat roots before infestation, while largely is unknown underlying this phenomenon. Here, we examined the transcriptional responses of both wheat roots and nematodes during the attraction stage by mRNA sequencing analysis (with and without reference genome, respectively). We found that consistent with their respective mobility, the immobile host wheat root only had 93 DEGs (27 up-regulated and 66 down-regulated), while the mobile plant parasitic nematode H. avenae reacted much more actively with 879 DEGs (867 up-regulated and 12 down-regulated). Among the DEGs, a number of wheat DEGs (most down-regulated) were involved in biotic stress pathways, while several putative effector genes (up-regulated) were found in the nematode DEGs. Results of the experiments demonstrated that nematode responds more actively than wheat during the attraction stage of parasitism, and the parasite responses mainly involved up-regulation whereas the host responses mainly involved down-regulation.
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Project description:LC-MS/MS-based LFQ proteomics of 150 wheat full-kernel flours from five different wheat species (common wheat, spelt, durum wheat, emmer, einkorn) grown at three different locations.
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