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PROVIDER: PRJNA1182498 | ENA |
REPOSITORIES: ENA
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Project description:Transcriptome analysis for the identification of spot blotch responsive genes and miRNAs in wheat [Triticum aestivum (fastq files) for Spot Blotch disease (SBR1: Susceptible and SBR2: Resistant)
| PRJNA1181582 | ENA
Project description:Hordeum vulgare ssp. spontaneum, accession Shechem 12-32, was submitted to 4 experimental treatments (C. sativus (spot blotch), P. hordei (leaf rust), and water and oil controls) to examine gene transcription differences triggered by biotrophic and hemi-biotrophic pathogens. Inoculated plants were arranged in a split plot design. Samples were collected at 12, 24, 36, & 48 hours after inoculation. A total of 48 samples (4 treatments x 4 time points x 3 replicates) were subjected to GeneChip analysis. Made public: 2009-12-02 ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ben Millett. The equivalent experiment is BB61 at PLEXdb.] treated or untreated: C. sativus (spot blotch) - time: 12 hrs(3-replications); treated or untreated: C. sativus (spot blotch) - time: 24 hrs(3-replications); treated or untreated: C. sativus (spot blotch) - time: 36 hrs(3-replications); treated or untreated: C. sativus (spot blotch) - time: 48 hrs(3-replications); treated or untreated: water control - time: 12 hrs(3-replications); treated or untreated: water control - time: 24 hrs(3-replications); treated or untreated: water control - time: 36 hrs(3-replications); treated or untreated: water control - time: 48 hrs(3-replications); treated or untreated: P. hordei (leaf rust) - time: 12 hrs(3-replications); treated or untreated: P. hordei (leaf rust) - time: 24 hrs(3-replications); treated or untreated: P. hordei (leaf rust) - time: 36 hrs(3-replications); treated or untreated: P. hordei (leaf rust) - time: 48 hrs(3-replications); treated or untreated: oil control - time: 12 hrs(3-replications); treated or untreated: oil control - time: 24 hrs(3-replications); treated or untreated: oil control - time: 36 hrs(3-replications); treated or untreated: oil control - time: 48 hrs(3-replications)
2011-11-22 | E-GEOD-33401 | biostudies-arrayexpress
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: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: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
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.
2020-08-20 | GSE152973 | GEO
Project description:Water-deficit stress negatively affects wheat yield and quality. Abiotic stress on the parental plants during reproduction could have transgenerational effects on the progenies. Here we investigated the transgenerational influence of pre-anthesis water-deficit stress by detailed analysis of the yield components, grain quality traits, and physiological traits in durum wheat. Next-generation sequencing analysis profiled the small RNA-omics, mRNA transcriptomics, and mRNA degradomics in the progenies. Parental water-deficit stress had positive impacts on the progenies in certain traits like harvest index and protein content in given genotype. Small RNA-seq identified 1739 conserved and 774 novel microRNAs (miRNAs). Transcriptome-seq characterised the expression of 66,559 genes while degradome-seq profiled the miRNA-guided mRNA cleavage dynamics. Differentially expressed miRNAs and genes were identified, with significant regulatory patterns subject to trans- and inter- generational stress. Integrated analysis based on the three omics revealed the significant biological interactions between stress-responsive miRNA and targets, with possible contributions towards transgenerational stress tolerance via pathways such as hormone signalling and nutrient metabolism. Our study provides the first confirmation of the transgenerational effects of water-deficit stress in durum wheat. New insights gained on the molecular level indicate that key miRNA-mRNA modules are potential candidates in transgenerational stress improvement.
2021-02-03 | GSE162008 | GEO