Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1232436 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR32671914_1.fastq.gz | Fastqsanger.gz | |||
| SRR32671914_2.fastq.gz | Fastqsanger.gz | |||
| SRR32671915_1.fastq.gz | Fastqsanger.gz | |||
| SRR32671915_2.fastq.gz | Fastqsanger.gz |
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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:To provide a global study of transcriptome changes under drought stress, the gene expression levels of a durum wheat genotype (Triticum durum Desf. cultivar Creso) and two bread wheat genotypes (Triticum aestivum L. cultivar Chinese Spring -CS- and its deletion line CS_5AL-10) were investigated. The 5A chromosome deletion line (5AL-10) lacks the distal part (43%) of the long arm of chromosome 5A. Each genotype was subjected to two different levels of water stress at the grain filling stage. After anthesis, three different levels of soil water content (SWC) were induced as described below: control (CTRL; SWC=28%), moderate stress (MS; SWC=18%), and severe stress (SS; SWC=12.5%). For each sample, three biological replicates were performed, for a total of 27 hybridizations. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA23 at PLEXdb.]
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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:To provide a global study of transcriptome changes under drought stress, the gene expression levels of a durum wheat genotype (Triticum durum Desf. cultivar Creso) and two bread wheat genotypes (Triticum aestivum L. cultivar Chinese Spring -CS- and its deletion line CS_5AL-10) were investigated. The 5A chromosome deletion line (5AL-10) lacks the distal part (43%) of the long arm of chromosome 5A. Each genotype was subjected to two different levels of water stress at the grain filling stage. After anthesis, three different levels of soil water content (SWC) were induced as described below: control (CTRL; SWC=28%), moderate stress (MS; SWC=18%), and severe stress (SS; SWC=12.5%). For each sample, three biological replicates were performed, for a total of 27 hybridizations. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA23 at PLEXdb.] genotype: Creso - stress condition: Control(3-replications); genotype: Creso - stress condition: Mild stress(3-replications); genotype: Creso - stress condition: Severe stress(3-replications); genotype: CS - stress condition: Control(3-replications); genotype: CS - stress condition: Mild stress(3-replications); genotype: CS - stress condition: Severe stress(3-replications); genotype: CS-5AL - stress condition: Control(3-replications); genotype: CS-5AL - stress condition: Mild stress(3-replications); genotype: CS-5AL - stress condition: Severe stress(3-replications)
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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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