Transcriptome analysis of Barley flag leaf during senescence
Ontology highlight
ABSTRACT:
ORGANISM(S): Hordeum vulgare
PROVIDER: GSE179555 | GEO | 2021/07/07
REPOSITORIES: GEO
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Project description:The assays performed are aimed at reflecting the immense physiological changes taking place in a senescing barley flag leaf, compared to a non-senescing young flag.
2014-02-06 | E-MTAB-2133 | biostudies-arrayexpress
Project description:Senescence is the last developmental phase of plant tissues, plant organs and, in the case of monocarpic senescence, entire plants. In monocarpic crops such as barley, it leads to massive remobilization of nitrogen (primarily from degradation of photosynthetic proteins) and other nutrients to developing seeds. Senescence has therefore a major impact on both yield and seed/grain quality. To further investigate this process, a proteomic comparison of flag leaves of late-senescing barley variety ‘Karl’ and a near-isogenic early-senescing line, ‘10_11’, was performed at 14 and 21 days past anthesis, using both two-dimensional gel-based and label-free quantitative mass spectrometry-based (‘shotgun’) proteomic techniques. Overall, this approach identified >9,000 barley proteins, and one-third of them were quantified. Analysis focused on proteins that were significantly (P-value ≤0.05; difference ≥1.5-fold) upregulated in early-senescing line ‘10_11’ as compared to ‘Karl’, as these may be functionally important for the senescence process. Many proteins in this group, including several membrane and intracellular receptors, glucanases, enzymes with possible roles in cuticle modification, classical pathogenesis-related proteins, membrane transporters and proteins involved in DNA repair, have likely or putative functions in plant pathogen defense. Additionally, several proteases and elements of the ubiquitin-proteasome system were upregulated in line ‘10_11’; these proteins may be involved in nitrogen remobilization, and in the regulation of both senescence and plant defense reactions. Together, our data shed new light, at the protein level, on the importance of plant defense reactions during senescence, on senescence regulation, and possibly on crosstalk between senescence regulation and plant-pathogen interaction.
2022-02-28 | PXD002333 | Pride
Project description:Transcriptome analysis of Barley flag leaf during senescence
| PRJNA744188 | ENA
Project description:Senescence is the ultimate stage of plant development. Among the different levels of senescence processes, flag leaf senescence plays a crucial role in determining grain quality in rice. In the present study, efforts are made to identify the possible involvement of miRNAs in flag leaf senescence. Four small RNA libraries were generated from different stages of flag leaf senescence and sequenced by Illumina deep sequencing. A total of 29 known miRNA families and 494 novel miRNAs were identified in the senescing flag leaves. 21 known and 116 novel miRNAs exhibited differential expression pattern. Computational prediction and analysis of putative targets of detected miRNAs revealed that miRNAs regulate the flag leaf senescence mainly by regulating transcription factors and hormone metabolism genes. The present study gives a clue about the senescence-associated miRNAs which can be used as a tool for manipulating flag leaf senescence in rice and other crops.
2021-11-30 | GSE123171 | GEO
Project description:Senescence is the last developmental phase of plant tissues, plant organs and, in the case of monocarpic senescence, entire plants. In monocarpic crops such as barley, it leads to massive remobilization of nitrogen (primarily from degradation of photosynthetic proteins) and other nutrients to developing seeds. Senescence has therefore a major impact on both yield and seed/grain quality. To further investigate this process, a proteomic comparison of flag leaves of late-senescing barley variety ‘Karl’ and a near-isogenic early-senescing line, ‘10_11’, was performed at 14 and 21 days past anthesis, using both two-dimensional gel-based and label-free quantitative mass spectrometry-based (‘shotgun’) proteomic techniques. Overall, this approach identified >9,000 barley proteins, and one-third of them were quantified. Analysis focused on proteins that were significantly (P-value ≤0.05; difference ≥1.5-fold) upregulated in early-senescing line ‘10_11’ as compared to ‘Karl’, as these may be functionally important for the senescence process. Many proteins in this group, including several membrane and intracellular receptors, glucanases, enzymes with possible roles in cuticle modification, classical pathogenesis-related proteins, membrane transporters and proteins involved in DNA repair, have likely or putative functions in plant pathogen defense. Additionally, several proteases and elements of the ubiquitin-proteasome system were upregulated in line ‘10_11’; these proteins may be involved in nitrogen remobilization, and in the regulation of both senescence and plant defense reactions. Together, our data shed new light, at the protein level, on the importance of plant defense reactions during senescence, on senescence regulation, and possibly on crosstalk between senescence regulation and plant-pathogen interaction.
2017-02-08 | PXD002307 | Pride
Project description:Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments.
2014-10-22 | GSE62539 | GEO
Project description:1. Comparison of two near isogenic lines between which the genome differs only for the region of the leaf-yellowing QTL Y3-4 on chromosome III.<br> Experiment description: <br><br> The lines HIF404-Sha and HIF404-Bay were grown on 3 mM nitrate in growth chamber according to Loudet et al . (2002, TAG 104:1173-84) until phenotypic yellowing symptoms differed between them. Plants were collected 49 days after sowing.<br><br> 2. Comparison of sugar effect on the leaf senescence progress using three RIL from the Bay-0 x shahdara population that exhibited differential leaf yellowing symptoms.<br> Experiment description: The recombinant inbred lines RIL310 (hypersenescing and early-senescing), RIL232 (early--senescing) et RIL045 (late-senescing) were grown in petri dishes (4,7 mM Nitrogen, with (LNG) or without (LN) glucose 2% until some difference of Fv/Fm trait can be observed (Wingler et al. 2004, New Phytol, 161 : 781-789). Growth experiments were performed in A. Wingler lab, University College of London.
2006-04-01 | E-MEXP-387 | biostudies-arrayexpress
Project description:This study was aimed at deciphering the impact of drought and heat on genome-wide gene expression in flag leaf of barley. We employed high-throughput sequencing of mRNA to identify genes that are associated with response to drought or heat and to their combination. Our study demonstrated that under combined stress, drought was the dominant factor affecting genes expression. It was also confirmed for phenotypic traits and chlorophyll fluorescence parameters. Drought- and heat-responsive genes were associated majorly with photosynthesis, abscisic acid signaling and lipids transport. Dehydrin encoding genes were found to be universal stress-responsive genes. Stress-induced genes specific to the flag leaf size were also found. This research provided novel insight into molecular mechanisms of barley flag leaf that determine drought and heat response, also during their co-occurrence.
2022-12-28 | E-MTAB-12438 | biostudies-arrayexpress
Project description:Time-course transcriptional profiling of senescing barley leaves. In this model, the senescence process was induced by continued incubation of the seedlings in darkness. Plant samples for the expression analysis were collected before senescence induction (Day 0) and after 3,7 and 10 days of incubation in the dark. The goal was to find the genes differentially expressed during the senescence process . Additionally, a list of the genes with the invariant expression was generated as a resource for selecting references suitable for qPCR or ddPCR experiments. Time-course experiment, two-color, common reference design. All of the data were obtained from material collected in three independent, time-separated leaf senescing experiments (biological replicates). In each replicate, samples from senescing leaves (3 Days, 7 Days, 10 Days) were compared to samples collected before the senescence induction (Day 0). 3 biological replicates.Cy5-labeled samples of interest (Day 0, Day 3, Day 7 and Day 10 from each biological replicate) were each hybridized against a Cy3-labeled common reference (RNA pool of all samples) on a total of 12 microarrays.
2014-10-22 | E-GEOD-62539 | biostudies-arrayexpress
Project description:Two sets of wheat lines near-isogenic to Lr34 were used to compare gene expression profiles of wheat: 1. with and without Lr34 gene; 2. rust and mock inoculation; 3. distal and basal portion of the flag leaves. The two sets of wheat near-isogenic lines were used to subtract genetic background variations and to enrich Lr34-regulated gene expression profiles. The study is aimed to better understand the mechanisms of the well-known durable leaf rust resistance gene, Lr34, mediated resistance at the transcriptome level. Keywords: Distal and basal leaf halves of near-isogenic lines
2007-02-01 | GSE6227 | GEO