E-GEOD-89233
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-89233 | ExpressionAtlas | 2023-06-15
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-89233-analysis-methods.tsv | Tabular | |||
| E-GEOD-89233-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-89233-coexpressions.tsv.gz | Tabular | |||
| E-GEOD-89233-configuration.xml | Xml | |||
| E-GEOD-89233-factors.xml | Xml |
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Project description:Flag (FL) and second leaves (SL) in rice show differential aging patterns during monocarpic senescence. Coordination of aging programs in the top leaves is important for effective grain-filling. However, molecular bases for differential aging programs in the top leaves have not been systematically explored in rice. Here, we performed mRNA-sequencing of FL and SL at six time points during the grain-filling period. mRNA expression data revealed 6,365 genes showing aging-dependent expression changes in FL and/or SL. Of them, while 3047 genes showed shared aging-dependent expression patterns between FL and SL, 3058 genes showed differential expression patterns, which were classified into 5 major groups (G1-5) based on their differential expression patterns. Of the groups, G3 representing amino acid (AA) transport showed consistent differential age-dependent expression patterns in independent samples, whereas the other groups showed inconsistent differential expression patterns. Moreover, of AA transporters (AATs) in G3, long-distance AATs showed invariant differential age-dependent expression patterns after panicle removal, consistent to panicle removal-invariant differential nitrogen contents between FL and SL, known to be associated with protein concentration in grains. Our results suggest that long-distance AA transport is an invariant core transcriptional program of differential aging in rice top leaves for nitrogen remobilization during grain-filling.
2017-09-22 | GSE89233 | GEO
Project description:Fundamental molecular bases for differential transcriptional programs of top leaves during grain-filling in rice
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Project description:Enhancing grain production of rice (Oryza sativa L.) is a top priority in ensuring food security for human being. One approach to increase yield is to delay leaf senescence and to extend the available time for photosynthesis. microRNAs (miRNAs) are key regulators for aging and cellular senescence in eukayotes. However, miRNAs and their roles in rice leaf senescence remain unexplored. Here, we report identification of miRNAs and their putative target genes by deep sequencing of six small RNA libraries, six RNA-seq libraries and two degradome libraries from the leaves of two super hybrid rice, Nei-2-You 6 (N2Y6, age-resistant rice) and Liang-You-Pei 9 (LYP9, age-sensitive rice). Totally 372 known miRNAs and 162 miRNA candidates were identified, and 1145 targets were identified. Compared with the expression of miRNAs in the leaves of LYP9, the numbers of miRNAs up-regulated and down-regulated in the leaves of N2Y6 were 47 and 30 at early stage of grain-filling, 21 and 17 at the middle stage, and 11 and 37 at the late stage, respectively. Six miRNA families, osa-miR159, osa-miR160 osa-miR164, osa-miR167, osa-miR172 and osa-miR1848, targeting the genes encoding APETALA2 (AP2), zinc finger proteins, salicylic acid-induced protein 19 (SIP19), Auxin response factors (ARF) and NAC transcription factors, respectively, were found to be involved in leaf senescence through phytohormone signaling pathways. These results provided valuable information for understanding the miRNA-mediated leaf senescence of rice, and offered an important foundation for rice breeding. [miRNA] sample 1:The flag leaves at early stage of grain-filling of N2Y6 rice; sample 2: The flag leaves at middle stage of grain-filling of N2Y6 rice;sample 3:The flag leaves at late stage of grain-filling of N2Y6 rice; sample 4:The flag leaves at early stage of grain-filling of LYP9 rice; sample 5: The flag leaves at middle stage of grain-filling of LYP9 rice;sample 6:The flag leaves at late stage of grain-filling of LYP9 rice. [DGE]: samples 7-12 [degradome (targets)]: samples 13:The flag leaves at mixed stages of grain-filling of N2Y6 rice; sample 14:The flag leaves at mixed stages of grain-filling of LYP9 rice
2015-01-01 | E-GEOD-62200 | biostudies-arrayexpress
Project description:A heat and drought tolerant rice cultivar (N22) was grown in the field under control and drought conditions during the dry season in 2013. Drought was applied during early grain filling and resulted in simultaneous heat stress, leading to reduced grain yield and quality. Total RNA was extracted from developing seeds under stress and control (fully flooded) conditions and RNA-seq analysis was performed. These samples are a part of a bigger experiment analysing the responses of three contrasting rice cultivars (N22, Dular, Anjali) to combined heat and drought stress including different organs (developing seeds, flag leaves, flowering spikelets) and developmental stages (early grain filling, flowering) at the transcriptomic level.
2020-11-04 | GSE153030 | GEO
Project description:Popular rice mega varieties lack sufficient key micronutrients (e.g., Fe, Zn), vitamins and a balanced amino acid composition that are essential for a healthy diet. The major bottleneck for improving the nutritional quality of popular rice varieties through conventional breeding or gene technology is our lack of an integrated understanding of the biochemical and molecular processes that occur during rice grain filling (and their determining genes or loci). In this project, we will perform molecular expression profiling on specific tissue layers of the rice grain. To perform this experiment, the material will be developing rice seeds from plants grown hydroponically under controlled greenhouse conditions. Then, the laser microdissection approach will be applied to dissect different parts of the grain (i.e, vascular trace, aleurone, nucellar epidermis, etc). Total RNA will be extracted from these dissected parts and RNA sequencing will be performed. In this project, we will learn how the synthesis and deposition of grain nutrients is regulated, particularly, during grain filling.
2020-09-16 | GSE153954 | GEO
Project description:Modern rice cultivars have large panicle, however, yield potential of these cultivars is often not fully achieved due to the poor grain-filling of their late-flowering inferior spikelets (IS). Our earlier work suggests broad transcriptional reprogramming during grain filling and shows a difference in gene expression between IS and the earlier-flowering superior spikelets (SS). However, the links between the abundance of transcripts and their corresponding proteins are unclear. In this study, a SWATH-MS (sequential window acquisition of all theoretical spectra-mass spectrometry) -based quantitative proteomic analysis has been applied between SS and IS. A total of 304 proteins, ranging from cellular components to biological processes, were observed to be differentially expressed between IS and SS. Detailed gene ontology analysis indicated that several biological processes including photosynthesis, protein metabolism, and energy metabolism are differentially regulated. Further correlation analysis revealed that abundance of most of the differentially expressed proteins is not correlated to the transcript levels, indicating an extra layer of gene regulation which may exist during rice grain filling. These findings raise an intriguing possibility that these candidate proteins may be crucial in determining the poor grain-filling of IS. Therefore, we hypothesize that the regulation of proteome changes not only occurs at the transcriptional, but also at the post-transcriptional level, during grain filling in rice.
2017-07-03 | PXD005401 | Pride
Project description:Rice leaves consist of three distinct regions along a proximal-distal axis, namely, the leaf blade, sheath, and blade-sheath boundary region. Each region has a unique morphology and function, however,but the genetic programs underlying the development of each region are poorly understood. To capture the entire picture of rice leaf development and to discover genes with unique functions in rice and grasses, it is crucial to explore genome-wide transcriptional profiles during the development of the three regions. In this study, we performed microarray analysis to profile the spatial and temporal patterns of gene expression in the rice leaf using dissected parts of leaves sampled in broad developmental stages.
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Project description:Phosphorus remobilisation from rice flag leaves during grain filling.
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Project description:Plant diurnal oscillation is a 24-hour period based variation. The correlation between diurnal genes and biological pathways was widely revealed by microarray analysis in different species. Rice (Oryza sativa) is the major food staple for about half of the world's population. The rice flag leaf is essential in providing photosynthates to the grain filling. However, there is still no comprehensive view about the diurnal transcriptome for rice leaves. In this study, we applied rice microarray to monitor the rhythmically expressed genes in rice seedling and flag leaves. We developed a new computational analysis approach and identified 6,266 (10.96%) diurnal probe sets in seedling leaves, 13,773 (24.08%) diurnal probe sets in flag leaves. About 65% of overall transcription factors were identified as flag leaf preferred. In seedling leaves, the peak of phase distribution was from 2:00am to 4:00am, whereas in flag leaves, the peak was from 8:00pm to 2:00am. The diurnal phase distribution analysis of gene ontology (GO) and cis-element enrichment indicated that, some important processes were waken by the light, such as photosynthesis and abiotic stimulus, while some genes related to the nuclear and ribosome involved processes were active mostly during the switch time of light to dark. The starch and sucrose metabolism pathway genes also showed diurnal phase. We conducted comparison analysis between Arabidopsis and rice leaf transcriptome throughout the diurnal cycle. In summary, our analysis approach is feasible for relatively unbiased identification of diurnal transcripts, efficiently detecting some special periodic patterns with non-sinusoidal periodic patterns. Compared to the rice flag leaves, the gene transcription levels of seedling leaves were relatively limited to the diurnal rhythm. Our comprehensive microarray analysis of seedling and flag leaves of rice provided an overview of the rice diurnal transcriptome and indicated some diurnal regulated biological processes and key functional pathways in rice. we generate rice diurnal gene expression profiles of seedling leaves and flag leaves using 57K Affymetrix rice whole genome array. keywords: rice (Oryza sativa L.), seedling leaves, flag leaves, diurnal, molecular functions, microarray
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Project description:A near-isogenic rice line CSSL50-1 with high chalkiness and Asominori (the parental line) with normal grain endosperm were used for comparative studies of rice grain endosperm chalkiness,transcriptome comparison of 15 DAF caryopses using Affymetrix rice GeneChip identified differential expressed genes between these two lines.
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