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Transcript profiling of transgenic rice lines where the OsMADS26 gene is over-expressed or down growing cultivated in standard or osmotic stress condition

ABSTRACT: Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g; flowering and floral organ identity), in stress-related developmental processes such as abscission, fruit ripening and senescence and the role of some of them in stress response regulation was reported. The aim of this study was to decipher the genes that are under the control of the OsMADS26 transcription factor in rice in standard or osmotic stress condition. Transcriptome analysis in over-expressor and down-regulated OsMADS26 rice transgenic lines revealed that several major regulators of biotic and abiotic stress responses are mis-regulated compared to control plants, suggesting that OsMADS26 acts as an upstream negative regulator of stress-associated genes.

ORGANISM(S): Oryza sativa

PROVIDER: GSE52640 | GEO | 2015/11/20

SECONDARY ACCESSION(S): PRJNA229564

REPOSITORIES: GEO

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Transcript profiling of transgenic rice lines where the OsMADS26 gene is over-expressed or down growing cultivated in standard or osmotic stress condition

Project description:Functional analyses of MADS-box transcription factors in plants have unraveled their role in major developmental programs (e.g; flowering and floral organ identity), in stress-related developmental processes such as abscission, fruit ripening and senescence and the role of some of them in stress response regulation was reported. The aim of this study was to decipher the genes that are under the control of the OsMADS26 transcription factor in rice in standard or osmotic stress condition. Transcriptome analysis in over-expressor and down-regulated OsMADS26 rice transgenic lines revealed that several major regulators of biotic and abiotic stress responses are mis-regulated compared to control plants, suggesting that OsMADS26 acts as an upstream negative regulator of stress-associated genes. Transgenic plants over-expressing or down-regulated (by RNA interference) for OsMADS26 were obtained and used to study the impact of this transcription factor on gene regulation in plants cultivated in standard or osmotic stress (100 mM manitol) condition.

2015-11-20 | E-GEOD-52640 | biostudies-arrayexpress

Gene expression analysis in wild-type and OsHOX24 rice overexpression line under control and drought stress conditions

Project description:Several homeobox genes belonging to HD-ZIP I subfamily are highly induced by drought stress at various developmental stages in rice. To analyze the role of a candidate HD-ZIP I subfamily member, OsHOX24, we constitutively overexpressed it in rice. The physiological analyses revealed that overexpression of OsHOX24 gene reduced drought stress tolerance in transgenic plants as compared to wild-type. We used microarrays to study the global effect of OsHOX24 overexpression in rice as compared to wild-type under control and drought stress condition.

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Abscission layer (AL) at the base of flower in rice using laser micro-dissection: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL

Project description:Tissue-specific transcriptional profiling of the abscission layer (AL) at the base of young flower in rice using laser micro-dissection: NIL(qSH1) vs. Nipponbare. We used two rice varieties, NIL(qSH1) and Nipponbare. NIL(qSH1) is a nearly isogenic line containing the seed shattering gene qSH1. Seed shattering is easy in NIL(qSH1), but it is not in Nipponbare. So, we used some stages of young flower in NIL(qSH1) and some in Nipponbare. Four regions: 1. abscission layer region of NIL(qSH1), 2. upper abscission region of NIL(qSH1), 3. lower abscission layer region of NIL(qSH1), and 4. abscission layer region of Nipponbare. Sample experiments: NIL(qSH1) AL vs. Nipponbare AL, NIL(qSH1) AL vs. NIL(qSH1) upper region of AL, and NIL(qSH1) AL vs. NIL(qSH1) lower region of AL.

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Oil Palm Fruit Abscission Zone Transcriptome

Project description:To determine the mechanisms of fleshy fruit abscission of the monocot oil palm (Elaeis guineensis Jacq.) compared with other abscission systems, we performed multi-scale comparative transcriptome analyses on fruit targeting the developing primary AZ and adjacent tissues. Combining between-tissue developmental comparisons with exogenous ethylene treatments, and naturally occurring abscission in the field, RNAseq analysis revealed a robust core set of 168 genes with differentially regulated expression, spatially associated with the ripe fruit AZ, and temporally restricted to the abscission timing. The expression of a set of candidate genes was validated by qRT-PCR in the fruit AZ of a natural oil palm variant with blocked fruit abscission, which provides evidence for their functions during abscission. Our results substantiate the conservation of gene function between dicot dry fruit dehiscence and monocot fleshy fruit abscission. The study also revealed major metabolic transitions occur in the AZ during abscission, including key senescence marker genes and transcriptional regulators, in addition to genes involved in nutrient recycling and reallocation, alternative routes for energy supply and adaptation to oxidative stress. The study provides the first reference transcriptome of a monocot fleshy fruit abscission zone and provides insight into the mechanisms underlying abscission by identifying key genes with functional roles and processes, including metabolic transitions, cell wall modifications, signalling, stress adaptations and transcriptional regulation, that occur during ripe fruit abscission of the monocot oil palm. The transcriptome data comprises an original reference and resource useful towards understanding the evolutionary basis of this fundamental plant process.

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Expression data from rice inflorescences of osmads32 mutant and wild type

Project description:MADS family genes in rice control flowering and inflorescence development. In the early flower stages of plant, MADS-box transcripion factors could form protein-protein interaction complexes with other floral homeotic genes and regulate the expression of downstram genes. OsMADS32 in rice is an important transcription factor in controlling flower development We used microarrays to detail the expression of downstream genes under the control of OsMADS32 during the early inflorescence stages in rice

2018-06-28 | GSE116322 | GEO

Project description:Tissue-specific transcriptional profiling of the abscission layer (AL) at the base of young flower in rice using laser micro-dissection: NIL(qSH1) vs. Nipponbare.

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smRNA under high osmotic stress

Project description:To identifiy osmotic stress responsive smRNAs, we used a deep-sequencing technique to profile small RNA populations in leaf and root tissues of plants under high osmotic stress and control conditions. We treated 30day-old plants with high osmotic stress and sampled leaves and roots from the same plant with 3 biologial replicates. Then, 3 replicates were pooled and total RNA was extracted and prepared for smRNA deep sequencing. After normalization and annotation, we selected potential osmotic stress responsive smRNAs.

2012-09-19 | E-GEOD-36560 | biostudies-arrayexpress

Expression profiling of tomato pre-abscission pedicels

Project description:Organ abscission is a general activity found in plants and its regulation is an important agronomical concern because the trait directly affects the harvesting efficiency of fruits or grains and the yields. Generally, abscission takes place at a specialized cell layer, which is called abscission zones (AZs). So far, investigations on organ abscission have been focused mainly on the cell activities during organ detachment. By contrast, little attention has been paid to the properties of AZ cells at the pre-abscission stage. The pre-abscission cells are at a turning point for initiating abscission; until an abscission initiating signal is provided, the AZ cells keep their physiological state, while once the signal occurs, the cells immediately change their state into the onset of abscission. In this study, to screen the genes involved in the regulation of abscission at the pre-abscission state, we investigated the gene expression profiles of tomato flower pedicels at anthesis. The screening revealed many genes that characterize cell identities in each pedicel region.

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