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A Gene Expression Profiling of Early Rice Stamen Development that Reveals Inhibition of Photosynthetic Genes by OsMADS58

ABSTRACT: Plant organ formation, or organogenesis is the process in which the primordium derived from shoot apical meristem develops into an organ with a given shape and proper function, through a series of cell division and differentiation. To decipher the genetic program underling plant organ formation, we targeted early rice stamen development that covers most important events in male organ formation and germ cell initiation in plants.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE53347 | GEO | 2013/12/17

SECONDARY ACCESSION(S): PRJNA231768

REPOSITORIES: GEO

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Gene expression profiling for early rice stamen

Project description:Plant organ formation, or organogenesis is the process in which the primordium derived from shoot apical meristem develops into an organ with a given shape and proper function, through a series of cell division and differentiation. To decipher the genetic program underling plant organ formation, we targeted early rice stamen development that covers most important events in male organ formation and germ cell initiation in plants. Totally, seven samples were used in this experiment. Stamens of stages 2-6 was collected through microdissection under microscope. And to ensure the stamen primordia collected are at corresponding stages, rice panicles were cut in half longitudinally, one half for paraffin sectioning to confirm developmental stages and the other half for preparing GEP samples. Samples of primordial and just-expanded third leaves were used as controls because leaf and stamen are homolog organs. RNA was extracted and amplified with Two-Cycle Eukaryotic Target Labeling Assay kit, and then hybridized to microarrays. Three biological replicates were applied for each sample.

2013-12-17 | E-GEOD-53347 | biostudies-arrayexpress

Global expression profiling applied to the analysis of Arabidopsis stamen development

Project description:To obtain detailed information about gene expression during stamen development in Arabidopsis thaliana, we compared, by microarray analysis, the gene expression profile of wild-type inflorescences to those of the floral mutants apetala3, sporocyteless/nozzle, and male sterile 1, in which different aspects of stamen formation are disrupted. These experiments led to the identification of groups of genes with predicted expression at early, intermediate and late stages of stamen development. Additional experiments aimed at characterizing gene expression specifically during microspore formation. To this end, we compared the gene expression profiles of wild-type flowers of distinct developmental stages to those of the male sterile 1 mutant. Computational analysis of the datasets derived from this experiment led to the identification of genes that are likely involved in the control of key developmental processes during microsporogenesis. Keywords: mutant comparison, developmental series

2007-08-31 | GSE8864 | GEO

Transcription profiling of stamen abscission zone cells from Arabidopsis over five developmental stages from prepollination to organ shed

Project description:We conducted transcriptional profiling of laser-captured stamen abscission zone cells over five developmental stages from prepollination to organ shed.

2008-06-15 | E-MEXP-1474 | biostudies-arrayexpress

The founder-cell transcriptome in the Arabidopsis apetala1 cauliflower inflorescence meristem

Project description:Although the pattern of lateral organ formation from apical meristems establishes species-specific plant architecture, the positional information that confers cell fate to cells as they transit to the meristem flanks where they differentiate, remains largely unknown. We have combined fluorescence-activated cell sorting and RNA-seq to characterise the cell-type-specific transcriptome at the earliest developmental time-point of lateral organ formation using DORNRÖSCHEN-LIKE::GFP to mark founder-cell populations at the periphery of the inflorescence meristem (IM) in apetala1 cauliflower double mutants, which overproliferate IMs. Within these founder-cells, floral primordium identity genes are upregulated and stem-cell identity markers are downregulated. The transcriptional network of differentially expressed genes supports the hypothesis that lateral organ founder-cell specification involves the creation of polarity from the centre to the periphery of the IM and the establishment of a boundary from surrounding cells, consistent with bract initiation. In contrast to the established paradigm that sites of auxin response maxima pre-pattern lateral organ initiation in the IM, only subtle transcriptional reprogramming within the global auxin network was observed, suggesting that auxin response might play a minor role in the earliest stages of lateral floral initiation.

2016-11-03 | GSE81401 | GEO

Comparative Transcriptomes Profiling of Photoperiod-sensitive Male Sterile Rice Nongken 58S between Short Day and Long Day Condition

Project description:Nongken 58S is photoperiod-sensitive genic male sterile (PGMS) rice. Its pollens are fully sterile when it is treated with LD condition from glume primordium differentiation stage to pistil/stamen primordium forming stage, and its pollens are fertile when treated with SD condition during these stages. We used microarrays to detail the global programme of leaf gene expression under LD and SD condition for investigating the transcriptomes in the male sterility transition in PGMS rice to find out the genes related to this transition We compared the transcriptomes of Nongken 58S under shortday (SD) and longday (LD) at the glume primordium differentiation stage and pistil/stamen primordium forming stage, respectively. 12 samples were analyzed, and each treatment had biological triplicates. Supplementary files: SD vs LD during the glume primordium differentiation stage and the pistil/stamen primordium forming stage.

2012-07-29 | E-GEOD-29820 | biostudies-arrayexpress

Time-series RNAseq analysis following lateral root induction by gravistimulation

Project description:We report the comparison of transcriptomic profiles in specific lateral root tissues for Col-0 wild type and puchi-1 mutant seedlings. Lateral root organogenesis is a key process in plant root system development and adaptation to the environment. To dissect the molecular events occurring during the early phase, we generated time-series transcriptomic datasets profiling lateral root development in puchi-1 and wild type backgrounds. Consistent with a mutually inhibitory mechanism, transcriptomic and reporter analysis revealed meristem-related genes were ectopically expressed during early stages of lateral root primordium formation in puchi-1. We conclude that PUCHI participates to the coordination of lateral root patterning and represses ectopic establishment of meristematic cell identities during early stages of organ development.

2022-03-25 | GSE199142 | GEO

Barley stamen maturation

Project description:Barley stamen transcriptomes at maturation stages W9.25 and W9.35

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Transcriptome Profile Analysis Reveals the Regulation Mechanism of Stamen Abortion in Handeliodendron bodinieri（Levl.）Rehd

Project description:To elucidate the molecular mechanism of stamen abortion underlying sex differentiation from transcriptomic aspects in Handeliodendron bodinieri, we use abnormal stamens before and after abortion in female flowers and normal stamen in male flowers at the same stage as control material. Key genes regulating stamen abortion was identified by using RNA-seq technique. The results show that it was abortion science stage 6 during anther development, at the same time, HbGPAT, HbAMS, HbLAP5, HbLAP3 and HbTES were down-regulated , and HbML5 was up-regulated. Therefore, these information will provide theoretical foundation for the conservation, breeding, scientific research and application of Handeliodendron bodinieri.

2021-07-31 | GSE181240 | GEO

Transcriptional regulators of stamen development in Arabidopsis identified by transcriptional profiling

Project description:In Arabidopsis, jasmonate is required for stamen and pollen maturation. Mutants deficient in jasmonate synthesis, such as opr3, are male-sterile but become fertile when jasmonate is applied to developing flower buds. We have used ATH1 oligonucleotide arrays to follow gene expression in opr3 stamens for 22 hours following jasmonate treatment. In these experiments, a total of 821 genes were specifically induced by jasmonate and 480 repressed. Comparisons with data from previous studies indicate that these genes constitute a stamen-specific jasmonate transcriptome, with a large proportion (70%) of the genes expressed in the sporophytic tissue but not in the pollen. Bioinformatics tools allowed us to associate many of the induced genes with metabolic pathways that are likely up-regulated during jasmonate-induced maturation. Our pathway analysis led to the identification of specific genes within larger families of homologues that apparently encode stamen-specific isozymes. Extensive additional analysis of our dataset identified 13 transcription factors that may be key regulators of the stamen maturation processes triggered by jasmonate. Two of these transcription factors, MYB21 and MYB24, are the only members of subgroup 19 of the R2R3 family of MYB proteins. A myb21 mutant obtained by reverse genetics exhibited shorter anther filaments, delayed anther dehiscence and greatly reduced male fertility. A myb24 mutant was phenotypically wild type, but production of a myb21 myb24 double mutant indicated that introduction of the myb24 mutation exacerbated all three aspects of the myb21 phenotype. Exogenous jasmonate could not restore fertility to myb21 or myb21 myb24 mutant plants. Together with the data from transcriptional profiling, these results indicate that MYB21 and MYB24 are induced by jasmonate and mediate important aspects of the jasmonate response during stamen development. Keywords: Time course analysis

2006-04-27 | GSE4733 | GEO

Transcriptomic responses of Arabidopsis wild-type and amp1 seedlings after hyperphyllin treatment [AraGene-1_1-st array]

Project description:ALTERED MERISTEM PROGRAM1 (AMP1) is a member of the M28 family of carboxypeptidases with a pivotal role in plant development and stress adaptation. Its most prominent mutant defect is a unique hypertrophic shoot phenotype combining a strongly increased organ formation rate with enhanced meristem size and the formation of ectopic meristem poles. However, so far the role of AMP1 in shoot development could not be assigned to a specific molecular pathway nor is its biochemical function resolved. We used a chemical genetic approach to identify the drug hyperphyllin (HP), which specifically mimics the shoot defects of amp1, including plastochron reduction and enlargement and multiplication of the shoot meristem. To further assess whether hyperphyllin acts in an AMP1-dependent manner we compared the transcriptonal responses of hyperphyllin-treated wild-type and amp1 mutant seedlings.

2017-11-08 | GSE106659 | GEO

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