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. 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.
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.
Project description:We conducted transcriptional profiling of laser-captured stamen abscission zone cells over five developmental stages from prepollination to organ shed.
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.
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
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
Project description:In the current study we did microarray of upland rice cultivar Nagina22 for drought stress at reproductive stage (panicle initiation) and analyzed drought stress responsive genes. We have taken flag leaf for our study as it is most essential organ for photosynthesis in rice. Normal watering Vs Drought Stress Flag leaf of Control (Three biological replicates) plant of Nagina22: C1, C2, C3 Flag leaf of drought stressed (Three biological replicates) plant of Nagina 22: S1, S2, S3
Project description:Transcriptional programs are important for the development of complex eukaryotic organisms. Suites of genes expressed with temporal and spatial controls by regulatory networks in response to environmental cues are the cornerstone for achieving the specification of morphology and physiology of the tissue or organ systems. Thus, an important issue of developmental biology is to define the subsets of expressed genes and their expression patterns that are related to the organ or tissue system. Rice is a model plant for cereal genome research. Although large amounts of data of whole genome expression have been generated in recent years in rice, the majority of the studies were designed to identify differentially expressed genes between controls and treatments with certain experimental conditions such as biotic, abiotic or light, or to investigate the comparative expression patterns between wild type and mutants of certain genes. Only in a few cases were the datasets designed for studying the transcriptomes of a limited number of organs and cell types. Thus, there is still insufficiency in the available datasets that would allow for the establishment of expression patterns for suits of genes during the developmental processes of rice. In this study, we collected 39 tissues/organs covering the life cycle of the rice from two indica varieties Minghui 63 and Zhenshan 97, and the Affymetrix GeneChip Rice Genome Array was used to investigate the transcriptomes of these organs. The objective was to develop a genomic resource of genome-wide dynamic transcriptome of the rice plant, which could be used as the reference gene expression map for rice and other cereals. Also, the dataset is used to identify the candidates of genes with potential functions in regulating the development of rice or breeding practice. Keywords: rice, expression profiling, life cycle, development, inflorescence To dissect the developmental transcriptomes of rice, a total of 39 tissues covering the entire tissue culture process and life cycle were sampled from two indica varieties Minghui 63 and Zhenshan 97. And the Affymetrix Genechip rice Genome Array was used to investigate their dynamic transcriptomes. Two independent biological replicates were sampled from most tissues, except two seedling and three panicle tissues, for which three independent biological replicates each with two technical replicates were sampled, resulting in a dataset of 190 microarrays.
Project description:The receptor-like kinases (RLKs) plays critical roles in signal transduction through sensing the extracellular signals and activating the downstream signal transduction by phosphorylating their targets. Up to now, there are only a few RLKs have been functionally identified. In this study, we systemically analyzed the expression pattern of rice genes, especially the RLK coding genes during embryo and endosperm development. Rice Ovary and three development stages of embryo and endosperm (embryo 3, 9, 12 DAF; Endosperm 3, 9, 16 DAF) were analyzed, all of them were biologically repeated two times.
Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. Keywords: developmental stage comparison, tissue comparison, platform comparison Anther development of rice from hypodermal archesporial cells formation to tri-cellular mature pollens were divided into eight stages. Three or four biological replicates at each stage were analyzed with Affymetrix Rice Genome Array, and total number of samples in this series is 26.
Project description:Gene expression throughout the reproductive process in rice (Oryza sativa) beginning with primordia development through pollination/fertilization to zygote formation was analyzed. We analyzed 25 stages/organs of rice reproductive development including early microsporogenesis stages with 57,381 probe sets, and identified around 26,000 expressed probe sets in each stage. Fine dissection of 25 reproductive stages/organs combined with detailed microarray profiling revealed dramatic, coordinated and finely tuned changes in gene expression. Decrease of expressed genes in the pollen maturation process was observed in a similar way with Arabidopsis and maize. An almost equal number of ab initio predicted genes and cloned genes appeared or disappeared coordinated with developmental stage progression. A large number of organ-/stage-specific genes were identified; notably 2,593 probe sets for developing anther, including 932 probe sets corresponding to ab initio predicted genes. Analysis of cell cycle-related genes revealed that several CDKs, cyclins and components of SCF E3 ubiquitin ligase complexes were expressed specifically in reproductive organs. Cell wall biosynthesis or degradation protein genes and transcription factor genes expressed specifically in reproductive stages were also newly identified. Rice genes homologous to reproduction-related genes in other plants showed expression profiles both consistent and inconsistent with their predicted functions. The rice reproductive expression atlas is likely to be the deepest and most comprehensive dataset available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed. Keywords: developmental stage comparison, tissue comparison, platform comparison Anther development of rice from hypodermal archesporial cells formation to tri-cellular mature pollens were divided into eight stages. Two biological replicates at each stage were analyzed with Agilent Rice 60mer oligo DNA microarray 4x44K RAP-DB, and total number of samples in this series is 16. In this series, we analyzed the RNA samples used in GSE13988 for platform comparison.