Unknown,Transcriptomics,Genomics,Proteomics

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Transcriptomes of developing rice ovules

ABSTRACT: We aimed to reveal transitions of gene expression profile in developing female gametophytes of rice in this study. The developmental process of rice female gametophyte, from megaspore mother cell at pre-meiotic stage to mature embryo sac, was separated into six stages. Developing ovules at each stage were separated from surrounding sporophyte tissues and collected using LMD. RNA samples extracted from them were subjected to microarray analysis. Dynamic gene expression profiles during female gametogenesis were revealed. Comparison of transcriptome in developing female gametophytes with those of male gametophyes revealed both conserved and diverged features between male and female gametogenesis. A lot of characteristic genes, such as a subset of transposable elements, auxin responsive genes and transcription factor genes, which showed dynamic expression profiles during female gametogenesis, were identified in this study. We believe that our transcriptome data will serve as a backbone of further focused biological analysis to understand the molecular basis in female gametogenesis of plant. Gene expression profiles of developing ovules were analyzed according to stage progression. Three or four biological replicates were prepared for each stage, and a total of nineteen samples were analyzed.

ORGANISM(S): Oryza sativa

SUBMITTER: Nori Kurata

PROVIDER: E-GEOD-35760 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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. This SuperSeries is composed of the following subset Series: GSE13988: Rice expression atlas (1): Anther development GSE14298: Rice expression atlas (2): Pollination - Fertilization GSE14299: Rice expression atlas (3): Early embryogenesis GSE14300: Rice expression atlas (4): Vegetative tissues GSE14301: Rice expression atlas (5): Anther development (Agilent data) Refer to individual Series

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.

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Transcriptomes of developing rice ovules

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