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| Status |
Public on Jun 10, 2011 |
| Title |
Analysis of anther transcriptomes to identify genes contributing to meiosis and male gametophyte development in rice |
| Platform organism |
Oryza sativa |
| Sample organism |
Oryza sativa Indica Group |
| Experiment type |
Expression profiling by array
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| Summary |
Background – In flowering plants, the anther is the site of male gametophyte development. Two major events in the development of the male germline are meiosis and the asymmetric division in the male gametophyte that gives rise to the vegetative and generative cells, and the following mitotic division in the generative cell that produces two sperm cells. Anther transcriptomes have been analyzed at progressive stages of development by using microarray and sequence by synthesis technologies to identify genes that regulate anther development. Here we have carried out a comprehensive analysis of rice anther transcriptomes at four distinct stages of development with a focus to identify regulatory components contributing to male meiosis and germline development. Further, these transcriptomes have been compared with transcriptomes of 10 stages of rice vegetative and seed development to identify genes that express specifically during anther development. Results - To understand the molecular processes that lead to male gametophyte development, transcriptome profiling of four stages of anther development in rice [pre-meiotic (PMA), meiotic (MA), anthers at single-celled (SCP) and tri-nucleate pollen (TPA)] was conducted. Around 22,000 genes were found to be expressed in at least one of the anther developmental stages, with the highest number in MA (18,090) and lowest (15,465) in TPA. Comparison of these transcriptome profiles to an in-house generated microarray-based transcriptomics database comprising of 10 stages/tissues of vegetative as well as reproductive development in rice resulted in the identification of 1,000 genes that are specifically expressed in anther stages. Of them the expression of 453 genes was found to be specific to TPA, whereas 78 and 184 genes were expressed specifically in MA and SCP. Gene ontology and pathway analysis of specifically expressed genes revealed that transcription factors and protein folding, sorting and degradation pathway genes dominated in MA, whereas in TPA, those coding for cell structure and signal transduction components were in abundance. Interestingly, about 50% of the genes with anther-specific expression have not been annotated so far. Conclusions - These data not only provide the transcriptome constituents of four landmark stages of anther development but also identify genes that express exclusively in these stages and therefore may contribute to specific aspects of anther and/or male gametophyte development in rice. Moreover, these gene sets assist in building a deeper understanding of underlying regulatory networks and in selecting candidates for gene function validation.
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| Overall design |
Overall twelve samples were analyzed representing four anther development stages, with three replicates of each stage.
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| Contributor(s) |
Deveshwar P, Bovill WD, Sharma R, Able JA, Kapoor S |
| Citation(s) |
21554676 |
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| Submission date |
Mar 07, 2011 |
| Last update date |
Dec 27, 2017 |
| Contact name |
Sanjay Kapoor |
| E-mail(s) |
kapoors@genomeindia.org
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| Phone |
91 11 65171135
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| URL |
http://www.dpmb.ac.in/
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| Organization name |
University of Delhi South Campus
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| Department |
Department of Plant Molecular Biology
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| Street address |
Benito Juarez Road
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| City |
New Delhi |
| State/province |
Delhi |
| ZIP/Postal code |
110021 |
| Country |
India |
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| Platforms (1) |
| GPL2025 |
[Rice] Affymetrix Rice Genome Array |
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| Samples (12)
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| GSM686458 |
Pre-meiotic anther, Biological replicate 1 |
| GSM686459 |
Pre-meiotic anther, Biological replicate 2 |
| GSM686460 |
Pre-meiotic anther, Biological replicate 3 |
| GSM686461 |
Meiotic anther, Biological replicate 1 |
| GSM686462 |
Meiotic anther, Biological replicate 2 |
| GSM686463 |
Meiotic anther, Biological replicate 3 |
| GSM686464 |
Anther with single celled pollen, Biological replicate 1 |
| GSM686465 |
Anther with single celled pollen, Biological replicate 2 |
| GSM686466 |
Anther with single celled pollen, Biological replicate 3 |
| GSM686467 |
Anther with trinucleate pollen, Biological replicate 1 |
| GSM686468 |
Anther with trinucleate pollen, Biological replicate 2 |
| GSM686469 |
Anther with trinucleate pollen, Biological replicate 3 |
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| Relations |
| BioProject |
PRJNA138101 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE27726_RAW.tar |
58.2 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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