Journal Article

Rice Expression Atlas In Reproductive Development

Masahiro Fujita, Youko Horiuchi, Yayoi Ueda, Yoko Mizuta, Takahiko Kubo, Kentaro Yano, Shinichiro Yamaki, Katsutoshi Tsuda, Toshifumi Nagata, Mitsuru Niihama, Hirotaka Kato, Shunsuke Kikuchi, Kazuki Hamada, Takako Mochizuki, Takeshi Ishimizu, Hiroaki Iwai, Nobuhiro Tsutsumi and Nori Kurata

in Plant and Cell Physiology

Published on behalf of Japanese Society of Plant Physiologists

Volume 51, issue 12, pages 2060-2081
Published in print December 2010 | ISSN: 0032-0781
Published online November 2010 | e-ISSN: 1471-9053 | DOI:

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  • Biochemistry
  • Molecular and Cell Biology
  • Plant Sciences and Forestry


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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. A decrease in 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 which 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 cyclin-dependent kinases (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 most extensive and most comprehensive data set available, indispensable for unraveling functions of many specific genes in plant reproductive processes that have not yet been thoroughly analyzed.

Keywords: Ab initio predicted genes; Flower development; Microarray; Reproductive stage; Rice; Transcriptome

Journal Article.  12845 words.  Illustrated.

Subjects: Biochemistry ; Molecular and Cell Biology ; Plant Sciences and Forestry

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