title: Genome-wide analysis of spatiotemporal gene expression patterns during early embryogenesis in rice.
abstract: Embryogenesis in rice is different from that of most dicotolydonous plants in that it shows a non-stereotypic cell division pattern, formation of dorsal-ventral polarity, and endogenous initiation of the radicle. To reveal the transcriptional features associated with developmental events during rice early embryogenesis, we used microarray analysis coupled with laser microdissection to obtain both spatial and temporal transcription profiles. Our results allowed us to determine spatial expression foci for each expressed gene in the globular embryo, which revealed the importance of phytohormone-related genes and a suite of transcription factors to early embryogenesis. Our analysis showed the polarized expression of a small number of genes along the apical-basal and dorsal-ventral axes in the globular embryo, which tended to fluctuate in later developmental stages. We also analyzed gene expression patterns in the early globular embryo and how this relates to expression in embryonic organs at later stages. We confirmed the accuracy of the expression patterns found by microarray analysis of embryo subdomains using in situ hybridization. Our study identified homologous genes from Arabidopsis thaliana with known functions in embryogenesis in addition to unique and uncharacterized genes that show polarized expression patterns during embryogenesis. The results of this study are presented in a database to provide a framework for spatiotemporal gene expression during rice embryogenesis, to serve as a resource for future functional analysis of genes, and as a basis for comparative studies of plant embryogenesis.
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan ajunito@mail.ecc.u-tokyo.ac.jp.
authors.forename: Jun-Ichi
authors.initials: J
authors.lastname: Itoh
authors.affiliation: Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Sato
authors.affiliation: Department of Bioresource Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Sato
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.
authors.forename: Ken-Ichiro
authors.initials: K
authors.lastname: Hibara
authors.affiliation: Department of Bioresource Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan.
authors.forename: Sae
authors.initials: S
authors.lastname: Shimizu-Sato
authors.affiliation: Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan.
authors.forename: Hiromi
authors.initials: H
authors.lastname: Kobayashi
authors.affiliation: Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Hinako
authors.initials: H
authors.lastname: Takehisa
authors.affiliation: Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA.
authors.forename: Karen A
authors.initials: KA
authors.lastname: Sanguinet
authors.affiliation: Genome Informatics Department, Mitsubishi Space Software Co., Ltd., Takezono 1-6-1, Tsukuba, Ibaraki 305-0032, Japan.
authors.forename: Nobukazu
authors.initials: N
authors.lastname: Namiki
authors.affiliation: Genome Resource Unit, Agrogenomics Research Center, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8602, Japan.
authors.forename: Yoshiaki
authors.initials: Y
authors.lastname: Nagamura
mesh_terms: D017360:Arabidopsis / Q000196:embryology*; D002455:Cell Division / Q000502:physiology; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000196:embryology*; D010937:Plant Growth Regulators / Q000235:genetics*
chemical_list: D010937:Plant Growth Regulators
keywords: Embryogenesis; Gene expression; Microarray; Microdissection; Rice; Transcriptome