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Spatio-temporal transcriptional profiling of early embryogenesis in rice

ABSTRACT: Embryogenesis in rice shows a non-stereotypic cell division pattern, the formation of dorsal-ventral polarity, and endogenous initiation of the radicle, which differs from most dicotyledonous plants. To reveal the transcriptional features associated with developmental events during early embryogenesis in rice, we obtained transcriptome data, including the spatial and temporal data sets, using microarray experiments combined with a laser microdissection. We could predict the spatial expression foci of each expressed gene in the globular embryo, which revealed that the expression bias along the apical-basal and dorsal-ventral axes was correlated with temporal changes in expression levels during early embryogenesis. The spatial expression patterns of transcripts was suggestive of a potential contribution of phytohormone-related genes to early embryogenesis and was a characteristic feature of transcription factor genes. We also analyzed the relationship between expression sites of the genes in the globular embryo and those in embryonic organs at later stages. Based on in silico prediction of gene expression sites, we developed potential marker genes expressed in specific domains of the early embryo. The results and database will provide a framework for spatio-temporal gene expression in rice embryogenesis and increase our understanding of developmental diversity of plant embryogenesis.

ORGANISM(S): Oryza sativa Oryza sativa Japonica Group

PROVIDER: GSE63110 | GEO | 2014/11/08

SECONDARY ACCESSION(S): PRJNA266658

REPOSITORIES: GEO

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Project description:Plants initially undergo a period of vegetative development, in which it produces leaves from shoot apical meristem (SAM) and roots from the root apical meristem. Later in development, the SAM undergoes a change in fate and enters reproductive development called as floral transition, producing flowers and seeds. Our understanding of the molecular and genetic mechanisms that underlie reproductive development in plants has increased tremendously in the past decade, essentially through the work on Arabidopsis. In this study, we have analyzed the spatial and temporal gene expression in various tissues/organs and developmental stages of rice using microarray technology to identify the genes differentially expressed during various stages of reproductive development. Experiment Overall Design: Various rice tissues/organs (seedling root, mature leaf and Y leaf) and stages of reproductive (panicle and seed) development were used for RNA extraction and hybridization on Affymetrix microarrays. Three biological replicates of each sample were used for microarray analysis. We sought to obtain developmental and temporal gene expression profiles at each stage to identify the differentially expressed genes. Different stages of panicle and seed development have been categorized according to panicle length and days after pollination, respectively, based on landmark developmental events as follows: up to 0.5 mm, shoot apical meristem and rachis meristem (SAM); 0-3 cm, floral transition and floral organ development (P1); 3-10 cm, meiotic stage (P2 and P3); 10-15 cm, young microspore stage (P4); 15-22 cm, vacuolated pollen stage (P5); 22-30 cm, mature pollen stage (P6); 0-2 dap, early globular embryo (S1); 3-4 dap, middle and late globular embryo (S2); 5-10 dap, embryo morphogenesis (S3); 11-20 dap, embryo maturation (S4); 21-29, dormancy and desiccation tolerance (S5). These stage specifications are approximations based on information from Itoh et al., 2005, Plant Cell Physiol, 46, 23-47.

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Spatio-temporal transcriptional profiling of early embryogenesis in rice

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