Spatio-temporal transcriptional profiling of early embryogenesis in rice

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. We designed microarray experiments for two types of dataset; i.e., spatial and temporal datasets. For temporal datasets, the entire embryonic tissues at 2, 3 and 4 DAP were collected using laser microdissection. For spatial datasets, 3-DAP embryos were separated into half parts of the embryo along the A-B and D-V axis using LM, which resulted in four tissues derived from the apical, basal, dorsal and ventral regions of the embryo. In addition to the spatial datasets for early embryos, we obtained sub-spatial datasets from tissues of 7-DAP embryos. Embryo tissues closely associated with four embryonic organs; namely, the shoot, scutellem, root (radicle), and epiblast/coleorhizae, were separated and collected by LM. These 11 samples were obtained in triplicate and used to perform the 44K rice microarray.