The functions of the plant body rely on interactions among distinct and nonequivalent cell types. The comparison of transcriptomes from different cell types should expose the transcriptional networks that underlie cellular attributes and contributions. Using laser microdissection and microarray profiling, we have produced a cell type transcriptome atlas that includes 40 cell types from rice (Oryza sativa) shoot, root and germinating seed at several developmental stages, providing patterns of cell specificity for individual genes and gene classes. Cell type comparisons uncovered previously unrecognized properties, including cell-specific promoter motifs and coexpressed cognate binding factor candidates, interaction partner candidates and hormone response centers. We inferred developmental regulatory hierarchies of gene expression in specific cell types by comparison of several stages within root, shoot and embryo.
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Gene Expression Omnibus
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We thank N. Li for valuable database advice and assistance and P. Wu (Zhejiang University) for the rice root micrograph in Figure 3. This work was supported by US National Science Foundation Plant Genome Program grant DBI-0325821 to T.N., X.-W.D. and H.Z. T.L. and M.C. were supported in part by Peking-Yale Monsanto Fellowships.
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