*Stomata are adjustable pores in the plant epidermis that regulate gas exchange between the plant and atmosphere; they are present on the aerial portions of most higher plants. Genetic pathways controlling stomatal development and distribution have been described in some detail for one dicot species, Arabidopsis, in which three paralogous bHLH transcription factors, FAMA, MUTE and SPCH, control discrete sequential stages in stomatal development. Orthologs of FAMA, MUTE and SPCH are present in other flowering plants. This observation is of particular interest when considering the grasses, because both the morphology of guard cells and their tissue distributions differ substantially between Arabidopsis and this group. By examining gene expression patterns, insertional mutants and cross-species complementation studies, we find evidence that FAMA function is conserved between monocots and dicots, despite their different stomatal morphologies, whereas the roles of MUTE and two SPCH paralogs are somewhat divergent.KEY WORDS: Stomata, Monocotyledon, Rice, Arabidopsis, Maize, bHLH Development 136, 2265Development 136, -2276Development 136, (2009 DEVELOPMENT 2266Stomatal development in grasses can be divided into five stages (Stebbins, 1960) (Fig. 1B). Here, stomatal development exhibits a strong spatiotemporal gradient with early stages taking place in the proximal portions of the leaf and guard cells differentiating later in distal regions. In stage one, cell files that are capable of forming stomata are determined (blue shading at leaf base, Fig. 1B). Asymmetric division of cells in these files (stage two, middle leaf section, Fig. 1B) generates GMCs as the smaller daughters. A second asymmetric division then occurs in the cells adjacent to the newly specified GMCs to produce a pair of subsidiary mother cells (SMCs), so at this third stage the guard cell complex consists of a GMC and two subsidiary cells. In the fourth stage, the GMC divides symmetrically into two box-shaped guard cells. During the final stage, guard cells undergo extensive elongation and morphogenetic changes to form the final pair of dumbbell-shaped cells with a central pore between them (red cells at tip of leaf, Fig. 1B) (Sack, 1994).Despite the differences in stomatal ontogeny, morphology and pattern between monocots and dicots, protein sequences of the key regulatory genes SPCH, MUTE and FAMA are highly conserved between representatives of these two angiosperm divisions. In this study, we identify likely orthologs of Arabidopsis SPCH, MUTE and FAMA in two grass species: rice (Oryza sativa) and maize (Zea mays). Through mutation, transgenics, and by monitoring gene expression in situ, we demonstrate that there is significant conservation of function of the FAMA gene between monocots and dicots. By contrast, although MUTE and the two SPCH genes maintain some common functions in grasses, they have diverged in their roles and domains of expression. MATERIALS AND METHODS Plant growth conditionsArabidopsis thaliana Columbia ecotype seeds were ste...

SUMMARYUnlike the situation in animals, the final morphology of the plant body is highly modulated by the environment. During Arabidopsis development, intrinsic factors provide the framework for basic patterning processes. CLASS III HOMEODOMAIN LEUCINE ZIPPER (HD-ZIPIII) transcription factors are involved in embryo, shoot and root patterning. During vegetative growth HD-ZIPIII proteins control several polarity set-up processes such as in leaves and the vascular system. We have identified several direct target genes of the HD-ZIPIII transcription factor REVOLUTA (REV) using a chromatin immunoprecipitation/DNA sequencing (ChIP-Seq) approach. This analysis revealed that REV acts upstream of auxin biosynthesis and affects directly the expression of several class II HD-ZIP transcription factors that have been shown to act in the shadeavoidance response pathway. We show that, as well as involvement in basic patterning, HD-ZIPIII transcription factors have a critical role in the control of the elongation growth that is induced when plants experience shade. Leaf polarity is established by the opposed actions of HD-ZIPIII and KANADI transcription factors. Finally, our study reveals that the module that consists of HD-ZIPIII/KANADI transcription factors controls shade growth antagonistically and that this antagonism is manifested in the opposed regulation of shared target genes.

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.