Being sessile, a plant's development is exquisitely controlled by its environment. In response to impending shade, a plant's architecture undergoes a profound morphological change, including stem elongation and accelerated flowering. This phenotype has consequences in agriculture, where shade avoidance responses in densely grown plants may reduce the growth of harvestable organs. As such, the perturbation of signaling pathways required for shade avoidance may produce crops with better yields. Previous studies of the model plant Arabidopsis thaliana have shown that shade signals because a rapid increase in the synthesis of the phytohormone auxin in leaves. Auxin is subsequently transported to stems to promote elongation growth. Therefore, it is likely that specific cell types have specialized responses to shade. However, the analysis of cell-specific expression changes in the Arabidopsis shoot has been lacking, primarily due to limitations in techniques required to isolate a given cell population. Here, the recently developed INTACT methodology will be used to study gene expression changes in shoot cell types. The leaf and cotyledons sense many light signals, and nuclear transcripts from the three major tissues of these organs, the mesophyll, epidermis and vasculature, will be purified. Using RNA-Sequencing technology, this proposal will test the changes in gene expression in these cells in response to simulated shade. By comparing these changes with that of mutant plants defective for shade-induced auxin biosynthesis, it will be determined if the gene expression changes in a given cell type are in part downstream of auxin signals. Using the information gleaned from this analysis, available T-DNA insertion mutants of potentially interesting cell-specific shade-regulated genes will be tested for defects in shade avoidance phenotypes. Interesting candidate genes would be auxin biosynthesis genes, which may be spatially controlled, or transcriptional regulators, some of which are already known to have a role in the shade avoidance phenotype. The gene's cell-specific role in modulating plant architecture will be assessed by expressing the gene under relevant cell-specific promoters and testing how this affects plant environmental responses. This analysis will place novel and previously identified factors required for shade avoidance into a spatial, cell-type specific context. Ultimately, the spatial perturbation of the genes identified here may generate plants where architectural changes in response to shade are controlled in an organ-specific manner. This may be advantageous in commercial plant species, where shade responses can be spatially tuned to produce maximum yield in a given environment. Furthermore, the proposal seeks to understand how environmental change is transduced at the cellular level to affect an organism's body plan during development.
A plant optimizes its organ shape and size to its local environment, providing an excellent system for the study of developmental plasticity in response to environmental challenges. This proposal seeks to better understand the spatial and cell-specific changes that occur in plants to generate organs of different shapes in response to light, the perturbation of which may be useful to generate commercial crops with higher yields. In addition, these studies may be suggestive of common evolutionary themes of how different cell types in both plants and animals are coordinated to produce complex organs, and how these processes can go awry to affect human health.