Joint NSF/ERA-CAPS: Phytochrome Control of Resource Allocation and Growth in Arabidopsis and in Brassicaceae Crops

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PI: Jennifer Nemhauser (University of Washington-Seattle)ERA-CAPS Collaborators: Karen Halliday (University of Edinburgh, Scotland, UK) and Mark Stitt (Max Planck Institute of Molecular Plant Physiology, Golm, Germany)For plants, light is a signal that carries information about the environment, and a source of energy for photosynthesis. Phytochromes are proteins that change activity when exposed to light, and, in turn, light-activated phytochromes direct many changes in plant cells, including massive re-programming of which genes are being turned on and which are being kept off. For example, phytochromes enable plants to detect nearby vegetation through subtle shifts in the quality of light hitting the plant cell. This light-activated surveillance mechanism initiates changes in plant architecture, biomass formation and the timing of reproduction, all traits that are strongly linked to crop yield. These changes in growth strategy require corresponding adjustments in resource deployment and yet little is known about how this is accomplished. This project will start to fill in this critical knowledge gap that will lead to new ideas for improving crop performance. With regard to outreach and training, this project will provide international research training opportunities for a diverse group of undergraduate and graduate students. In addition, the project will extend existing outreach efforts to include a yearly 12-week residency for a visual artist to develop new visualization tools for molecular genetic concepts, particularly those relating to agriculture and biofuels. This project builds on new research from the partner labs showing that cross talk between phytochrome and carbon signaling is central to C resource use efficiency and resource conservation. A principal aim will be to determine the role of phytochrome in C resource management. The project will also delineate the genetic basis and impact of shading-induced N re-allocation in canopies. This trait strongly impacts on N use efficiency and stand photosynthesis, and in many crops is closely linked to yield. The project will conduct a systematic study across scales, delivering mechanistic information about signal integration, time-resolved transcriptome and metabolite profiles, and quantitative information about biomass accumulation, defined as the flux of carbon to protein and cell wall components, and growth dynamics. The experimental findings will be integrated into models to test hypotheses and to gain understanding at a system level. An aim will be to build models that predict the dual action of phytochrome and photosynthesis on resource management and biomass production. The project will run parallel work programs in the reference species, Arabidopsis thaliana, and the closely related crop Brassica rapa. The rapid life cycle and larger resource pool of the reference species will accelerate knowledge acquisition. B. rapa brings the advantage of larger size, and allows new insights to be directly applied to a food crop. Results will be made broadly accessible through national and international meetings and through publications in leading international journals. All datasets will be accessible through the consortium website, as well as through long-term repositories that include but are not limited to the Biological Data Repository (BioDare; https://www.biodare.ed.ac.uk/) and the Plant Systems Biology Modelling (PlaSMo;http://www.plasmo.ed.ac.uk/) database. The consortium website will also serve to advertise the general aims and advances of this project with links to more general dissemination of information, including outreach targeted to non-scientists.