Collaborative Research: RESEARCH-PGR NSF-SNSF: Comparative high-resolution analysis of transcription factor binding sites in plant organ formation

About This Grant

Plants create a variety of lateral organs, such as roots, leaves, and flowers, as they grow. Each of these new organs has specific functions that are important for plants, and they all impact agricultural yields in crop plants. Research suggests that there are both developmental similarities and differences between the different organ types. The basis of this is unclear. Many genes are known to contribute to the creation of lateral organs, with some genes impacting one organ type and others impact more than one. Understanding the common and different functions of plant genes in the development of different organ types is an important goal which can help crop improvement. However, there is a limitation in the technology available to study this at a scale that will be informative. The goal of this proposal is to create a semi-automated system to determine what genes are active in different lateral organ types. This system will be able to look at many genes in parallel, an advantage over older technologies. The project will also compare two divergent plant species and define the role of a cell signaling pathway on gene function in different organ types to help understand how evolution and cell signaling pathways shape lateral organ formation. Lastly, the project will create databases for other scientists to use in their research, and a workshop to train other scientists on the use of the semi-automated system, which will enable other researchers to use this approach in their studies. Lateral organ production, including flowers and roots, is a critical feature of many crop traits and as such the project will help inform future efforts to improve crop productivity and ensure food security. During plant development common signaling pathways and transcription factors (TFs) often operate in seemingly distinct processes. Understanding how individual plant signaling pathways and TFs are repurposed in different contexts remains a challenge. Traditional methods for defining individual TF functions are time consuming and labor intensive. As the number of TFs impacting plant processes increases, this creates a technical bottleneck. To address this, this proposal will develop a new high-throughput platform to identify TF targets in vivo and use this platform to identify context-specific TF binding sites during lateral organ development across tissue types and across species. The project team has identified a peptide signaling pathway as a novel driver of lateral organ formation in roots and shoots and identified a suite of TFs that impact peptide-mediated lateral organ formation. As such, the project will also use this platform to define how peptide signaling shapes TF targeting in different lateral organs and interrogate the mechanisms underlying context-specific TF binding sites using a combination of genetic, biochemical, and genomics approaches. The project will also generate web-based interfaces for other researchers to explore and utilize data from the project, and hands-on workshops to train researchers in the use of the platform, expanding the impact of the project. This award was funded as part of a lead agency opportunity between NSF and Swiss NSF where NSF funds the US investigator, Swiss NSF funds the Swiss partner. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.