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Genes2Shape_From genes to shape: Towards development of a computable flower

Subject Area Plant Cell and Developmental Biology
Term from 2018 to 2022
Project identifier Deutsche Forschungsgemeinschaft (DFG) - Project number 355241834
 
Final Report Year 2022

Final Report Abstract

The genes2shape project aimed at understanding how molecular regulation integrates with mechanics to control overall plant shape, an unresolved problem with wide implications for both fundamental and applied biology. The problem was addressed using Arabidopsis flowers, which are amongst the best characterised systems in plant developmental biology and are important as being the reproductive structures. From a mechanistic point of view, it is widely accepted that regulatory molecular networks are important for generating the differentiation pattern during organ formation and it is assumed that the molecular patterns interfere with the properties of the structural cellular elements (cell wall, cytoskeleton) to induce particular growth patterns. How this occurs and how this is coordinated in space is not known. To obtain a mechanistic understanding of such a complex process, we collected information from multiple scales, from molecular networks to physical properties and geometry have to be combined into a single description. Building on our complementary experience in interdisciplinary research on plant development, we used a combination of live imaging, imaging processing methods and computational modelling to generate the most coherent quantitative description of early flower development to date. By creating a cell-based template where molecular information was mapped - a flower atlas - we were able to address the questions on how the regulatory pattern is set up and how this relates to growth in different regions of the flower. We found that despite the extensive literature on flower development, additional regulatory hypotheses were required in our models to explain the molecular patterns, and we could extract how different genes contribute to growth by a combinatorial investigation of multiple genes and subdomains of the flower. Further, we could confirm the change in growth rates predicted by our analysis with mutant data. The flower atlas is disseminated via an interactive graphical web interface freely available to the community via Morphonet. This transforms the way data is provided to the community by integrating multiple data types and allowing users to browse the data and build their experiments and models on the latest information and insights. We have further addressed the connection between expression pattern domains and mechanical changes by analysing and modelling shape changes appearing when cell wall components are perturbed. By using a novel set of spatially localised perturbations, where wall components are disrupted only in specific domains of the flower, we have been able to show how growth and mechanics within flower organs and in boundaries between the organs contribute to the overall morphology of the flower. By working on a single cell resolution and identifying spatially localised regions of importance for changes in morphology at the early stages of flower development, the project outcomes will contribute to the ability to efficiently identify where and when to apply changes for generating desired effects on the morphology of fully developed flowers. Together with the predictive models, this can transform the way breeding is approached in the future.

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