Periodic Reporting for period 1 - CFQMLD (A Computational Framework For Quantitative Modeling of Leaf Development in Arabidopsis and Cardamine)
Berichtszeitraum: 2017-01-01 bis 2018-12-31
Understanding how form emerges in living organisms is a fundamental challenge in biology. Progress, however, has been confounded by the complex chain of interactions linking the organization of mature organ forms to molecular processes. As such, insights into the manner in which individual genes contribute to the development of form have been elusive; even in well-studied model organisms. In this context, leaves are a striking example of the self-organization of form – displaying remarkable diversity within and between species. To study the molecular basis of leaf shape and its diversity the Tsiantis lab has exploited Arabidopsis thaliana and Cardamine hirsuta, two closely related species with distinct leaf shapes. Leaves of A. thaliana have a simple contour (also termed margin) adorned with small protrusions. By contrast, those of C. hirsuta are compound, meaning their leaves are comprised of many leaf-like segments, connected to a common stalk. By comparing the development of these two species the Tsiantis lab has identified many of the key genetic factors underlying their distinct leaf shapes. This opens the door to a detailed understanding of mechanisms shaping leaf form development.
Due to the complexity of leaf development, however, understanding how leaf shape is organized requires computational models, informed by detailed quantitative measurements of growth and gene expression. Such models permit the systematic examination of the interactions linking genetic regulation, cell division and tissue growth to final form. An objective of this project was to develop such a computational modelling framework, as well as the advanced quantification tools required to analyse leaf growth and form. The next objective was to combine these tools with experimental efforts in the Tsiantis lab to obtain fundamental insights into how leaf form is regulated, thus providing essential insights into shape regulation in eukaryotic systems. In this context, a primary aim of this work was achieving a mechanistic explanation of the basis of simple and compound leaf shape development in A. thaliana and C. hirsuta. As leaves are the primary organs for light capture in plants, and their photosynthetic efficiency is influenced by their shape, our work provides an important step towards the engineering of leaf shape for crop improvement.
Due to the complexity of leaf development, however, understanding how leaf shape is organized requires computational models, informed by detailed quantitative measurements of growth and gene expression. Such models permit the systematic examination of the interactions linking genetic regulation, cell division and tissue growth to final form. An objective of this project was to develop such a computational modelling framework, as well as the advanced quantification tools required to analyse leaf growth and form. The next objective was to combine these tools with experimental efforts in the Tsiantis lab to obtain fundamental insights into how leaf form is regulated, thus providing essential insights into shape regulation in eukaryotic systems. In this context, a primary aim of this work was achieving a mechanistic explanation of the basis of simple and compound leaf shape development in A. thaliana and C. hirsuta. As leaves are the primary organs for light capture in plants, and their photosynthetic efficiency is influenced by their shape, our work provides an important step towards the engineering of leaf shape for crop improvement.
To complement genetic and cellular-level time-lapse imaging studies of leaf development, we developed computational models and quantification techniques at multiple-scales (working with the Smith group, MPIPZ). Each class of model was aimed at capturing a range of phenomena relevant to the organization of organ shape. Simple cell-population models were implemented to study organ size and proportion. To study the integration of local growth and patterning at the leaf margin with overall leaf growth, physically based models were developed using the Finite Element Method (FEM). To examine how growth and patterning of the leaf margin influence protrusion shape we devised minimal geometric models of leaf margin development. Finally to examine the relation between tissue level growth and cell-shape, we created physically based cellular models of the leaf epidermis based on mass-spring networks and 3D FEM simulations.
To quantify leaf shape and development we developed a system to quantify mature leaf shapes (Leaf Interrogator, LeafI) and plug-ins for cellular and organ-wide quantification in the widely used MorphoGraphX software. LeafI provided an integrated software package for the analysis of leaf contours extracted from images, including both the computation of simple measures of shape (e.g. how circular or convex the forms were) as well as ‘shape spaces’ inferred from collections of contours. Many techniques used to quantify leaf contours can also be used for cell-shape. This prompted us to port the shape measures from LeafI into MorphoGraphX, for use in the quantification of time-lapse data. Finally, to quantify global and regional aspects of cellular behaviors (e.g. growth and proliferation) we developed techniques relying on the location of cells within developing organs, based on their absolute position (global) or distance from important landmarks (regional).
Together, the models and quantification techniques we developed provide a rich computational framework to study how growth, patterning and cellular behaviors are integrated during leaf shape development in different species and genetic backgrounds.
Combining these computational tools with time-lapse confocal imaging in A. thaliana and C. hirsuta allowed us to achieve the key aim of the project: understanding the mechanistic basis of simple and compound leaf development. Additional project results elucidated fundamental aspects of lateral organ development in plants. We linked tissue growth in leaves and other lateral organs to the morphology of epidermal cells and explained the emergence of their curious “puzzle-like” shape. Additionally, we also explored the role of the gene LATE MERISTEM IDENTITY1 (LMI1) in regulating organ proportions in leaves and stipules. Together, these biological results underscore the advances provided by the computational tools developed in the scope of this project.
Many of these results have now been published, in eLife and Genes & Development, and publication of the remaining major results of the project is underway. The results of this project have been broadly disseminated through social media and public outreach through the Max Planck Institute for Plant Breeding Research, as well as attendance and presentation of results at scientific conferences and workshops by the researcher (3 meetings), his supervisor (8 meetings) and key collaborators (7 meetings).
To quantify leaf shape and development we developed a system to quantify mature leaf shapes (Leaf Interrogator, LeafI) and plug-ins for cellular and organ-wide quantification in the widely used MorphoGraphX software. LeafI provided an integrated software package for the analysis of leaf contours extracted from images, including both the computation of simple measures of shape (e.g. how circular or convex the forms were) as well as ‘shape spaces’ inferred from collections of contours. Many techniques used to quantify leaf contours can also be used for cell-shape. This prompted us to port the shape measures from LeafI into MorphoGraphX, for use in the quantification of time-lapse data. Finally, to quantify global and regional aspects of cellular behaviors (e.g. growth and proliferation) we developed techniques relying on the location of cells within developing organs, based on their absolute position (global) or distance from important landmarks (regional).
Together, the models and quantification techniques we developed provide a rich computational framework to study how growth, patterning and cellular behaviors are integrated during leaf shape development in different species and genetic backgrounds.
Combining these computational tools with time-lapse confocal imaging in A. thaliana and C. hirsuta allowed us to achieve the key aim of the project: understanding the mechanistic basis of simple and compound leaf development. Additional project results elucidated fundamental aspects of lateral organ development in plants. We linked tissue growth in leaves and other lateral organs to the morphology of epidermal cells and explained the emergence of their curious “puzzle-like” shape. Additionally, we also explored the role of the gene LATE MERISTEM IDENTITY1 (LMI1) in regulating organ proportions in leaves and stipules. Together, these biological results underscore the advances provided by the computational tools developed in the scope of this project.
Many of these results have now been published, in eLife and Genes & Development, and publication of the remaining major results of the project is underway. The results of this project have been broadly disseminated through social media and public outreach through the Max Planck Institute for Plant Breeding Research, as well as attendance and presentation of results at scientific conferences and workshops by the researcher (3 meetings), his supervisor (8 meetings) and key collaborators (7 meetings).
The advances made during this project greatly contribute to our understanding of organogenesis in plants. In the course of the project we have developed the first computational model explicitly linking developmental gene activity in the leaf to the amount and direction of growth. Furthermore, by combining advanced quantification of time-lapse imaging and computational modeling we were able to explain the distinction between simple and compound leaves. This is a key aspect of leaf shape diversity, but one whose precise cellular and molecular basis was previously unknown. Similarly, both the function of ‘puzzle-cell’ shapes in the epidermis of leaves and other lateral organs, as well as the mechanism underlying the emergence of these shapes has been unclear. We showed that the ‘puzzle-like’ shape of epidermal cells of plants reduces the mechanical stress induced by turgor on their outer facing cell-wall, and that changing cell geometry to reduce this stress leads to the emergence of puzzle-shaped cells in tissues (like leaves) which expand in two-directions. These results explain both the form and function of ‘puzzle cells’, link tissue level growth to that of cells, and provide critical insights to spur further work.
The computational frameworks for modeling and quantification of organ shape and development created during this project were critical to all of the preceding advances. Altogether, this work has enriched our understanding of how form emerges in living organisms. It also provides important case studies for the engineering of plant form, and is thus an important stepping-stone for the future efforts to modify leaf shape for the purposes of crop improvement.
The computational frameworks for modeling and quantification of organ shape and development created during this project were critical to all of the preceding advances. Altogether, this work has enriched our understanding of how form emerges in living organisms. It also provides important case studies for the engineering of plant form, and is thus an important stepping-stone for the future efforts to modify leaf shape for the purposes of crop improvement.