Quantifying morphogenesis in plants in 4D

Old school, new rules: floral meristem development revealed by 3D gene expression atlases and high-resolution transcription factor-chromatin dynamics

The intricate morphology of the flower is primarily established within floral meristems in which floral organs will be defined and from where the developing flower will emerge. Floral meristem development involves multiscale-level regulation, including lineage and positional mechanisms for establishing cell-type identity, and transcriptional regulation mediated by changes in the chromatin environment. However, many key aspects of floral meristem development remain to be determined, such as: 1) the exact role of cellular location in connecting transcriptional inputs to morphological outcomes, and 2) the precise interactions between transcription factors and chromatin regulators underlying the transcriptional networks that regulate the transition from cell proliferation to differentiation during floral meristem development. Here, we highlight recent studies addressing these points through newly developed spatial reconstruction techniques and high-resolution transcription factor-chromatin environment interactions in the model plant Arabidopsis thaliana. Specifically, we feature studies that reconstructed 3D gene expression atlases of the floral meristem. We also discuss how the precise timing of floral meristem specification, floral organ patterning, and floral meristem termination is determined through temporally defined epigenetic dynamics for fine-tuning of gene expression. These studies offer fresh insights into the well-established principles of floral meristem development and outline the potential for further advances in this field in an age of integrated, powerful, multiscale resolution approaches.

Methods to Visualize and Quantify Cortical Microtubule Arrays in Arabidopsis Conical Cells

Many studies from different model organisms have demonstrated that microtubules are essential for various cellular processes, including cell division, cell morphogenesis, and intracellular trafficking. In interphase plant cells, oriented cortical microtubule arrays are highly characteristic in cells that display various morphologies, such as elongated hypocotyl cells and root cells, jigsaw-puzzled leaf pavement cells, and petal epidermal conical cells. Conical cells represent a specialized epidermal cell type found in the petal epidermis of many flowering plants. It has been suggested that in the model plant Arabidopsis thaliana, the petal adaxial epidermal cells develop from a roughly hemispherical morphology to a conical shape, correlating with the reorientation of cortical microtubules from random to well-ordered circumferential arrays. This chapter presents an overview of the methods available to visualize the microtubule cytoskeleton in living conical cells via confocal microscopy.

Cell type-specific dynamics underlie cellular growth variability in plants

Coordination of growth, patterning and differentiation is required for shaping organs in multicellular organisms. In plants, cell growth is controlled by positional information, yet the behavior of individual cells is often highly heterogeneous. The origin of this variability is still unclear. Using time-lapse imaging, we determined the source and relevance of cellular growth variability in developing organs of Arabidopsis thaliana. We show that growth is more heterogeneous in the leaf blade than in the midrib and petiole, correlating with higher local differences in growth rates between neighboring cells in the blade. This local growth variability coincides with developing stomata. Stomatal lineages follow a specific, time-dependent growth program that is different from that of their surroundings. Quantification of cellular dynamics in the leaves of a mutant lacking stomata, as well as analysis of floral organs, supports the idea that growth variability is mainly driven by stomata differentiation. Thus, the cell-autonomous behavior of specialized cells is the main source of local growth variability in otherwise homogeneously growing tissue. Those growth differences are buffered by the immediate neighbors of stomata and trichomes to achieve robust organ shapes.

Live-imaging provides an atlas of cellular growth dynamics in the stamen

Development of multicellular organisms is a complex process involving precise coordination of growth among individual cells. Understanding organogenesis requires measurements of cellular behaviors over space and time. In plants, such a quantitative approach has been successfully used to dissect organ development in both leaves and external floral organs, such as sepals. However, the observation of floral reproductive organs is hampered as they develop inside tightly closed floral buds, and are therefore difficult to access for imaging. We developed a confocal time-lapse imaging method, applied here to Arabidopsis (Arabidopsis thaliana), which allows full quantitative characterization of the development of stamens, the male reproductive organs. Our lineage tracing reveals the early specification of the filament and the anther. Formation of the anther lobes is associated with a temporal increase of growth at the lobe surface that correlates with intensive growth of the developing locule. Filament development is very dynamic and passes through three distinct phases: (1) initial intense, anisotropic growth, and high cell proliferation; (2) restriction of growth and proliferation to the filament proximal region; and (3) resumption of intense and anisotropic growth, displaced to the distal portion of the filament, without cell proliferation. This quantitative atlas of cellular growth dynamics provides a solid framework for future studies into stamen development.

X-ray microscopy enables multiscale high-resolution 3D imaging of plant cells, tissues, and organs

Capturing complete internal anatomies of plant organs and tissues within their relevant morphological context remains a key challenge in plant science. While plant growth and development are inherently multiscale, conventional light, fluorescence, and electron microscopy platforms are typically limited to imaging of plant microstructure from small flat samples that lack a direct spatial context to, and represent only a small portion of, the relevant plant macrostructures. We demonstrate technical advances with a lab-based X-ray microscope (XRM) that bridge the imaging gap by providing multiscale high-resolution three-dimensional (3D) volumes of intact plant samples from the cell to the whole plant level. Serial imaging of a single sample is shown to provide sub-micron 3D volumes co-registered with lower magnification scans for explicit contextual reference. High-quality 3D volume data from our enhanced methods facilitate sophisticated and effective computational segmentation. Advances in sample preparation make multimodal correlative imaging workflows possible, where a single resin-embedded plant sample is scanned via XRM to generate a 3D cell-level map, and then used to identify and zoom in on sub-cellular regions of interest for high-resolution scanning electron microscopy. In total, we present the methodologies for use of XRM in the multiscale and multimodal analysis of 3D plant features using numerous economically and scientifically important plant systems.

The Search for Geometrical Parameters That Represent the Dynamic Nature of Phyllotaxis in Plants

The shoot apical meristem (SAM) is the main growth centre that produces lateral organs such as leaves in specific and precise symmetrical patterns. The main goal of this commentary is to explore the link between phyllotactic parameters such as the plastochrone ratio (R) as well as Γ (relationship between the size of the SAM and the size of primordia) and growth processes involved in the expression of symmetrical patterns at the level of the SAM. It is also possible to deduce the values of these parameters from measures of the apical area and the radius of the SAM. A comparative analysis of phyllotactic parameters for three species (Begonia scabrida, Euterpe oleracea, and Anagallis arvensis) for which ‘dynamic’ data are available reveals that empirical and theoretical values of R and Γ can differ, indicating that characters defining these parameters are subject to developmental constraints that in turn determine the boundary conditions for the dynamic manifestation of phyllotactic patterns. One of the main challenges that remains is the ability to consistently and effectively observe the dynamic changes taking place at the SAM (in real time) over an extended period.

Shaping the Organ: A Biologist Guide to Quantitative Models of Plant Morphogenesis

Organ morphogenesis is the process of shape acquisition initiated with a small reservoir of undifferentiated cells. In plants, morphogenesis is a complex endeavor that comprises a large number of interacting elements, including mechanical stimuli, biochemical signaling, and genetic prerequisites. Because of the large body of data being produced by modern laboratories, solving this complexity requires the application of computational techniques and analyses. In the last two decades, computational models combined with wet-lab experiments have advanced our understanding of plant organ morphogenesis. Here, we provide a comprehensive review of the most important achievements in the field of computational plant morphodynamics. We present a brief history from the earliest attempts to describe plant forms using algorithmic pattern generation to the evolution of quantitative cell-based models fueled by increasing computational power. We then provide an overview of the most common types of "digital plant" paradigms, and demonstrate how models benefit from diverse techniques used to describe cell growth mechanics. Finally, we highlight the development of computational frameworks designed to resolve organ shape complexity through integration of mechanical, biochemical, and genetic cues into a quantitative standardized and user-friendly environment.

Leaf Shape Diversity: From Genetic Modules to Computational Models

Plant leaves display considerable variation in shape. Here, we introduce key aspects of leaf development, focusing on the morphogenetic basis of leaf shape diversity. We discuss the importance of the genetic control of the amount, duration, and direction of cellular growth for the emergence of leaf form. We highlight how the combined use of live imaging and computational frameworks can help conceptualize how regulated cellular growth is translated into different leaf shapes. In particular, we focus on the morphogenetic differences between simple and complex leaves and how carnivorous plants form three-dimensional insect traps. We discuss how evolution has shaped leaf diversity in the case of complex leaves, by tinkering with organ-wide growth and local growth repression, and in carnivorous plants, by modifying the relative growth of the lower and upper sides of the leaf primordium to create insect-digesting traps.

Network analysis of Arabidopsis mitochondrial dynamics reveals a resolved tradeoff between physical distribution and social connectivity

Mitochondria in plant cells exist largely as individual organelles which move, colocalize, and interact, but the cellular priorities addressed by these dynamics remain incompletely understood. Here, we elucidate these principles by studying the dynamic "social networks" of mitochondria in Arabidopsis thaliana wildtype and mutants, describing the colocalization of individuals over time. We combine single-cell live imaging of hypocotyl mitochondrial dynamics with individual-based modeling and network analysis. We identify an inevitable tradeoff between mitochondrial physical priorities (an even cellular distribution of mitochondria) and “social” priorities (individuals interacting, to facilitate the exchange of chemicals and information). This tradeoff results in a tension between maintaining mitochondrial spacing and facilitating colocalization. We find that plant cells resolve this tension to favor efficient networks with high potential for exchanging contents. We suggest that this combination of physical modeling coupled to experimental data through network analysis can shed light on the fundamental principles underlying these complex organelle dynamics. A record of this paper’s transparent peer review process is included in the supplemental information.

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Dynamic social networks of plant mitochondria reflect physical organellar encounters

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Network analysis and modeling show priorities and tradeoffs for mitochondrial motion

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Mitochondria in plant cells trade off physical spacing against social connectivity

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Plant cells favor efficient networks with high potential for information exchange

Linking Genes to Shape in Plants Using Morphometrics

A transition from qualitative to quantitative descriptors of morphology has been facilitated through the growing field of morphometrics, representing the conversion of shapes and patterns into numbers. The analysis of plant form at the macromorphological scale using morphometric approaches quantifies what is commonly referred to as a phenotype. Quantitative phenotypic analysis of individuals with contrasting genotypes in turn provides a means to establish links between genes and shapes. The path from a gene to a morphological phenotype is, however, not direct, with instructive information progressing both across multiple scales of biological complexity and through nonintuitive feedback, such as mechanical signals. In this review, we explore morphometric approaches used to perform whole-plant phenotyping and quantitative approaches in capture processes in the mesoscales, which bridge the gaps between genes and shapes in plants. Quantitative frameworks involving both the computational simulation and the discretization of data into networks provide a putative path to predicting emergent shape from underlying genetic programs.

Quantification of plant morphology and leaf thickness with optical coherence tomography

Optical coherence tomography (OCT) can be a valuable imaging tool for in vivo and label-free digital plant phenotyping. However, for imaging leaves, air-filled cavities limit the penetration depth and reduce the image quality. Moreover, up to now quantification of leaf morphology with OCT has been done in one-dimensional or two-dimensional images only, and has often been limited to relative measurements. In this paper, we demonstrate a significant increase in OCT imaging depth and image quality by infiltrating the leaf air spaces with water. In the obtained high-quality OCT images the top and bottom surface of the leaf are digitally segmented. Moreover, high-quality en face images of the leaf are obtained from numerically flattened leaves. Segmentation in three-dimensional OCT images is used to quantify the spatially resolved leaf thickness. Based on a segmented leaf image, the refractive index of an infiltrated leaf is measured to be 1.345±0.004, deviating only 1.2% from that of pure water. Using the refractive index and a correction for refraction effects at the air-leaf interface, we quantitatively mapped the leaf thickness. The results show that OCT is an efficient and promising technique for quantitative phenotyping on leaf and tissue level.

Live imaging of microtubules in petal conical cells

The microtubule cytoskeleton plays an important role in cell shape and plant development. During the past decades, the ability to use confocal microcopy to observe microtubules in living cells using fluorescent protein fusions has given plant scientists the opportunity to answer outstanding biological questions. Plants contain diverse epidermal cells with distinct morphologies and physiological functions. For example, flowering plants have specialized petal conical cells that likely facilitate functions such as providing grips for bee pollinators. Here, we summarize recent progress on live imaging of the microtubule cytoskeleton in conical cells. Firstly, we present a simple method for live-cell confocal imaging of conical cells, which is suitable for the quantification of the cell geometry. Secondly, we describe a method for observing microtubule organization in conical cells of Arabidopsis thaliana expressing green fluorescent protein (GFP)-tagged α-tubulin 6 (GFP-TUA6). These live imaging approaches are likely to lead to rapid advances in our knowledge of the role of microtubules in conical cell shaping.

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.

Imaging plant germline differentiation within Arabidopsis flowers by light sheet microscopy

In higher plants, germline differentiation occurs during a relatively short period within developing flowers. Understanding of the mechanisms that govern germline differentiation lags behind other plant developmental processes. This is largely because the germline is restricted to relatively few cells buried deep within floral tissues, which makes them difficult to study. To overcome this limitation, we have developed a methodology for live imaging of the germ cell lineage within floral organs of Arabidopsis using light sheet fluorescence microscopy. We have established reporter lines, cultivation conditions, and imaging protocols for high-resolution microscopy of developing flowers continuously for up to several days. We used multiview imagining to reconstruct a three-dimensional model of a flower at subcellular resolution. We demonstrate the power of this approach by capturing male and female meiosis, asymmetric pollen division, movement of meiotic chromosomes, and unusual restitution mitosis in tapetum cells. This method will enable new avenues of research into plant sexual reproduction.

In silico study of the role of cell growth factors in photosynthesis using a virtual leaf tissue generator coupled to a microscale photosynthesis gas exchange model

Computational tools that allow in silico analysis of the role of cell growth and division on photosynthesis are scarce. We present a freely available tool that combines a virtual leaf tissue generator and a two-dimensional microscale model of gas transport during C3 photosynthesis. A total of 270 mesophyll geometries were generated with varying degrees of growth anisotropy, growth extent, and extent of schizogenous airspace formation in the palisade mesophyll. The anatomical properties of the virtual leaf tissue and microscopic cross-sections of actual leaf tissue of tomato (Solanum lycopersicum L.) were statistically compared. Model equations for transport of CO2 in the liquid phase of the leaf tissue were discretized over the geometries. The virtual leaf tissue generator produced a leaf anatomy of tomato that was statistically similar to real tomato leaf tissue. The response of photosynthesis to intercellular CO2 predicted by a model that used the virtual leaf tissue geometry compared well with measured values. The results indicate that the light-saturated rate of photosynthesis was influenced by interactive effects of extent and directionality of cell growth and degree of airspace formation through the exposed surface of mesophyll per leaf area. The tool could be used further in investigations of improving photosynthesis and gas exchange in relation to cell growth and leaf anatomy.

Cortical Microtubule Organization during Petal Morphogenesis in Arabidopsis

Cortical microtubules guide the direction and deposition of cellulose microfibrils to build the cell wall, which in turn influences cell expansion and plant morphogenesis. In the model plant Arabidopsis thaliana (Arabidopsis), petal is a relatively simple organ that contains distinct epidermal cells, such as specialized conical cells in the adaxial epidermis and relatively flat cells with several lobes in the abaxial epidermis. In the past two decades, the Arabidopsis petal has become a model experimental system for studying cell expansion and organ morphogenesis, because petals are dispensable for plant growth and reproduction. Recent advances have expanded the role of microtubule organization in modulating petal anisotropic shape formation and conical cell shaping during petal morphogenesis. Here, we summarize recent studies showing that in Arabidopsis, several genes, such as SPIKE1, Rho of plant (ROP) GTPases, and IPGA1, play critical roles in microtubule organization and cell expansion in the abaxial epidermis during petal morphogenesis. Moreover, we summarize the live-confocal imaging studies of Arabidopsis conical cells in the adaxial epidermis, which have emerged as a new cellular model. We discuss the microtubule organization pattern during conical cell shaping. Finally, we propose future directions regarding the study of petal morphogenesis and conical cell shaping.

Long-term live-cell imaging approaches to study lateral root formation in Arabidopsis thaliana

Lateral roots comprise the majority of the branching root system and are important for acquiring nutrients and water from soil in addition to providing anchorage. Lateral roots develop post-embryonically from existing root parts and originate from a subset of specified pericycle cells (lateral root founder cells) located deep inside roots. Small numbers of these specified pericycle cells undergo several rounds of cell division to create a dome-shaped primordium, which eventually organizes a meristem, an essential region for plant growth with active cell division, and emerges from its parental root as a lateral root. Observing cellular and molecular processes for an extended time at various scales are crucial for understanding biological processes during organogenesis. Lateral root formation is an example of the successful application of live-cell imaging approaches to understand various aspects of developmental events in plants, including cell fate determination, cell proliferation, cell-to-cell interaction and cell wall modification. Here I review the recent progress in understanding the molecular mechanisms of lateral root formation and the contribution of live-cell imaging approaches.

Growth and biomechanics of shoot organs

Plant organs arise through complex interactions between biological and physical factors that control morphogenesis. While there has been tremendous progress in the understanding of the genetics behind development, we know much less about how mechanical forces control growth in plants. In recent years, new multidisciplinary research combining genetics, live-imaging, physics, and computational modeling has begun to fill this gap by revealing the crucial role of biomechanics in the establishment of plant organs. In this review, we provide an overview of our current understanding of growth during initiation, patterning, and expansion of shoot lateral organs. We discuss how growth is controlled by physical forces, and how mechanical stresses generated during growth can control morphogenesis at the level of both cells and tissues. Understanding the mechanical basis of growth and morphogenesis in plants is in its early days, and many puzzling facts are yet to be deciphered.

Multicellular Systems Biology: Quantifying Cellular Patterning and Function in Plant Organs Using Network Science

Organ function is at least partially shaped and constrained by the organization of their constituent cells. Extensive investigation has revealed mechanisms explaining how these patterns are generated, with less being known about their functional relevance. In this paper, a methodology to discretize and quantitatively analyze cellular patterning is described. By performing global organ-scale cellular interaction mapping, the organization of cells can be extracted and analyzed using network science. This provides a means to take the developmental analysis of cellular organization in complex organisms beyond qualitative descriptions and provides data-driven approaches to inferring cellular function. The bridging of a structure-function relationship in hypocotyl epidermal cell patterning through global topological analysis provides support for this approach. The analysis of cellular topologies from patterning mutants further enables the contribution of gene activity toward the organizational properties of tissues to be linked, bridging molecular and tissue scales. This systems-based approach to investigate multicellular complexity paves the way to uncovering the principles of complex organ design and achieving predictive genotype-phenotype mapping.

A Simple Protocol for Imaging Floral Tissues of Arabidopsis with Confocal Microscopy

We present a simple protocol to image floral tissues with confocal laser scanning microscopy (CLSM). Recently, new imaging techniques have emerged that improve the image quality of plant tissues. In this protocol, as an example, we focus on the fluorescence detection of the miRNA MIR164c precursor. Briefly, the method involves tissue clearing, cell wall staining, and the visualization of fluorescence in tissues in young floral buds of Arabidopsis with CLSM with the use of water dipping lenses.

Leaf development and evolution

Plant leaves are differentiated organs that arise sequentially from a population of pluripotent stem cells at the shoot apical meristem (SAM). There is substantial diversity in leaf shape, much of which depends on the size and arrangement of outgrowths at the leaf margin. These outgrowths are generated by a patterning mechanism similar to the phyllotactic processes producing organs at the SAM, which involves the transcription factors CUP-SHAPED COTYLEDON and the phytohormone auxin. In the leaf, this patterning mechanism creates sequential protrusions and indentations along the margin. The size, shape, and distribution of these protrusions also depend on the overall growth of the leaf lamina. Globally, growth is regulated by a complex genetic network controlling the distribution of cell proliferation and the timing of differentiation. Evolutionary changes in margin form arise from changes in two different classes of homeobox genes that modify the outcome of marginal patterning in diverse ways, and are under intense investigation.

Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument's ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

3D Reconstruction of Lipid Droplets in the Seed of Brassica napus

Rapeseed is one of the most important and widely cultured oilseed crops for food and nonfood purposes worldwide. Neutral lipids are stored in lipid droplets (LDs) as fuel for germination and subsequent seedling growth. Most of the LD detection in seeds was still in 2D levels, and some of the details might have been lost in previous studies. In the present work, the configuration of LDs in seeds was obtained by confocal imaging combined with 3D reconstruction technology in Brassica napus. The size and shape of LDs, LD numbers, cell interval spaces and cell size were observed and compared at 3D levels in the seeds of different materials with high and low oil content. It was also revealed that different cells located in the same tissue exhibited various oil contents according to the construction at the 3D level, which was not previously reported in B. napus. The present work provides a new way to understand the differential in cell populations and enhance the seed oil content at the single cell level within seeds.

Network-based approaches to quantify multicellular development

Multicellularity and cellular cooperation confer novel functions on organs following a structure-function relationship. How regulated cell migration, division and differentiation events generate cellular arrangements has been investigated, providing insight into the regulation of genetically encoded patterning processes. Much less is known about the higher-order properties of cellular organization within organs, and how their functional coordination through global spatial relations shape and constrain organ function. Key questions to be addressed include: why are cells organized in the way they are? What is the significance of the patterns of cellular organization selected for by evolution? What other configurations are possible? These may be addressed through a combination of global cellular interaction mapping and network science to uncover the relationship between organ structure and function. Using this approach, global cellular organization can be discretized and analysed, providing a quantitative framework to explore developmental processes. Each of the local and global properties of integrated multicellular systems can be analysed and compared across different tissues and models in discrete terms. Advances in high-resolution microscopy and image analysis continue to make cellular interaction mapping possible in an increasing variety of biological systems and tissues, broadening the further potential application of this approach. Understanding the higher-order properties of complex cellular assemblies provides the opportunity to explore the evolution and constraints of cell organization, establishing structure-function relationships that can guide future organ design.

Spatio-temporal orientation of microtubules controls conical cell shape in Arabidopsis thaliana petals

The physiological functions of epidermal cells are largely determined by their diverse morphologies. Most flowering plants have special conical-shaped petal epidermal cells that are thought to influence light capture and reflectance, and provide pollinator grips, but the molecular mechanisms controlling conical cell shape remain largely unknown. Here, we developed a live-confocal imaging approach to quantify geometric parameters of conical cells in Arabidopsis thaliana (A. thaliana). Through genetic screens, we identified katanin (KTN1) mutants showing a phenotype of decreased tip sharpening of conical cells. Furthermore, we demonstrated that SPIKE1 and Rho of Plants (ROP) GTPases were required for the final shape formation of conical cells, as KTN1 does. Live-cell imaging showed that wild-type cells exhibited random orientation of cortical microtubule arrays at early developmental stages but displayed a well-ordered circumferential orientation of microtubule arrays at later stages. By contrast, loss of KTN1 prevented random microtubule networks from shifting into well-ordered arrays. We further showed that the filamentous actin cap, which is a typical feature of several plant epidermal cell types including root hairs and leaf trichomes, was not observed in the growth apexes of conical cells during cell development. Moreover, our genetic and pharmacological data suggested that microtubules but not actin are required for conical cell shaping. Together, our results provide a novel imaging approach for studying petal conical cell morphogenesis and suggest that the spatio-temporal organization of microtubule arrays plays crucial roles in controlling conical cell shape.

How cells achieve their final shapes is a fundamental question in biology. Most flowering plants have special conical-shaped petal epidermal cells that are thought to attract pollinators, but the molecular and genetic mechanisms that control conical cell shape remain unknown. In this study, we developed a live-confocal imaging approach for the quantitative study of conical cell morphogenesis. Through genetic screens, we showed that A. thaliana KTN1, ROP GTPases, and SPIKE1 are required for conical cell shaping. Live-cell imaging showed that loss of KTN1 prevented random microtubule networks from shifting into well-ordered microtubule arrays at later developmental stages, which is correlated with the tip sharpening of conical cells. Moreover, genetic and pharmacological data suggested that microtubules but not actin are required for conical cell shaping. Together, our findings provide significant insights into the spatio-temporal organization of microtubules that controls conical cell development.

Analysis of 3D Cellular Organization of Fixed Plant Tissues Using a User-guided Platform for Image Segmentation

The advent of non-invasive, high-resolution microscopy imaging techniques and computational pipelines for high-throughput image processing has contributed to gain insights in plant organ morphogenesis at the cellular level. Confocal scanning laser microscopy (CSLM) allows the generation of three dimensional images constituted of serial optical sections reporting on stained subcellular structures. Fluorescent labels of cell walls or cell membranes, either chemically or through reporter proteins, are particularly useful for the analyses of tissue organization and cellular shapes in 3D. Image segmentation based on cell boundary signals is used as an input to generate 3D-segments representing cells. These digitalized, 3D objects provide quantitative data on cell shape, size, geometry, position or on (intercellular) intensity signals if additional reporters are used. Herein, we report a detailed, annotated workflow for image segmentation using microscopic data. We used it in the context of a study of tissue patterning during ovule primordium development in Arabidopsis thaliana. Whole carpels are stained for cell boundaries using a modified pseudo-Schiff propidium iodide (mPS-PI) protocol, 3D images are acquired at high resolution by CSLM, segmented and annotated for individual cell types using ImarisCell. This allows for quantitative analyses of cell shape and cell number that are relevant for tissue morphodynamic studies.

DRACO-STEM: An Automatic Tool to Generate High-Quality 3D Meshes of Shoot Apical Meristem Tissue at Cell Resolution

Context: The shoot apical meristem (SAM), origin of all aerial organs of the plant, is a restricted niche of stem cells whose growth is regulated by a complex network of genetic, hormonal and mechanical interactions. Studying the development of this area at cell level using 3D microscopy time-lapse imaging is a newly emerging key to understand the processes controlling plant morphogenesis. Computational models have been proposed to simulate those mechanisms, however their validation on real-life data is an essential step that requires an adequate representation of the growing tissue to be carried out. Achievements: The tool we introduce is a two-stage computational pipeline that generates a complete 3D triangular mesh of the tissue volume based on a segmented tissue image stack. DRACO (Dual Reconstruction by Adjacency Complex Optimization) is designed to retrieve the underlying 3D topological structure of the tissue and compute its dual geometry, while STEM (SAM Tissue Enhanced Mesh) returns a faithful triangular mesh optimized along several quality criteria (intrinsic quality, tissue reconstruction, visual adequacy). Quantitative evaluation tools measuring the performance of the method along those different dimensions are also provided. The resulting meshes can be used as input and validation for biomechanical simulations. Availability: DRACO-STEM is supplied as a package of the open-source multi-platform plant modeling library OpenAlea (http://openalea.github.io/) implemented in Python, and is freely distributed on GitHub (https://github.com/VirtualPlants/draco-stem) along with guidelines for installation and use.

In-vivo analysis of morphogenesis in plants

Although many molecular regulators of morphogenesis have been identified in plants, it remains largely unknown how the molecular networks influence local cell shape and how cell growth, form, and position are coordinated during tissue and organ formations. So far, analyses of gene function in morphogenesis have mainly focused on the qualitative analysis of phenotypes, often providing limited mechanistic insight into how particular factors act. For this reason, there has been a growing interest in mathematical and computational models to formalize and test hypotheses. These require much more rigorous, quantitative approaches; in parallel, new quantitative and correlative imaging pipelines have been developed to study morphogenesis. Here, we describe a number of such methods, focusing on live imaging.

A method to generate the surface cell layer of the 3D virtual shoot apex from apical initials

BACKGROUND

The development of cell pattern in the surface cell layer of the shoot apex can be investigated in vivo by use of a time-lapse confocal images, showing naked meristem in 3D in successive times. However, how this layer is originated from apical initials and develops as a result of growth and divisions of their descendants, remains unknown. This is an open area for computer modelling. A method to generate the surface cell layer is presented on the example of the 3D paraboloidal shoot apical dome. In the used model the layer originates from three apical initials that meet at the dome summit and develops through growth and cell divisions under the isotropic surface growth, defined by the growth tensor. The cells, which are described by polyhedrons, divide anticlinally with the smallest division plane that passes depending on the used mode through the cell center, or the point found randomly near this center. The formation of the surface cell pattern is described with the attention being paid to activity of the apical initials and fates of their descendants.

RESULTS

The computer generated surface layer that included about 350 cells required about 1200 divisions of the apical initials and their derivatives. The derivatives were arranged into three more or less equal clonal sectors composed of cellular clones at different age. Each apical initial renewed itself 7-8 times to produce the sector. In the shape and location and the cellular clones the following divisions of the initial were manifested. The application of the random factor resulted in more realistic cell pattern in comparison to the pure mode. The cell divisions were analyzed statistically on the top view. When all of the division walls were considered, their angular distribution was uniform, whereas in the distribution that was limited to apical initials only, some preferences related to their arrangement at the dome summit were observed.

CONCLUSIONS

The realistic surface cell pattern was obtained. The present method is a useful tool to generate surface cell layer, study activity of initial cells and their derivatives, and how cell expansion and division are coordinated during growth. We expect its further application to clarify the question of a number and permanence or impermanence of initial cells, and possible relationship between their shape and oriented divisions, both on the ground of the growth tensor approach.

3D Imaging of Whole-Mount Ovules at Cellular Resolution to Study Female Germline Development in Rice

Recent advances in fluorescence-based staining of cellular compartments coupled with confocal microscopy imaging have allowed the visualization of three-dimensional (3D) structures with cellular resolution in various intact plant tissues and species. Such approaches are of particular interest for the analysis of the reproductive lineage in plants including the meiotic precursor cells deeply embedded within the ovary of the gynoecium enclosed in the flower. Yet, their relative inaccessibility and the lack of optical clarity of plant tissues prevent robust staining and imaging across several cell layers. Several whole-mount tissue staining and clearing techniques are available. One of them specifically allows staining of cellular boundaries in thick tissue samples while providing extreme optical clarity, using an acidic treatment followed by a modified Pseudo-Schiff propidium iodide (mPS-PI) method. While commonly used for Arabidopsis tissues, its application to other species like the model crop rice required protocol adaptations for obtaining robust staining that we present here. The procedure comprises six steps: (a) Material sampling; (b) Material fixation; (c) Tissue preparation; (d) Staining; (e) Sample mounting; and (d) Microscopy imaging. Particularly, we use ethanol and acetic anhydride as fixative reagents. A modified enzymatic treatment proved essential for starch degradation influencing optical clarity hence allowing acquisition of images at high resolution. This improved protocol is efficient for analyzing the megaspore mother cells in rice (Oryza sativa) ovary but is broadly applicable to other crop tissues of complex composition, without the need for tissue sectioning.

Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity

Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.

Emerging concepts in chromatin-level regulation of plant cell differentiation: timing, counting, sensing and maintaining

Plants are characterized by a remarkable phenotypic plasticity that meets the constraints of a sessile lifestyle and the need to adjust constantly to the environment. Recent studies have begun to reveal how chromatin dynamics participate in coordinating cell proliferation and differentiation in response to developmental cues as well as environmental fluctuations. In this review, we discuss the pivotal function of chromatin-based mechanisms in cell fate acquisition and maintenance, within as well as outside meristems. In particular, we highlight the emerging role of specific epigenomic factors and chromatin pathways in timing the activity of stem cells, counting cell divisions and positioning cell fate transitions by sensing phytohormone gradients.

25 Years of Cell Cycle Research: What's Ahead?

We have reached 25 years since the first molecular approaches to plant cell cycle. Fortunately, we have witnessed an enormous advance in this field that has benefited from using complementary approaches including molecular, cellular, genetic and genomic resources. These studies have also branched and demonstrated the functional relevance of cell cycle regulators for virtually every aspect of plant life. The question is - where are we heading? I review here the latest developments in the field and briefly elaborate on how new technological advances should contribute to novel approaches that will benefit the plant cell cycle field. Understanding how the cell division cycle is integrated at the organismal level is perhaps one of the major challenges.