Quantifying leaf venation patterns: two-dimensional maps

The leaf vasculature plays crucial roles in transport and mechanical support. Understanding how vein patterns develop and what underlies pattern variation between species has many implications from both physiological and evolutionary perspectives. We developed a method for extracting spatial vein pattern data from leaf images, such as vein densities and also the sizes and shapes of the vein reticulations. We used this method to quantify leaf venation patterns of the first rosette leaf of Arabidopsis thaliana throughout a series of developmental stages. In particular, we characterized the size and shape of vein network areoles (loops), which enlarge and are split by new veins as a leaf develops. Pattern parameters varied in time and space. In particular, we observed a distal to proximal gradient in loop shape (length/width ratio) which varied over time, and a margin-to-center gradient in loop sizes. Quantitative analyses of vein patterns at the tissue level provide a two-way link between theoretical models of patterning and molecular experimental work to further explore patterning mechanisms during development. Such analyses could also be used to investigate the effect of environmental factors on vein patterns, or to compare venation patterns from different species for evolutionary studies. The method also provides a framework for gathering and overlaying two-dimensional maps of point, line and surface morphological data.     

Inducible Repression of Multiple Expansin Genes Leads to Growth Suppression during Leaf Development

Expansins are cell wall proteins implicated in the control of plant growth via loosening of the extracellular matrix. They are encoded by a large gene family, and data linked to loss of single gene function to support a role of expansins in leaf growth remain limited. Here, we provide a quantitative growth analysis of transgenics containing an inducible artificial microRNA construct designed to down-regulate the expression of a number of expansin genes that an expression analysis indicated are expressed during the development of Arabidopsis (Arabidopsis thaliana) leaf 6. The results support the hypothesis that expansins are required for leaf growth and show that decreased expansin gene expression leads to a more marked repression of growth during the later stage of leaf development. In addition, a histological analysis of leaves in which expansin gene expression was suppressed indicates that, despite smaller leaves, mean cell size was increased. These data provide functional evidence for a role of expansins in leaf growth, indicate the importance of tissue/organ developmental context for the outcome of altered expansin gene expression, and highlight the separation of the outcome of expansin gene expression at the cellular and organ levels.     

Quantifying Shape Changes and Tissue Deformation in Leaf Development

The analysis of biological shapes has applications in many areas of biology, and tools exist to quantify organ shape and detect shape differences between species or among variants. However, such measurements do not provide any information about the mechanisms of shape generation. Quantitative data on growth patterns may provide insights into morphogenetic processes, but since growth is a complex process occurring in four dimensions, growth patterns alone cannot intuitively be linked to shape outcomes. Here, we present computational tools to quantify tissue deformation and surface shape changes over the course of leaf development, applied to the first leaf of Arabidopsis (Arabidopsis thaliana). The results show that the overall leaf shape does not change notably during the developmental stages analyzed, yet there is a clear upward radial deformation of the leaf tissue in early time points. This deformation pattern may provide an explanation for how the Arabidopsis leaf maintains a relatively constant shape despite spatial heterogeneities in growth. These findings highlight the importance of quantifying tissue deformation when investigating the control of leaf shape. More generally, experimental mapping of deformation patterns may help us to better understand the link between growth and shape in organ development.The analysis of biological shapes is a field of broad interest, with diverse applications ranging from medical imaging to comparative anatomy and botany (Lestrel, 2011). Within plant biology, the wide variation of leaf shapes among species has long intrigued evolutionary biologists, physiologists, and developmental biologists alike. Leaves typically develop into flat structures that maximize photosynthetic surface, with variations that may help to facilitate gas exchange, offset water loss, improve convective cooling, increase mechanical support, or reduce resistance to physical environmental forces, for example (for review, see Tsukaya, 2006; Cronk, 2009). The processes controlling leaf shape development, therefore, are important to plant survival and biomass accumulation and hence have important agricultural implications.Understanding how leaf shape is controlled typically involves studying shape variation among related species and in shape mutants and requires tools to quantify phenotypic differences. In recent years, several sophisticated semiautomatic methods have been developed to analyze leaf shapes in terms of their two-dimensional (2D) profiles. Analyses range from simple length and width measurements and allometric ratios to statistical analysis of outline coordinates (Langlade et al., 2005; Bylesjö et al., 2008; Weight et al., 2008; Backhaus et al., 2010).Leaf shape can also be quantified in terms of a three-dimensional (3D) surface, which can range from flat to curved or ruffled, as observed in nature and in many leaf shape mutants. Approaches to 3D shape analysis based on flattened and unflattened leaf dimensions in the proximodistal and mediolateral axes have been presented by Liu et al. (2010) and Wu et al. (2007). Kaminuma et al. (2004) developed a technique for obtaining coordinates of the leaf surface in vivo, from which they measured the angle of the surface across the leaf and fit curves along the leaf proximodistal and mediolateral axes to characterize blade epinasty.These existing methods for leaf shape analysis are very useful for detecting and quantitatively describing shape differences, but they do not provide information about the underlying mechanisms that give rise to those shape differences. For example, the correspondence between evenly spaced outline points (Langlade et al., 2005; Bylesjö et al., 2008; Weight et al., 2008; Backhaus et al., 2010) is arbitrary. Furthermore, existing work has not provided an analysis of leaf shape in terms of both 2D and 3D phenotypic features together, and with the exception of Kaminuma et al. (2004), the methods are destructive and cannot be used to measure changes in shape in vivo.Differences in shapes between two organs arise through differences in how the organs grow. It is impossible, however, to ascertain from differences in final organ shape what differences in growth gave rise to them, as the possible combinations of spatial and temporal alterations in growth patterns that could be responsible for the final shape are endless. By the same token, it can be difficult to conceptualize from growth patterns how the interconnected tissues will deform and, thus, how overall organ shape will change.To address this issue, Kennaway et al. (2011) recently proposed a simulation modeling framework to investigate how a shape may locally and globally deform under the control of spatially distributed growth- and polarity-regulating substances. This framework was used to hypothesize how growth and shape deformation may be controlled in flowers (Green et al., 2010; Sauret-Güeto et al., 2013) and leaves (Kuchen et al., 2012). However, to date, shape deformation patterns have not been quantified experimentally. Here, we use data collected for a study on leaf growth (Remmler and Rolland-Lagan, 2012) to develop a method for describing 3D surface shape and shape deformations during leaf development. In particular, we generate experimental maps of tissue deformation, which offer a new approach to investigating shape differences and uncovering the link between growth and shape during development.     

PIN1-Independent Leaf Initiation in Arabidopsis

Phyllotaxis, the regular arrangement of leaves and flowers around the stem, is a key feature of plant architecture. Current models propose that the spatiotemporal regulation of organ initiation is controlled by a positive feedback loop between the plant hormone auxin and its efflux carrier PIN-FORMED1 (PIN1). Consequently, pin1 mutants give rise to naked inflorescence stalks with few or no flowers, indicating that PIN1 plays a crucial role in organ initiation. However, pin1 mutants do produce leaves. In order to understand the regulatory mechanisms controlling leaf initiation in Arabidopsis (Arabidopsis thaliana) rosettes, we have characterized the vegetative pin1 phenotype in detail. We show that although the timing of leaf initiation in vegetative pin1 mutants is variable and divergence angles clearly deviate from the canonical 137° value, leaves are not positioned at random during early developmental stages. Our data further indicate that other PIN proteins are unlikely to explain the persistence of leaf initiation and positioning during pin1 vegetative development. Thus, phyllotaxis appears to be more complex than suggested by current mechanistic models.     

Studies on the Growth of Spinach Leaves (Spinacea oleracea)

The growth of spinach leaves has been studied from approximately1 cm long to full size. Over-all growth was measured in termsof area and total number of cells. The differential growth ofleaves was measured by the changes in the shape of squares drawnon the leaf surface. Growth differentials in terms of numbersof cells and number displaying mitotic figures were measuredin leaf discs taken from different positions within leaves. It was found that cell division in spinach leaves continueduntil the leaves reach from one-third to one-half full size.Cell division within the lamina of the leaves was not uniformbut ceased at an early stage of development in the leaf tipregion and continued for an extended period at the base.     

拟南芥YUAN1基因调控器官形状和大小

器官形状和大小的控制是一个基本的发育生物学过程, 受细胞分裂和细胞扩展的影响。到目前为止, 人们对植物器官形状和大小的调控机制知之甚少。本实验室前期研究发现了一个种子和器官大小的调控基因DA1, 其编码一个泛素受体。在拟南芥(Arabidopsis thaliana)中, DA1通过抑制细胞的分裂来限制种子和器官的大小。本研究通过激活标签的方法在da1-1突变体背景下筛选到一个叶子形状发生改变的半显性突变体(yuan1-1D)。yuan1-1D形成短而圆的叶片和短的叶柄, 细胞学分析显示, 叶片和叶柄变短的主要原因是细胞的长向扩展降低导致的。YUAN1编码一个含有PHD锌指结构域的蛋白。GFP-YUAN1融合蛋白定位在细胞核内。过量表达YUAN1基因导致叶片和叶柄变短。遗传学分析显示, YUAN1和DA1、ROT3以及ROT4在控制叶片形状和大小方面作用于不同的遗传途径中。因此, 本研究鉴定了一个新的控制器官形状和大小的基因YUAN1, 为阐明植物器官形状和大小调控的分子机制提供了重要线索。     

Cellulose orientation at the surface of the Arabidopsis seedling. Implications for the biomechanics in plant development

In diffuse growing cells the orientation of cellulose fibrils determines mechanical anisotropy in the cell wall and hence also the direction of plant and organ growth. This paper reports on the mean or net orientation of cellulose fibrils in the outer epidermal wall of the whole Arabidopsis plant. This outer epidermal wall is considered as the growth-limiting boundary between plant and environment. In the root a net transverse orientation of the cellulose fibrils occurs in the elongation zone, while net random and longitudinal orientations are found in subsequent older parts of the differentiation zone. The position and the size of the transverse zone is related with root growth rate. In the shoot the net orientation of cellulose fibrils is transverse in the elongating apical part of the hypocotyl, and longitudinal in the fully elongated basal part. Leaf primordia and very young leaves have a transverse orientation. Throughout further development the leaf epidermis builds a very complex pattern of cells with a random orientation and cells with a transverse or a longitudinal orientation of the cellulose fibrils. The patterns of net cellulose orientation correlate well with the cylindrical growth of roots and shoots and with the typical planar growth of the leaf blade. On both the shoot and the root surface very specific patterns of cellulose orientation occur at sites of specific cell differentiation: trichome-socket cells complexes on the shoot and root hairs on the root.     

Whole organ, venation and epidermal cell morphological variations are correlated in the leaves of Arabidopsis mutants

Despite the large number of genes known to affect leaf shape or size, we still have a relatively poor understanding of how leaf morphology is established. For example, little is known about how cell division and cell expansion are controlled and coordinated within a growing leaf to eventually develop into a laminar organ of a definite size. To obtain a global perspective of the cellular basis of variations in leaf morphology at the organ, tissue and cell levels, we studied a collection of 111 non-allelic mutants with abnormally shaped and/or sized leaves, which broadly represent the mutational variations in Arabidopsis thaliana leaf morphology not associated with lethality. We used image-processing techniques on these mutants to quantify morphological parameters running the gamut from the palisade mesophyll and epidermal cells to the venation, whole leaf and rosette levels. We found positive correlations between epidermal cell size and leaf area, which is consistent with long-standing Avery's hypothesis that the epidermis drives leaf growth. In addition, venation parameters were positively correlated with leaf area, suggesting that leaf growth and vein patterning share some genetic controls. Positional cloning of the genes affected by the studied mutations will eventually establish functional links between genotypes, molecular functions, cellular parameters and leaf phenotypes.     

Initiation of axillary and floral meristems in Arabidopsis

Shoot development is reiterative: shoot apical meristems (SAMs) give rise to branches made of repeating leaf and stem units with new SAMs in turn formed in the axils of the leaves. Thus, new axes of growth are established on preexisting axes. Here we describe the formation of axillary meristems and floral meristems in Arabidopsis by monitoring the expression of the SHOOT MERISTEMLESS and AINTEGUMENTA genes. Expression of these genes is associated with SAMs and organ primordia, respectively. Four stages of axillary meristem development and previously undefined substages of floral meristem development are described. We find parallels between the development of axillary meristems and the development of floral meristems. Although Arabidopsis flowers develop in the apparent absence of a subtending leaf, the expression patterns of AINTEGUMENTA and SHOOT MERISTEMLESS RNAs during flower development suggest the presence of a highly reduced, "cryptic" leaf subtending the flower in Arabidopsis. We hypothesize that the STM-negative region that develops on the flanks of the inflorescence meristem is a bract primordium and that the floral meristem proper develops in the "axil" of this bract primordium. The bract primordium, although initially specified, becomes repressed in its growth.     

Quantitative trait loci mapping of floral and leaf morphology traits in Arabidopsis thaliana: evidence for modular genetic architecture

Summary Morphological variation within organisms is integrated and often modular in nature. That is to say, the size and shape of traits tend to vary in a coordinated and structured manner across sets of organs or parts of an organism. The genetic basis of this morphological integration is largely unknown. Here, we report on quantitative trait loci (QTL) analysis of leaf and floral organ size in Arabidopsis thaliana. We evaluate patterns of genetic correlations among traits and perform whole-genome scans using QTL mapping methods. We detected significant genetic variation for the size and shape of each floral and leaf trait in our study. Moreover, we found large positive genetic correlations among sets of either flower or leaf traits, but low and generally nonsignificant genetic correlations between flower and leaf traits. These results support the hypothesis of independent floral and vegetative modules. We consider co-localization of QTL for different traits as support for a pleiotropic basis of morphological integration and modularity. A total of eight QTL affecting flower and three QTL affecting leaf traits were identified. Most QTL affected either floral or leaf traits, providing a general explanation for high correlations within and low correlations between modules. Only two genomic locations affected both flower and leaf growth. These results are discussed in the context of the evolution of modules, pleiotropy, and the putative homologous relationship between leaves and flowers.     

Organ shape and size: a lesson from studies of leaf morphogenesis

Control of the shape and size of indeterminate organs, such as roots and stems, is directly related to the control of the shape and size of the cells in these organs, as predicted by orthodox cell theory. For example, the polarity-dependent growth of leaf cells directly affects the polar expansion of leaves. Thus, the control of leaf shape is related to the control of the shape of cells within the leaf, as suggested by cell theory. By contrast, in determinate organs, such as leaves, the number of cells does not necessarily reflect organ shape or size. Genetic evidence shows that a compensatory system(s) is involved in leaf morphogenesis, and that an increase in cell volume can be triggered by a decrease in cell number and vice versa. Studies of chimeric leaves also suggest interaction between leaf cells that coordinates the behaviour of these cells at the organ level. Moreover, leaf size also appears to be coordinated at the whole-plant level. The recently hypothesised neo cell theory describes how leaf shape- and size-control mechanisms control leaf shape at the organ-level via cell-cell interaction.     

The Arabidopsis embryonic shoot fate map

A fate map has been constructed for the shoot apical region of the embryo of the dicotyledonous plant Arabidopsis thaliana using spontaneously arising clonal albino sectors caused by the chloroplast mutator 1-2 mutation. Chimeric seedlings exhibiting albino sectors shared between the cotyledons and first true leaves revealed patterns of organ inclusion and exclusion. Frequencies of clone sharing were used to calculate developmental distances between organs based on the frequency of clonal sectors failing to extend between different organs. The resulting fate map shows asymmetry in the developmental distances between the cotyledons (embryonic leaves) which in turn predicts the location of the first post-germination leaf and the handedness of the spiral of leaf placement around the central stem axis in later development. The map suggests that embryonic leaf fate specification in the cotyledons may represent a developmental ground state necessary for the formation of the shoot apical meristem.     

LeafAnalyser: a computational method for rapid and large-scale analyses of leaf shape variation

A comprehensive understanding of leaf shape is important in many investigations in plant biology. Techniques to assess variation in leaf shape are often time-consuming, labour-intensive and prohibited by complex calculation of large data sets. We have developed LeafAnalyser, software that uses image-processing techniques to greatly simplify the measurement of leaf shape variation. LeafAnalyser places a large number of evenly distributed landmarks along leaf margins and records the position of each automatically. We used LeafAnalyser to analyse the variation in 3000 leaves from 400 plants of Antirrhinum majus . We were able to summarise the major trends in leaf shape variation using a principal components (PC) analysis and assess the changes in size, width and tip-to-base asymmetry within our leaf library. We demonstrate how this information can be used to develop a model that describes the range and variation of leaf shape within standard wild-type lines, and illustrate the shape transformations that occur between leaf nodes. We also show that information from LeafAnalyser can be used to identify novel trends in shape variation, as low-variance PCs that only affect a subset of position landmarks. These results provide a high-throughput method to calculate leaf shape variation that allows a large number of leaves to be visualised in higher-dimensional phenotypic space. To illustrate the applicability of LeafAnalyser we also calculated the leaf shape variation in 300 leaves from Arabidopsis thaliana .     

Genome-Dependent Factors in the Development of Leaf Phototrophic Tissues in Diploid and Alloploid Wheat Species

Growth and mesostructure of the photosynthetic apparatus were studied in leaves of ten Triticum L. species. Plants with the A^u genome were shown to develop larger leaf assimilation areas due to expanding areas of individual leaves and an increase in the absolute growth rate. Leaf and mesophyll thickness and mesophyll cell size decreased in the G-genome species. Leaf compactness, which depended on cell size and number per unit leaf area and leaf folding, determined the specific patterns of internal leaf organization in wheat species with diverse genotypes. These patterns did not affect cell plastid-to-cytoplasm ratio as shown by the stable indices of cell surface area/cell volume, cell surface area per chloroplast, and cell volume per chloroplast. The structural indices of leaf phototrophic tissues, mesophyll density, and mesophyll CO₂ conductance in alloploids, as compared to diploid species, depended on both ploidy and genome constitution.     

Targeted manipulation of leaf form via local growth repression

A classical view is that leaf shape is the result of local promotion of growth linked to cell proliferation. However, an alternative hypothesis is that leaf form is the result of local repression of growth in an otherwise growing system. Here we show that leaf form can indeed be manipulated in a directed fashion by local repression of growth. We show that targeting expression of an inhibitor of a cyclin-dependent kinase (KRP1) to the sinus area of developing leaves of Arabidopsis leads to local growth repression and the formation of organs with extreme lobing, including generation of leaflet-like organs. Directing KRP1 expression to other regions of the leaf using an miRNA target sequence tagging approach also leads to predictable novel leaf forms, and repression of growth in the leaf margin blocks the outgrowth of lobes, leading to a smoother perimeter. In addition, we show that decreased growth around the perimeter and across the leaf abaxial surface leads to a change in 3D form, as predicted by mechanical models of leaf growth. Our analysis provides experimental evidence that local repression of growth influences leaf shape, suggesting that it could be part of the mechanism of morphogenesis in plants in the context of an otherwise growing system.     

Biological Properties,Trunk Anatomy and Growth Patterns of Cycas panzhihuaensis

Cycas panzhihuaensis L. Zhou et S. Y. Yang is a rare and endangered Cycad that grows in dry-hot valley of Jinsha River. The biological properties, trunk anatomy and growth patterns were studied by field investigation and location observation. The results showed as follows: The sex ratio of cones was strongly male based on reproductive episode. There were no significant sexual differences in leaf number, leaf size, trunk size and ramet number. More than 70% of the adult plants produce ramets, with a mean number of ramets per adult plant of about 2.8. The proportion of individuals with ramets and the number of ramets was positively correlated with trunk height. Maximum mean trunk diameter and mean number of leaves were reached when the plant reached 30--40 cm tall. Further increase of leaf width ceased when the plant reached 5 years old. Leaf reached its maximum length when the trunk was 10 cm tall. Growth units of trunk showed a linear relationship with height. The estimated age could be obtained by counting growth units of the trunk. The survival curve of leaves was well described by Deevey type Ⅰ . The survival time of many leaves was two growth units. The rate of leaf mortality abruptly increased after two growth units. Few leaves could survive five units.