Simulation of organ patterning on the floral meristem using a polar auxin transport model

Auxin and CmAP1 regulate the reproductive development of axillary buds in Chinese chestnut (Castanea mollissima)

Auxin accumulation upregulates the expression of APETALA1 (CmAP1) and subsequently activates inflorescence primordium development in axillary buds of chestnut. The architecture of fruiting branches is a key determinant of chestnut yield. Normally, axillary buds at the top of mother fruiting branches develop into flowering shoots and bear fruits, and the lower axillary buds develop into vegetative shoots. Decapitation of the upper axillary buds induces the lower buds to develop into flowering shoots. How decapitation modulates the tradeoff between vegetative and reproductive development is unclear. We detected inflorescence primordia within both upper and lower axillary buds on mother fruiting branches. The level of the phytohormones 3-indoleacetic acid (IAA) and trans-zeatin (tZ) increased in the lower axillary buds in response to decapitation. Exogenous application of the synthetic analogues 1-naphthylacetic acid (NAA) or 6-benzyladenine (6-BA) blocked or promoted, respectively, the development of the inflorescence primordia in axillary buds. The transcript levels of the floral identity gene CmAP1 increased in axillary buds following decapitation. An auxin response element TGA-box is present in the CmAP1 promoter and influenced the CmAP1 promoter-driven expression of β-glucuronidase (GUS) in floral organs in Arabidopsis, suggesting that CmAP1 is induced by auxin. We propose that decapitation releases axillary bud outgrowth from inhibition caused by apical dominance. During this process, decapitation-induced accumulation of auxin induces CmAP1 expression, subsequently promoting the reproductive development of axillary buds.

Hormones and Flower Development in Arabidopsis

Sexual reproduction requires the participation of two gametes, female and male. In angiosperms, gametes develop in specialized organs, pollen (containing the male gametes) develops in the stamens, and the ovule (containing the female gamete) develops in the gynoecium. In Arabidopsis thaliana, the female and male sexual organs are found within the same structure called flower, surrounded by the perianth, which is composed of petals and sepals. During flower development, different organs emerge in an established order and throughout their development distinct tissues within each organ are differentiated. All this requires the coordination and synchronization of several biological processes. To achieve this, hormones and genes work together. These components can interact at different levels generating hormonal interplay and both positive and negative feedback loops, which in turn, gives robustness, stability, and flexibility to flower development. Here, we summarize the progress made on elucidating the role of different hormonal pathways during flower development in Arabidopsis thaliana.

Arabidopsis TWISTED DWARF1 regulates stamen elongation by differential activation of ABCB1,19-mediated auxin transport

Despite clear evidence that a local accumulation of auxin is likewise critical for male fertility, much less is known about the components that regulate auxin-controlled stamen development. In this study, we analyzed physiological and morphological parameters in mutants of key players of ABCB-mediated auxin transport, and spatially and temporally dissected their expression on the protein level as well as auxin fluxes in the Arabidopsis stamens. Our analyses revealed that the FKBP42, TWISTED DWARF1 (TWD1), promotes stamen elongation and, to a lesser extent, anther dehiscence, as well as pollen maturation, and thus is required for seed development. Most of the described developmental defects in twd1 are shared with the abcb1 abcb19 mutant, which can be attributed to the fact that TWD1-as a described ABCB chaperone-is a positive regulator of ABCB1- and ABCB19-mediated auxin transport. However, reduced stamen number was dependent on TWD1 but not on investigated ABCBs, suggesting additional players downstream of TWD1. We predict an overall housekeeping function for ABCB1 during earlier stages, while ABCB19 seems to be responsible for the key event of rapid elongation at later stages of stamen development. Our data indicate that TWD1 controls stamen development by differential activation of ABCB1,19-mediated auxin transport in the stamen.

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.

Sex biased expression of hormone related genes at early stage of sex differentiation in papaya flowers

Sex types of papaya are controlled by a pair of nascent sex chromosomes, but molecular genetic mechanisms of sex determination and sex differentiation in papaya are still unclear. We performed comparative analysis of transcriptomic profiles of male and female floral buds at the early development stage before the initiation of reproductive organ primordia at which there is no morphological difference between male and female flowers. A total of 1734 differentially expressed genes (DEGs) were identified, of which 923 showed female-biased expression and 811 showed male-biased expression. Functional annotation revealed that genes related to plant hormone biosynthesis and signaling pathways, especially in abscisic acid and auxin pathways, were overrepresented in the DEGs. Transcription factor binding motifs, such as MYB2, GAMYB, and AP2/EREBP, were enriched in the promoters of the hormone-related DEGs, and transcription factors with those motifs also exhibited differential expression between sex types. Among these DEGs, we also identified 11 genes in the non-recombining region of the papaya sex chromosomes and 9 genes involved in stamen and carpel development. Our results suggested that sex differentiation in papaya may be regulated by multiple layers of regulation and coordination and involved transcriptional, epigenetic, and phytohormone regulation. Hormones, especially ABA and auxin, transcription factors, and genes in the non-recombination region of the sex chromosome could be involved in this process. Our findings may facilitate the elucidation of signal transduction and gene interaction in sex differentiation of unisexual flowers in papaya.

A Sight on Single-Cell Transcriptomics in Plants Through the Prism of Cell-Based Computational Modeling Approaches: Benefits and Challenges for Data Analysis

Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants' features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem's solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells' spatial localization in the initial plant organ-one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.

Auxin and Flower Development: A Blossoming Field

The establishment of the species-specific floral organ body plan involves many coordinated spatiotemporal processes, which include the perception of positional information that specifies floral meristem and floral organ founder cells, coordinated organ outgrowth coupled with the generation and maintenance of inter-organ and inter-whorl boundaries, and the termination of meristem activity. Auxin is integrated within the gene regulatory networks that control these processes and plays instructive roles at the level of tissue-specific biosynthesis and polar transport to generate local maxima, perception, and signaling. Key features of auxin function in several floral contexts include cell nonautonomy, interaction with cytokinin gradients, and the central role of MONOPTEROS and ETTIN to regulate canonical and noncanonical auxin response pathways, respectively. Arabidopsis flowers are not representative of the enormous angiosperm floral diversity; therefore, comparative studies are required to understand how auxin underlies these developmental differences. It will be of great interest to compare the conservation of auxin pathways among flowering plants and to discuss the evolutionary role of auxin in floral development.

A design principle for floral organ number and arrangement in flowers with bilateral symmetry

The bilateral symmetry of flowers is a striking morphological achievement during floral evolution, providing high adaptation potential for pollinators. The symmetry can appear when floral organ primordia developmentally initiate. Primordia initiation at the ventral and dorsal sides of the floral bud is differentially regulated by several factors, including external organs of the flower and CYCLOIDEA (CYC) gene homologues, which are expressed asymmetrically on the dorso-ventral axis. It remains unclear how these factors control the diversity in the number and bilateral arrangement of floral organs. Here, we propose a mathematical model demonstrating that the relative strength of the dorsal-to-ventral inhibitions and the size of the floral stem cell region (meristem) determines the number and positions of the sepal and petal primordia. The simulations reproduced the diversity of monocots and eudicots, including snapdragon Antirrhinum majus and its cyc mutant, with respect to organ number, arrangement and initiation patterns, which were dependent on the inhibition strength. These theoretical results suggest that diversity in floral symmetry is primarily regulated by the dorso-ventral inhibitory field and meristem size during developmental evolution.

Two-stage patterning dynamics in conifer cotyledon whorl morphogenesis

Background and Aims

Conifer embryos, unlike those of monocots or dicots, have variable numbers of cotyledons, even within the same species. Cotyledons form in a single whorl on a dome-shaped embryo. The closely spaced cotyledons are not found outside this ring, indicating a radial control on where they can form. Polar transport of the hormone auxin affects outgrowth of distinct cotyledons, but not the radial aspect of the whorl or the within-whorl spacing between cotyledons. A quantitative model of plant growth regulator patterning is needed to understand the dynamics of this complex morphogenetic process.

Methods

A two-stage reaction-diffusion model is developed for the spatial patterning of growth regulators on the embryo surface, with a radial pattern (P1) constraining the shorter-wavelength cotyledon pattern (P2) to a whorl. These patterns drive three-dimensional (3-D) morphogenesis by catalysing local surface growth.

Key Results

Growth driven by P2 generates single whorls across the experimentally observed range of two to 11 cotyledons, as well as the circularly symmetric response to auxin transport interference. These computations are the first corroboration of earlier theoretical proposals for hierarchical control of whorl formation. The model generates the linear relationship between cotyledon number and embryo diameter observed experimentally. This accounts for normal integer cotyledon number selection, as well as the less common cotyledon fusings and splittings observed experimentally. Flattening of the embryo during development may affect the upward outgrowth angle of the cotyledons.

Conclusions

Cotyledon morphogenesis is more complex geometrically in conifers than in angiosperms, involving 2-D patterning which deforms a surface in three dimensions. This work develops a quantitative framework for understanding the growth and patterning dynamics involved in conifer cotyledon development, and applies more generally to the morphogenesis of whorls with many primordia.

Virtual Plant Tissue: Building Blocks for Next-Generation Plant Growth Simulation

Motivation: Computational modeling of plant developmental processes is becoming increasingly important. Cellular resolution plant tissue simulators have been developed, yet they are typically describing physiological processes in an isolated way, strongly delimited in space and time. Results: With plant systems biology moving toward an integrative perspective on development we have built the Virtual Plant Tissue (VPTissue) package to couple functional modules or models in the same framework and across different frameworks. Multiple levels of model integration and coordination enable combining existing and new models from different sources, with diverse options in terms of input/output. Besides the core simulator the toolset also comprises a tissue editor for manipulating tissue geometry and cell, wall, and node attributes in an interactive manner. A parameter exploration tool is available to study parameter dependence of simulation results by distributing calculations over multiple systems. Availability: Virtual Plant Tissue is available as open source (EUPL license) on Bitbucket (https://bitbucket.org/vptissue/vptissue). The project has a website https://vptissue.bitbucket.io.

Computational Modeling of Auxin: A Foundation for Plant Engineering

Since the development of agriculture, humans have relied on the cultivation of plants to satisfy our increasing demand for food, natural products, and other raw materials. As we understand more about plant development, we can better manipulate plants to fulfill our particular needs. Auxins are a class of simple metabolites that coordinate many developmental activities like growth and the appearance of functional structures in plants. Computational modeling of auxin has proven to be an excellent tool in elucidating many mechanisms that underlie these developmental events. Due to the complexity of these mechanisms, current modeling efforts are concerned only with single phenomena focused on narrow spatial and developmental contexts; but a general model of plant development could be assembled by integrating the insights from all of them. In this perspective, we summarize the current collection of auxin-driven computational models, focusing on how they could come together into a single model for plant development. A model of this nature would allow researchers to test hypotheses in silico and yield accurate predictions about the behavior of a plant under a given set of physical and biochemical constraints. It would also provide a solid foundation toward the establishment of plant engineering, a proposed discipline intended to enable the design and production of plants that exhibit an arbitrarily defined set of features.

A dynamical phyllotaxis model to determine floral organ number

How organisms determine particular organ numbers is a fundamental key to the development of precise body structures; however, the developmental mechanisms underlying organ-number determination are unclear. In many eudicot plants, the primordia of sepals and petals (the floral organs) first arise sequentially at the edge of a circular, undifferentiated region called the floral meristem, and later transition into a concentric arrangement called a whorl, which includes four or five organs. The properties controlling the transition to whorls comprising particular numbers of organs is little explored. We propose a development-based model of floral organ-number determination, improving upon earlier models of plant phyllotaxis that assumed two developmental processes: the sequential initiation of primordia in the least crowded space around the meristem and the constant growth of the tip of the stem. By introducing mutual repulsion among primordia into the growth process, we numerically and analytically show that the whorled arrangement emerges spontaneously from the sequential initiation of primordia. Moreover, by allowing the strength of the inhibition exerted by each primordium to decrease as the primordium ages, we show that pentamerous whorls, in which the angular and radial positions of the primordia are consistent with those observed in sepal and petal primordia in Silene coeli-rosa, Caryophyllaceae, become the dominant arrangement. The organ number within the outmost whorl, corresponding to the sepals, takes a value of four or five in a much wider parameter space than that in which it takes a value of six or seven. These results suggest that mutual repulsion among primordia during growth and a temporal decrease in the strength of the inhibition during initiation are required for the development of the tetramerous and pentamerous whorls common in eudicots.

Why do most eudicot flowers have either four or five petals? This fundamental and attractive problem in botany has been little investigated. Here, we identify the properties responsible for organ-number determination in floral development using mathematical modeling. Earlier experimental and theoretical studies showed that the arrangements of preexisting organs determine where a new organ will arise. Expanding upon those studies, we integrated two interactions between floral organs: (1) spatially and temporally decreased inhibition of new organ initiation by preexisting organs, and (2) mutual repulsion among organs such that they are “pushed around” during floral development. In computer simulations incorporating such initiation inhibition and mutual repulsion, the floral organs spontaneously formed several circles, consistent with the concentric circular arrangement of sepals and petals in eudicot flowers. Each circle tended to contain four or five organs arranged in positions that agreed quantitatively with the organ positions in the pentamerous flower, Silene coeli-rosa, Caryophyllaceae. These results suggest that the temporal decay of initiation inhibition and the mutual repulsion among growing organs determine the particular organ number during eudicot floral development.

Cytokinin-auxin crosstalk in cell type specification

Auxin and cytokinin affect cell fate specification transcriptionally and non-transcriptionally, and their roles have been characterised in several founder cell specification and activation contexts. Similarly to auxin, local cytokinin synthesis and response gradients are instructive, and the roles of ARABIDOPSIS RESPONSE REGULATOR 7/15 (ARR7/15) and the negative cytokinin response regulator ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6, as well as auxin signalling via MONOPTEROS/BODENLOS, are functionally conserved across different developmental processes. Auxin and cytokinin crosstalk is tissue- and context-specific, and may be synergistic in the shoot apical meristem (SAM) but antagonistic in the root. We review recent advances in understanding the interactions between auxin and cytokinin in pivotal developmental processes, and show that feedback complexity and the multistep nature of specification processes argue against a single morphogenetic signal.

A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network

Various environmental signals integrate into a network of floral regulatory genes leading to the final decision on when to flower. Although a wealth of qualitative knowledge is available on how flowering time genes regulate each other, only a few studies incorporated this knowledge into predictive models. Such models are invaluable as they enable to investigate how various types of inputs are combined to give a quantitative readout. To investigate the effect of gene expression disturbances on flowering time, we developed a dynamic model for the regulation of flowering time in Arabidopsis thaliana. Model parameters were estimated based on expression time-courses for relevant genes, and a consistent set of flowering times for plants of various genetic backgrounds. Validation was performed by predicting changes in expression level in mutant backgrounds and comparing these predictions with independent expression data, and by comparison of predicted and experimental flowering times for several double mutants. Remarkably, the model predicts that a disturbance in a particular gene has not necessarily the largest impact on directly connected genes. For example, the model predicts that SUPPRESSOR OF OVEREXPRESSION OF CONSTANS (SOC1) mutation has a larger impact on APETALA1 (AP1), which is not directly regulated by SOC1, compared to its effect on LEAFY (LFY) which is under direct control of SOC1. This was confirmed by expression data. Another model prediction involves the importance of cooperativity in the regulation of APETALA1 (AP1) by LFY, a prediction supported by experimental evidence. Concluding, our model for flowering time gene regulation enables to address how different quantitative inputs are combined into one quantitative output, flowering time.

A computational framework for 3D mechanical modeling of plant morphogenesis with cellular resolution

The link between genetic regulation and the definition of form and size during morphogenesis remains largely an open question in both plant and animal biology. This is partially due to the complexity of the process, involving extensive molecular networks, multiple feedbacks between different scales of organization and physical forces operating at multiple levels. Here we present a conceptual and modeling framework aimed at generating an integrated understanding of morphogenesis in plants. This framework is based on the biophysical properties of plant cells, which are under high internal turgor pressure, and are prevented from bursting because of the presence of a rigid cell wall. To control cell growth, the underlying molecular networks must interfere locally with the elastic and/or plastic extensibility of this cell wall. We present a model in the form of a three dimensional (3D) virtual tissue, where growth depends on the local modulation of wall mechanical properties and turgor pressure. The model shows how forces generated by turgor-pressure can act both cell autonomously and non-cell autonomously to drive growth in different directions. We use simulations to explore lateral organ formation at the shoot apical meristem. Although different scenarios lead to similar shape changes, they are not equivalent and lead to different, testable predictions regarding the mechanical and geometrical properties of the growing lateral organs. Using flower development as an example, we further show how a limited number of gene activities can explain the complex shape changes that accompany organ outgrowth.

Polarity in the early floral meristem of Arabidopsis

The diversity of angiosperm flowers depends on organ meristy and position. However, the signaling pathways that establish polarity and positional information remain largely unelucidated. Use of the founder-cell marker DORNRÖSCHEN-LIKE (DRNL) in Arabidopsis has recently highlighted the importance of the abaxial-adaxial axis for early floral development. We have extended the use of DRNL::GFP to further characterize floral organogenesis in genotypes that are altered in floral organ meristy or position, including ettin (ett-3) and blade-on-petiole (bop)1-11 bop2-4 double mutants. The creation of supernumery sepals by the splitting of sepal founder-cell populations along an ab-/adaxial axis strengthens the importance of the ab-/adaxial developmental axis in early floral meristem development. Furthermore, we confirm the dependency of the wildtype sequence of sepal initiation on bract suppression and demonstrate that supernumery stamens derive from the imprecise resolution of a ring of DRNL expression. Expression of DRNL in apetala1 (ap1-1) and ap2-8 mutants reflect the altered whorl structure and show that these homeotic genes function upstream of DRNL. Analyzing the dynamism of early floral meristem ontogeny at a fine temporal and spatial resolution in Arabidopsis can reveal mechanisms of organogenesis and is applicable to other species with differing floral body plans in a comparative evolutionary context.

Arabidopsis floral phytomer development: auxin response relative to biphasic modes of organ initiation

In the Arabidopsis inflorescence meristem (IM), auxin is considered a prepatterning signal for floral primordia, whereas a centripetal mode of positional information for floral organ identity is inherent to the ABCE model. However, spatio-temporal patterns of organ initiation in each whorl at the earliest initiation stages are largely unknown. Evidence suggests that initial flower development occurs along an abaxial/adaxial axis and conforms to phytomer theory. Use of the founder cell marker DORNRÖSCHEN-LIKE (DRNL) as a tool in leafy, puchi, and apetala 1 cauliflower mutant backgrounds suggests that bract founder cells are marked at the IM periphery. The DRNL transcription domain in the wild-type IM is spatially discrete from DR5 expression, suggesting that bract initiation is independent of canonical auxin response. When bracts develop in lfy and puchi mutant floral primordia the initiation of lateral sepals precedes the specification of medial sepals compared with wild type, showing an interplay between bract and abaxial sepal founder cell recruitment. In the perianthia (pan) mutant background, DRNL expression indicates that a radial outer whorl arrangement derives from splitting of sepal founder cell populations at abaxial and adaxial positions. This splitting of incipient sepal primordia is partially dependent on PRESSED FLOWER (PRS) activity and implies that sepal specification is independent of WUSCHEL and CLAVATA3 expression, as both marker genes only regain activity in stage-2 flowers, when patterning of inner floral organs switches to a centripetal mode. The transition from an initially abaxial/adaxial into a centripetal patterning programme, and its timing represent an adaptive trait that possibly contributes to variation in floral morphology, especially unidirectional organ initiation.

A division in PIN-mediated auxin patterning during organ initiation in grasses

The hormone auxin plays a crucial role in plant morphogenesis. In the shoot apical meristem, the PIN-FORMED1 (PIN1) efflux carrier concentrates auxin into local maxima in the epidermis, which position incipient leaf or floral primordia. From these maxima, PIN1 transports auxin into internal tissues along emergent paths that pattern leaf and stem vasculature. In Arabidopsis thaliana, these functions are attributed to a single PIN1 protein. Using phylogenetic and gene synteny analysis we identified an angiosperm PIN clade sister to PIN1, here termed Sister-of-PIN1 (SoPIN1), which is present in all sampled angiosperms except for Brassicaceae, including Arabidopsis. Additionally, we identified a conserved duplication of PIN1 in the grasses: PIN1a and PIN1b. In Brachypodium distachyon, SoPIN1 is highly expressed in the epidermis and is consistently polarized toward regions of high expression of the DR5 auxin-signaling reporter, which suggests that SoPIN1 functions in the localization of new primordia. In contrast, PIN1a and PIN1b are highly expressed in internal tissues, suggesting a role in vascular patterning. PIN1b is expressed in broad regions spanning the space between new primordia and previously formed vasculature, suggesting a role in connecting new organs to auxin sinks in the older tissues. Within these regions, PIN1a forms narrow canals that likely pattern future veins. Using a computer model, we reproduced the observed spatio-temporal expression and localization patterns of these proteins by assuming that SoPIN1 is polarized up the auxin gradient, and PIN1a and PIN1b are polarized to different degrees with the auxin flux. Our results suggest that examination and modeling of PIN dynamics in plants outside of Brassicaceae will offer insights into auxin-driven patterning obscured by the loss of the SoPIN1 clade in Brassicaceae.

Computational models and functional studies using the plant Arabidopsis thaliana have led to competing models for how the PIN-FORMED1 (PIN1) auxin transporter polarizes in the cell to create both the maxima required for organ initiation and the narrow streams required for vein patterning. Here we identify a previously uncharacterized PIN protein most closely related to PIN1 that is present in all flowering plants but lost in the Brassicaceae, including Arabidopsis. We localized this protein, here termed Sister-of-PIN1 (SoPIN1), along with duplicate members of PIN1 (PIN1a and PIN1b), in two grass species. Our localization data provide striking evidence for a spatial and temporal split between SoPIN1 and the two PIN1s during organ initiation in grasses. Based on our localization results we created a computational model showing that the observed patterns of expression and polarization of the grass PINs can emerge assuming SoPIN1 polarizes up the gradient of auxin concentration while the PIN1 members polarize with the auxin flux. This model reveals a minimal framework of necessary functions involved in auxin-transport-mediated patterning in the shoot and demonstrates that work outside of Arabidopsis is essential to understanding how auxin-transport mediates patterning in most flowering plants.

Auxin polar transport in stamen formation and development: how many actors?

In flowering plants, proper development of stamens, the male reproductive organs, is required for successful sexual reproduction. In Arabidopsis thaliana normally six stamen primordia arise in the third whorl of floral organs and subsequently differentiate into stamen filaments and anthers, where male meiosis occurs, thus ending the early developmental phase. This early phase is followed by a late developmental phase, which consists of a rapid elongation of stamen filaments coordinated with anther dehiscence and pollen maturation, and terminates with mature pollen grain release at anthesis. Increasing evidence suggests that auxin transport is necessary for both early and late phases of stamen development. It has been shown that different members of PIN (PIN-FORMED) family are involved in the early phase, whereas members of both PIN and P-glycoproteins of the ABCB (PGP) transporter families are required during the late developmental phase. In this review we provide an overview of the increasing knowledge on auxin transporters involved in Arabidopsis stamen formation and development and we discuss their role and functional conservation across plant species.

What lies beyond the eye: the molecular mechanisms regulating tomato fruit weight and shape

Domestication of fruit and vegetables resulted in a huge diversity of shapes and sizes of the produce. Selections that took place over thousands of years of alleles that increased fruit weight and altered shape for specific culinary uses provide a wealth of resources to study the molecular bases of this diversity. Tomato (Solanum lycopersicum) evolved from a wild ancestor (S. pimpinellifolium) bearing small and round edible fruit. Molecular genetic studies led to the identification of two genes selected for fruit weight: FW2.2 encoding a member of the Cell Number Regulator family; and FW3.2 encoding a P450 enzyme and the ortholog of KLUH. Four genes were identified that were selected for fruit shape: SUN encoding a member of the IQD family of calmodulin-binding proteins leading to fruit elongation; OVATE encoding a member of the OVATE family proteins involved in transcriptional repression leading to fruit elongation; LC encoding most likely the ortholog of WUSCHEL controlling meristem size and locule number; FAS encoding a member in the YABBY family controlling locule number leading to flat or oxheart shape. For this article, we will provide an overview of the putative function of the known genes, when during floral and fruit development they are hypothesized to act and their potential importance in regulating morphological diversity in other fruit and vegetable crops.

Racemose inflorescences of monocots: structural and morphogenetic interaction at the flower/inflorescence level

BACKGROUND

Understanding and modelling early events of floral meristem patterning and floral development requires consideration of positional information regarding the organs surrounding the floral meristem, such as the flower-subtending bracts (FSBs) and floral prophylls (bracteoles). In common with models of regulation of floral patterning, the simplest models of phyllotaxy consider only unbranched uniaxial systems. Racemose inflorescences and thyrses offer a useful model system for investigating morphogenetic interactions between organs belonging to different axes.

SCOPE

This review considers (1) racemose inflorescences of early-divergent and lilioid monocots and their possible relationship with other inflorescence types, (2) hypotheses on the morphogenetic significance of phyllomes surrounding developing flowers, (3) patterns of FSB reduction and (4) vascular patterns in the primary inflorescence axis and lateral pedicels.

CONCLUSIONS

Racemose (partial) inflorescences represent the plesiomorphic condition in monocots. The presence or absence of a terminal flower or flower-like structure is labile among early-divergent monocots. In some Alismatales, a few-flowered racemose inflorescence can be entirely transformed into a terminal 'flower'. The presence or absence and position of additional phyllomes on the lateral pedicels represent important taxonomic markers and key features in regulation of flower patterning. Racemose inflorescences with a single floral prophyll are closely related to thyrses. Floral patterning is either unidirectional or simultaneous in species that lack a floral prophyll or possess a single adaxial floral prophyll and usually spiral in the outer perianth whorl in species with a transversely oriented floral prophyll. Inhibitory fields of surrounding phyllomes are relevant but insufficient to explain these patterns; other important factors are meristem space economy and/or the inhibitory activity of the primary inflorescence axis. Two patterns of FSB reduction exist in basal monocots: (1) complete FSB suppression (cryptic flower-subtending bract) and (2) formation of a 'hybrid' organ by overlap of the developmental programmes of the FSB and the first abaxial organ formed on the floral pedicel. FSB reduction affects patterns of interaction between the conductive systems of the flower and the primary inflorescence axis.

Hormonal interactions and gene regulation can link monoecy and environmental plasticity to the evolution of dioecy in plants

Most models for dioecy in flowering plants assume that dioecy arises directly from hermaphroditism through a series of independent feminizing and masculinizing mutations that become chromosomally linked. However, dioecy appears to evolve most frequently through monoecious grades. The major genetic models do not explain the evolution of unisexual flowers in monoecious and submonoecious populations, nor do they account for environmentally induced sexual plasticity. In this review, we explore the roles of environmental stress and hormones on sex determination, and propose a model that can explain the evolution of dioecy through monoecy, and the mechanisms of environmental sex determination. Environmental stresses elicit hormones that allow plants to mediate the negative effects of the stresses. Many of these same hormones are involved in the regulation of floral developmental genes. Recent studies have elucidated the mechanisms whereby these hormones interact and can act as switchpoints in regulatory pathways. Consequently, differential concentrations of plant hormones can regulate whole developmental pathways, providing a mechanism for differential development within isogenic individuals such as seen in monoecious plants. Sex-determining genes in such systems will evolve to generate clusters of coexpressed suites. Coexpression rather than coinheritance of gender-specific genes will define the sexual developmental fate. Therefore, selection for gender type will drive evolution of the regulatory sequences of such genes rather than their synteny. Subsequent mutations to hyper- or hyposensitive alleles within the hormone response pathway can result in segregating dioecious populations. Simultaneously, such developmental systems will remain sensitive to external stimuli that modify hormone responses.

Cell patterns emerge from coupled chemical and physical fields with cell proliferation dynamics: the Arabidopsis thaliana root as a study system

A central issue in developmental biology is to uncover the mechanisms by which stem cells maintain their capacity to regenerate, yet at the same time produce daughter cells that differentiate and attain their ultimate fate as a functional part of a tissue or an organ. In this paper we propose that, during development, cells within growing organs obtain positional information from a macroscopic physical field that is produced in space while cells are proliferating. This dynamical interaction triggers and responds to chemical and genetic processes that are specific to each biological system. We chose the root apical meristem of Arabidopsis thaliana to develop our dynamical model because this system is well studied at the molecular, genetic and cellular levels and has the key traits of multicellular stem-cell niches. We built a dynamical model that couples fundamental molecular mechanisms of the cell cycle to a tension physical field and to auxin dynamics, both of which are known to play a role in root development. We perform extensive numerical calculations that allow for quantitative comparison with experimental measurements that consider the cellular patterns at the root tip. Our model recovers, as an emergent pattern, the transition from proliferative to transition and elongation domains, characteristic of stem-cell niches in multicellular organisms. In addition, we successfully predict altered cellular patterns that are expected under various applied auxin treatments or modified physical growth conditions. Our modeling platform may be extended to explicitly consider gene regulatory networks or to treat other developmental systems.

The emergence of tumors results from altered cell differentiation and proliferation during organ and tissue development. Understanding how such altered or normal patterns are established is still a challenge. Molecular genetic approaches to understanding pattern formation have searched for key central genetic controllers. However, biological patterns emerge as a consequence of coupled complex genetic and non-genetic sub-systems operating at various spatial and temporal scales and levels of organization. We present a two-dimensional model and simulation benchmark that considers the integrated dynamics of physical and chemical fields that result from cell proliferation. We aim at understanding how the cellular patterns of stem-cell niches emerge. In these, organizer cells with very low rates of proliferation are surrounded by stem cells with slightly higher proliferation rates that transit to a domain of active proliferation and then of elongation and differentiation. We quantified such cellular patterns in the Arabidopsis thaliana root to test our theoretical propositions. The results of our simulations closely mimic observed root cellular patterns, thus providing a proof of principle that coupled physical fields and chemical processes under active cell proliferation give rise to stem-cell patterns. Our framework may be extended to other developmental systems and to consider gene regulatory networks.

A mathematical basis for plant patterning derived from physico-chemical phenomena

The position of leaves and flowers along the stem axis generates a specific pattern, known as phyllotaxis. A growing body of evidence emerging from recent computational modeling and experimental studies suggests that regulators controlling phyllotaxis are chemical, e.g. the plant growth hormone auxin and its dynamic accumulation pattern by polar auxin transport, and physical, e.g. mechanical properties of the cell. Here we present comprehensive views on how chemical and physical properties of cells regulate the pattern of leaf initiation. We further compare different computational modeling studies to understand their scope in reproducing the observed patterns. Despite a plethora of experimental studies on phyllotaxis, understanding of molecular mechanisms of pattern initiation in plants remains fragmentary. Live imaging of growth dynamics and physicochemical properties at the shoot apex of mutants displaying stable changes from one pattern to another should provide mechanistic insights into organ initiation patterns.

The flux-based PIN allocation mechanism can generate either canalyzed or diffuse distribution patterns depending on geometry and boundary conditions

Growth and morphogenesis in plants require controlled transport of the plant hormone auxin. An important participant is the auxin effluxing protein PIN, whose polarized subcellular localization allows it to effectively transport auxin large distances through tissues. The flux-based model, in which auxin flux through a wall stimulates PIN allocation to that wall, is a dominant contender among models determining where and in what quantity PIN is allocated to cell walls. In this paper we characterise the behaviour of flux-based PIN allocation models in various tissues of the shoot apical meristem. Arguing from both mathematical analysis and computer simulations, we describe the natural behaviours of this class of models under various circumstances. In particular, we demonstrate the important dichotomy between sink- and source- driven systems, and show that both diffuse and canalized PIN distributions can be generated simultaneously in the same tissue, without model hybridization or variation of PIN-related parameters. This work is performed in the context of the shoot apical and floral meristems and is applicable to the construction of a unified PIN allocation model.

Auxin controls petal initiation in Arabidopsis

Floral organs are usually arranged in concentric whorls of sepals, petals, stamens and carpels. How founder cells of these organs are specified is unknown. In Arabidopsis, the PETAL LOSS (PTL) transcription factor functions in the sepal whorl, where it restricts the size of the inter-sepal zone. Genetic evidence suggests that PTL acts to support a petal initiation signal active in the adjacent whorl. Here we aimed to characterise the signal by identifying enhancers that disrupt initiation of the remaining petals in ptl mutants. One such enhancer encodes the auxin influx protein AUX1. We have established that auxin is a direct and mobile petal initiation signal by promoting its biosynthesis in the inter-sepal zone in ptl mutant plants and restoring nearby petal initiation. Consistent with this, loss of PTL function disrupts DR5 expression, an auxin-inducible indicator of petal-initiation sites. The signalling network was extended by demonstrating that: (1) loss of RABBIT EARS (RBE) function apparently disrupts the same auxin influx process as PTL; (2) the action of AUX1 is supported by AXR4, its upstream partner in auxin influx; (3) polar auxin transport, which is controlled by PINOID (PID) and PIN-FORMED1 (PIN1), functions downstream of PTL; and (4) the action of pmd-1d, a dominant modifier of the ptl mutant phenotype, is dependent on auxin transport. Thus, loss of PTL function disrupts auxin dynamics, allowing the role of auxin in promoting petal initiation to be revealed.

PETAL LOSS is a boundary gene that inhibits growth between developing sepals in Arabidopsis thaliana

Flower primordia are partitioned by boundaries during their early development. Such boundaries occur between whorls of organs, and also between organs within whorls. PETAL LOSS (PTL) is a trihelix transcription factor gene that is expressed in boundaries between sepal primordia in the outer whorl. Over-expression of PTL results in growth suppression suggesting that PTL normally inhibits growth between newly arising sepals. We have tested this by examining the consequences of loss of PTL function using confocal imaging. The size of the inter-sepal zone in stage 4 buds expands radially by 35-40% in ptl-1 mutants as a consequence of additional cell proliferation. There is no change in the size of PTL-expressing cells. PTL expression does not overlap with the sites of petal initiation identified using the DR5 auxin response reporter. The latter are closer to the centre of the flower. Thus the consequence of loss of PTL function on petal initiation is indirect, perhaps through interference with a mobile petal-initiation signal or movement of the PTL protein. CUP-SHAPED COTYLEDON (CUC) genes are also involved in defining inter-sepal boundaries. However, genetic studies combining ptl with loss of cuc1 function, and gain of CUC function in extra early petals-1 (miR164c) mutants, have revealed that CUC and PTL act differently. CUC suppresses growth of sepal tissues from the boundary region whereas PTL acts to keep the size of the boundary in check.

Integrating two patterning processes in the flower

Spatial organ arrangement plays an important role in flower development. The position and the identity of floral organs is influenced by various processes, in particular the expression of MADS-box transcription factors for identity and dynamics of the plant hormone auxin for positioning. We are currently integrating patterning processes of MADS and auxin into our computational models, based on interactions that are known from experiments, in order to get insight in how these define the floral body plan. The resulting computational model will help to explore hypothetical interactions between the MADS and auxin regulation networks in floral organ patterning.

Dynamic regulation of growing domains for elongating and branching morphogenesis in plants

With their continuous growth, understanding how plant shapes form is fundamentally linked to understanding how growth rates are controlled across different regions of the plant. Much of a plant's architecture is generated in shoots and roots, where fast growth in tips contrasts with slow growth in supporting stalks. Shapes can be determined by where the boundaries between fast- and slow-growing regions are positioned, determining whether tips elongate, branch, or cease to grow. Across plants, there is a diversity in the cell wall chemistry through which growth operates. However, prototypical morphologies, such as tip growth and branching, suggest there are common dynamic constraints in localizing chemical growth catalysts. We have used Turing-type reaction-diffusion mechanisms to model this spatial localization and the resulting growth trajectories, characterizing the chemistry-growth feedback necessary for maintaining tip growth and for inducing branching. The mechanism defining the boundaries between fast- and slow-growing regions not only affects tip shape, it must be able to form new boundaries when the pattern-forming dynamics break symmetry, for instance in the branching of a tip. In previous work, we used an arbitrary concentration threshold to switch between two dynamic regimes of the growth catalyst in order to define growth boundaries. Here, we present a chemical dynamic basis for this threshold, in which feedback between two pattern-forming mechanisms controls the extent of the regions in which fast growth occurs. This provides a general self-contained mechanism for growth control in plant morphogenesis (not relying on external cues) which can account for both simple tip extension and symmetry-breaking branching phenomena.