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Bamboo with its remarkable growth rate and economic significance, offers an ideal system to investigate the molecular basis of organogenesis in rapidly growing plants, particular in monocots, where gene regulatory networks governing the maintenance and differentiation of shoot apical and intercalary meristems remain a subject of controversy. We employed both spatial and single-nucleus transcriptome sequencing on 10× platform to precisely dissect the gene functions in various tissues and early developmental stages of bamboo shoots. Our comprehensive analysis reveals distinct cell trajectories during shoot development, uncovering critical genes and pathways involved in procambium differentiation, intercalary meristem formation, and vascular tissue development. Spatial and temporal expression patterns of key regulatory genes, particularly those related to hormone signaling and lipid metabolism, strongly support the hypothesis that intercalary meristem origin from surrounded parenchyma cells. Specific gene expressions in intercalary meristem exhibit regular and dispersed distribution pattern, offering clues for understanding the intricate molecular mechanisms that drive the rapid growth of bamboo shoots. The single-nucleus and spatial transcriptome analysis reveal a comprehensive landscape of gene activity, enhancing the understanding of the molecular architecture of organogenesis and providing valuable resources for future genomic and genetic studies relying on identities of specific cell types., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

The primary vascular system of plants (the stele) has attracted interest from paleobotanists, developmental biologists, systematists, and physiologists for nearly two centuries. Ferns, with their diverse stelar morphology, deep evolutionary history, and prominent fossil record, have been a major focus in studies of the stele. To explain the diversity of stelar morphology, past adaptive hypotheses have invoked biomechanics, hydraulics, and drought tolerance as key selection pressures in the evolution of stelar complexity; but, these hypotheses often isolate the stele from a whole-plant developmental context, ignoring potential covariation between vascular patterning and shoot morphology. Furthermore, incongruence between expected patterns and observed data challenge adaptive hypotheses, precluding a comprehensive explanation of stelar evolution. While ontogeny has been previously recognized as a factor in stelar diversification, it has not been fully integrated into a comprehensive framework. Here we synthesize 150-years of research on stelar morphology, incorporating developmental, physiological, and phylogenetic data to present the ontogenetic hypothesis of stelar evolution. This hypothesis posits that stelar morphology is an integrated feature of whole-plant ontogeny, not a trait shaped by direct selection for adaptive patterns. This shift in perspective provides an updated framework for understanding the determinants of stelar morphology and focusses future efforts to ask more incisive questions about the evolution and function of primary vascular architecture., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Barley (Hordeum vulgare) is an important global cereal crop and a model in genetic studies. Despite advances in characterising barley genomic resources, few mutant studies have identified genes controlling root architecture and anatomy, which plays a critical role in capturing soil resources. Our phenotypic screening of a TILLING mutant collection identified line TM5992 exhibiting a short-root phenotype compared with wild-type (WT) Morex background. Outcrossing TM5992 with barley variety Proctor and subsequent SNP array-based bulk segregant analysis, fine mapped the mutation to a cM scale. Exome sequencing pinpointed a mutation in the candidate gene HvPIN1a, further confirming this by analysing independent mutant alleles. Detailed analysis of root growth and anatomy in Hvpin1a mutant alleles exhibited a slower growth rate, shorter apical meristem and striking vascular patterning defects compared to WT. Expression and mutant analyses of PIN1 members in the closely related cereal brachypodium (Brachypodium distachyon) revealed that BdPIN1a and BdPIN1b were redundantly expressed in root vascular tissues but only Bdpin1a mutant allele displayed root vascular defects similar to Hvpin1a. We conclude that barley PIN1 genes have sub-functionalised in cereals, compared to Arabidopsis (Arabidopsis thaliana), where PIN1a sequences control root vascular patterning., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Gene silencing is crucial in crop breeding for desired trait development. RNA interference (RNAi) has been used widely but is limited by ectopic expression of transgenes and genetic instability. Introducing an upstream start codon (uATG) into the 5'untranslated region (5'UTR) of a target gene may 'silence' the target gene by inhibiting protein translation from the primary start codon (pATG). Here, we report an efficient gene silencing method by introducing a tailor-designed uATG-containing element (ATGE) into the 5'UTR of genes in plants, occupying the original start site to act as a new pATG. Using base editing to introduce new uATGs failed to silence two of the tested three rice genes, indicating complex regulatory mechanisms. Precisely inserting an ATGE adjacent to pATG achieved significant target protein downregulation. Through extensive optimization, we demonstrated this strategy substantially and consistently downregulated target protein expression. By designing a bidirectional multifunctional ATGE4, we enabled tunable knockdown from 19% to 89% and observed expected phenotypes. Introducing ATGE into Waxy, which regulates starch synthesis, generated grains with lower amylose, revealing the value for crop breeding. Together, we have developed a programmable and robust method to knock down gene expression in plants, with potential for biological mechanism exploration and crop enhancement., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Vascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flower heads. We imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism. The vascular system in the head of the model plant Gerbera hybrida is qualitatively different from those of Bellis perennis and Helianthus annuus, characterized previously. Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, and Tanacetum vulgare represent variants of the Bellis and Helianthus systems. In each species, the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values. In spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature., (© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation.)

Summary: PIN‐FORMED auxin efflux transporters, a subclass of which is plasma membrane‐localised, mediate a variety of land‐plant developmental processes via their polar localisation and subsequent directional auxin transport. We provide the first characterisation of PIN proteins in liverworts using Marchantia polymorpha as a model system. Marchantia polymorpha possesses a single PIN‐FORMED gene, whose protein product is predicted to be plasma membrane‐localised, MpPIN1.To characterise MpPIN1, we created loss‐of‐function alleles and produced complementation lines in both M. polymorpha and Arabidopsis. In M. polymorpha, gene expression and protein localisation were tracked using an MpPIN1 transgene encoding a translationally fused fluorescent protein.Overexpression of MpPIN1 can partially complement loss of an orthologous gene, PIN‐FORMED1, in Arabidopsis. In M. polymorpha, MpPIN1 influences development in numerous ways throughout its life cycle. Most notably, MpPIN1 is required to establish gemmaling dorsiventral polarity and for orthotropic growth of gametangiophore stalks, where MpPIN1 is basally polarised.PIN activity is largely conserved within land plants, with PIN‐mediated auxin flow providing a flexible mechanism to organise growth. Specifically, PIN is fundamentally linked to orthotropism and to the establishment of de novo meristems, the latter potentially involving the formation of both auxin biosynthesis maxima and auxin‐signalling minima. [ABSTRACT FROM AUTHOR]

Decades of research have primarily emphasized genetic blueprint as the driving force behind plant regeneration. The flow of information from genetics, which manifests as biochemical properties, including hormones, has been extensively implicated in plant regeneration. However, recent advancements have unveiled additional intrinsic modules within this information flow. Here, we explore the three core modules of plant regeneration: biochemical properties, mechanical forces acting on cells, and cell geometry. We debate their roles and interactions during morphogenesis, emphasizing the potential for multiple feedbacks between these core modules to drive pattern formation during regeneration. We propose that de novo organ regeneration is a self-organized event driven by multidirectional information flow between these core modules., (© 2023 The Authors New Phytologist © 2023 New Phytologist Foundation.)

Summary: Characterising the processes that control auxin dynamics is essential to understanding how auxin regulates plant development. Over recent years, several studies have investigated auxin diffusion through plasmodesmata, characterising this cell‐to‐cell diffusion and demonstrating that it affects auxin distributions. Furthermore, studies have shown that plasmodesmatal auxin diffusion affects developmental processes, including phototropism, lateral root emergence and leaf hyponasty. This short Tansley Insight review describes how these studies have contributed to our understanding of auxin dynamics and discusses potential future directions in this area. [ABSTRACT FROM AUTHOR]

Summary: Phyllotactic patterns are some of the most conspicuous in nature. To create these patterns plants must control the divergence angle between the appearance of successive organs, sometimes to within a fraction of a degree. The most common angle is the Fibonacci or golden angle, and its prevalence has led to the hypothesis that it has been selected by evolution as optimal for plants with respect to some fitness benefits, such as light capture.We explore arguments for and against this idea with computer models. We have used both idealized and scanned leaves from Arabidopsis thaliana and Cardamine hirsuta to measure the overlapping leaf area of simulated plants after varying parameters such as leaf shape, incident light angles, and other leaf traits.We find that other angles generated by Fibonacci‐like series found in nature are equally optimal for light capture, and therefore should be under similar evolutionary pressure.Our findings suggest that the iterative mechanism for organ positioning itself is a more likely target for evolutionary pressure, rather than a specific divergence angle, and our model demonstrates that the heteroblastic progression of leaf shape in A. thaliana can provide a potential fitness benefit via light capture. See also the Commentary on this article by Sicard, 225: 13–15. [ABSTRACT FROM AUTHOR]

Characterising the processes that control auxin dynamics is essential to understanding how auxin regulates plant development. Over recent years, several studies have investigated auxin diffusion through plasmodesmata, characterising this cell-to-cell diffusion and demonstrating that it affects auxin distributions. Furthermore, studies have shown that plasmodesmatal auxin diffusion affects developmental processes, including phototropism, lateral root emergence and leaf hyponasty. This short Tansley Insight review describes how these studies have contributed to our understanding of auxin dynamics and discusses potential future directions in this area., (© 2021 The Author. New Phytologist © 2021 New Phytologist Foundation.)

Broad-scale evolutionary comparisons have shown that branching forms arose by convergence in vascular plants and bryophytes, but the trajectory of branching form diversification in bryophytes is unclear. Mosses are the most species-rich bryophyte lineage and two sub-groups are circumscribed by alternative reproductive organ placements. In one, reproductive organs form apically, terminating growth of the primary shoot (gametophore) axis. In the other, reproductive organs develop on very short lateral branches. A switch from apical to lateral reproductive organ development is proposed to have primed branching form diversification., Moss gametophores have modular development and each module develops from a single apical cell. Here we define the architectures of 175 mosses by the number of module classes, branching patterns and the pattern in which similar modules repeat. Using ancestral character state reconstruction we identify two stages of architectural diversification., During a first stage there were sequential changes in the module repetition pattern, reproductive organ position, branching pattern and the number of module classes. During a second stage, vegetative changes occurred independently of reproductive fate., The results pinpoint the nature of developmental change priming branching form diversification in mosses and provide a framework for mechanistic studies of architectural diversification. [ABSTRACT FROM AUTHOR]

519I.519II.520III.520IV.527V.530530References530 Summary: The development and growth of plants, as well as their successful adaptation to a variety of environments, is highly dependent on the conduction of water, nutrients and other important molecules throughout the plant body. Xylem is a specialized vascular tissue that serves as a conduit of water and minerals and provides mechanical support for upright growth. Wood, also known as secondary xylem, constitutes the major part of mature woody stems and roots. In the past two decades, a number of key factors including hormones, signal transducers and (post)transcriptional regulators have been shown to control xylem formation. We outline the main mechanisms shown to be essential for xylem development in various plant species, with an emphasis on Arabidopsis thaliana, as well as several tree species where xylem has a long history of investigation. We also summarize the processes which have been shown to be instrumental during xylem maturation. This includes mechanisms of cell wall formation and cell death which collectively complete xylem cell fate. [ABSTRACT FROM AUTHOR]

The ability of the plant hormone auxin to enter a cell is critical to auxin transport and signaling. Auxin can cross the cell membrane by diffusion or via auxin-specific influx carriers. There is little knowledge of the magnitudes of these fluxes in plants., Radiolabeled auxin uptake was measured in protoplasts isolated from roots of Arabidopsis thaliana. This was done for the wild-type, under treatments with additional unlabeled auxin to saturate the influx carriers, and for the influx carrier mutant auxin resistant 1 ( aux1). We also used flow cytometry to quantify the relative abundance of cells expressing AUX1- YFP in the assayed population., At pH 5.7, the majority of auxin influx into protoplasts - 75% - was mediated by the influx carrier AUX1. An additional 20% was mediated by other saturable carriers. The diffusive influx of auxin was essentially negligible at pH 5.7., The influx of auxin mediated by AUX1, expressed as a membrane permeability, was 1.5 ± 0.3 μm s−1. This value is comparable in magnitude to estimates of efflux permeability. Thus, auxin-transporting tissues can sustain relatively high auxin efflux and yet not become depleted of auxin. [ABSTRACT FROM AUTHOR]

To provide a comparative framework to understand the evolution of auxin regulation in vascular plants, the effect of perturbed auxin homeostasis was examined in the lycophyte Selaginella kraussiana., Polar auxin transport was measured by tracing tritiated IAA in excised shoots. Shoots were cultured in the presence of auxin efflux inhibitors and exogenous auxin, and developmental abnormalities were documented., Auxin transport in Selaginella shoots is exclusively basipetal, as in angiosperms. Perturbed auxin transport results in the loss of meristem maintenance and abnormal shoot architecture. Dichotomous root branching in Selaginella appears to be regulated by an antagonistic relationship between auxin and cytokinin., The results suggest that basipetal polar auxin transport occurred in the common ancestor of lycophytes and euphyllophytes. Although the mechanisms of auxin transport appear to be conserved across all vascular plants, distinct auxin responses govern shoot growth and development in lycophytes and euphyllophytes. [ABSTRACT FROM AUTHOR]

This paper presents two models of carrier-dependent long-distance auxin transport in stems that represent the process at different scales. [ABSTRACT FROM AUTHOR]

Summary • The SOS signaling pathway plays an important role in plant salt tolerance. However, little is known about how the SOS pathway modulates organ development in response to salt stress. Here, the involvement of SOS signaling in NaCl-induced lateral root (LR) development in Arabidopsis was assessed. • Wild-type and sos3-1 mutant seedlings on iso-osmotic concentrations of NaCl and mannitol were analyzed. The marker lines for auxin accumulation, auxin transport, cell division activity and stem cells were also examined. • The results showed that ionic effect alleviates the inhibitory effects of osmotic stress on LR development. LR development of the sos3-1 mutant showed increased sensitivity specifically to low salt. Under low-salt conditions, auxin in cotyledons and LR primordia (LRP) of the sos3-1 mutant was markedly reduced. Decreases in auxin polar transport of mutant roots may cause insufficient auxin supply, resulting in defects not only in LR initiation but also in cell division activity in LRP. • Our data uncover a novel role of the SOS3 gene in modulation of LR developmental plasticity and adaptation in response to low salt stress, and reveal a new mechanism for plants to sense and adapt to small changes of salt. [ABSTRACT FROM AUTHOR]

The co-ordination between floret initiation and meristem expansion, and their relationships with carbon availability, were studied and quantified in sunflower (Helianthus annuus) plants subjected to light or water shortages. Meristem size, number of floret primordia, primordium size, rate of plant biomass accumulation, leaf area, photosynthetic rate, and soluble sugar content in the capitulum were measured until completion of floret initiation. Although treatments differentially affected tissue expansion and biomass acquisition, a common relationship between the final number of florets and the rate and duration of meristem expansion was conserved. In the absence of water deficit, changes in relative expansion rate in the meristem paralleled changes in soluble sugar content. Water deficit reduced tissue expansion both in leaves and in the capitulum, and induced the accumulation of soluble sugars in the meristem. Use of these sugars at re-watering was associated with increased meristem growth and higher floret numbers compared with control plants. Floret initiation and meristem tissue expansion remained strongly co-ordinated under all studied circumstances, and both depended on local carbon availability when water supply was unlimited. Transient water deficits favoured reproductive meristem growth and floret production. Equations accounting for these results constitute a framework for phenotyping the response to drought. [ABSTRACT FROM AUTHOR]

• Lycopodium represents a phylogenetically distinct clade of basal vascular plants with anatomical characters that have no parallel in other lineages. Thus, knowledge of lycopod structure and development may reveal important information about the common ancestors of all vascular plants. Here we report the unique architecture of the conducting system in Lycopodium annotinum and Lycopodium clavatum. • Based on multiple series of anatomical sections, we reconstructed spatial relationships between microphylls and the stelar system. • Analysis revealed that protoxylem ribs (PXR) were vertical, regardless of type of phyllotaxis, and their numbers were variable. Microphyll traces (MTr) were randomly distributed between ribs, resulting in the absence of defined sympodia and varied lengths of MTr. Dichotomous branching contributed to additional features, for example occurrence of mesarch protoxylem, affecting stele structure and PXR numbers. • Our data showed limited interrelationships between lycopod vasculature and microphyll phyllotaxis. This may suggest that both systems developed independently, then evolved together to form the integrated supply system. Thus vasculature in extant lycophytes may be less functionally efficient than in seed plants, where consistent leaf-trace lengths guarantee predictable energy utilization during ontogeny. Differences may result from the phylogenetically different origin of microphylls, and the level of vascular complexity. [ABSTRACT FROM AUTHOR]

The article discusses the biotrophic interaction between Lotus japonicus and the rust fungus Uromyces loti. The symbiotic relationship is probably the most important plant-fungus interaction. One common feature of biotrophic interactions is the formation of elaborate intracellular accommodation structures that maintain an intimate coexistence of both fungal and plant cells over a prolonged period. A genetic approach is used in a study to unravel the overlap between mutualistic and parasitic biotrophy.

The article highlights the issues that emerged during the 14th New Phytologist Symposium held at the Royal Society in London, England in January 2006. The symposium addressed the broad goal of ecological development. Ecological development aims to close the gap between mechanisms and ecology, and provide a genuinely integrated view of plant development in its real environmental context. Knowledge of genetic mechanisms may be essential in understanding the degree of correlation or independence of plant responses to different environmental factors.

The ability of a genotype to change its phenotype was once considered rather a nuisance – making it difficult to define a genotype. This led to the idea that there was a problem called ‘instability’. But quite early it was recognized that stability was under genetic control, and was a character like other attributes of an individual. From this realization came the idea that there were two sides to the character of ‘instability’, and that the ability to change could be important. This ability was thus given the title of ‘plasticity’. Once recognized, it became clear from surveys of different species and populations that plasticity can (i) be a complex character, and (ii) be selected to fit species to the particular demands of different environments. For plants, which cannot meet variations in environment like animals by behavioural responses, phenotypic plasticity can be very important. Plants should therefore be valuable tools for unravelling the mechanisms of plasticity whilst also demonstrating its contribution to fitness experimentally. We ought also to be able to demonstrate that appropriate genetic variability is available through which complex responses can be built up by selection. Genes must exist not only to determine character means, but also to determine character response, which adds interesting complexity to our ideas about evolution. [ABSTRACT FROM AUTHOR]

Summary 1I. Introduction 1II. The shoot apical meristem: the creation of a field of cells from which leaves can be formed 2III. Patterning: the selection of leaf initiation site 2IV. Morphogenesis: the initial stages of leaf formation 4V. Differentiation and determination: transcriptional networks controlling determinancy 6VI. The elaboration of leaf form 6VII. Early steps in leaf histogenesis 7VIII. Later steps in leaf differentiation: epidermal cell fate 8IX. Compound and simple leaves: variation on a theme? 9X. Changes in leaf form: developmental and environmental influences 9XI. A model of leaf formation 9 Acknowledgements 10 References 10The formation of a leaf is a basic aspect of plant development. This review provides an overview of our present understanding of the process from initiation to the final form of the leaf. Molecular genetic and cell biology approaches have yielded significant advances in this area, adding not only to our knowledge of leaf development but also to fundamental principles in plant biology. These principles will be highlighted, as well as areas where our understanding is still incomplete, in particular the problem of coordinating the multifaceted steps involved in the generation of the leaf structure.New Phytologist(2004)doi: 10.1111/j.1469-8137.2004.01292.x© New Phytologist(2004) [ABSTRACT FROM AUTHOR]

The article provides a quantitative analysis of the process of capitulum growth and the gradual but controlled process by which elements within the capitulum become destined to form individual flowers. The data provide a foundation for the modelling of flower formation and for linking the observed parameters of floral morphogenesis with the wealth of molecular data on organogenesis in plants. An analysis of auxin flux and distribution during leaf initiation is also presented. The situation in the capitulum may be linked with the spatial and temporal control of factors specific to flower formation.

The article highlights the XII International Congress on Molecular Plant-Microbe Interactions in Yucatán, Mexico in December 2005. The aim of the meetings is to present data at the forefront of research over a wide field of interactions between plants, fungi, bacteria, viruses and nematodes. The emphasis is on the genetic and molecular analysis of the processes under study. Several of the speakers at the conference focused on nonhost resistance and the importance of pathogen-associated molecular pattern perception and transduction.

• The SOS signaling pathway plays an important role in plant salt tolerance. However, little is known about how the SOS pathway modulates organ development in response to salt stress. Here, the involvement of SOS signaling in NaCl-induced lateral root (LR) development in Arabidopsis was assessed. • Wild-type and sos3-1 mutant seedlings on iso-osmotic concentrations of NaCl and mannitol were analyzed. The marker lines for auxin accumulation, auxin transport, cell division activity and stem cells were also examined. • The results showed that ionic effect alleviates the inhibitory effects of osmotic stress on LR development. LR development of the sos3-1 mutant showed increased sensitivity specifically to low salt. Under low-salt conditions, auxin in cotyledons and LR primordia (LRP) of the sos3-1 mutant was markedly reduced. Decreases in auxin polar transport of mutant roots may cause insufficient auxin supply, resulting in defects not only in LR initiation but also in cell division activity in LRP. • Our data uncover a novel role of the SOS3 gene in modulation of LR developmental plasticity and adaptation in response to low salt stress, and reveal a new mechanism for plants to sense and adapt to small changes of salt., (© 2010 The Authors. New Phytologist © 2010 New Phytologist Trust.)