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Individual variability refers to the differences observed among genetically identical plants or cells grown in the same environment. Phenotypic and transcriptional variability have been extensively described in unicellular organisms and mammalian cells. However, increasing evidence now points to both intra- and inter-individual variability in plants. Cell-to-cell variability in gene expression within a single plant (intra-individual variability) is now recognised as a key factor contributing to the robustness of plant development as well as environmental responses. At a broader scale, multiple studies strongly suggest that inter-individual variability, often involving gene expression differences between individual seedlings, can be associated with an adaptive value at the population level under challenging environmental conditions. This review first aims to describe what is currently known about intra- and inter-individual variability in plants, with a main focus on gene expression variation and highlighting the importance of chromatin modifications. We then illustrate how the extent of individual variability can differ depending on environmental conditions, and discuss how the plasticity of such variability may enhance the ability of plants to respond to challenging situations. These observations finally underline the relevance of investigating individual variability in the context of agriculture.
Plants regulate root development in response to fluctuating environmental conditions, including establishing symbiotic relationships with arbuscular mycorrhizal fungi and nitrogen-fixing bacteria under nutrient limitation. These processes are orchestrated by plant hormones, particularly gibberellins, and the repressors of gibberellin signalling, DELLA proteins. Gibberellin and DELLAs serve as critical regulators in symbiotic signalling and root organogenesis, integrating hormonal and environmental cues with cellular patterning to direct plant development. This review explores the current understanding of gibberellin and DELLA function in symbiosis and root development, including an analysis of the conservation and divergence of their function in land plant evolution. DELLA proteins play a pivotal role in the common symbiotic signalling pathway, modulating transcriptional responses essential for both arbuscular mycorrhizal and rhizobial symbioses. While gibberellin suppresses early symbiotic signalling and microbial infection by promoting DELLA degradation, gibberellin positively regulates nodule organogenesis and function, demonstrating a cell- and stage-dependent role in symbiotic associations. Indeed, precise spatial and temporal dynamics of gibberellin signalling occurs during nodulation and root development. Key avenues for future research are identified, including understanding how the crosstalk between gibberellin and other key plant hormones fine-tune symbiosis and root development.
Plant metabolism underpins the food, fiber, and fuel that support our economy, driving strong interest in new strategies to rewire plant metabolism for emerging applications. While most synthetic biology efforts are reliant on genetic engineering, plants can be manipulated in many other ways that remain comparatively underexplored. Across nature, diverse organisms, including bacteria, fungi, and insects, have evolved sophisticated mechanisms to exploit plant metabolic richness, reshaping it for purposes that span from basic nutrition to the construction of complex, novel structures for shelters. These interspecies interactions and non-model systems represent unique manners in which plants can be reprogrammed or hijacked by other organisms, offering inspiration for novel approaches to engineering plant metabolism. By better understanding the basis of how organisms induce these remarkable transformations in plants, we can expand the conceptual boundaries of synthetic biology and reveal alternative routes to manipulating plants for the production of a diverse array of valuable compounds and materials. Deeper insight into these mechanisms will yield novel blueprints for rethinking the scope and breadth in which we can redesign plant metabolism across many applications.
Lipids are fundamental biomolecules that function not only as structural components of cellular membranes and as major energy reserves, but also as dynamic signaling entities that coordinate plant responses to environmental challenges. Under abiotic stresses such as drought, salinity, and nutrient deficiency, plants undergo extensive lipid remodeling to maintain membrane integrity and cellular homeostasis. Diverse lipid classes, including phosphoglycerolipids, sphingolipids, glycoglycerolipids, sterol lipids and oxylipins, generate signaling cues that activate intracellular cascades governing stress adaptation. For instance, a recently discovered stepwise decoding mechanism for heat sensing directly connects membrane lipid remodeling to a nuclear signaling cascade, exemplifying how dynamic lipid changes trigger specific transcriptional outputs. Lipid metabolism also elicits plant immune responses, modulating defense gene expression and programmed cell death during biotic interactions. Notably, a breakthrough in plant immunity revealed that the dual phosphorylation of diacylglycerol kinase 5 (DGK5) triggers a phosphatidic acid (PA) burst, which subsequently regulates reactive oxygen species (ROS) production to execute defense responses. Here, we summarize recent advances illustrating how lipid metabolic pathways are integrated into plant signaling networks that underline both abiotic and biotic stress responses. Beyond their canonical structural and storage roles, lipids constitute a sophisticated communication system that enables plants to sense environmental perturbations and orchestrate coordinated physiological and transcriptional responses. Deciphering this lipid-centric regulatory network will be critical for developing strategies to enhance plant resilience under climate change.
Diseases caused by plant pathogens are a major factor decreasing crop yields that lead to food insecurity. To protect against pathogen threats, plants possess a multifaceted immune system that perceive threats derived from plant pathogens, resulting in the activation of immune responses. Evolutionary pressures allow plant pathogens to evolve rapidly and evade recognition by nucleotide-binding leucine-rich repeat (NLR) receptors. In recent years, advancements in our understanding of the molecular and structural basis of effector recognition by NLRs have enabled targeted strategies for engineered receptors that contain novel or expanded recognition profiles. In conjunction with advancements in structural modeling and synthetic biology tools, this has transformed our ability to manipulate plant receptors with precision. Here, we highlight structure-based approaches toward engineering plant NLRs, including integrated domain (ID) engineering and leucine-rich repeat resurfacing, discuss challenges associated with NLR engineering, and highlight future engineering approaches to enhance the plant immune system against pathogen threats.
Developmental phase transitions in plants represent irreversible shifts in growth and identity and must therefore be precisely controlled. These transitions rely heavily on epigenetic mechanisms and are tightly coordinated with environmental cues. The VIVIPAROUS/ABSCISIC ACID INSENSITIVE3 (ABI3)-LIKE (VAL) family of B3 domain transcription factors has emerged as a central regulatory node throughout plant development. VAL proteins act as sequence-specific DNA-binding factors that mediate the assembly of Polycomb Repressive Complexes (PRCs) and associate chromatin modifiers, thereby ensuring stable transcriptional silencing at key developmental regulators. Through this function, VAL proteins specify which genes must be epigenetically repressed to allow transitions from embryogenesis to seedling growth, from juvenile to adult vegetative phases, and ultimately to flowering. Most mechanistic insights into VAL protein function come from Arabidopsis thaliana, although recent studies in other species reinforce VAL conserved role in chromatin silencing and epigenetic integration. Here, we synthesize current knowledge on VAL-mediated regulation and highlight conceptual advances in understanding how sequence-specific repressors interface with chromatin machinery in plants. We further discuss the evolutionary conservation of VAL structural domains and outline open questions surrounding VAL functional roles in chromatin regulation.
Pectins are major determinants of plant cell wall mechanics, hydration, adhesion, and signaling. Synthesized in the Golgi as structurally diverse polymers, pectins are deposited and remodeled in spatially restricted patterns that generate wall domains with distinct biochemical and mechanical properties. This review summarizes recent advances in pectin biosynthesis, modification, and crosslinking, including emerging views of homogalacturonan organization beyond the classical egg-box model. We highlight growing evidence that pectins function not only as structural materials but also as signaling platforms that integrate extracellular wall status with intracellular responses. Stomata provide a compelling system in which pectin heterogeneity underlies both morphogenesis and physiological function. During stomatal development, localized pectin biosynthesis, secretion, de-methyl-esterification, and degradation contribute to guard mother cell division, pore initiation, and the establishment of bilateral symmetry. In mature stomata, patterned pectin chemistry generates mechanical asymmetries that support the "Fix and Flex" framework, in which stiffened polar domains constrain guard cell deformation while more flexible regions enable pore opening and closing. Comparisons between dicot and grass stomata further suggest that conserved mechanical logic can be achieved through lineage-specific wall chemistries. We also discuss how polarized trafficking, exocyst-mediated secretion, and candidate wall-sensing receptor systems may connect pectin remodeling to cell polarity pathways during stomatal morphogenesis. Taken together, pectin is positioned as a dynamic extracellular regulator that couples biosynthesis, mechanics, signaling, and polarity to control stomatal development and function.
The spatially constrained nature of plant cells makes them highly reliant on targeted membrane vesicle trafficking, which sustains proper cellular function, tissue organization, and overall plant growth and development. These mechanisms are regulated by small GTPases, which function assembling tethering complexes and later serve as their effectors. Tethering factors facilitate the initial contact between the target membrane and incoming vesicles, thereby playing a pivotal role in vesicle targeting and fusion. This review focuses on two tethering complexes, the class C core vacuole/endosome tethering (CORVET) and the homotypic fusion and vacuole protein sorting (HOPS) tethering complex, which have been best studied in the model plant Arabidopsis thaliana. The activity of these complexes has been linked to the regulation of multivesicular endosomes with the vacuole membrane. However, recent reports propose additional functions for specific HOPS subunits regulating other fusion events. Despite these advances, our understanding of HOPS/CORVET function and regulation, including the input of small GTPases, remains incomplete. Thus, in this review, we emphasize the essential role of the HOPS/CORVET tethering complex in plant growth and development while identifying key gaps for future research.
Plants have a layered immune system, comprising PAMP-pattern triggered immunity (PTI), effector-triggered immunity (ETI), and systemic acquired resistance (SAR), which enables them to detect and respond to microbial threats. Several studies on plant immunity have advanced our understanding of how nucleotide-binding leucine-rich repeat receptors (NLRs) function within these defense layers. Sensor NLRs recognize pathogen effectors, while helper NLRs form resistosome complexes that drive downstream signaling, including calcium influx, reactive oxygen species production, and transcriptional activation. Moreover, single-cell and spatial omics have revealed heterogeneity in immune activation, identifying specialized "PRIMER" cells that initiate strong local responses and "bystander" cells that respond to cues from neighboring tissues to maintain broader immunity. Additionally, structural analyses have clarified the assembly of resistosomes, and proteomic and interactome studies highlight how protein networks shape signaling specificity and intensity. Epigenetic and RNA-mediated mechanisms further modulate NLR expression and responsiveness. In this review, we focus on an integrative overview of how receptor activation, gene-regulatory circuits, protein interaction hubs, and chromatin dynamics collectively influence immune outcomes. We also discuss the insights of systems and synthetic biology approaches that may guide rational engineering of more durable and broad-spectrum disease resistance in crops.
Plant genome biology is entering a new era defined by fully phased, chromosome-scale, telomere-to-telomere assemblies, enabled by the convergence of long-read sequencing technologies, improved assembly algorithms, and powerful scaffolding strategies. Gapless, haplotype-resolved genomes are now feasible even for polyploid species, shifting the bottleneck from assembly to annotation and interpretation. Genome annotation remains one of the greatest opportunities and challenges in plant biology. While ab initio methods still form the backbone of structural prediction, evidence-based frameworks that integrate RNA sequencing, chromatin accessibility, methylation, and 3D genome data are rapidly advancing the field. At the same time, artificial intelligence-driven protein-coding gene predictors are redefining ab initio gene finding, and large-scale orthology networks continue to improve functional inference. The next frontier is extending annotation beyond protein-coding genes into regulatory and structural dimensions, a goal increasingly enabled by single-cell and multi-omic technologies. Looking forward, the integration of AI, multi-omics, and large language models promises to standardize and automate workflows from DNA isolation to functional annotation. These innovations will accelerate fundamental plant biology discovery, enable next-generation biodiversity conservation, and transform strategies for crop improvement and biotechnology.
Functionally related genes are frequently organized into clusters in plant genomes, including homologous gene clusters (HGCs) derived from duplicated genes and biosynthetic gene clusters (BGCs) composed of genes involved in the same metabolic pathway. Genes within a BGC are often co-expressed in a tissue- and time-specific manner, enabling the controlled production of specialized metabolites in specific plant tissues or in response to specific environmental cues. A few recent studies have revealed that transcriptional super-enhancers (SEs) play a central role in coordinating the co-expression of genes within BGCs. In Arabidopsis thaliana, SEs have been identified for a substantial proportion of BGCs. In addition, these clusters, together with their cognate SEs, are embedded within the same topologically associating domains. Disruption of these SEs through T-DNA insertions or clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas)-induced deletions can alter the expression of entire gene clusters. Notably, SEs linked to gene clusters can be readily predicted and mapped using tissue-specific chromatin accessibility datasets. Molecular dissection of SE-mediated regulation of BGCs holds great promise for advancing synthetic biology, metabolic engineering, and crop improvement.
Single-cell technologies are redefining plant cell identity. Traditional classifications based on position, morphology, and a few marker genes yielded static, coarse cell categories. In contrast, single-cell and single-nucleus RNA sequencing reveal hidden cellular heterogeneity and reconstruct developmental trajectories in ostensibly well-characterized plant tissues including vasculature and mesophyll. Environmental cues such as pathogen attack, drought, and wounding generate transient, spatially restricted cell states that bulk profiling masks, and these dynamics are best resolved by integrating single-cell data with spatial transcriptomics and live imaging. Comparative single-cell analyses extend these insights across evolution, revealing conserved core cell-type groups, lineage-specific innovations, and rapid transcriptomic rewiring in particular cell types. Emerging computational strategies mitigate orthology issues caused by genome duplications, enabling robust cross-species atlas alignment. These advances demonstrate that plant cell identity is dynamic, context-dependent, and distributed along continuous spectra. We argue that future frameworks should balance discrete cell-type labels with flexible state-based descriptions and integrate multiomic and spatial information to capture the full plasticity of plant cells, from ephemeral stress responses to millennial evolutionary changes.
Asymmetric cell division (ACD) is a central mechanism that generates cellular diversity and tissue patterning in plants. Because they are constrained by rigid cell walls, plant cells often employ precisely oriented divisions to generate distinct daughter-cell fates. While classic studies have identified where ACD occurs and genetic studies have uncovered key regulators, the mechanisms linking early asymmetries to fate specification remain incompletely understood. Here, we synthesize insights from diverse plants and algae about symmetry-breaking in their zygotes and specialized cell lineages. We then discuss how initial asymmetries are translated into stable daughter-cell identities and how cells integrate positional information, lineage, and signaling networks to decide between self-renewal and differentiation. We also highlight emerging tools that could be applied to resolve current blind spots in symmetry breaking, asymmetric inheritance, and fate specification. Together, these perspectives reveal how plants repeatedly reinvent asymmetry to pattern tissues reproducibly yet flexibly, providing a framework to probe the mechanisms and evolution of plant ACD.
Land plant evolution has been marked by bursts of novelty, often underpinned by extensive genomic innovation. A key mechanism driving these changes is horizontal gene transfer (HGT), the process by which genes move between species and even across taxonomic kingdoms. HGT can accelerate evolutionary change through the rapid introduction of new genes yet its importance in plant biology is only beginning to be understood. Here, we review the functional contributions of HGT during the origin and diversification of land plants. We discuss the occurrence of HGT throughout plant evolution and its impact on the origin of defining traits from cell walls to developmental programs. Beyond ancient contributions, HGT continues to drive the emergence of lineage-specific innovations. Recently acquired bacterial and fungal genes make complex functional contributions to processes including stress response, pathogen defence, and development across plant phylogeny. These observations suggest that HGT was, and continues to be, a major force shaping plant evolution, exemplifying the potential significance of HGT in eukaryotic biology more broadly.
Wheat produces unbranched inflorescences (spikes) composed of smaller inflorescences (spikelets) as their fundamental building units. The spikelet number per spike (SNS) is a major determinant of grain yield and the gene networks that regulate this trait are the focus of this review. Spikelet development starts with the transition of the shoot apical meristem into an inflorescence meristem (IM) that produces lateral spikelet meristems (SMs). The rate at which SMs are produced and the timing of the IM transition into a terminal spikelet (IM→TS) determine the final SNS. These two traits are regulated by genes expressed in the IM (e.g. meristem identity genes), as well as by the amount of FLOWERING LOCUS T1 (florigen) transported from leaves to developing spikes. Spikelet number can also be increased by the production of spikes with supernumerary spikelets (SS) or branch-like structures that resemble small spikes. Mutations that promote a reversion from SM to IM identity can induce the formation of SS or branches. Initial efforts to incorporate these mutations into commercial wheat varieties have faced trade-offs in fertility and grain weight, which will require additional research and breeding efforts. Meanwhile, genes and allele combinations that increase SNS without affecting the number of spikelets per node have been identified and are being deployed in wheat breeding programs. Recent spatial transcriptomics, single-cell analyses, and multi-omics studies of wheat spike development are accelerating the discovery of new genes affecting SNS and enhancing our ability to engineer more productive wheat spikes.
Transposable elements (TEs) are ubiquitous components of the genome whose mobility can be triggered by environmental stress and influenced by genotype-environment interactions. In plants, TEs constitute a substantial proportion of the genome and frequently cause large-effect mutations that impact gene regulation, methylation, and phenotype expression. These characteristics have recently positioned TEs as potential drivers of rapid local adaptation. However, this perspective is not always integrated with the broader understanding of fitness effects and neutral processes. Despite numerous associations between TEs and fitness-related traits, clear cases directly linking TE insertion, phenotype, and fitness in natural populations-i.e., genuine examples of local adaptation-remain rare in plants. Emerging population-genomic evidence presents a more complex picture: while some TE insertions may facilitate adaptation or rapid responses to environmental change, most are selected against and act as deleterious, selfish elements. The evolutionary dynamics of TEs are further modulated by genome architecture, reproductive system, and ecological context, underscoring their system-specific behavior. In this opinion piece, I argue that generalizing about the significance of TEs in local adaptation in plants is fraught with complexity and risks oversimplification. As sequencing technologies advance, integrating theoretical population genetics with large-scale comparative analyses and simulations across a wider range of species will be essential to more fully characterize the dynamics of TEs.
Vascular tissues form the central transport and support system in plants, integrating water and nutrient uptake with long-distance signaling and growth regulation. In roots, vascular development occurs dynamically along both apical-basal and radial axes and must stay responsive to changing environmental conditions. Recent studies have shown that intercellular communication through plasmodesmata is key to this process, allowing the movement of regulatory molecules such as peptides, transcription factors, and small RNAs that coordinate cell division, fate determination, and differentiation. This review summarizes current knowledge on how mobile regulatory factors influence the development of xylem, phloem, and vascular cambium in Arabidopsis thaliana roots. We discuss how spatially restricted and directional signal mobility sets tissue boundaries, maintains stem cell activity, and guides lineage progression. We also explore how the dynamic regulation of plasmodesmata permeability incorporates environmental signals-including abiotic and biotic stresses-into vascular developmental programs by controlling the range and timing of intercellular signaling. Overall, these findings position plasmodesmata-mediated intercellular mobility as a crucial regulatory layer that links vascular patterning to developmental resilience. Understanding how this layer is modulated under stress conditions will be vital for explaining how root vascular tissues stay functional while adapting to changing environments.
Noncoding RNAs are emerging as major regulators in plant development and environmental response. MicroRNAs, small RNAs, and ribosomal RNAs have established mechanisms for generation, maturation, and function. However, long noncoding RNAs (lncRNAs) currently lack a robust classification according to their function. lncRNAs are here defined as noncoding RNAs that are longer than 200 nucleotides and generally transcribed by RNA polymerase II. They often exhibit low expression and limited sequence conservation yet display tissue or stress-specific regulation. Furthermore, lncRNAs are categorized based on their location relative to nearby genes, including sense (overlapping a gene on the same strand), antisense (overlapping on the opposite strand), intronic (located within intron), intergenic (found between genes), and bidirectional (transcribed in the opposite direction from a nearby gene). Here, we summarized the last years of work in the field of lncRNA, but instead of grouping them into the biological processes they are involved in, we attempt to group them into general functions in plants. This will not be an exhaustive grouping of known functions for lncRNA, rather a list of established functions with several characterized cases.
Tandem arrays, genomic loci comprising adjacent paralogs that share high sequence identity, concentrate in plant genome regions shaped by strong adaptive pressure, from nucleotide-binding leucine-rich repeat (NLR) resistance clusters to specialized metabolism loci. Yet these biologically informative neighborhoods are precarious bioinformatically. Short-read assemblies often result in assembly collapse, compressing multi-member tandem arrays into a single consensus sequence. Annotation pipelines compound this error through annotation fusion, which merges distinct array members into elongated gene models, and annotation omission, which drops true array members even when assemblies preserve local structure. The result is systemic distortion: collapsed references misrepresent tandem array copy number, confounded expression quantification across array members, and obscured tandem-array copy number variation (CNV) in population-genomic analyses. Graph pangenomes built from long-read, haplotype-resolved assemblies offer a direct remedy. By representing alternative locus structures as paths in a pangenome graph, these references restore tandem arrays as discoverable, measurable objects. Individual array members retain distinct coordinates, enabling array-member-resolved expression analysis and accurate genotyping of tandem-array CNV. This shift turns tandem-array-rich loci from systemic blind spots into accessible windows on adaptive genome evolution.
Plants are multicellular organisms in which numerous specialized cell types must communicate to function as a unified system. Plant cells are enclosed by rigid walls, and therefore, intercellular communication requires the presence of plasmodesmata (PD), cytoplasmic channels bridging neighboring cells. These structures are crucial for coordinating developmental stages across tissues. To ensure proper growth and development, the movement of signaling molecules, RNAs, proteins, and nutrients through PD must be tightly controlled, underscoring the importance of regulating their selectivity. Despite their essential role, direct evidence for PD involvement in developmental processes is limited and the mechanisms governing PD regulation remain incompletely understood. Recent studies suggest the existence of diverse regulatory mechanisms beyond the classical callose-based model, revealing a likely complex interplay of several PD regulators across development. In this review, we summarize recent findings on the role of PD in various plant developmental programs, discuss emerging regulatory mechanisms, and highlight how much remains to be discovered.