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Plant digital twins (DTs) are dynamic, data-aware virtual representations that integrate plant structure, physiology, and environmental inputs to simulate plant function, growth, and performance. By combining process-based models, phenomics data, and environmental states in a continuous feedback loop linking physical and virtual plants, DTs offer a novel approach for investigating complex biological systems. In this opinion article, we outline the conceptual foundations of DTs and how they offer new opportunities to bridge the genotype-to-phenotype gap and aid in crop improvement. Despite their promise, major challenges remain in DT development, scalability, and accessibility. Addressing these challenges will be critical for enabling the broad adoption of DTs as transformative tools for accelerating plant science research and crop improvement.
Cytokinin signaling, long regarded primarily as a developmental regulator, has emerged as a central integrator of plant terrestrial adaptation. Comparative genomic and structural phylogenetics indicate a stepwise assembly of the phosphorelay, where receptor domains diversified alongside lineage-specific shifts in cytokinin usage, from cis-zeatin-enriched systems in early-diverging lineages toward trans-zeatin-dominant signaling in vascular plants, while downstream executors remained evolutionarily constrained. Cross-lineage transcriptomic comparisons under heat stress suggest a rewiring of physiological outputs. Although growth repression is deeply conserved, broader metabolic responses differ across clades: trehalose-associated osmoprotection in early land plants, whereas angiosperms transitioned to redox- and transport-based strategies. Overall, cytokinin signaling forms a modular framework that enabled early environmental buffering and was subsequently refined to support the complex architectures of vascular plants.
Abscisic acid (ABA) is a central regulator of plant stress responses and development, but its evolutionary history extends far beyond terrestrial plants (Embryophyta). Emerging phylogenomic evidence reveals that the plastidial ABA biosynthetic pathway originates from cyanobacteria-indicating that plastid-based ABA production predates terrestrialization. In contrast, the signaling framework evolved through stepwise modular innovations. The protein phosphate 2C-sucrose non-fermenting 1-related protein kinase2 core is ancient, whereas the canonical ABA-binding capacity of pyrabactin resistance/pyrabactin resistance 1-like/regulatory component of ABA receptors emerged during the evolution of land plants (Embryophyta) from ancestral Zygnematophyceae algae, with further refinement in angiosperms. By integrating noncanonical receptors, such as chloroplast Mg-chelatase H, we propose a continuous evolutionary trajectory of ABA from prokaryotes to embryophytes, highlighting how receptor innovation facilitated the transition to a terrestrial lifestyle.
Understanding how positional information within plant tissues shapes developmental programs in real time has long remained a challenge due to technical limitations in precisely accessing and manipulating defined cellular domains within complex tissues. Recent advances in single-cell laser ablation, particularly when combined with confocal microscopy, now allow precise spatiotemporal perturbation of selected cells. This technology has enabled researchers to dissect cellular functions, communication dynamics, and mechanical responses with unprecedented accuracy. Here, we review how laser ablation has emerged as a transformative approach in plant biology, from unraveling the signaling networks governing meristem maintenance and root patterning to modeling wound responses and immune activation.
Plant awareness disparity is the human tendency to overlook plants, with negative consequences for education, biodiversity conservation, and sustainability. Philosophy, as a way of life, can promote plant awareness by re-examining how humans perceive and value plant life. I propose four complementary modes of perception, based on hierarchy, similarity, relation, and otherness, each revealing how cultural assumptions shape human attention and ethical attitudes toward plants. Drawing on phenomenology, Indigenous worldviews, Eastern thought, ecofeminism, everyday aesthetics, and vegetal ontology traditions, I integrate philosophical thought with the emerging construct of plant awareness. Practicing seeing plants differently through philosophy can retrain human perception toward them and nurture humility, gratitude, and responsibility. Such reflection on the plant-human bond reinforces the dialogue between science, education, and the humanities, and strengthens the ethical foundations of sustainability.
Phototropins are blue-light receptors that regulate diverse light-driven processes, including phototropism, chloroplast movement, stomatal opening, leaf positioning, and leaf flattening, all of which optimise photosynthesis and promote plant growth. These autophosphorylating serine/threonine kinases initiate signalling from the plasma membrane by altering protein phosphorylation patterns. Nearly 3 decades of research have uncovered numerous phosphorylation events pivotal for distinct phototropin-mediated responses. Here, we summarise major advances in understanding phototropin autophosphorylation, the identification of substrate proteins, and how phosphorylation at specific sites, collectively termed the phototropin phosphocode, controls protein function. We also discuss the emerging role of protein phosphatases in modulating this phosphocode and the potential to engineer these regulatory mechanisms to enhance photosynthetic performance and plant biomass.
High-throughput phenotyping (HTP) has advanced rapidly in recent decades, driven by technological developments across research and agricultural frameworks. Despite its success in measuring traits, it remains underutilized in field crop breeding programs. While the most critical and labor-intensive selection is conducted on heterozygous single plants or small plots at early stages, most phenotyping research focuses on stable genotypes grown in large plots. Here, we reconsider how HTP can be effectively integrated into breeding by accounting for methodologies, scale-related constraints, and technological limitations. Our focus remains on self-pollinated field crops, the predominant global food source. In light of climate change and food security needs, improving the integration of breeding and phenomics can accelerate genetic and technological advances in developing elite varieties.
The traditional model of plant-arbuscular mycorrhizal (AM) fungal coevolution, based solely on interactions between plants and AM fungi, became obsolete with the discovery of the critical roles that belowground microbiomes play in the function of mycorrhizal symbiosis. Based on insights into hyphosphere microbiota, we expand the plant-AM fungus-bacterium continuum into a multipartite AM fungal-orchestrated holobiont (H-AMF) framework, where AM fungi integrate plant roots with soil microbiota into a cross-kingdom ecological unit. A division of labor exists among plants, AM fungi, and hyphosphere microbes in the mycocentric H-AMF perspective. We summarize mechanisms by which AM fungi sustain cooperative relationships with plants and hyphosphere microbiota and propose holobiont-scale methodologies to advance understanding of plant-fungal-microbial interactions and their ecological functions.
The use of cover crops (CCs) is increasingly promoted to diversify cropping systems and advance agricultural sustainability. Yet, CC adoption can involve context-dependent trade-offs, including resource competition and elevated greenhouse gas (GHG) emissions. In this opinion article, we propose enhanced rock weathering (ERW) as a complementary strategy to improve biogeochemical synchrony within CC systems. By synthesizing emerging evidence, we show how CC-ERW interactions can synergistically enhance carbon sequestration, nutrient cycling, GHG mitigation, and soil food-web functioning, mainly via root-driven weathering processes and soil feedbacks. We further outline opportunities for application across diverse agroecosystems and highlight key challenges for scaling, including weathering thresholds, potential metal risks, and governance constraints. Overall, harnessing the CC-ERW nexus offers a promising pathway toward climate-resilient and multifunctional agriculture.
Plants thrive in complex and often hostile environments by continuously sensing and responding to a wide array of biotic and abiotic challenges. Central to this surveillance system are cell surface receptors, including receptor kinases and receptor proteins. Recent advances have revealed how these receptors not only recognize pathogen- and damage-associated molecular patterns but also perceive endogenous peptides and environmental signals. Importantly, emerging evidence highlights extensive crosstalk between immune and abiotic stress signaling, with shared components and co-regulatory mechanisms shaping an integrated response. In this review, we synthesize recent discoveries on the diverse roles of cell surface receptors in detecting external and internal signals, coordinating defense and stress tolerance, and balancing these processes with nutrient acquisition.
As sessile organisms, plants must constantly survey their surroundings and make appropriate responses in their metabolism or development. Numerous receptors and kinases, as well as phytocytokines that play key roles in signal transduction for a multitude of cues, have been revealed in the past 2 decades. However, the mechanisms coordinating these responses remain poorly understood. Recently, the conserved plant metacaspase family emerged as a versatile switch that plays multiple roles, from early signal perception to downstream propagation, by proteolysis of propeptides or other signaling proteins to mediate their conversion to activated forms. In addition, evidence for proteolysis-independent functions of plant metacaspases has also emerged. In this feature review, we summarize advances in plant metacaspase functions and consider approaches to unravel their complex impacts.
Plants have evolved two primary innate immune strategies, pattern-triggered immunity and effector-triggered immunity, to prevent excessive microbial infection. As the 'second genome' of plants, microbiota also regulates the plant growth-immune tradeoff. In this opinion article, we propose that beneficial microbes expand the plant immune threshold by coordinately regulating above-ground and below-ground immune signaling. We integrate this concept into the existing framework of plant immune strategies to construct a novel model of plant immunity. Building upon this foundation, we introduce a novel perspective regarding dose-dependent immune responses. We propose that, in natural systems, non-pathogen-plant interactions should be evaluated not only based on the specific recognition of microbe-associated molecular patterns (MAMPs) but also by incorporating the dose-dependent effects of MAMPs into the assessment framework.
Plants require dynamic mechanisms of cellular organization to continuously adapt to fluctuating environmental conditions. Biomolecular condensation, which refers to nonstoichiometric assembly of macromolecules into membraneless compartments via phase separation, emerges as an essential regulatory strategy for plant development and stress responses. Unlike membrane-bound organelles, condensates can dynamically assemble/disassemble in response to different environmental cues. Increasing evidence indicates that versatile plant condensates associate with cellular membranes to regulate processes such as signal transduction, intracellular trafficking, organelle biogenesis, and gene expression. In this review, we summarize recent progress on representative condensates in association with the plant endomembrane system. We also highlight methodological advances, from multiscale in vivo characterization to in vitro reconstitution, which enable quantitative dissection of membrane-condensate interactions, with an emphasis on the biophysical principles governing them.
Nitric oxide (NO) and melatonin (MT) are ubiquitous plant stress signals, yet their interplay is often reduced to simple antioxidant additivity or fixed synergy. In this review, we synthesize current evidence into an evidence-supported working framework in which NO-MT crosstalk functions as a reversible, stress-state-dependent signaling module governed by NO set-point control, redox-encoded post-translational modifications, and phase-, tissue-, and network-gated feedback. We distinguish three operational states: feed-forward activation, buffering restraint, and network integration. We further define minimum diagnostic criteria for state assignment, including NO kinetics, blockability, turnover/denitrosation capacity, and target-selective S-nitrosation. This framework clarifies when NO-MT coupling is causal, when it is buffered, and when it is redirected by broader reactive oxygen species/calcium/hormone/hydrogen sulfide.
Seed dispersal is a key process in plant regeneration and persistence. While vertebrates such as birds and mammals are widely recognised as endozoochores, a growing body of evidence reveals that invertebrates also contribute meaningfully to seed dispersal through ingestion and defaecation. This review extends the prevailing vertebrate-centred paradigm, arguing that invertebrate gut passage is a recurrent, testable, and ecologically meaningful process. We synthesise current findings on invertebrate-mediated endozoochory across arthropods, gastropods, and other groups, highlighting their effectiveness, ecological relevance, and overlooked roles in shaping plant recruitment, especially in insular or fragmented systems. We adapt the seed dispersal effectiveness framework to invertebrate-mediated dispersal, identify key knowledge gaps, and call for systematic integration of invertebrates into seed-dispersal research and conservation planning.
Climate-driven variability is reducing our ability to accurately predict crop performance across environments, limiting genetic gain in breeding programs. Sustained progress requires predictive frameworks that capture plant-environment interactions across diverse genetics and management conditions. Integrating mechanistic insights from plant science into predictive models offers a path to improve the accuracy, precision, and interpretability of breeding decisions under changing environments. We present emerging hierarchical genome-phenome frameworks and outline how they can be leveraged within breeding programs to evaluate how biological knowledge informs predictions across target environments and supports long-term genetic gain.
Plant science relies on collaborative, infrastructure-rich, and long-term research, yet evaluation remains dominated by simplified citation-based metrics. This mismatch shapes research culture and incentives. More responsible assessment should combine quantitative indicators with contribution-aware, context-sensitive approaches that better reflect how plant science is conducted.
Trehalose 6-phosphate (T6P), a trehalose synthesis intermediate and sugar phosphate, serves as a signaling molecule coordinating sucrose status with plant growth and development. Beyond its metabolic role, the T6P pathway integrates exogenous and other endogenous cues to regulate key developmental transitions, including embryogenesis, seed maturation and filling, shoot branching, vegetative and reproductive phase transitions, and tuber and lateral root formation. Dynamic spatiotemporal expression patterns of T6P-pathway genes correlate with developmental stages, though their specific contributions to the initiation and progression of these transitions remain under investigation. Here, we provide recent insights and future perspectives on the T6P pathway, emphasizing its role in orchestrating diverse plant developmental programs across model and crop species and highlighting emerging mechanistic insights into its functions.
Extrachromosomal circular DNA (eccDNA) is now recognized as a widespread and functionally significant feature of plant genomes. Evidence indicates that eccDNAs contribute to genome plasticity and gene regulation, particularly during abiotic stress. This review synthesizes current knowledge on the composition, dynamics, and functions of plant eccDNAs, including those enriched in transposable elements, protein-coding genes, and repetitive sequences, and their emerging roles in stress tolerance. We evaluate leading models of eccDNA biogenesis, emphasizing mechanisms tied to DNA damage repair and recombination, informed by plant and nonplant systems. We also highlight recent discoveries on eccDNA accumulation, transmission, and regulatory potential, underscoring the need to integrate eccDNA biology into mainstream plant genomics and stress-adaptation research.
Breeding for complex traits is constrained by limited predictive accuracy and transferability, particularly when nonadditive genetic effects and genotype-by-environment interactions dominate performance. In this review, we propose 'Click Breeding', a design-driven paradigm that shifts emphasis from ranking individual candidates to generating and stress-testing entire multigenerational breeding programs. In this framework, objectives and constraints are encoded as machine-readable plans; candidate strategies are evaluated via simulations that integrate genetics, physiology, and environment; and selected designs become traceable experimental workflows with governance checkpoints. Click Breeding connects genomic prediction, crop modeling, and laboratory automation into a coherent, auditable design cycle that complements the breeder's judgment. We discuss conceptual foundations, assess technology maturity, and identify biological, computational, and regulatory challenges to making programmable crop design operational.