Once viewed mainly as metabolic intermediates, small metabolites are increasingly recognized as spatially and temporally regulated signals that coordinate plant development and adaptation. Understanding these metabolite-based regulatory processes could reveal new strategies to improve crop resilience, productivity, and sustainability under changing environmental conditions.
Castilleja (Orobanchaceae), commonly known as Indian paintbrush, is a genus of approximately 200 hemiparasitic species found primarily across the Americas. Long studied for its taxonomic complexity, vibrant floral displays, and ecological interactions with host plants, Castilleja has recently emerged as a versatile research system spanning parasitic biology, specialized metabolism, conservation genetics, and pharmacology. The availability of whole-genome sequencing is transforming the field, revealing expanded gene families involved in host recognition, enabling genomic species delimitation of cryptic taxa, and providing frameworks for mapping biosynthetic pathways of bioactive compounds, including iridoid glycosides and phenylethanoid glycosides. This review synthesizes advances across these disciplines and highlights how genomics serves as an integrative force connecting taxonomy, ecology, phytochemistry, and parasitic biology in this genus.
Plants respond to spatially and temporally variable soil nutrients through root architectural plasticity, regulation of uptake and assimilation per root unit, and plant-soil-microbiome interactions. Although often viewed as complementary, these responses can also behave as compensatory strategies. Under non-optimal nutrient distributions, plants may invest either in greater root proliferation or in higher uptake capacity per root unit. We propose that this development-transport relationship should be understood as an optimization problem, rather than an additive response. Comparable morphology-physiology trade-offs occur in other resource-acquiring organs, including the gut and the lungs. Tuning or partially uncoupling these constraints could redefine crop ideotypes as dynamic combinations of root architecture, physiological elasticity, and controlled rhizosphere outsourcing, opening new routes to improve nutritional efficiencies.
Auxin and calcium (Ca2+) are central plant signals that coordinate growth, development, and responses to environmental cues. Typically studied as largely parallel pathways, they are now increasingly recognized as interconnected networks whose activities converge at multiple regulatory levels. Recent advances in live imaging, biosensors, optogenetics, and structural approaches have revealed that auxin can rapidly trigger Ca2+ influx from the apoplast via TRANSPORT INHIBITOR RESPONSE1 (TIR1)/AUXIN-SIGNALING F-BOX (AFB)-dependent signaling mechanisms and Ca2+ channels, presumably involving cyclic nucleotides produced by TIR1/AFB auxin receptors. Conversely, Ca2+ signals arising from mechanosensing, wounding, and environmental stress can modulate auxin transport, signaling, and transcriptional outputs. Together, these discoveries highlight a dynamic, reciprocal signaling axis where Ca2+ acts both downstream and upstream of auxin to shape growth, development, tropisms, and regeneration.
Angiosperms rose to ecological dominance through innovations that enhanced photosynthetic capacity and water-use efficiency. We propose that a pivotal, yet underappreciated, contributor was the hydroactive stomatal mechanism, an abscisic acid-mediated, metabolically driven control of guard-cell turgor. Unlike passive hydraulic responses to changes in water status, hydroactive regulation enables rapid, multisignal integration and minute-scale adjustment of stomatal aperture, synchronising carbon gain with hydraulic safety under fluctuating light, CO2, and evaporative demand. We argue that this water-status control module complemented other stomatal signalling pathways responsive to light, CO2, and metabolism, improving physiological coordination in dynamic environments. This perspective reframes stomata as decision-making nodes linking leaf anatomical evolution, physiological plasticity, and angiosperm diversification and offers a foundation for engineering climate-resilient crops under climate change.
Producing enough food to feed the world in an environmentally sustainable way represents a major challenge for humanity. It requires a bold paradigm that maximises options for the future. In contrast, organic farming has serious limitations, as it is based on an oversimplified assumption that natural substances are safe and artificial substances are unsafe. This approach severely constrains options for using synthetic inputs or new breeding techniques (NBTs) because they are perceived as 'unnatural'. In this opinion article, we encourage a more objective evaluation of the contribution of synthetic inputs and NBTs to sustainability. We argue that crop production per se is not a natural situation and that it is important to keep options open for the future.
Hydrogen sulfide (H2S) is widely implicated in plants’ adaptive responses to salinity, regulating processes ranging from ionic homeostasis to antioxidant defense and is often described as a central signaling hub due to its interaction with core signaling pathways, such as Ca2+, reactive oxygen species, nitric oxide, and phytohormones. However, most evidence remains correlative and relies heavily on pharmacological interventions. This review critically examines the mechanistic gaps, causality, and specificity of H2S-mediated signaling in regulating salinity adaptive responses in plants. We argue that moving from phenomenological observations to causal mechanisms requires a strategic shift towards advanced genetic tools, in vivo dynamic imaging, synthetic biology, and systems-level interrogation. Addressing these challenges is essential to harness the translational potential of H2S signaling for improving crop resilience in saline environments.
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.
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.
Phytohormones are predominantly produced in tissues that are spatially separated from their perceptive target tissues. Consequently, short- and long-distance phytohormone movement is a prerequisite for their function, and the underpinning transport mechanisms are crucial for phytohormone action. Strigolactones (SLs) are the most recently identified class of phytohormones. While SL synthesis and signaling pathways are well established, knowledge of active SL transport is scarce, limiting a system-level understanding of SL mechanisms and functions. Following the characterization of several SL transporters in the context of crop protection for two crops of global importance, we review our current knowledge on SL transport and highlight critical knowledge gaps with the aim of providing a conceptual framework for future studies.
The process by which plants synthesize the insecticidal compound nicotine remained unexpectedly elusive for many decades. In a new report, Chang et al. shed light on a five-component metabolon that catalyzes the final steps of the nicotine biosynthetic pathway, offering promising prospects for engineering plant resistance.
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.
The colonization of land by plants reshaped the global carbon cycle, with distinct functional contributions from different lineages. Mosses, a diverse group of nonvascular plants, inhabit environments ranging from arid rock surfaces to high-latitude peatlands and possess traits that strongly influence the global carbon cycle. Although small in stature, mosses frequently dominate primary production at higher latitudes and contribute to long-term carbon storage in peatland and tundra ecosystems. Emerging evidence indicates that moss physiological responses to elevated CO2 and changing climate conditions may alter ecosystem carbon balance in ways not currently captured by Earth system models. This review discusses the moss lifestyle, their historical and current influence on the carbon cycle, and their responses to elevated CO2 levels.
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.
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.
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.
