Symbiotic nitrogen fixation (SNF) is an effective strategy for legumes and actinorhizal plants to acquire atmospheric nitrogen (N₂) for their growth and development. Like other enzymatic processes in roots, the efficiency of SNF is highly dependent on soil temperature. Since global atmospheric temperature change also affects soil temperature, it is essential to know the temperature response of different types of plant-microbial symbioses capable of SNF at the molecular, physiological, and ecosystem levels on air and soil temperature changes. This is of particular significance, because the ability of nitrogen-fixing microbial symbionts to deal with temperature changes in the soil can affect growth and development of legumes and actinorhizal plants and, hence, the sustainability of ecosystems in a changing climate. However, temperature response may differ between different groups of nitrogen-fixing microbial symbionts (e.g., rhizobia vs. Frankia) and between different strains of the same microbial symbiont. In the present review, we summarize current knowledge on the temperature response of SNF, describe unexplored research topics, and propose future basic and applied research avenues under controlled conditions and in field studies. It provides a holistic view on the subject to encourage interdisciplinary research on this subject which has been largely neglected during the last decades, but of increasing significance due to global climate change.

Rice is a staple food for more than half of the world's population, particularly in Asia. Cadmium (Cd) contamination in rice poses serious risks to human health through the food chain. Understanding the mechanisms governing Cd uptake, translocation, and tissue distribution, as well as its interaction with essential metals such as iron (Fe), zinc (Zn), and manganese (Mn), is critical for improving rice safety. Over the past two decades, key transporters involved in Cd and micronutrient homeostasis have been identified, providing insights into their crosstalk and competition. In this review, we summarize current knowledge on Cd and essential metal transport in rice and discuss the challenges and trade-offs in limiting Cd accumulation while maintaining plant growth and micronutrient balance, highlighting strategies for developing rice varieties with reduced Cd content and enhanced food safety.

The domestication of crops originates from their wild ancestors and typically begins with the selection of phenotypes carrying specific alleles within wild populations. Subsequently, artificial hybridization and the retention of novel mutations introduce new alleles, leading to the continual creation of new phenotypes. The modern maize (Zea mays L.), as one of the most important food crops worldwide, has long attracted significant attention from researchers regarding its domestication and origin. In this review, we have summarized the related advances in clarifying hybrid origin and identifying related genes and allelic origins in maize. Modern maize was initially domesticated from Zea mays ssp. parviglumis approximately 9,000 years ago, followed by hybridization with Z. mays ssp. mexicana around 6,000 years ago, which gave rise to the modern maize lineage. Modern maize, as a hybrid lineage, possesses extensive genetic admixture that serves as the foundation for its phenotypic diversity and wide adaptability to various cultivation environments. Compared to ssp. parviglumis and mexicana, the unique phenotypes of maize were shaped through the selection of allelic combinations from both ancestors and/or the accumulation of novel mutations. Elite alleles from both ancestors hold significant value for biotic and abiotic stress resistance. Identifying these alleles and the underlying molecular mechanisms and incorporating them into modern breeding programs could facilitate the development of new maize germplasm with enhanced adaptability to today's changing environments and improved agricultural productivity.

Plants, as sessile organisms, continuously encounter challenges posed by fluctuating environmental conditions. To adapt to these stresses, they have developed dynamic regulatory mechanisms, including post-translational modifications (PTMs) such as SUMOylation. Small ubiquitin-like modifier (SUMO) proteins are covalently attached to target proteins, resulting in alterations to their stability, localization, activity, and interactions. Over the past two decades, SUMOylation has emerged as a critical regulator of responses to various abiotic and biotic stresses in plants. This review summarizes recent advancements in the roles of SUMOylation in response to temperature stress, drought conditions, salinity stress, and pathogen attacks. Furthermore, we discuss the mechanism by which SUMOylation functions as an essential molecular switch that balances developmental processes and stress responses, and provide a perspective on future investigations in this field. By integrating current knowledge with future perspectives, this summary and perspective will deepen our understanding of the roles of PTMs in plant stress responses and offer insights for improving crop yields and resistance.

The accelerating global population growth and increasing environmental pressures driven by climate change have made food security an urgent scientific objective. In addition to genetic modifications aimed at yield improvement, minimizing yield reduction and postharvest decay caused by pathogenic infections is essential for reinforcing global food supply systems. Metabolites, as fundamental biochemical constituents of life, form the basis of many plant defense strategies that have evolved over millions of years to counter pathogen invasion—functioning both as direct antimicrobial and anti‐herbivory agents as well as inducers of internal immune signaling networks. Despite the extensive diversity and intricate biosynthetic pathways of plant metabolites, advances in high‐performance mass spectrometry and nucleotide sequencing have clarified the immune‐related roles of several metabolites through conventional genetic and transcriptomic analyses. The emergence of artificial intelligence (AI) has provided a transformative means by which to integrate and interpret complex, large‐scale data sets, offering insights unattainable through traditional approaches and expediting the mapping of metabolite–immunity interactions. This review summarizes recent progress in elucidating the functions of various plant metabolites, including primary metabolites and secondary metabolites, in plant immune responses. This study also details their reprogramming by pathogens. Finally, it examines the prospective applications of nanoscience, de novo domestication, and artificial intelligence in the rational design of next‐generation artificial elicitors.

Genetic variation underlying phenotypic diversity between wild and domesticated species has been extensively studied, the contribution of higher‐order chromatin architecture to these processes remains less explored. Advances in Hi‐C and related genomic technologies have revealed that plant genomes exhibit complex three‐dimensional (3D) genome organization, hierarchically structured into A/B compartments, and topologically associated domains (TADs). TADs represent self‐interacting genomic regions that can constrain or regulate without directly determining transcriptional outcomes. Alterations to TAD organization or boundary have been associated with changes in chromatin interactions and gene regulatory potential in specific developmental or environmental contexts. In plants, emerging evidence indicates that TAD structure can be genetically and environmentally modulated, despite the absence of canonical architectural proteins such as CTCF. Both environmental stress and genetic perturbations have been shown to remodel chromatin organization, with context‐dependent changes in gene expression. Such plasticity in chromatin dynamics that contribute to adaptive responses raises a potential link between 3D genomic structure and cryptic genetic variations (CGVs). CGVs remain phenotypically silent under normal conditions but can be revealed under environmental or genetic perturbations, representing an additional layer of regulatory potential in plant genomes. Here, we propose that stress‐induced chromatin organization, including changes in TAD organization and chromatin compartmentalization, may influence accessibility and expression of CGVs in a context‐dependent manner. While a direct mechanistic link between TADs and CGVs remains largely unexplored. Here, we reviewed recent findings from model plants and major crops to highlight how variation in 3D genome organization can contribute to transcriptional plasticity, stress responses, and lineage‐specific regulatory evolution. By integrating 3D genomics, chromatin accessibility, and multi‐omics data, we outline a conceptual framework for generating hypotheses and open questions on how TAD‐associated chromatin dynamics and CGVs together may shape transcriptional plasticity, stress responses, and long‐term adaptive evolution in plants with implications for future crop improvement strategies.

Plant immunity requires not only intracellular recognition of pathogen invasion but also downstream execution mechanisms that directly restrict pathogen proliferation and spread. Nucleotide-binding leucine-rich repeat receptors (NLRs) function as core components of innate immunity in both plants and animals. In animals, NLR activation initiates caspase-dependent immune signaling pathways. In contrast, plants lack caspases but instead contain metacaspases (MCAs/MCs). MCs are Ca²⁺-dependent cysteine proteases that mediate selective proteolysis during immune-associated cellular reprogramming. In the context of plant antiviral immunity, recent studies support roles for MCs in antiviral defense and position their activation within NLR-mediated immune networks. Notably, Ca²⁺ influx downstream of NLR activation is proposed to contribute to the coupling of immune recognition and proteolytic execution. In this review, we synthesize current advances in NLR- and MC-mediated plant immunity, with a particular emphasis on antiviral immunity, and propose a conceptual framework in which recognition and proteolytic execution constitute coordinated yet mechanistically distinct layers of plant immune responses, with implications for immune engineering aimed at enhancing resistance against diverse viral diseases.

Ubiquitination is a central mechanism that regulates receptor kinases (RKs) in plants, where the ubiquitin code controls RK stability, endocytosis, and kinase activity, ensuring precise signaling during development and immunity. As transmembrane signaling hubs, RKs are dynamically controlled by E3 ubiquitin ligases, whose activity is itself regulated by RK phosphorylation, forming intricate feedback loops. Ubiquitination directs RKs toward degradation via either the endocytic-vacuolar or 26S proteasome pathways, with emerging evidence suggesting functional interplay between these routes. Beyond proteolysis, ubiquitination can also directly suppress RK activity. Phosphorylation of E3 ligases by activated RKs or their co-receptors modulates ligase activity, substrate binding, and ubiquitin chain linkage, enabling dynamic signal regulation. This reciprocal control establishes a sophisticated network that maintains receptor homeostasis and signaling fidelity. Despite significant progress, key questions remain about degradation pathway integration, structural mechanisms of E3-substrate-E2 complexes, and crosstalk with other post-translational modifications. Elucidating these regulatory circuits will deepen our understanding of RK-mediated cellular signaling and provide strategies to enhance crop resilience and symbiotic efficiency.

The cellular heterogeneity associated with plant form and function is often overlooked in traditional bulk-tissue analyses. Emerging single-cell technologies provide new opportunities for dissecting this complexity at higher resolution. In this review, we summarize how single-cell multi-omics approaches, integrating transcriptomics, epigenomics, and spatial omics, can be used to characterize the regulatory landscapes associated with crop development, stress responses, and evolution. We discuss the application of these technologies across the crop life cycle, with a focus on identifying cell-type-specific programs related to key agronomic traits and tracing developmental trajectories. Furthermore, we describe how single-cell tools contribute to the analysis of plant responses to abiotic and biotic stresses and provide insights into the evolution of specialized cell types. We also discuss current challenges, including technical difficulties in protoplast isolation, the computational integration of multi-modal data, and scalability across diverse species. Finally, we outline potential future directions for combining machine learning and spatial transcriptomics to connect cellular-level observations with tissue-level functions, thereby supporting advances in functional genomics, precision breeding, and crop improvement.

Global agriculture urgently needs sustainable strategies to boost crop productivity while reducing environmental impact. Harnessing plant- exuded bioactive metabolites, such as polyphenols, flavonoids, and organic acids, as natural prebiotics offers a powerful yet underexploited avenue for modulating rhizosphere microbiomes. These prebiotics complement existing microbial inoculants by leveraging the plant's own chemistry to selectively recruit beneficial microbes, thereby enhancing disease suppression, nutrient acquisition, and soil health more reliably than introduced consortia, which often fail due to ecological instability. However, translating this promise into practice is hampered by the profound complexity of the soil–root–microbe interface. This review establishes a conceptual framework that positions plant prebiotics as actionable tools for precision microbiome engineering. We summarize the biosynthetic pathways and mechanisms through which these specialized metabolites stimulate specific beneficial microbial functions. Building on this synthesis, we introduce the PRE-DDV pipeline (decode–design–validate), a closed-loop strategy integrating multi-omics profiling, synthetic community design, and iterative field validation. To enable commercial-scale field application, we critically examine key translational considerations: Identifying scalable plant sources (including native flora and agro-industrial byproducts), advancing formulation and precision delivery to ensure stability and targeted release, and assessing the economic feasibility, environmental sustainability, and regulatory frameworks governing industrial-scale production. Together, these contributions position prebiotics within a concrete pathway that bridges biological mechanisms and practical scalability, transforming them from a promising concept into a practical cornerstone of sustainable, climate-resilient agriculture.

Flowering time is a key agronomic trait that influences plant reproductive success and crop yield, and its regulation is closely associated with soil nutrient availability. This review summarizes recent advances in understanding the molecular mechanisms through which macronutrients and micronutrients regulate flowering time in plants. An emerging central theme is that nutrient-derived signaling integrates with core flowering regulatory pathways, including the photoperiodic, gibberellin, vernalization, autonomous, and sugar pathways, with nitrogen and phosphorus being the most extensively studied. However, major knowledge gaps remain regarding the regulatory roles of potassium, sulfur, and micronutrients, as well as species-specific nutrient responses and the molecular basis of nutrient-nutrient and nutrient-environment interactions in flowering regulation. In addition, the role of nutrient-derived metabolites and rhizosphere microorganisms in flowering control remains largely unexplored. Addressing these challenges is essential for the rational development of crop varieties with optimized flowering time and enhanced nutrient use efficiency through targeted genetic engineering, molecular breeding, and innovative nutrient management strategies, thereby supporting sustainable agricultural development.

Engineered nanoparticles (ENPs) are increasingly recognized as promising tools for modulating plant stress responses; however, their underlying mechanisms and associated risks remain under debate. This review integrates recent advances showing that ENPs can reprogram plant redox homeostasis through multiple pathways, including direct surface redox activity, nanozyme‐like catalysis, ion release, and disruption of organellar electron transport. In addition, ENPs influence membrane physicochemical properties, transcriptional regulation, metabolic fluxes, hormonal crosstalk, epigenetic modifications, and the structure of the plant‐associated microbiome. These processes produce distinct reactive oxygen and nitrogen species (ROS/RNS) signatures that activate Ca²⁺ fluxes, mitogen‐activated protein kinase (MAPK) cascades, and downstream transcriptional networks. We emphasize the importance of dose‐dependent—often hormetic—responses, the critical role of the rhizosphere microbiome, and the application of spatially resolved techniques (e.g., μ‐XRF, NanoSIMS, and spatial omics) to link NP fate with localized redox dynamics. Finally, we propose a safe‐by‐design framework that incorporates standardized NP characterization, appropriate ionic and inert controls, and predictive modeling approaches. This framework aims to facilitate the risk‐informed and sustainable deployment of ENPs in agriculture.

Nitrogen pollution represents a critical challenge in the 21st century, highlighting the urgent need for sustainable alternatives to industrial nitrogen fixation. Diazotrophic bacteria, which uniquely convert dinitrogen (N₂) into bioavailable forms, offer a promising solution through biological nitrogen fixation (BNF). These bacteria typically perform nitrogen fixation under nitrogen‐limited conditions. Over the past 50 years, extensive research has elucidated the molecular mechanisms and regulatory pathways governing BNF. Recent microbiome studies have revealed that wild rice accessions harbor a greater abundance of diazotrophic bacteria, whereas a substantial proportion of these beneficial microbes have been lost in modern cultivated varieties. Advancements in synthetic biology have enabled the engineering of nitrogen-exporting diazotrophs, potentially reducing dependence on industrial nitrogen fertilizers. This review emphasizes the importance of targeted research to develop customized diazotrophic microbes in conjunction with synthetic microbial community that can serve as nitrogen exporters for rice. Furthermore, it highlights the necessity of identifying rice cultivars that are particularly responsive to these microbial interventions. Finally, it provides a comprehensive roadmap addressing key challenges and opportunities in deploying BNF to supplement plant nitrogen nutrition and advance sustainable agriculture.

Hypoxic conditions caused by submergence or soil waterlogging constrain plant growth and productivity. To survive, plants coordinately reprogram both sugar metabolism and phytohormone signaling to trigger adaptive responses; yet, the integrative regulatory frameworks governing this interaction remain unresolved. Here, we synthesize current knowledge on how sugars, acting as both metabolites and signals, intersect with phytohormone networks to regulate growth and survival under low-oxygen stress. Under hypoxia, ethylene and auxin reshape root architecture, while cytokinin mediates sugar-dependent regulation of shoot branching to optimize resource allocation. The dynamic interplay between abscisic acid and sugars is central to maintaining energy balance under cyclic day–night hypoxia. This interaction modulates the stomatal aperture, facilitates controlled starch degradation, and coordinates sucrose transport to sustain metabolism. Furthermore, crosstalk between primary sugars, gibberellin, and brassinosteroid fine-tunes critical developmental transitions, including seed germination and internode elongation. Although individual signaling pathways under hypoxia have been well studied, their integration via sugar–hormone crosstalk remains elusive. To address these issues, we propose integrating synthetic low-oxygen sensors that initially detect hypoxic stress with engineered sugar–hormone balancing circuits that subsequently fine-tune metabolic and hormonal responses, thereby creating closed-loop feedback systems for adaptive stress resilience. Such systems could enable “Sensing, Metabolism, Adaptation, and Regulation Technology” (SMART) crops to autonomously sense and adapt to hypoxia stress. By synthesizing current knowledge and existing gaps, our work proposes future directions to advance the development of hypoxia-resilient crops through optimizing growth and yield stability under stress.