Membrane transporters, including ion channels and carriers, maintain ionic and nutrient homeostasis vital for growth and stress resilience in plants. Their activity is finely regulated, enabling dynamic responses to internal and external signals. Transporters often exist in an ‘autoinhibited’ resting state that can be switched on by post-translational modifications in response to environmental cues. Specifically, protein phosphorylation functions as a molecular switch that relieves autoinhibition of channels and carriers to modulate their activities. We examine the phospho-regulation of exemplary transporters involved in nutrient allocation, stress resistance, and signal transduction, providing a perspective on how plants orchestrate membrane transport processes to sustain ion and nutrient balance and adapt to environmental challenges.

High day and night temperatures impair grain yield and quality in major cereal crops such as rice, maize, and wheat, posing a major challenge under global warming. In this review, we have highlighted advances that govern flowering through clock genes, key genetic regulatory mechanisms of the complex processes that regulate inflorescence architecture and grain filling efficiency, which are affected by heat stress. This unraveled knowledge offers opportunities to improve grain yield and quality without tradeoffs, leading to higher grain number, more efficient grain filling, and maintaining uncompromised starch-to-protein accumulation under high day and night temperatures.

Phenotypic datasets are increasingly rich and heterogeneous, with images, time courses, manual measurements, processed variables, and metadata. The management of such datasets navigates between partly incompatible objectives: (i) facilitate data analysis by extracting, organizing, and storing relevant variables; and (ii) allow reuse of raw, synthesized, and computed data (FAIR principles). For the first objective, ‘dedicated datasets’ can be extracted from raw information and tailored for the user’s data analysis, but they result in a massive loss of information. We advocate that, for the second objective, ‘sensu stricto phenomic datasets’, upstream of dedicated datasets, should organize data without loss of information with data-science tools, in a ‘theory-agnostic’ way. They allow different users to build their own ‘dedicated datasets’ according to planned data analysis.

Controlled environment agriculture (CEA) provides unprecedented opportunities to accelerate the translation of plant science breakthroughs into agricultural impact. By precisely controlling growth conditions, CEA enables the reliable and tightly regulated deployment of beneficial optimized traits by integrating emerging breeding, genomic, and synthetic biology tools. In this review we highlight both the progress and the remaining challenges enabled by CEA to reimagine crop design, including enhanced photosynthesis that operates independently of seasonal and circadian limitations, improvements in resource and metabolic efficiency, customized plant architecture, and the reliable, controllable production of high-value compounds. These capabilities position CEA as both a versatile research platform and an efficient, high-yielding production system, bridging fundamental discoveries with real-world crop outcomes to support sustainable, climate-resilient agriculture into the future.

A recent study by Zhang et al. demonstrates that a microbial compound, cyclo(Leu–Pro), mimics plant hormones to regulate rice tillering via strigolactone signaling. This finding underscores the crucial role of the root microbiome in crop development and opens up potential for microbiome-based eco-friendly strategies to optimize crop architecture and yield.

Since the discovery of auxins as cell division factors a century ago, impressive scientific advances related to phytohormones have revolutionized plant sciences and human progress. This review examines the key features of the ten hormonal groups that operate in plants, here referred to as the ‘classical ten’: auxins, gibberellins (GAs), cytokinins (CKs), abscisic acid (ABA), ethylene (ETH), salicylates (SAs), jasmonates (JAs), brassinosteroids (BRs), peptide hormones (PEPs), and strigolactones (SLs). By leveraging historical data and sharpening the essentials of each hormonal group, their major functions are presented, with a discussion on what makes a compound a phytohormone and how it can be differentiated from hormone-like compounds and other signaling molecules. Hormonal receptors, long-distance transport, and differences between hormonal crosstalk, interactions, and complementation are discussed to illustrate the basics of hormonal action in plants.

Wheat rust diseases pose major threats to global food security; accelerated gene discovery is critical for developing resistant varieties. The Mutational Omics Discovery Pipeline (MODP) integrates ethyl methanesulfonate (EMS) mutagenesis (typically 0.3–1.2% v/v) with multi-omics analyses to accelerate the identification of resistance genes in wheat. EMS can induce G→A and C→T transitions, which may result in the loss of disease resistance due to mutation in the target genes. In the M2 generation, by inoculating with the rust pathogens and employing high-throughput phenotyping, we can efficiently identify susceptible independent mutants.

A significant proportion of flowers in crop plants fail to produce seeds, particularly under heat and drought stress. This outcome reflects a regulated developmental process of reproductive abortion, shaped by a complex interplay of genetic, hormonal, and environmental factors that limit crop yield. Unlike abscission, reproductive abortion can occur at multiple developmental stages. In this review, we examine how internal and external cues disrupt the development of florets, ovules, embryos, and seeds in major food crops, including cereals, legumes, and brassicas, under both optimal and stress conditions. Drawing from research in arabidopsis and extending to crop systems, we identify conserved and crop-specific mechanisms, highlight critical knowledge gaps, and propose strategies to enhance reproductive resilience and seed set under abiotic stresses.

Unicellular green algae are a diverse and ecologically crucial group, serving as primary producers in a wide range of aquatic ecosystems and producing valuable biomolecules in human hands, thanks to their remarkable phenotypic and metabolic plasticity. Among the different regulatory mechanisms explaining these capacities, epigenetics plays a key role. This review focuses on the epigenetic regulation of the model species Chlamydomonas reinhardtii, focusing on the role of DNA methylation [C5-methylcytosine (5mC), N6-methyladenine (6mA)], histone post-translational modifications (PTMs), and noncoding RNAs (ncRNAs) in modulating gene expression, maintaining genome stability, and enabling acclimation to several environments. This review also explores the evolutionary significance of these marks and the potential role of the unique epigenetic patterns in this species.

MicroRNAs (miRNAs) guide post-transcriptional gene silencing in plants and shape developmental outcomes and environmental responses by precisely tuning gene expression. miRNAs originate from primary transcripts (pri-miRNAs) whose structural features – including internal loops, mismatches, and sequence motifs – facilitate interactions with the miRNA processing complex composed of DICER-LIKE 1 (DCL1), HYPONASTIC LEAVES 1 (HYL1), and SERRATE (SE). In vitro structural analyses of DCL1, HYL1, and SE proteins have elucidated their interactions with each other and with pri-miRNAs at unprecedented resolution. These findings highlight plant-specific processing features that are distinct from those of animals and suggest new avenues for manipulating miRNA pathways. We review recent progress in understanding the structural determinants of pri-miRNA processing, knowledge that may also be valuable for future applications in crop species through targeted genome editing.

Specific accumulation of auxin contributes to the regulation of many developmental processes. Auxin uptake is mediated by AUX1 (AUXIN1) and LAX (Like-AUX1) proteins, but their mechanism of action has been unclear. Recent studies by Yang et al. and Ung et al. provide structures suggesting how auxin uptake is coupled to proton flux.

Synthetic biology holds great potential to transform agriculture, yet its progress is constrained by the complexity of multigenomic, multitrait, and multi-environment data. Desirable traits often arise from complex gene networks acting across diverse conditions, making them difficult to predict and optimize manually. In the past decade, artificial intelligence (AI) has supported this process, but its large data needs and poor integration limit its role to pattern recognition rather than explanatory trait design. We argue that hybrid AI can more effectively navigate multiomics complexity to engineer climate-smart, high-yield crops. Already reducing trial and error in crop engineering, guiding gRNA design, and identifying key regulators, hybrid AI has outperformed traditional data-driven approaches, but its full potential requires clear pipelines, curated datasets, and automation platforms.

Advances in genome engineering have paved the way for targeted epigenome engineering, providing fundamental insights into the role of epigenetic modifications in trait inheritance. Engineered epialleles have already delivered stable, heritable changes in agronomic traits. Despite this capacity, progress in the field has not yet achieved its potential, leaving many avenues of research unexplored. In this review we examine the factors influencing this progress, including the advances in current epigenome editing techniques, the key research goals and translational applications, and the challenges in the selection of ideal target loci. We propose that improved tools for the selection of target loci, particularly in large and complex genomes, are needed to propel the field forward.

Plants have developed sophisticated signaling mechanisms to adapt to environmental changes, and secreted peptides play crucial roles. Sulfated tyrosine (sTyr) peptides are important regulators of plant growth, nutrient uptake, defense responses, and seed development. This study delves into the evolution of sTyr peptides, their receptors, and the enzyme tyrosylprotein sulfotransferase (TPST) that is responsible for their activation. By exploring the evolutionary timeline of sTyr peptide function, we aim to determine their significance in the emergence of land plants. We map the distribution of sTyr peptides, their receptors, and TPST across different plant species, and identify key sites essential for their activity. These findings provide a comprehensive overview of the functional and evolutionary significance of sTyr peptidesand offer insights into their potential agricultural applications.

Wheat is a primary staple crop worldwide, grown in a wide range of environments, leading to significant yield variation. Improving wheat yield potential and resilience against abiotic and biotic stresses are critical to food security. A perennial debate is to breed for yield potential or for adaptation to specific conditions. In this review, we show that often selection for yield potential also improves crop yield under stress with no trade-offs. We examine agronomic and physiological traits associated with yield that are less likely to exhibit crossover or scaling effects, and we discuss their implications for breeding.

The SEC14-GOLD family of phosphatidylinositol (PI) transfer proteins, known as PATELLIN (PATL) proteins in plants, are key regulators of plasma membrane (PM)-related signaling processes. They function through multifaceted interactions involving a SEC14 lipid-binding domain, GOLD domain, and their N-terminal region. Protein phosphorylation is crucial for modulating protein and phospholipid interactions, but phosphorylation of SEC14 proteins remains understudied. Phosphoproteomics data from Arabidopsis thaliana indicates two major phosphorylation hubs within the N-terminal and the conserved SEC14-GOLD regions in the PATLs. These phosphorylation patterns vary in response to environmental and hormonal stress-related factors. Understanding how PATL proteins are phosphorylated can offer insights into PATL–membrane interactions and their functional roles in cell physiology, providing new strategies for plant adaptation and stress resilience in crops.

As a biomolecular interaction assay, MicroScale thermophoresis (MST) represents an innovative analytical technique that integrates the high precision of fluorescence detection with the dynamic sensitivity of thermophoresis. MST operates under in vivo-mimicking conditions, enabling quantitative characterization of binding affinities through the observation of differential migration patterns of fluorescently labeled biomolecules. MST technology validated and quantified the interactions between multiple plant receptors and RALF peptides.

Proteins are integral components of root exudates that mediate plant–microbe interactions, nutrient mobilization, and stress responses. Despite their importance, our understanding of their composition, regulation, and function is limited. Here, we summarize recent advances on root-exuded proteins, highlight pivotal outstanding questions, and propose future research directions.

Coenzyme Q (CoQ) is vital for human health, but structural differences limit its supplementation from crops. In a recent study, Xu et al. traced its diversification across plant lineages and identified distinct targets for precise engineering. Their work highlights how utilising evolutionary signatures can enable crop biofortification and guide future strategies to enhance nutritional value.

Salicylic acid (SA) is a vital phytohormone produced from isochorismate in arabidopsis (Arabidopsis thaliana). However, SA in most plant species is produced from phenylalanine, a pathway that has long remained unresolved. Three recent studies filled this major knowledge gap and elucidated a multistep SA biosynthesis pathway that is ancestral in the plant kingdom.