Trends in Plant Science

Understanding the genetics of cotton regeneration to help improve cotton Plant regeneration in cotton remains confined to a few genotypes. Xu et al. linked competence to chromatin accessibility and AGL15, while Tang et al. showed auxin–chromatin interplay guiding embryogenesis. Together, they highlight regeneration as an integrated program of accessibility, transcription, and hormonal control to overcome recalcitrance in crops.

Understanding the genetics of cotton regeneration to help improve cotton #plantscience

LEC2 unlocks totipotency by unlocking chromatin Plants exhibit a unique regenerative capacity, exemplified by somatic embryogenesis (SE), that is, the formation of embryos from somatic cells. In a recent study, Peng et al. identified LEAFY COTYLEDON2 (LEC2) as a central regulator of SE by remodeling chromatin and activating totipotency regulators through epigenetic and hormonal pathways, enabling somatic cells to reset their developmental fate.

LEC2 unlocks totipotency by unlocking chromatin #plantscience

Delighted to share that the 2026 Rank Prize for Nutrition has been awarded to Professor David E. Salt & Martin Broadley! 🏆👏 Congratulations both!

Read more 👉 www.rankprize.org/prize/nutrit...

@uniofnottingham.bsky.social @rothamsted.bsky.social #plantscience

Phased telomere-to-telomere super-pangenome: definitive reference genome in plants With falling sequencing costs and the rise of computational methods, plant genomics is entering a new paradigmatic shift. Combination of phased telomere-to-telomere assemblies and super-pangenome is emerging as the ultimate reference needed in plants. Together they provide a gold standard for genetic dissection, molecular-design breeding, and resource conservation.

Phased telomere-to-telomere super-pangenome: definitive reference genome in plants #plantscience

Fighting citrus Huanglongbing with evolutionary principles Conventional pest management often accelerates the evolution of resistance in pests, resulting in an unsustainable cycle of control. By contrast, evolution-informed pest management (EIPM) can outmaneuver pests by anticipating and exploiting their adaptive constraints. This perspective synthesizes evolutionary principles from wild and cultivated plants to develop durable defenses. As classical biocontrol uses living natural enemies, which is not stable, efficient, or adaptable enough, we highlight the emergence of EIPM, where artificial intelligence (AI) and synthetic biology enable precise design of new biocontrol. As a case study, our recent research identified resistant protein PUB21DN and micropeptide APP3-14 as promising tools against citrus Huanglongbing (HLB), demonstrating the value of combining evolutionary insights with advanced technologies for sustainable agricultural solutions.

Fighting citrus Huanglongbing with evolutionary principles #plantscience

Twenty years of wheat genomics (2005–2025) Twenty years of sustained global efforts in wheat genomics reached the latest milestone in 2025 with the publication of two articles reporting complete wheat genome sequences. This forum article includes milestones from early drafts to recent breakthroughs, highlighting how this latest resource will accelerate improvement of this globally important crop.

Twenty years of wheat genomics (2005–2025) #plantscience

Toward a logic-based framework for plant epigenetic control Genome editing enables precise sequence alteration, but remains limited by binary logic and irreversible outcomes. By contrast, epigenome editing offers reversible and multilayered regulation without altering the DNA sequence. Yet current implementations remain inert – unable to sense, compute, or adapt. Here, we survey emerging plant epigenome editing modalities and explore their integration with logic-based synthetic gene circuits. We propose design strategies, such as multiplexer-driven flowering switches in Arabidopsis (Arabidopsis thaliana) and Boolean logic-gated fruit ripening in Solanum lycopersicum. Underpinned by plant-tailored roadmaps and pitfall mitigation strategies synthesized here, these architectures could transform static editing into programmable, context-aware regulation. This convergence gestures toward a future of composite epigenome engineering, where epigenetic plasticity and synthetic logic integrate to support scalable, predictive control of traits.

Toward a logic-based framework for plant epigenetic control #plantscience

The genetics of paradoxes: CLE peptide signaling in the Arabidopsis root tip Signaling of secreted CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides via CLV1-type receptor kinases is a central mechanism regulating stem cell pool size. Originally characterized in the context of shoot meristem maintenance, this network has been increasingly scrutinized in recent years for its role in Arabidopsis thaliana (Arabidopsis) root meristem maintenance and organization. These analyses revealed unique, often seemingly paradoxical facets, which can be understood from the rewiring of CLE signaling networks in the root compared with the shoot. Here, we review the intricate interplay between distinct and antagonistic CLE signaling pathways in the primary root meristem, which suggests that the core function of CLE signaling in roots is to dynamically buffer antagonism between positive and negative signaling inputs, thereby enhancing developmental robustness.

The genetics of paradoxes: CLE peptide signaling in the Arabidopsis root tip #plantscience

Expanding the plant epigenetic code: histone short-chain acylation Gene expression regulation in plants involves complex epigenetic mechanisms. Historically, histone acetylation and methylation have been recognized as central determinants of chromatin dynamics and transcriptional regulation. However, recent studies have identified novel types of short-chain lysine acylation – including crotonylation, butyrylation, β-hydroxybutyrylation, 2-hydroxyisobutyrylation, succinylation, and lactylation – as emerging players in epigenetic control. Although these modifications have been extensively characterized in mammals, accumulating evidence now confirms their presence in plants. We focus on plant-specific findings related to histone acylation and analyze its metabolic sources, writers, and erasers, as well as its functional roles in plant development and stress adaptation. Investigation of these modifications in higher plants may unveil unique regulatory mechanisms that underlie developmental plasticity and resilience, and thereby open new avenues for crop improvement and sustainable agriculture.

Expanding the plant epigenetic code: histone short-chain acylation #plantscience

MAP kinases and stomatal regulation: current updates and future perspectives Stomata are essential structures for gas exchange and water regulation in plants. Their development and movement are controlled by complex signaling networks. The mitogen-activated protein kinase (MAPK) cascade serves as a central hub, integrating endogenous and exogenous signals to regulate both stomatal development and aperture dynamics. This review summarizes recent advances in the molecular mechanisms underlying MAPK cascade-mediated stomatal regulation. It highlights the dual roles of the MAPK networks in development and stress adaptation across Arabidopsis thaliana, grasses, and woody species. Understanding MAPK-mediated stomatal control provides valuable insights for engineering climate-resilient crops with enhanced stress resistance.

MAP kinases and stomatal regulation: current updates and future perspectives #plantscience

November Issue. Read FREE:Nanomaterial-based gene delivery in plants (see cover); Dosing requirements to untangle hormesis; Epigenome editing for herbicide-resistant crops; Negative impacts of climate change on crop yields are underestimated &much more www.cell.com/trends/plant...
#plantscience

Plant-to-plant signaling: building networks for resilience to stress, or merely eavesdropping? The overall function of an ecosystem is determined by the richness of its biodiversity and the complex interactions formed between the different species that inhabit it. Understanding how global change factors (including climate change), and their combinations, are affecting the intricate species-to-species relationships formed within different ecosystems and agro-ecosystems is becoming therefore increasingly important to our future. Here, we discuss how improved plant-to-plant and plant-to-microbiome signaling, achieved via research, intervention, and altered practices, can be used to form resilient plant communities that will help us shape our environment and successfully address some of our current and future anthropogenically generated critical challenges.

Plant-to-plant signaling: building networks for resilience to stress, or merely eavesdropping? #plantscience

Promoter/enhancer replacement by genome editing for crop improvement Genome editing is a technology that enables targeted mutagenesis. Notably, site-directed nucleation (SDN)-1 genome editing, which does not involve the incorporation of foreign DNA sequences and can introduce the same mutations as naturally occurring mutations, is not subject to genetically modified organism (GMO) regulations in many countries if transgenes are segregated out. This makes it an attractive strategy for crop improvement. Multiple DNA double-strand breaks introduced via genome editing may lead to inversions or translocations. If these genomic alterations involve promoter regions, a promoter/enhancer replacement may occur, thereby altering target gene expression as desired. Because conventional SDN-1 genome editing primarily induces loss-of-function mutations, promoter/enhancer replacement by genome editing (PERGE) represents a new paradigm in genome editing for crop improvement.

Promoter/enhancer replacement by genome editing for crop improvement #plantscience

Transport engineering of glucosinolates for future brassica crops Glucosinolates (GLS) are key defense metabolites in brassicaceous plants, but major anti-nutritional (especially goitrogenic) factors in Brassica oilseed crops. In the 1970s, breeding of ‘double-low’ rapeseed cultivars with canola-quality seeds low in erucic acid and GLS resulted in feed-quality press cake but limited genetic and GLS diversity of the crop. To develop the press cake into protein food, seed GLS levels must be further reduced. Targeting recently identified transporters in Arabidopsis thaliana with key roles in GLS seed loading prevented GLS accumulation in seeds without altering their presence elsewhere in the plant. Transport engineering has potential as a novel breeding approach to decouple seed and leaf GLS, broaden genetic diversity, and improve both seed quality and pest resistance in Brassica oilseed crops.

Transport engineering of glucosinolates for future brassica crops #plantscience

From curse to blessing: sulfur-availability enhances forest resilience? Sulfur, often regarded as a pollutant, is an essential macronutrient for plant immunity and stress responses in all studied plant families. Declining atmospheric sulfur deposition via pollution-controlling may weaken tree defenses, leading to increased disease vulnerability, especially under increased climate stress. While sulfur is known to enhance crop resilience, its role in forest ecosystems remains poorly understood. Limited field data and challenges in extrapolating from agriculture highlight the need for targeted research. Understanding sulfur’s potential to enhance forest health via sulfur-induced resistance could provide new strategies for managing forest stress. In this opinion article we outline sulfur’s shifting role in forests, from curse to blessing, and depict the need for targeted, interdisciplinary research to determine its potential contribution to climate resilience.

From curse to blessing: sulfur-availability enhances forest resilience? #plantscience

Role of cAMP in TIR1/AFB auxin signaling: open issues The canonical mechanism by which the phytohormone auxin regulates transcription has been one of the cornerstones of plant signaling. The recent unexpected discovery of cyclic AMP (cAMP) as a second messenger in this pathway has revised its foundations while leaving many open questions and gaps in our understanding; these will be discussed in this forum article.

Role of cAMP in TIR1/AFB auxin signaling: open issues #plantscience

Phenolamides: metabolic architects of plant adaptation Phenolamides are specialized plant metabolites with important roles in plant disease resistance and stress tolerance. They serve as biomarkers and effectors of oxidative stress. Moreover, they enhance plant metabolic diversity and potential for acclimation to stress. In this opinion article we focus on recent progress in phenolamide research, including phenolamide biosynthesis, decoration, and transport mechanisms, and we highlight the important role of technological advances in the discovery of new phenolamides and the identification of their biosynthetic genes. We also discuss phytohormone-regulated phenolamide biosynthesis networks and their multifunctional roles in environmental adaptation. We posit that a deeper mechanistic understanding of phenolamide biology will be essential for leveraging these molecules to develop high-value phytoprotectants and advance sustainable agriculture.

Phenolamides: metabolic architects of plant adaptation #plantscience

The expanding world of plant NLR pairs Three recent studies, by Zhu et al., Klymiuk et al., and Hu et al., identified paired nucleotide-binding site–leucine-rich repeat receptors (NLRs) in wheat against different pathogens, providing new insights into the genomic organization, domain architecture, and function of plant NLR pairs. Another study, by Du et al., showed that cross-species transfer of NLR partners confers resistance, highlighting the translational potential of NLR pairs in crop improvement.

The expanding world of plant NLR pairs #plantscience

Environmental regulation of plant vascular networks The plant vascular system, a cornerstone of terrestrial adaptation, enables the long-distance transport of water, nutrients, and signaling molecules and provides mechanical support. Its anatomy also underpins stress resilience; yet, how environmental cues regulate vascular development remains poorly understood. In this review, we synthesize recent advances in molecular mechanisms underlying vascular plasticity in response to abiotic and biotic stresses, including temperature, light, drought, salinity, mechanical forces, nutrient deficiencies, and pathogens. We highlight conserved and species-specific pathways and discuss unresolved questions, such as how plants integrate multiple stressors to optimize vascular development. Finally, we propose applying single-cell omics and genome editing to decode these adaptive strategies with potential implications for crop resilience and sustainable biomass production.

Environmental regulation of plant vascular networks #plantscience

Equipping the next generation of plant taxonomists: Insights and recommendations Plant taxonomy underpins biodiversity research and conservation, but global disparities in training and resources hinder progress, especially in biodiversity-rich regions. Through a global survey of taxonomists and trainers, we reveal that 48% of countries have fewer than ten active plant taxonomists, and that there are stark regional gaps in access to basic tools and infrastructure. A 'limitations index' highlights Angola, Benin, Botswana, Colombia, Sierra Leone, and Venezuela as facing the greatest challenges. To address these imbalances and build crucial taxonomic capacity, we advocate for inclusive and regionally adapted programs with improved access to infrastructure, engaging teaching methods, cascading mentorship, and stronger collaboration. Strategic investment in plant taxonomy training is essential to realizing the full potential of global plant diversity.

Equipping the next generation of plant taxonomists: Insights and recommendations #plantscience

Guardians of arid lands: deep-rooted defense against desertification and climate change Deep-rooted plants (DRPs) are vital ecological engineers in arid regions, combating desertification through distinctive adaptations such as rapid root growth and hydraulic lift. By tapping into groundwater beyond a depth of 5 m, they stabilize soils, sequester carbon, and support biodiversity, while delivering socioeconomic benefits. Despite their resilience, DRPs are increasingly threatened by climate change and pressure of human activities such as overgrazing. In this feature review we consolidate the vital roles of DRPs in ecosystem services and land restoration, advocating for conservation strategies that integrate drip irrigation, rotational grazing policies, and United Nations Convention to Combat Desertification (UNCCD) targets. We highlight the potential of DRPs to achieve land degradation neutrality (LDN) and urge prompt research and management actions to safeguard these keystone species in our climate change adaptation toolkit for drylands.

Guardians of arid lands: deep-rooted defense against desertification and climate change #plantscience

Manipulating microRNAs to enhance biomass yield and biofuel production Woody biomass is a vital carbon sink and biofuel feedstock, but lignocellulosic ethanol production faces cell wall recalcitrance. miRNA-mediated cell wall bioengineering presents an efficient and promising approach to address the high costs associated with biofuel production. In this review, we examine the critical role of miRNAs in plants, with a particular focus on woody species. We systematically analyzed the internal factors influencing biofuel production from an integrated perspective of plant science and chemical basis. Notably, we proposed a schematic framework for miRNA-mediated cell wall engineering, to reduce lignocellulosic recalcitrance and enhance biomass accumulation. Finally, we highlight key questions and suggest potential procedures for the manipulation of miRNAs to facilitate the efficient utilization of forestry-derived biofuels.

Manipulating microRNAs to enhance biomass yield and biofuel production #plantscience

Acidic soils: sustainable mitigation technologies The growing human population is intensifying agriculture, often resulting in overuse of agrochemicals and widespread soil acidification. This increases the solubility of toxic metals like aluminum (Al) and manganese, harming root growth, disrupting microbial communities, and limiting nutrient uptake, ultimately reducing yields and threatening food security. Soil acidity management is key to soil health and long-term sustainable crop productivity.

Acidic soils: sustainable mitigation technologies #plantscience

Strategies to intensify CO2 capture by microalgae for the circular bioeconomy In this review, we explore pathways of coupling between microscale metabolic engineering with macroscale bioprocess design to transform microalgae into intelligent carbon management platforms, focusing on strategies that enhance CO2 fixation capacity, including synthetic enhancement of carbon-concentrating mechanisms (CCMs) and metabolic reprogramming. The integration of microalgae with microbial consortia further stabilizes carbon flow and supports system resilience under environmental fluctuations. Emerging hybrid cultivation systems – powered by renewable energy and guided by artificial intelligence (AI)-based modeling – enable scalable, adaptive, and cost-effective CO2 removal. These innovations are framed within circular bioeconomy models, where microalgae convert waste carbon into bioenergy and bioproducts. Coupling of molecular, ecological, and engineering advances can overcome current deployment barriers. We propose new directions for future research that prioritize feasibility, sustainability, and multifunctionality.

Strategies to intensify CO2 capture by microalgae for the circular bioeconomy #plantscience

Land plant evolution: from microbial interaction to horizontal gene transfer Microbe interaction not only plays an integral role in plant growth and adaptation, but also may lead to genetic integration. Horizontal gene transfer (HGT) from microbes occurs in all major plant groups and appears to be frequent in charophytes and bryophytes. Horizontally acquired microbial genes have contributed to major physiological and structural innovations in land plants. This paper discusses microbial interactions and genetic integration, with a particular focus on recent data regarding the role of horizontally acquired microbial genes in land plant evolution. We suggest that microbes are essential resources for plants, both as an ecological component and as a source of novel genetic material, and that plant colonization of land and further diversification represent a process of exploitation of microbial resources.

Land plant evolution: from microbial interaction to horizontal gene transfer #plantscience

The emerging role of apoplastic H+ in plant signaling Protons (H+), commonly measured as pH, represent a fundamental physiological parameter in cellular systems. In plants, cytoplasmic H+ levels are tightly regulated to maintain homeostasis, whereas apoplastic H+ concentrations fluctuate dynamically in response to stress and developmental cues. This review discusses and scrutinizes the roles of apoplastic H+ fluctuations in transmitting stress and developmental cues, focusing on their interactions with established regulatory elements, such as phytohormones, H2O2, and peptide–receptor complexes, as well as other functional proteins, within stress and developmental signaling networks. Recent advances in understanding the mechanisms underlying apoplastic H+ as a pivotal regulator of plant adaptation and development open promising avenues for future research to enhance plant resilience and productivity under diverse environmental challenges.

The emerging role of apoplastic H+ in plant signaling #plantscience

Advances in plant spatial multi-omics data analysis Recent advances in plant spatial omics, including transcriptomics and metabolomics, have enabled fine-scale cellular insights by registering spatial information. Combining spatial approaches with droplet-based single-cell technologies has further enhanced our understanding of many complex biological processes. However, the unique features of plants, such as rigid cell walls and size variability, require adaptation of mammalian-derived analytical methods. This review summarizes current strategies for acquiring plant spatial multi-omics data, with a focus on widely accessible commercial platforms. We also outline analysis workflows, from preprocessing to downstream interpretation, and provide a practical tutorial using demonstration datasets. This resource offers researchers a concise guide to experimental and computational approaches for plant spatial multi-omics.

Advances in plant spatial multi-omics data analysis #plantscience

Transforming toxic element remediation: a necessary path for 21st-century food security Toxic element contamination poses a serious threat to global food security. However, traditional remediation methods offer only temporary solutions. Emerging gene-editing, synthetic biology, and hybrid technologies now promise transformative, scalable, and permanent strategies to detoxify soils, reclaim polluted land, and secure sustainable agriculture in a rapidly changing global landscape.

Transforming toxic element remediation: a necessary path for 21st-century food security #plantscience

An updated perspective: what genes make a tree a tree? We learn early on how to tell trees apart from other plants. However, it has proved hard to distinguish trees from other plants at the genetic level, and it is believed that there are no unique ‘tree genes’. With the rapid increase in available tree genomes, we can perform new comparative and evolutionary analyses of plant life histories and growth forms. Here we provide a fresh perspective on the genetic foundation for woodiness and perenniality in angiosperms by analyzing selection pressures and gene family evolution in the rosids using genomic data. We examine genes distinguishing trees from herbs and discuss future directions for uncovering the genetic factors that define a tree in this new era of tree genomics.

An updated perspective: what genes make a tree a tree? #plantscience

Xerobranching: a ROS-triggered Aux/IAA multimerization-based adaptive strategy The mechanisms by which plants modulate root morphology, architecture, and the associated molecular pathways to cope with conditions of water deficit remain incompletely understood. Recently, Roy et al. elucidated novel aspects of an adaptive trait, termed xerobranching, which plays a critical role in fine-tuning drought adaptation.

Xerobranching: a ROS-triggered Aux/IAA multimerization-based adaptive strategy #plantscience