J. Exp. Bot. [JOURNAL]
Sun
200 papers
Single-Cell Atlases as Meta-Analytic Compasses for Developmental Biology: A Case Study Using the Arabidopsis Root.
Chen M, Kari S, Szekely P … +2 more , Bargmann BOR, Shahan R
J Exp Bot · 2026 Jul · PMID 42403114 · Publisher ↗
Plant development arises from the coordinated execution of gene regulatory programs across diverse cell types. While classical genetic and genomic approaches have revealed many of the genes required for plant growth and...
Plant development arises from the coordinated execution of gene regulatory programs across diverse cell types. While classical genetic and genomic approaches have revealed many of the genes required for plant growth and patterning, these methods often average signals across heterogeneous tissues, thereby obscuring how regulatory programs operate within individual cells. Resolving gene expression at cellular resolution is therefore essential for understanding how developmental decisions are made, integrated, and propagated during organ growth. The Arabidopsis root, with its simple anatomy and invariant cell lineages, provides an ideal system for addressing these questions. Recent advances in single-cell and single-nucleus transcriptomics have enabled the construction of comprehensive cellular atlases that capture gene expression dynamics across cell identities and developmental trajectories. In this Expert Views article, we highlight recent conceptual and technical developments that illustrate how single-cell atlases have transformed studies of root development. We emphasize how these atlases both serve as community resources to inform the interpretation of new datasets, including those generated from mutants and in response to perturbation, as well as provide a platform for meta-analysis to initiate new studies. Using auxin signaling as a meta-analysis case study, we demonstrate how legacy transcriptomic data can be reinterpreted within a cell lineage-resolved framework. Finally, we highlight how spatial transcriptomics and rigorous data-sharing practices will extend cellular atlases across tissues and species, thereby enabling increasingly precise strategies for understanding and engineering plant growth and resilience.
A sugar flow model predicts cell dynamics, weight and quality of tomato at varying sink-source ratios and temperatures.
De Visser PHB, Molenaar J, Struik PC
J Exp Bot · 2026 Jul · PMID 42400357 · Publisher ↗
A new tomato fruit model predicts cell numbers, cell sizes, sugar contents, and fresh weight. Transport of water and saccharides from plant stem to fruit cells is computed following biophysical rules. Saccharide fruit si...
A new tomato fruit model predicts cell numbers, cell sizes, sugar contents, and fresh weight. Transport of water and saccharides from plant stem to fruit cells is computed following biophysical rules. Saccharide fruit sink is based on sugar metabolism, rates of cell division and expansion, and starch and cell wall dynamics. Osmotic and hydraulic potentials in cells and their vacuoles drive water import at given cell-wall extensibility. The interaction of demand and transport determines saccharide flow and biomass. We incorporated physiological responses to temperature, pruning, and plant shading. Existing and new parameters were calibrated with data from fruit heating and fruit pruning experiments of contrasting tomato cultivars. Model validation for different strategies of fruit heating and pruning, and plant shading was successful. Increased fruit temperature was shown to reduce fruit weight, as expected. Growth response to fruit pruning or shading were fully explained by changes in phloem sucrose concentration. Hydraulic conductivity of vascular tissue as well as sucrose and hexose carrier capacities were crucial fruit properties determining sugar flux. Model scenarios on knockdown of sucrose synthase and active hexose uptake affected sugar composition. The model creates an important step towards predicting fruit quality and taste under diverse growth conditions.
Crosstalks between plant proteostasis and chromatin remodeling machineries.
Albacete-Rodríguez M, Rubio V
J Exp Bot · 2026 Jul · PMID 42400263 · Publisher ↗
To ensure survival, plants must rely on efficient signalling pathways that allow them to adjust rapidly to sudden changes and external cues. Such responses depend not only on the precise control of protein abundance but...
To ensure survival, plants must rely on efficient signalling pathways that allow them to adjust rapidly to sudden changes and external cues. Such responses depend not only on the precise control of protein abundance but also on the coordinated regulation of gene expression. This dynamic control of gene expression is achieved, in part, by the regulatory function of chromatin remodelers whose protein levels, localisation and functional integrity need to be carefully controlled. In recent years, several E3 ubiquitin ligases have been shown to influence the stability and function of key chromatin regulators. This convergence between plant chromatin and proteostasis machineries has been relatively understudied. However, given that epigenetic states underpin multiple stress responses, developmental transitions and the maintenance of genome integrity, understanding how E3 ubiquitin ligases shape these processes provides a valuable perspective on plant biology while also opening new possibilities for improving crop performance in increasingly variable environments. Some of these examples, along with their implications and future research perspectives, will be critically discussed in this review.
Novel Imaging Approaches for Visualising Root-Mycorrhizal Fungal Interactions.
Birt HWG, Paisey SJ, Möhl P … +5 more , Hind J, Xu J, Pickett J, Tredwell M, Johnson D
J Exp Bot · 2026 Jul · PMID 42397066 · Publisher ↗
Mycorrhizal fungi form essential symbiotic relationships with plant roots, facilitating nutrient exchange and promoting plant health. Understanding their interactions can benefit from advanced imaging techniques capable...
Mycorrhizal fungi form essential symbiotic relationships with plant roots, facilitating nutrient exchange and promoting plant health. Understanding their interactions can benefit from advanced imaging techniques capable of visualising nutrient exchange and structural colonisation at subcellular resolutions across large sample sizes. This review explores novel imaging approaches that are revolutionising our understanding of root-mycorrhizal fungal symbioses. Several techniques can now visualise and characterise mycorrhizal fungi and associated root structures non-destructively and in three dimensions, for example, X-ray computed tomography (micro-CT), X-ray fluorescence (XRF) and X-ray absorption near edge structure (XANES) spectroscopy. Metabolic processes and nutrient exchange can be tracked through positron emission tomography (PET), fluorescent nanoparticles (FNPs), and the monitoring of electrical signalling. AI-powered image processing software is enabling high-throughput analysis of complex images generated from a range of sources. Mycorrhiza systems are also able to be tracked in-field at multiple scales: hyperspectral imaging can detect mycorrhizal associations at the kilometre scale, while portable MRI imagers can detect changes at the tissue scale. These converging technologies enable the direct, continuous measurement of structural and metabolic root-mycorrhizal fungi interactions, paving the way for a mechanistic understanding of these vital symbiotic partnerships and their impact on plant health and ecosystem functioning.
The ga3ox1b mutation reveals the crosstalk between gibberellin and other phytohormones in controlling the growth and development of female flowers in Cucurbita pepo.
Gautam K, Segura M, García A … +5 more , Castro-Cegrí A, Palma F, Garrido D, Martínez C, Jamilena M
J Exp Bot · 2026 Jul · PMID 42389928 · Publisher ↗
Cucurbita pepo is a monoecious species with female and male unisexual flowers on the same plant. The large size of its flowers makes this species a model for studying the regulation of sex determination and sex-associate...
Cucurbita pepo is a monoecious species with female and male unisexual flowers on the same plant. The large size of its flowers makes this species a model for studying the regulation of sex determination and sex-associated developmental traits. Because male flowers appear at earlier stages of plant development than female flowers, the plant has evolved a system in which female flowers grow and open much faster than male flowers in order to synchronize male and female flowering for proper pollination and fertilization. In this paper, we show that this differential growth of female and male flowers is controlled by gibberellin (GA). We identify and characterize a loss-of-function mutation in the GA biosynthetic gene CpGA3ox1B, which results in a deficiency of active GA in various vegetative and reproductive organs. The dwarf phenotype of the ga3ox1b mutant is similar to that of other plants deficient in GA, but surprisingly, the GA mutation affects only the development of female flowers, which are much smaller, do not open, and are completely sterile. However, male flowers develop normally, reaching the same size and fertility as male WT flowers. In the WT, female flowers have higher expression of CpGA3ox1B than male flowers, causing them to accumulate more active GA and grow faster than male flowers. The mutant dwarf plant and flower phenotypes were rescued by GA3, but not ethylene or JA, indicating that the ga3ox1b flower did not reach the appropriate size to become sensitive to ethylene and JA, the hormones controlling petal expansion and flower opening in later stages of female flower development. The GA mutation does not affect ethylene-regulated sex determination at the earliest floral meristem, but it does affect the growth of the corolla and pistil once the meristem is determined to be a female flower. The transcriptomic changes and differential accumulation of other phytohormones in the WT and ga3ox1b female organs revealed that the function of GA depends on its interaction with other phytohormones, including auxin and cytokinin as GA synergists and ethylene, ABA, and JA as GA antagonists in the development of female floral organs. Completely opposite transcriptomic changes in the ovary of ga3ox1b and the ethylene-insensitive mutant etr2b demonstrate the mutual exclusion of ethylene and GA signaling at different stages of female flower development and highlight the importance of several transcription factors, such as MYB62, for the integration of ethylene and GA in the regulation of both sex determination and flower organ growth and development in C. pepo.
Increased grain weight conferred by GW2 mutations in wheat does not translate into yield gains in multi-year field trials of near-isogenic lines.
Simmonds J, Crane P, Eade S … +9 more , Montemayor-Lara A, Kerton M, Bird N, Tailby P, Jackson P, Warner D, Hayes C, Schafer D, Uauy C
J Exp Bot · 2026 Jul · PMID 42388144 · Publisher ↗
Multiple studies have identified genes affecting grain morphology, yet their capacity to deliver yield gains under field conditions remains unclear. We performed a multiyear, multilocation factorial evaluation of GRAIN W...
Multiple studies have identified genes affecting grain morphology, yet their capacity to deliver yield gains under field conditions remains unclear. We performed a multiyear, multilocation factorial evaluation of GRAIN WIDTH2 (TaGW2) mutants in hexaploid wheat using BC4 near-isogenic lines, sowing-density treatments and semi-dwarfing RHT1 backgrounds. Loss-of-function mutations in TaGW2 increased grain size and thousand grain weight (TGW) additively; with the aaBBDD single mutant showing the most stable single-locus effect, while the aabbdd triple mutant achieved ∼20% higher TGW across twelve field trials. However, overall grain yield remained unchanged or slightly reduced, reflecting a compensatory trade-off with grain number. Spike phenotyping of both main and secondary tillers showed comparable increases in TGW and spike yield despite fewer grains per spike, indicating that limited yield gain primarily reflects reduced spike number per unit area rather than decreased spike-level productivity. Effects were stable across sowing densities, whereas interactions with semi-dwarfing alleles were allele-specific: RHT-B1b partially suppressed TGW gains and accentuated yield penalties, whereas RHT-D1b maintained the large-grain phenotype and productivity. Across experiments, the TaGW2-A1D1 double mutant increased TGW (∼14%) while maintaining yield stability, identifying it as a promising genotype for breeding. We conclude that TaGW2 is a reliable modifier of grain size but not yield in isolation.
Serendipita indica promotes rice phosphorus uptake by plasma membrane H+-ATPase OsA1-stimulated root hair growth.
Xu F, Ding F, Zheng R … +12 more , Tong L, Bai C, Chen Z, Li J, Li P, Zhang J, Zhang Q, Liu J, Zhu Y, Zhang J, Pang J, Xu W
J Exp Bot · 2026 Jul · PMID 42388141 · Publisher ↗
Plasma membrane (PM) H+-ATPase is important for plant phosphorus (P) uptake. The endophytic fungus Serendipita indica (S. indica) can increase plant P acquisition under P deficiency conditions, but it is unclear whether...
Plasma membrane (PM) H+-ATPase is important for plant phosphorus (P) uptake. The endophytic fungus Serendipita indica (S. indica) can increase plant P acquisition under P deficiency conditions, but it is unclear whether PM H+-ATPase OsA1 is involved in S. indica-modulated P uptake in rice. Under low-P conditions, rice seedlings inoculated with S. indica showed a 90% increase in shoot P concentration and a 164% increase in root P concentration compared with the non-inoculated rice, largely due to significantly elongated root hairs. The relative expression of OsA1 in S. indica-inoculated plants was 73.2% higher than in non-inoculated S. indica plants under low-P conditions. Under low-P conditions, S. indica inoculation also enhanced root H+ efflux by 34% and PM H+-ATPase activity by 27% in wild-type rice compared with non-inoculated plants, whereas no such significant difference was observed in the osa1-1 or osa1-2 mutants. Taken together, our results suggest that S. indica promotes root hair growth under low-P conditions by modulating plasma membrane H+-ATPase OsA1. This cooperative interaction reveals a key mechanism through which S. indica enhances P acquisition, providing valuable insights for improving P-use efficiency in rice production.
The primary beta-galactosidase BGAL10 modulates pavement cell shape acquisition in Arabidopsis.
Yadav S, Kumar V, Heymans A … +6 more , Sabooni N, Jobert F, Lin M, Grones P, Bacete L, Robert S
J Exp Bot · 2026 Jul · PMID 42381545 · Publisher ↗
Cell shape acquisition is a fundamental biological process that allows cells to establish and maintain morphologies adapted to their specialised functions while preserving tissue integrity. In plants, this process is str...
Cell shape acquisition is a fundamental biological process that allows cells to establish and maintain morphologies adapted to their specialised functions while preserving tissue integrity. In plants, this process is strongly influenced by the presence of the cell wall, a dynamic extracellular network of polysaccharides and proteins that surrounds the plasma membrane and physically connects neighbouring cells. By constraining and directing cellular expansion, the cell wall plays a central role in controlling cell shape. In Arabidopsis leaves, epidermal pavement cells adopt a characteristic jigsaw-puzzle-like morphology through the formation of interdigitating lobes and necks, providing a powerful model system for dissecting the mechanisms underlying complex plant cell shape acquisition. Here, we demonstrate the involvement of the glycoside hydrolase BETA-GALACTOSIDASE 10 (BGAL10) in pavement cell morphogenesis. Using high-resolution time-series imaging, we analysed cell growth dynamics alongside the spatial expression and subcellular localisation of BGAL10, revealing a prominent role for BGAL10 in mature cells, particularly at curved regions of the cell wall along pavement cell lobes. Furthermore, Brillouin microscopy revealed altered mechanical properties in the bgal10-1 mutant, most notably at lobe-indentation interfaces and cell junctions. Together, our results indicate that BGAL10 fine-tunes lobe outgrowth, likely through modification of the hemicellulose matrix, thereby regulating cell wall extensibility and mechanical stress distribution during pavement cell shape acquisition.
The link between phosphate starvation-triggered anthocyanin biosynthesis and jasmonate-driven regulation in tomato.
Junco MC, Madrid-Espinoza J, Cabeza RA … +2 more , Ruiz-Lara S, Figueroa CR
J Exp Bot · 2026 Jun · PMID 42367112 · Publisher ↗
Phosphate Starvation Response (PSR) in plants integrates inorganic phosphate (Pi) sensing with hormonal and metabolic reprogramming. Recent evidence supports a PSR-jasmonate (JA)-anthocyanin axis in which the PSR-associa...
Phosphate Starvation Response (PSR) in plants integrates inorganic phosphate (Pi) sensing with hormonal and metabolic reprogramming. Recent evidence supports a PSR-jasmonate (JA)-anthocyanin axis in which the PSR-associated PHOSPHATE STARVATION RESPONSE (PHR)/PHR-like-SYG1-PHO81-XPR1-inositol pyrophosphate 8 (PHR/PHL-SPX-InsP8) module gates transcriptional activation, while the core JA components JASMONATE ZIM-DOMAIN (JAZ) and MYELOCYTOMATOSIS 2 (MYC2) mediate hormone-induced activation of secondary metabolism. In Solanum lycopersicum, PHR/PHL transcription factors (TFs) serve as core PSR hubs, with expanded regulatory networks and InsP-associated control layers that tune SPX buffering and transcriptional output. Downstream, JA signaling and MYC2-dependent transcription interface with anthocyanin regulators, including key MYB and bHLH TFs that form the MYB-basic helix-loop-helix (bHLH)-WD40 repeat (MBW) complex, thereby regulating tissue capacity for pigmentation under Pi starvation (PiS). Anthocyanin-rich tomato cultivars such as 'Indigo Rose' exemplify how genetic configuration can enhance MBW responsiveness and potentiate pigment accumulation under PiS. Here, we collate recent advances linking PSR gating, JA response, and anthocyanin biosynthesis regulation in tomato, and propose a working model with testable predictions to accelerate causal validation, and enable breeding strategies targeting phosphorus use efficiency and nutritional quality.
OsFLZ5 Enhances Drought Tolerance and ABA Sensitivity in Rice via Transcriptional Activation by OsbZIP23.
Li J, Tang Y, Li M … +6 more , Li Y, Shi G, Chen S, Wang Y, Ma Y, Yang C
J Exp Bot · 2026 Jun · PMID 42359475 · Publisher ↗
Drought stress presents a major challenge to global agriculture. FCS-Like Zinc Finger (FLZ) genes are transcriptionally responsive to environmental stimuli, yet their precise biological functions remain insufficiently ch...
Drought stress presents a major challenge to global agriculture. FCS-Like Zinc Finger (FLZ) genes are transcriptionally responsive to environmental stimuli, yet their precise biological functions remain insufficiently characterized. Here, we demonstrate that OsFLZ5, a drought- and abscisic acid (ABA)-induced gene, enhances drought tolerance and ABA sensitivity in rice (Oryza sativa L.), but does not exhibit obvious adverse effects on crucial agronomic traits including yield and plant height. Overexpression (OE) of OsFLZ5 significantly improved survival rate, seedling growth, and biomass under both polyethylene glycol6000 (PEG6000)-simulated and soil-based drought conditions, whereas knockout (KO) lines exhibited impaired performance. Consistently, OE lines showed heightened sensitivity to ABA, while KO mutants were less responsive. OsFLZ5 promotes soluble sugar accumulation and reduces malondialdehyde and hydrogen peroxide levels after drought exposure. RNA sequencing revealed that OsFLZ5 modulates a suite of drought-responsive genes. Notably, we identified the bZIP transcription factor OsbZIP23 as a direct upstream regulator of OsFLZ5; it binds to the OsFLZ5 promoter and activates its expression, thereby contributing to enhanced drought resilience and ABA sensitivity. These findings establish the OsbZIP23-OsFLZ5 regulatory module as a new mechanism in the rice drought and ABA response, providing targets for developing drought-tolerant crops.
From signaling to catabolism: terminal tails in plant hormone regulation.
Shabek N
J Exp Bot · 2026 Jun · PMID 42349878 · Publisher ↗
Plant hormone signaling is shaped not only by biosynthesis and perception but also by the controlled removal of bioactive molecules. Although catabolic pathways were long viewed as passive sinks, emerging evidence indica...
Plant hormone signaling is shaped not only by biosynthesis and perception but also by the controlled removal of bioactive molecules. Although catabolic pathways were long viewed as passive sinks, emerging evidence indicates that hormone inactivation can determine the amplitude and duration of signaling outputs. This review examines recent advances in phytohormone homeostasis, with emphasis on strigolactone (SL) and salicylic acid (SA), two systems in which the enzymatic basis of hormone deactivation has been resolved at mechanistic and structural levels. In SL biology, the receptor DWARF14 couples perception to hydrolysis but is not optimized for bulk hormone clearance. The identification of carboxylesterases such as CXE15 establishes a dedicated catabolic route in which activity is governed by conformational gating mediated by an N-terminal helix. In parallel, SA catabolism is mediated by 2-oxoglutarate-dependent oxygenases, including DOWNY MILDEW RESISTANT 6 and DMR6-LIKE OXYGENASE 1, which act in feedback control of immunity and are further regulated through ubiquitin-mediated degradation. Together, these examples show that hormone catabolism can operate as an active and tunable layer of plant signaling networks, with terminal protein regions contributing to the control of enzyme activity, stability, and signal duration.
Beyond the CO-FT regulatory module: E1 and PHYA emerge as players in photoperiodic regulation of flowering in legumes.
Henriques R, Benlloch R
J Exp Bot · 2026 Jun · PMID 42345120 · Publisher ↗
The legume family (Fabaceae) is the third largest in plants including several crop species that are able to fix Nitrogen, promote soil health and contribute to food security worldwide. Recent progress in legume genetics...
The legume family (Fabaceae) is the third largest in plants including several crop species that are able to fix Nitrogen, promote soil health and contribute to food security worldwide. Recent progress in legume genetics and genomics allowed the identification of photoperiod-dependent flowering loci, which were incorporated into specific signalling networks. Functional characterisation of these regulators revealed new roles for known photoreceptors such as phytochrome A, and it also identified legume-specific B3 domain transcriptional factors (E1 and E1-like proteins). This suggests some diversification from the traditional CONSTANS-FLOWERING LOCUS T module present in other angiosperms. Although most of the findings discussed in this review pertain to species from the two main legume clades, the galegoids (e.g., alfalfa, clover, pea, ) and the phaseoloids (e.g., common bean, soybean, cowpea, pigeon pea), research on flowering regulation in the basal genistoid clade (e.g., lupins) will also be addressed. We propose that functional diversification of photoperiod-dependent flowering strategies in the different legume species could have contributed to their environmental adaptation and allowed their geographical expansion and success worldwide.
Sulfur metabolism-dependent retrograde signalling for oxidative stress acclimation.
Furbank R, Plskova Z, Pogson B … +1 more , Chan KX
J Exp Bot · 2026 Jun · PMID 42345076 · Publisher ↗
Plant sulfur metabolism is crucial to the plant acclimation response to abiotic stresses, providing the redox-active compounds cysteine and glutathione for redox buffering as well as the chloroplast-to-nucleus retrograde...
Plant sulfur metabolism is crucial to the plant acclimation response to abiotic stresses, providing the redox-active compounds cysteine and glutathione for redox buffering as well as the chloroplast-to-nucleus retrograde signal 3'-phosphoadenosine 5'-phosphate (PAP) for activation of gene expression changes. Whilst these processes have been conventionally considered separately, here we review chloroplast retrograde signalling in the context of plant sulfur metabolism, with focus on the biosynthesis and degradation of PAP in secondary sulfur metabolism. We outline mechanisms by which primary sulfur metabolism via cysteine and glutathione contribute to the modulation of chloroplast retrograde signalling. We examine emerging questions in how plant sulfur metabolism is coordinated in different cell types of a plant leaf for synthesis and accumulation of PAP. Finally, while the majority of chloroplast retrograde signalling research has focused on the model Brassicaceae plant species Arabidopsis thaliana, here we outline the opportunities for novel insights from non-Brassicaceae plants to enable an integrated understanding of the intersection of sulfur metabolism and retrograde signalling.
Combining a high-caliber chromosome-level genome and root single-cell atlas resolves genetic diversity and root development in Olea europaea subsp. cuspidata.
Hu W, Jiang C, Zhao Q … +10 more , Wang W, Li X, Lu H, Chen L, Gao S, Xu F, Shen G, Zhu S, Fu Y, Niu E
J Exp Bot · 2026 Jun · PMID 42345073 · Publisher ↗
Olea europaea subsp. cuspidata, a subspecies of olive trees, stands out for its remarkable stress tolerance and commonly serves as a rootstock that enhances olive oil yield. To explore its genomic and cellular underpinni...
Olea europaea subsp. cuspidata, a subspecies of olive trees, stands out for its remarkable stress tolerance and commonly serves as a rootstock that enhances olive oil yield. To explore its genomic and cellular underpinnings for potential breeding applications, a chromosome-scale genome assembly and a root-specific single-cell atlas of O. europaea subsp. cuspidata was resolved. Using a combined survey evaluation strategy along with PacBio CLR and Hi-C sequencing technologies, a total genome of 1.62 Gb was obtained (23 chromosomes; N50: 55.72 Mb). Phylogenetic analysis revealed that Oleaceae plants diverged by approximately 17.2 Mya, with O. europaea subsp. cuspidata splitting from other O. europaea lineages at approximately 5.7 Mya. It is genetically closer to the cultivated olive O. europaea subsp. europaea cv. 'Arbequina' than to the wild olive O. europaea subsp. europaea var. sylvestris. Additionally, a dynamic molecular map of olive roots was generated at single-cell resolution to reconstruct the continuous root cell differentiation and developmental trajectory. This helps to unravel key regulatory genes in olive root development and adaptation to the external environment. This study explored the diversity of olive trees at genomic and root cellular levels, with insights to support the theoretical basis for enhanced stress tolerance, aiding the global introduction and promotion of olive trees.
Salicylic acid fine-tunes cell survival during plant senescence and pathogen infection.
Luo J, Chan Z, Zhang F
J Exp Bot · 2026 Jun · PMID 42342249 · Publisher ↗
Salicylic acid (SA) is a crucial plant hormone synthesized via two primary pathways: the ISOCHORISMATE SYNTHASE (ICS) pathway and the PHENYLALANINE AMMONIA-LYASE (PAL) pathway. SA biosynthesis and homeostasis are precise...
Salicylic acid (SA) is a crucial plant hormone synthesized via two primary pathways: the ISOCHORISMATE SYNTHASE (ICS) pathway and the PHENYLALANINE AMMONIA-LYASE (PAL) pathway. SA biosynthesis and homeostasis are precisely regulated in plants. Furthermore, SA functions in a concentration-dependent manner to enhance resistance to both abiotic stresses and pathogens, as well as to regulate plant senescence. However, the underlying mechanisms of SA action remain to be elucidated. Recent studies have demonstrated that in juvenile plants, age-related cues, autoimmunity, and autophagy contribute to maintaining SA at the basal level. In adult plants, moderate concentrations of SA enhance resistance by activating autophagy and the antioxidant system in response to abiotic stresses and pathogen infections. Elevated levels of SA initiate positive feedback loop involving reactive oxygen species (ROS) and the transcriptional regulator WRKY75, which serves as a core regulatory hub during natural senescence, abiotic stress-induced premature senescence, and pathogen infection-triggered hypersensitive response (HR). In the late stages of these processes, autophagy acts synergistically with high levels of SA to accelerate programmed cell death (PCD). This review summarizes recent advancements in SA biosynthesis and compares the associated signaling pathways during plant senescence and pathogen infection, providing theoretical insights into SA-regulated plant senescence and immunity.
Addressing the day-night divide.
McAusland L, Murchie EH
J Exp Bot · 2026 Jun · PMID 42341092 · Full text
This article comments on: 2026. Wheat leaf dark respiration acclimates more strongly at night than in the day when responding to nocturnal warming. Journal of Experimental Botany , 3777–3792. https://doi.org/10.1093/jxb...
This article comments on: 2026. Wheat leaf dark respiration acclimates more strongly at night than in the day when responding to nocturnal warming. Journal of Experimental Botany , 3777–3792. https://doi.org/10.1093/jxb/erag106
Floral identity and beyond: revisiting AGAMOUS-like transcription factor functions in rice.
Brazel AJ
J Exp Bot · 2026 Jun · PMID 42341091 · Full text
This article comments on: 2026. Genome-wide regulatory and interaction landscape underlying functional divergence of rice AGAMOUS-like transcription factors. Journal of Experimental Botany , 3637–3660. https://doi.org/1...
This article comments on: 2026. Genome-wide regulatory and interaction landscape underlying functional divergence of rice AGAMOUS-like transcription factors. Journal of Experimental Botany , 3637–3660. https://doi.org/10.1093/jxb/erag122
Through the looking glass: A single-cell view of plant-microbe interactions.
Magrath IRK, Wong SL, Palmer JW … +2 more , Saha A, Luginbuehl LH
J Exp Bot · 2026 Jun · PMID 42340022 · Publisher ↗
Plants interact with a vast variety of microbes that inhabit both above- and belowground tissues. Through their effect on host physiology and growth, plant-microbe interactions define the success of a plant's life cycle....
Plants interact with a vast variety of microbes that inhabit both above- and belowground tissues. Through their effect on host physiology and growth, plant-microbe interactions define the success of a plant's life cycle. A key aspect of these interactions is the requirement for highly cell-type-specific responses from the plant, be it to form symbiotic structures in certain cells or to mount a highly localised immune response. There has been long-standing interest in uncovering the cell-specific transcriptomic changes that underpin these processes to better understand the establishment, functioning, and regulation of plant-microbe interactions. The recent optimisation of single-cell and spatial transcriptomics for plants now allows us to investigate these interactions in unprecedented detail. Here, we discuss how single-cell technologies can help unravel the many mysteries of plant-microbe interactions. We focus on the key lessons we have learned from recent single-cell studies in the field and highlight the current limitations of single-cell technologies. We also offer promising avenues for future exploration and conclude by suggesting experimental and bioinformatic considerations to maximise insights from past and future studies and help make the most of this new single-cell era in the field of plant-microbe interactions.
Iron and zinc accumulation in the endosperm of transgenic rice through a multigene stacking system.
Gong C, Li W, Liu S … +8 more , Li J, Si X, Wang Z, Yang G, Kong L, Liu Y, Zhang W, Chen X
J Exp Bot · 2026 Jun · PMID 42339644 · Publisher ↗
Iron (Fe) and zinc (Zn) deficiencies severely threaten global human health. Thus, rice biofortification to enhance intrinsic Fe and Zn levels in grains represents an effective strategy to alleviate human Fe and Zn defici...
Iron (Fe) and zinc (Zn) deficiencies severely threaten global human health. Thus, rice biofortification to enhance intrinsic Fe and Zn levels in grains represents an effective strategy to alleviate human Fe and Zn deficiencies. Several biofortification strategies have successfully increased Fe and Zn concentrations in the rice endosperm, with multigene approaches demonstrating synergistic micronutrient accumulation. To enhance Fe and Zn accumulation in rice endosperm, we designed a transformation construct (NYFN) in which OsNRAMP7 and OsNAS2 were driven by the 35S promoter, OsYSL2 by the OsSUT1 promoter, and OsFER2 by the endosperm-specific OsGluA2 promoter. Multi-year field trials were conducted at two locations to evaluate Fe and Zn accumulation in transgenic NYFN rice plants derived from Nipponbare (NB) and commercial cultivar Huaidao 5 (HD5) genetic backgrounds. The results showed that transgenic NB lines exhibited 10.93-14.72 μg/g DW Fe and 33.01-48.33 μg/g DW Zn in polished grains, representing 4.9- to 6.3-fold increases in Fe and 2- to 2.7-fold increases in Zn compared to the NB control. Polished grains of HD5 transformants contained 10.24-13.35 μg/g DW Fe and 32.17-50.33 μg/g DW Zn, corresponding to 4- to 7.4-fold elevations in Fe and 2- to 2.3-fold elevations in Zn relative to the HD5 control. X-ray fluorescence spectroscopy (µ-XRF) and Perls' Prussian blue staining analyses confirmed the significantly enhanced Fe and Zn accumulation in transgenic grains. Transgenic NB lines exhibited significant changes in certain agronomic traits, including reduced 1000-grain weight, grain size, and grain filling rate, whereas transgenic HD5 lines showed no significant agronomic differences relative to the wild type. Total grain weight per plant remained unchanged in both the transgenic NB and HD5 lines compared to the wild type. The results demonstrate that the NYFN strategy enables sustainable Fe and Zn biofortification, representing a promising solution to the global challenge of human Fe and Zn deficiency.
TaR3H interacts with Pm21 and confers powdery mildew resistance.
Si C, Dong Z, Cao S … +9 more , Luo C, Hao S, Wang W, Hu W, Liu M, Zhang R, Liu J, Xing L, Cao A
J Exp Bot · 2026 Jun · PMID 42334443 · Publisher ↗
Wheat powdery mildew severely threats global wheat production. Previously, we cloned the broad-spectrum wheat powdery mildew resistance gene Pm21 which encoded a typical NLR immune receptor. In this study, we identified...
Wheat powdery mildew severely threats global wheat production. Previously, we cloned the broad-spectrum wheat powdery mildew resistance gene Pm21 which encoded a typical NLR immune receptor. In this study, we identified TaR3H as an interacting protein of the Pm21 coiled-coil (CC) domain (Pm21CC) and performed comprehensive biochemical and functional analysis to illustrate the defense pathway mediated by Pm21. TaR3H, a putative transcription factor, localizes to both the nucleus and plasma membrane, with its transcriptional activation function residing in the N-terminal region. We found that TaR3H interacts with Pm21CC, but not with full-length Pm21（Pm21FL）in uninfected cells, whereas it interacts with both Pm21CC and Pm21FL during Bgt infection, suggesting that the protein folding state or activity of Pm21CC modulates its interaction. Functional studies demonstrated that silencing TaR3H in Pm21-carrying resistant materials compromised resistance to Bgt, while overexpression of TaR3H in the susceptible cultivar enhanced powdery mildew resistance. Integrated transcriptomic and DAP-seq analysis indicated that TaR3H-mediated resistance enhancement is associated with hormone signaling pathway. This study reveals novel functions of TaR3H in the broad-spectrum powdery mildew resistance pathway, providing new insights into the molecular mechanism underlying Pm21-mediatd immunity.
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