The Plant Journal

The Agrobacterium vacuum infiltration method has made it possible to transform Arabidopsis thaliana without plant tissue culture or regeneration. In the present study, this method was evaluated and a substantially modified transformation method was developed. The labor-intensive vacuum infiltration process was eliminated in favor of simple dipping of developing floral tissues into a solution containing Agrobacterium tumefaciens, 5% sucrose and 500 microliters per litre of surfactant Silwet L-77. Sucrose and surfactant were critical to the success of the floral dip method. Plants inoculated when numerous immature floral buds and few siliques were present produced transformed progeny at the highest rate. Plant tissue culture media, the hormone benzylamino purine and pH adjustment were unnecessary, and Agrobacterium could be applied to plants at a range of cell densities. Repeated application of Agrobacterium improved transformation rates and overall yield of transformants approximately twofold. Covering plants for 1 day to retain humidity after inoculation also raised transformation rates twofold. Multiple ecotypes were transformable by this method. The modified method should facilitate high-throughput transformation of Arabidopsis for efforts such as T-DNA gene tagging, positional cloning, or attempts at targeted gene replacement.

Microalgae represent an exceptionally diverse but highly specialized group of micro-organisms adapted to various ecological habitats. Many microalgae have the ability to produce substantial amounts (e.g. 20-50% dry cell weight) of triacylglycerols (TAG) as a storage lipid under photo-oxidative stress or other adverse environmental conditions. Fatty acids, the building blocks for TAGs and all other cellular lipids, are synthesized in the chloroplast using a single set of enzymes, of which acetyl CoA carboxylase (ACCase) is key in regulating fatty acid synthesis rates. However, the expression of genes involved in fatty acid synthesis is poorly understood in microalgae. Synthesis and sequestration of TAG into cytosolic lipid bodies appear to be a protective mechanism by which algal cells cope with stress conditions, but little is known about regulation of TAG formation at the molecular and cellular level. While the concept of using microalgae as an alternative and renewable source of lipid-rich biomass feedstock for biofuels has been explored over the past few decades, a scalable, commercially viable system has yet to emerge. Today, the production of algal oil is primarily confined to high-value specialty oils with nutritional value, rather than commodity oils for biofuel. This review provides a brief summary of the current knowledge on oleaginous algae and their fatty acid and TAG biosynthesis, algal model systems and genomic approaches to a better understanding of TAG production, and a historical perspective and path forward for microalgae-based biofuel research and commercialization.

Advances in determination of polymer structure and in preservation of structure for electron microscopy provide the best view to date of how polysaccharides and structural proteins are organized into plant cell walls. The walls that form and partition dividing cells are modified chemically and structurally from the walls expanding to provide a cell with its functional form. In grasses, the chemical structure of the wall differs from that of all other flowering plant species that have been examined. Nevertheless, both types of wall must conform to the same physical laws. Cell expansion occurs via strictly regulated reorientation of each of the wall's components that first permits the wall to stretch in specific directions and then lock into final shape. This review integrates information on the chemical structure of individual polymers with data obtained from new techniques used to probe the arrangement of the polymers within the walls of individual cells. We provide structural models of two distinct types of walls in flowering plants consistent with the physical properties of the wall and its components.

A large number of morphologically normal, fertile, transgenic rice plants were obtained by co-cultivation of rice tissues with Agrobacterium tumefaciens. The efficiency of transformation was similar to that obtained by the methods used routinely for transformation of dicotyledons with the bacterium. Stable integration, expression and inheritance of transgenes were demonstrated by molecular and genetic analysis of transformants in the R0, R1 and R2 generations. Sequence analysis revealed that the boundaries of the T-DNA in transgenic rice plants were essentially identical to those in transgenic dicotyledons. Calli induced from scutella were very good starting materials. A strain of A. tumefaciens that carried a so-called 'super-binary' vector gave especially high frequencies of transformation of various cultivars of japonica rice that included Koshihikari, which normally shows poor responses in tissue culture.

MAPMAN is a user-driven tool that displays large data sets onto diagrams of metabolic pathways or other processes. SCAVENGER modules assign the measured parameters to hierarchical categories (formed 'BINs', 'subBINs'). A first build of TRANSCRIPTSCAVENGER groups genes on the Arabidopsis Affymetrix 22K array into >200 hierarchical categories, providing a breakdown of central metabolism (for several pathways, down to the single enzyme level), and an overview of secondary metabolism and cellular processes. METABOLITESCAVENGER groups hundreds of metabolites into pathways or groups of structurally related compounds. An IMAGEANNOTATOR module uses these groupings to organise and display experimental data sets onto diagrams of the users' choice. A modular structure allows users to edit existing categories, add new categories and develop SCAVENGER modules for other sorts of data. MAPMAN is used to analyse two sets of 22K Affymetrix arrays that investigate the response of Arabidopsis rosettes to low sugar: one investigates the response to a 6-h extension of the night, and the other compares wild-type Columbia-0 (Col-0) and the starchless pgm mutant (plastid phosphoglucomutase) at the end of the night. There were qualitatively similar responses in both treatments. Many genes involved in photosynthesis, nutrient acquisition, amino acid, nucleotide, lipid and cell wall synthesis, cell wall modification, and RNA and protein synthesis were repressed. Many genes assigned to amino acid, nucleotide, lipid and cell wall breakdown were induced. Changed expression of genes for trehalose metabolism point to a role for trehalose-6-phosphate (Tre6P) as a starvation signal. Widespread changes in the expression of genes encoding receptor kinases, transcription factors, components of signalling pathways, proteins involved in post-translational modification and turnover, and proteins involved in the synthesis and sensing of cytokinins, abscisic acid (ABA) and ethylene revealing large-scale rewiring of the regulatory network is an early response to sugar depletion.

Active oxygen species (AOS) are believed to have important roles in plants in general and in plant—pathogen interactions in particular. They are believed to be involved in signal transduction, cell wall reinforcement, hypersensitive response (HR) and phytoalexin production, and to have direct antimicrobial effects. Since current methods are inadequate for localizing AOS in intact plant tissue, most studies have been conducted using cell suspension culture/elicitors systems. 3,3‐diaminobenzidine (DAB) polymerizes instantly and locally as soon as it comes into contact with H2O2 in the presence of peroxidase, and it was found that, by allowing the leaf to take up this substrate, in‐vivo and in‐situ detection of H2O2 can be made at subcellular levels. This method was successfully used to detect H2O2 in developing papillae and surrounding haloes (cell wall appositions) and whole cells of barley leaves interacting with the powdery mildew fungus. Thus, H2O2 can be detected in the epidermal cell wall subjacent to the primary germ tube from 6 h after inoculation, and subjacent to the appressorium from 15 h. The earliest time point for observation of H2O2 in relation to epidermal cells undergoing HR is 15 h after inoculation, first appearing in the zones of attachment to the mesophyll cells underneath, and eventually in the entire epidermal cell. Furthermore, it was observed that proteins in papillae and HR cells are cross‐linked, a process believed to be fuelled by H2O2. This cross‐linking reinforces the apposition, presumably assisting the arrest of the pathogen.

Reactive oxygen species (ROS) play a key role in the acclimation process of plants to abiotic stress. They primarily function as signal transduction molecules that regulate different pathways during plant acclimation to stress, but are also toxic byproducts of stress metabolism. Because each subcellular compartment in plants contains its own set of ROS-producing and ROS-scavenging pathways, the steady-state level of ROS, as well as the redox state of each compartment, is different at any given time giving rise to a distinct signature of ROS levels at the different compartments of the cell. Here we review recent studies on the role of ROS in abiotic stress in plants, and propose that different abiotic stresses, such as drought, heat, salinity and high light, result in different ROS signatures that determine the specificity of the acclimation response and help tailor it to the exact stress the plant encounters. We further address the role of ROS in the acclimation of plants to stress combination as well as the role of ROS in mediating rapid systemic signaling during abiotic stress. We conclude that as long as cells maintain high enough energy reserves to detoxify ROS, ROS is beneficial to plants during abiotic stress enabling them to adjust their metabolism and mount a proper acclimation response.

Plant compounds that are perceived by humans to have color are generally referred to as 'pigments'. Their varied structures and colors have long fascinated chemists and biologists, who have examined their chemical and physical properties, their mode of synthesis, and their physiological and ecological roles. Plant pigments also have a long history of use by humans. The major classes of plant pigments, with the exception of the chlorophylls, are reviewed here. Anthocyanins, a class of flavonoids derived ultimately from phenylalanine, are water-soluble, synthesized in the cytosol, and localized in vacuoles. They provide a wide range of colors ranging from orange/red to violet/blue. In addition to various modifications to their structures, their specific color also depends on co-pigments, metal ions and pH. They are widely distributed in the plant kingdom. The lipid-soluble, yellow-to-red carotenoids, a subclass of terpenoids, are also distributed ubiquitously in plants. They are synthesized in chloroplasts and are essential to the integrity of the photosynthetic apparatus. Betalains, also conferring yellow-to-red colors, are nitrogen-containing water-soluble compounds derived from tyrosine that are found only in a limited number of plant lineages. In contrast to anthocyanins and carotenoids, the biosynthetic pathway of betalains is only partially understood. All three classes of pigments act as visible signals to attract insects, birds and animals for pollination and seed dispersal. They also protect plants from damage caused by UV and visible light.

Genome sequencing has resulted in the identification of a large number of uncharacterized genes with unknown functions. It is widely recognized that determination of the intracellular localization of the encoded proteins may aid in identifying their functions. To facilitate these localization experiments, we have generated a series of fluorescent organelle markers based on well-established targeting sequences that can be used for co-localization studies. In particular, this organelle marker set contains indicators for the endoplasmic reticulum, the Golgi apparatus, the tonoplast, peroxisomes, mitochondria, plastids and the plasma membrane. All markers were generated with four different fluorescent proteins (FP) (green, cyan, yellow or red FPs) in two different binary plasmids for kanamycin or glufosinate selection, respectively, to allow for flexible combinations. The labeled organelles displayed characteristic morphologies consistent with previous descriptions that could be used for their positive identification. Determination of the intracellular distribution of three previously uncharacterized proteins demonstrated the usefulness of the markers in testing predicted subcellular localizations. This organelle marker set should be a valuable resource for the plant community for such co-localization studies. In addition, the Arabidopsis organelle marker lines can also be employed in plant cell biology teaching labs to demonstrate the distribution and dynamics of these organelles.

Full-length cDNAs are essential for functional analysis of plant genes in the post-sequencing era of the Arabidopsis genome. Recently, cDNA microarray analysis has been developed for quantitative analysis of global and simultaneous analysis of expression profiles. We have prepared a full-length cDNA microarray containing approximately 7000 independent, full-length cDNA groups to analyse the expression profiles of genes under drought, cold (low temperature) and high-salinity stress conditions over time. The transcripts of 53, 277 and 194 genes increased after cold, drought and high-salinity treatments, respectively, more than fivefold compared with the control genes. We also identified many highly drought-, cold- or high-salinity- stress-inducible genes. However, we observed strong relationships in the expression of these stress-responsive genes based on Venn diagram analysis, and found 22 stress-inducible genes that responded to all three stresses. Several gene groups showing different expression profiles were identified by analysis of their expression patterns during stress-responsive gene induction. The cold-inducible genes were classified into at least two gene groups from their expression profiles. DREB1A was included in a group whose expression peaked at 2 h after cold treatment. Among the drought, cold or high-salinity stress-inducible genes identified, we found 40 transcription factor genes (corresponding to approximately 11% of all stress-inducible genes identified), suggesting that various transcriptional regulatory mechanisms function in the drought, cold or high-salinity stress signal transduction pathways.

Meiotic recombination is not only a key mechanism for sexual adaptation in eukaryotes but crucial for the accumulation of beneficial alleles in breeding populations. The effective manipulation of recombination requires, however, a better understanding of the mechanisms regulating the rate and distribution of recombination events in genomes. Here, we identified the genomic features that best explain the recombination variation among a diverse set of segregating populations of barley at a resolution of 1 Mbp and investigated how methylation and structural variants (SVs) determine crossover (CO) hotspots and coldspots at a high resolution of 10 kb. Hotspots were found to be in proximity to genes, and the genetic effects not assigned to methylation were found to be the most important factor explaining differences in recombination rates among populations, along with the methylation and the parental sequence divergence. Interestingly, coldspots were associated with the inheritance of a highly methylated genomic fragment from one parent only, but hotspots were identified at genomic segments where both parents were equally low methylated. The parental sequence divergence was shown to have a sigmoidal correlation with recombination, indicating an upper limit of mismatch among homologous chromosomes for CO formation. SVs were shown to be correlated with CO suppression, and their type and size were not found to influence that effect. The joint act of methylation and SVs was associated with the location of coldspots in barley, and the weight of their relative effect depends on the genomic region. Our findings suggest that recombination in barley is highly predictable, occurring mostly in multiple short sections located in proximity to genes and being modulated by local levels of methylation and SV load.

The Plant Journal is delighted to announce the successful 2026 TPJ Fellows—Martina Legris, Adam Bentham and Furong Liu. These early career group leaders have exciting scientific programmes and impressive research track records, as well as contributions to the wider plant science community. Congratulations to Martina, Adam and Furong. We welcome them to The Plant Journal team and look forward to supporting their careers.

Salvia miltiorrhiza Bunge is a valuable medicinal plant, yet its genetic manipulation has been limited by the lack of efficient and practical transformation methods. Here, we report a simplified, tissue culture-independent strategy enabling Agrobacterium-mediated gene delivery under non-sterile conditions, termed hypocotyl acupuncture. The method employs needle-assisted inoculation of intact seedlings at the hypocotyl, completely bypassing callus induction, regeneration, and repeated subculture. Following inoculation, EGFP-positive hairy roots are selectively cultivated for approximately 4 months and then induced to regenerate shoots within one additional month, yielding transgenic plantlets in approximately 5 months. Systematic optimization achieved a transformation efficiency of approximately 55% (defined as the percentage of explants producing EGFP-positive regenerants). ACCC10060 was selected as the optimal strain based on efficiency and root morphology. CRISPR/Cas9-mediated genome editing generated mutation frequencies of 53.8%-88.9% with no off-target effects. Targeted mutagenesis of SmCPS1, a gene encoding a key rate-limiting enzyme in tanshinone biosynthesis, resulted in altered root pigmentation. The method was successfully extended to Astragalus membranaceus, Platycodon grandiflorus, and Isatis indigotica, achieving transformation efficiencies of 25%-55%. This study provides an efficient, practical, and broadly applicable tool for genome editing and functional genomics in medicinal plants.

SUMMARY To investigate whether root‐sourced ethylene‐precursor 1‐aminocyclopropane‐1‐carboxylic acid (ACC) modulates long‐term salinity responses in tomato, a commercial variety ( Solanum lycopersicum L. Mill) was grafted onto three rootstocks differing in ACC/ethylene production: an ethylene‐overproducing mutant ( epinastic , epi ), a root‐specific ACC deaminase overexpressing transgenic line with reduced ACC availability for ethylene synthesis ( ACCD ) and the wild‐type cv. Micro‐Tom (WT). ACCD grafts exhibited low‐ACC concentrations, a branched root system and enhanced plant growth and yield stability under salinity, compared to epi and WT grafts, through modulating nutritional, metabolic, hormonal and transcriptional networks in the scion. Low root‐sourced ACC was linked to down‐ and upregulation of ABA biosynthesis ( NCED3 ) and catabolism ( CYP707A1/3 ), leading to reduced leaf ABA but induced signalling; activation of GA biosynthesis ( GA20ox , GA3ox ) and CK homeostasis ( ZOG , AHPT1L , ARR‐Bs , CRF2/4 ); induced steroid metabolism; improved leaf P ( SPX3 , PAP17, PEPC1 ), Ca and S nutrition, and limited Na + accumulation, leading to stable carbon metabolism, source–sink relations and yield under salt stress. High root‐sourced ACC in epi grafts mainly penalised reproductive growth but induced protective flavonoids and source activity in salinised leaves. These findings highlight the role of root‐derived ACC in modulating local and systemic responses to stress and its potential for improving crop yield stability under salinity.

The plant cuticle acts as a crucial barrier against abiotic stresses. In this study, the vulnerable anther (van) gene on chromosome D13 was map-based cloned in upland cotton and identified as GhMYB106_D13. It was demonstrated that the differential distribution of MYB106 between D13 and A13 may represent post-polyploidization convergent evolutionary events. Transcriptome analysis, metabolic profiling, and microscopic examination of anther cuticle in GhMYB106_D13 over-expression and knockout lines revealed that GhMYB106_D13 affects the wax and cuticle biosynthesis pathway. GC-MS analysis demonstrated that the loss of GhMYB106_D13 resulted in an ~27.6% reduction in total wax load, predominantly characterized by a decrease in very-long-chain alkanes, whereas overexpression (OE) led to wax accumulation. Key genes involved in the pathway including FACR2, LACS1, HHT1, and PXG4 were found to be changed dynamically. Specifically, GhMYB106_D13 likely activates the expression of LACS1, a gene involved in wax synthesis that was downregulated in Stage-8 anthers of the Ghmyb106_D13 mutant. Meanwhile, upregulation of FACR2, CYP704B1, and HHT1 was suggested to be potentially involved in cuticle metabolism, possibly through altered 16-feruloyloxypalmitic acid (16-FA) level. Thus, GhMYB106_D13 contributes to the formation of the first protective 'shield' for the anther against external stresses. Additionally, GhMYB106_D13 participates in trichome differentiation, which constitutes a second 'shield' that encloses the petals and sequesters the anther in the bud before flowering. Overall, these findings unveil the dual function of GhMYB106_D13 in physical protection of plant propagation and offer valuable insights for future strategies aimed at improving stress tolerance in crops.

The ubiquitin proteasome system (UPS) and autophagy cooperatively orchestrate plant immune homeostasis, while diverse phytopathogens deploy secreted effectors to disrupt their crosstalk for successful colonization. Proteaphagy, the autophagic turnover of intact 26S proteasome holoenzymes, is a conserved stress response co-opted by Pseudomonas syringae effector HopM1 to cripple host proteolysis. However, how the Huanglongbing (HLB) pathogen 'Candidatus Liberibacter asiaticus' (CLas) simultaneously manipulates UPS and autophagy to subvert citrus immunity remains largely uncharacterized. Here, we functionally characterize the secreted CLas effector SDE5640, which exacerbates HLB susceptibility in sweet orange (Citrus sinensis). SDE5640 directly binds the 19S proteasome chaperone CsPSMD10, whose homodimerization via Cys163/Cys190 disulfide bonds is required for immune suppression. CsPSMD10 overexpression enhances citrus susceptibility to CLas, whereas the dimerization-deficient CsPSMD10-C190S mutant confers robust HLB resistance. Mechanistically, CsPSMD10 targets CsATG8 isoforms for UPS-dependent degradation to restrain autophagic flux; SDE5640 competitively occupies the Ank2/Ank3 domains of CsPSMD10 to disrupt CsPSMD10-CsATG8c complexes, thereby stabilizing CsATG8c and triggering autophagy dependent on CsPSMD10. Moreover, SDE5640-induced autophagy drives selective autophagic degradation of the 20S proteasome catalytic subunit CsPBA1, which ultimately disrupts cellular proteasome activity and attenuates salicylic acid-mediated citrus immunity. Collectively, our findings identify a novel SDE5640-CsPSMD10-CsATG8c-CsPBA1 regulatory cascade, illustrating how a single CLas effector synchronously rewires the UPS-autophagy crosstalk to facilitate pathogen proliferation.

Pumilio (PUM) proteins comprise an evolutionarily conserved family of sequence-specific RNA-binding proteins that act as key post-transcriptional regulators in eukaryotes. In this study, we identified a maize PUM protein, named ZmDLR9 (Defective in Lateral Root 9), as a positive factor involved in lateral root development. Loss-of-function mutation in the ZmDLR9 (dlr9-1) severely impaired lateral root formation. Functional analysis revealed that ZmDLR9 localizes in the nucleolus and interacts with pre-rRNA processing-associated proteins, including BRX1-1 (BIOGENESIS OF RIBOSOMES IN XENOPUS 1-1), BRX1-2, and GRC3 (a subunit of the ITS2 processing complex). The dlr9-1 mutation resulted in aberrant accumulation of pre-rRNA processing intermediates, as well as defects in ribosome assembly and translation. Heterologous expression of ZmDLR9 partially rescued the growth defects of an Arabidopsis PUM loss-of-function mutant (apum24-2), demonstrating functional conservation of the PUM protein family across the plant kingdom. Furthermore, the dlr9-1 mutation disrupted nucleolar morphology, thereby inhibiting cell proliferation and delaying lateral root primordia emergence. Together, our results demonstrate that ZmDLR9, a Pumilio protein, is required for lateral root development by mediating pre-rRNA processing-dependent cell proliferation.

Jeal, K., Carpenter, S. J., Burt, C., Edwards, K. J. and Jill Harrison, C. (2025), Phylogeny, chromosomal mapping and expression analyses of wheat CLAVATA pathway components suggest differential selection on receptor-like kinases, CLEs and T3 WOXes. The Plant Journal, 124, e70580. https://doi.org/10.1111/tpj.70580. In the Acknowledgements section, funding from BBSRC grant BB/T008741/1 was inadvertently omitted. We apologize for this error and thank the BBSRC for funding this work. The published article has been updated to reflect this correction.

Heat stress (HS) severely limits plant growth and productivity, threatening agriculture and food security. Plants cope with recurrent HS through adaptive thermal memory, which allows them to retain a memory of prior moderate priming stress. However, while this process has been well studied in Arabidopsis thaliana, it remains unclear whether the same molecular mechanisms operate in horticultural crops such as tomato (Solanum lycopersicum). Here, we show that tomato plants display a longer thermal memory capacity than Arabidopsis. We found that thermal priming followed by recurrent HS enhanced yield of tomato plants under both controlled and field conditions. Consistent with previous reports, we show that HEAT SHOCK FACTOR A2 (SlHSFA2) is required for thermal priming, as hsfa2 CRISPR mutants lost priming capacity. SlHSFA2 acts as positive regulator of a subset of type II transcriptional thermal memory genes, including SlBAG6. SlHSFA2 physically interacts with ETHYLENE RESPONSE FACTORs, which function as co-activators of type II transcriptional thermal memory genes and further enhance the expression of those genes in response to heat. Together, these findings establish a regulatory module critical for heat adaptation in tomato.

Plant hypocotyls are central to seedling establishment in variable light environments. Although core photoreceptor pathways regulating hypocotyl elongation are well defined, the molecular basis of natural variation in this trait-particularly through posttranscriptional regulation-remains poorly understood. Here, we report that a high-altitude, high-light-adapted Arabidopsis ecotype from Tibet exhibits longer hypocotyls under low light compared to a low-altitude ecotype from Sichuan. Using recombinant inbred lines combined with fine-mapping and near-isogenic line validation, we identified the major locus LA1 (Light Adaptation 1) and pinpointed IAMH2 as the causal gene. Full-length transcriptomics revealed a natural structural variant in the IAMH2 3' UTR of high-altitude ecotypes that alters its length and disrupts a poly(U) motif. We further show that in low-altitude ecotypes, the RNA-binding proteins C3H14/C3H15 directly bind this poly(U)-rich region to posttranscriptionally downregulate IAMH2 mRNA levels, thereby attenuating IAMH2-dependent IAA accumulation and hypocotyl elongation. Analysis of 38 globally representative ecotype genomes confirmed that IAMH2 3' UTR variation correlates with light intensity and elevation, supporting its role in environmental adaptation. Collectively, our work reveals a previously unknown C3H14/C3H15-IAMH2 posttranscriptional module that dynamically adjusts hypocotyl elongation in response to light, providing new insights into the plasticity and adaptive evolution of seedling photomorphogenesis.