Journal of Experimental Botany
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Journal of Experimental Botany
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Founded in 1950, the Journal of Experimental Botany (JXB) is a top-ranking journal owned by the Society for Experimental Biology (SEB) and dedicated to publishing advances in plant science.

https://academic.oup.com/jxb

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🍅 SPECIAL ISSUE RESEARCH 🍅

The tomato dad1 mutant lacks jasmonate biosynthesis, forming seedless fruits. Expression data shows spatiotemporal localization of jasmonate regulates fruit set primarily by modulating gibberellin metabolism - Nomura et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 8 (shortened, full legend in paper): A working model for JA-mediated regulation of tomato fruit development. In the wild type (WT), the jasmonic acid (JA) biosynthesis gene SlDAD1 is specifically expressed in the filaments before anthesis, particularly at −2 days after anthesis (DAA). During this period, JA levels (red) transiently increase in the filaments and ovules, thereby suppressing ovary enlargement prior to anthesis. Consequently, in the absence of pollination the ovaries fail to develop into fruits. The signal, which is probably emitted through the ovules (dotted arrow), is not clear. In contrast, the Sldad1 mutant exhibits markedly low JA levels in both the filaments and ovules before anthesis.
December 7, 2025 at 5:48 PM
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🧬 SPECIAL ISSUE RESEARCH 🧬

🍅 Genome-edited tomato mutants for the SPATULA gene elucidated conserved functions during gynoecium development, improving our understanding of the SPT gene in fleshy fruits- Martínez-Estrada et al.

🔗 doi.org/10.1093/jxb/...
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Fig. 4.Effect of the lack of SlSPT function on pollen tube growth and ovary characteristics in slspt mutants and wild-type (WT; Micro-Tom) plants. (A) Pollen tube growth in the gynoecium. (B) Pollen tube staining measured as relative intensity units. (C) Micrographs of transverse sections of the ovary at anthesis, with a magnified view of the pericarp of the ovary at anthesis. (D, E) Comparison of cell layers and pericarp thickness between WT and slspt mutants. Different letters indicate statistically significant differences [ANOVA followed by Fisher's LSD test, P≤0.05, n=10, for (B), Kruskal–Wallis test followed by Dunn’s test, P≤0.05, n=15, for (D); Tukey’s range test, P≤0.05, n=15, for (E)]. Scale bars: 1 mm (A), 0.4 mm (C left); 50 µm (C right).
December 6, 2025 at 7:53 PM
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🍅✨ SPECIAL ISSUE REVIEW ✨🍅

The nutritional quality of fresh fruit is not just a matter of bioactive content but of all the structural and biochemical properties that develop from the field to the digestive tract - Bertin et al.

🔗 doi.org/10.1093/jxb/...

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Graphical abstract Fresh and processed tomatoes are a major source of phytonutrients in the human diet, and the beneficial health effects for consumers are largely attributed to carotenoids and polyphenols. The metabolic pathways and genetic regulatory factors involved in their synthesis are well described, enabling healthier varieties to be produced. However, the relationship between fruit metabolite content and expected health benefits is not straightforward, as many other factors are involved. These include cell division, cell wall properties, the expansion of storage compartments such as plastids and vacuoles, and metabolite synthesis and dilution by water. All of these factors impact the bioaccessibility and bioavailability of the nutrients accumulated and consumed in fresh and processed fruit.
December 6, 2025 at 4:18 PM
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🍅📘 SPECIAL ISSUE REVIEW 📘🍅

Wang & de Maagd discuss review recent progress and address remaining questions in relation to tomato fruit development and ripening transcriptional regulation, and highlight future challenges.

🔗 doi.org/10.1093/jxb/...

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Fig. 2.Transcriptional regulation network of fruit development, ripening initiation, and ripening progression. Transcription factors involved in fruit development and ripening are depicted as rounded rectangles in a putative temporal or developmental sequence from left to right. Arrows emanating from these TFs indicate transcriptional regulation. The thickness of the arrows shows the predicted strength of regulation. Arrows from C2H4 to EILs represent ethylene signal transduction. Arrows emanating from DML2 denote DNA cytosine demethylation. Circles depict phytohormones: ABA, abscisic acid; BR, brassinosteroids; GA, gibberellic acid; IAA, auxin. Created in BioRender. Wang, R. (2025) https://BioRender.com/4qtac55.
December 6, 2025 at 8:35 AM
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🌿🍅 SPECIAL ISSUE RESEARCH 🍅🌿

The wild tomato Solanum pennellii has specialized leaf design & photosynthetic machinery that boost photosynthetic capacity, which can be transferred to commercial tomato plants via non-GM grafting methods- Ganie et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 1.Whole plant leaf area and plant height of LEA and Lost. The growth patterns of LEA and Lost, particularly in terms of whole plant leaf area and height, were quantified throughout the experiment. (A) LEA consistently exhibited a significantly higher whole plant leaf area than Lost (B) Although LEA initially had greater plant height, Lost began to surpass LEA in height around 29 d after transplanting (DAT). Data are presented as mean values ±standard deviation (n=3–6). Statistical differences were assessed using Student's t-test: *P<0.05, **P<0.01, ***P<0.001.
December 5, 2025 at 6:51 PM
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⚙️🍅 SPECIAL ISSUE RESEARCH 🍅⚙️

A mechanical treatment applied to tomato seedlings enhances stem width, increases vascular bundle number, promotes early flowering & improves fruit yield, involving auxin & ethylene pathways - Castro-Estrada et al.

🔗 doi.org/10.1093/jxb/...
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Fig. 8 (shortened, full legend in paper): Schematic representation of the morphological and physiological impacts triggered by combined mechanical stress (MS) in tomato plants. Ten-day-old tomato plants exposed to mechanical treatment (MT) with a variable weight of 1.5–3 g, positioned on the upper part of the stem for 48 h, exhibited multiple layered responses. Initially, this exposure significantly increased stem width, stele diameter, and the number of xylem vessels, leading to a substantial increase in stem xylem area. All the changes were observed as early as 6 h after the initiation of MT and continued until nearly 10 DPT. MS also impacted the lignification of the stem tissues. MT induced changes in gene expression and altered plant metabolism to sustain the morphological and physiological changes, amplifying the initial responses throughout the entire life cycle of the plants.
December 5, 2025 at 4:12 PM
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🧬🍅 SPECIAL ISSUE RESEARCH 🍅🧬

Tomato cytoplasmic male sterility caused by incompatibility between nuclear and cytoplasmic genetic information is restored through the action of multiple fertility restorer genes of tomato wild relatives - Iki et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 2.Genomic structures of the LA1670, LA0166, and LA1673 RF lines. (A) Chromosome structural similarity between the three RF lines of LA1670 (SPI1.1ch01 to SPI1.1ch12), LA0166 (SCH1.0ch01 to SCH1.0ch12), and LA1673 (SLYcer1.1ch01 to SLYcer1.1ch12). Arrows indicate the RF1 and RF2 loci. (B) Genomic structural similarity between the RF1 loci on chromosome 1 of the three RF lines. Blue and red alignment links between the RF lines show regular and reversed orientations, respectively. Pentagons indicate PPR genes with gene ID colors (yellow, blue, and red) indicating orthologous genes.
December 5, 2025 at 1:41 PM
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🧬 🍅 SPECIAL ISSUE RESEARCH 🍅 🧬

MYB and WRKY transcription factors collaboratively regulate suberin biosynthesis in the tomato root exodermis. Antagonistic interactions may fine-tune suberization or act as a brake on overaccumulation - Jo et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 2 (shortened, full legend in paper): Perturbations of SlMYB41, SlMYB92, and SlWRKY71 expression affect the suberization of tomato exodermis. (A) Percentage of cross-sections showing a non-suberized, an early suberized (suberin in <50% of exodermal cells), or a late suberized (suberin in >50% of exodermal cells) exodermis phenotype in hairy root cultures of the control (empty vector), CRISPR knockout lines [Slmyb41-ko, Slmyb92-ko, Slwrky71-ko(4), and Slwrky71-ko(5)], and overexpressing lines (SlMYB41-OX, SlMYB92-OX, and SlWRKY71-OX). The number above the bars represents the number (n) of individual roots examined in each genotype. Asterisks denotes statistically significant differences between each line in comparison with the empty vector control, whereas n.s. indicates no significant differences (P<0.05, χ2 test).
December 5, 2025 at 11:23 AM
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🔬🪲 SPECIAL ISSUE RESEARCH 🔬🪲

Glandular trichomes function as ultra-fast biomechanical defense triggers in tomatoes, rupturing upon contact with insects and exposing them to sticky and toxic secretions - Popowski et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 3.Thrips nymphs rupture tomato trichomes. (A) Frames from a microscopy video (Supplementary Video S4) before, during, and after a thrips leg causes type VI glandular trichome rupture on an S. habrochaites tomato stem sample. Zoomed-in panels are shown below each frame, with illustrative labels for the leg, glandular head, and fluid filament formed afterward. The colors assigned to the frames indicate the time of the experiment in the leg position versus time plot of (B) The plot also tracks the formation and length of the filament over the course of the video, as the insect struggles to move.
December 5, 2025 at 8:00 AM
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🌟🔬 TECHNICAL INNOVATION 🔬🌟

Flores-Tornero et al. have created the first double fluorescent marker line for generative cell and sperm cells of tomato, as well as a protocol to isolate those cells using fluorescence-activated cell sorting 🍅

🔗 doi.org/10.1093/jxb/...

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Fig. 1.Micro-Tom flower, pollen, and pollen tube growth in vitro and semi-in vivo. (A) Micro-Tom plant growing in a reach-in chamber. (B) Structure of a mature flower (top), showing the conic anther surrounding the style and the ovary at the base (bottom). (C) Pollen release by the vibration method. (D) Bright field (top) and fluorescent field (bottom) of a bicellular pollen stained with DAPI, showing the generative cell and the vegetative nucleus. (E) Micro-Tom pollen tubes growing in vitro and (F) in semi-in vivo. GCN, generative cell nucleus; PG, pollen grain; PT, pollen tube; St, stigma; Sty, style; VN, vegetative nucleus. Scale bars: (B) 75 mm; (D) 10 µm; (E and F) 100 µm.
December 4, 2025 at 6:13 PM
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☀️🍅 SPECIAL ISSUE REVIEW 🍅☀️

Heuvelink et al. examine how light intensity, photoperiod, spectrum, directionality and energy regulate whole-plant physiological processes including morphogenesis, source–sink interactions and assimilate partitioning.

🔗 doi.org/10.1093/jxb/...
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Fig. 3.Schematic representation of the different photoreceptors in tomato, their respective absorption spectra, corresponding chromophores, and main functions. FAD, flavin adenine dinucleotide; FMN, flavin mononucleotide; PHY, phytochromobilin; Trp, tryptophan residues.
December 4, 2025 at 12:30 PM
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🖥️ 📈 SPECIAL ISSUE RESEARCH 📈 🖥️

🍅 A kinetic modeling approach is used to understand how gene expression influences ethylene biosynthesis and signaling during tomato ripening - Nguyen et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 6.Prediction of ethylene biosynthesis of ethylene treated winter and summer tomatoes during off-vine postharvest ripening. (A) ACC content, (B) MACC content, (C) ethylene production rate, (D) ACS activity, (E) ACO activity. Heat plots represent the distribution results from a Monte Carlo simulation. The black and white lines represent the mean and 95% confident interval, respectively. The points are measurement data. Error bars represent the standard error of the mean (n=5 for winter fruit and n=4 for summer fruit). ACC, 1-aminocyclopropane-1-carboxylic acid; ACO, 1-aminocyclopropane-1-carboxylic acid oxidase; ACS, 1-aminocyclopropane-1-carboxylic acid synthase; BR, breaker; LR, light red; MACC, 1-(malonylamino)cyclopropane-1-carboxylic acid; MG, mature green; ORG, orange; RR, red ripe; TRN, turning.
December 4, 2025 at 8:10 AM
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🔥🧂 SPECIAL ISSUE RESEARCH 🔥🧂

Using multi-omics, Pardo-Hernández et al. identified specific ABA-dependent and independent markers for single and combined abiotic stresses. These markers weren't initially detectable when using individual omics alone 🔍

🔗 doi.org/10.1093/jxb/...
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Fig. 1.Phenomics and ionomics analysis in tomato wild type (WT) and the ABA-deficient flacca mutant without (flc–) and with (flc+) application of exogenous ABA under control, salinity, heat, and combination of salinity and heat. (A) Photographs of the aerial part. (B) Data of physiological parameters. (C, D) Radial graphs of cations and anions of flc– (C) and flc+ (D) under all conditions normalized against WT plants grown under control conditions. Raw data for (C) and (D) can be found in Supplementary Table S2. A, photosynthesis; E, transpiration; gs, stomatal conductance; Ci/Ca, intercellular CO2/ambient CO2; Fv'/Fm', variable to maximal fluorescence (light); Φ PSII, PSII quantum yield; Φ CO2, quantum efficiency of CO2 assimilation; C, control; S, salinity; H, heat; S+H, salinity+heat.
December 3, 2025 at 7:40 PM
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🌟 Celebrating the JXB editors featured in Clarivate's Highly Cited Researchers 2025 🌟

📝 Editor-in-Chief John Lunn
📝 Darwin Reviews Editor Don Ort
📝 Associate Editor Tracy Lawson

Congratulations to all! 👏

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An announcement postcard "Celebrating JXB editors recognised in Clarivate's Highly Cited Researchers 2025". The JXB logo is the top, followed by three headshots of Don Ort (Darwin Reviews Editor), John Lunn (Editor-in-Chief) and Tracy Lawson (Associate Editor).
December 3, 2025 at 3:59 PM
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🫖 SPECIAL ISSUE RESEARCH 🫖

Compost tea enhances tomato fruit aroma by up-regulating LOX genes involved in fatty acid metabolism, facilitated by ethylene signaling and mediated through transcription factor SlERF.E4. 🍅

✍️ Li et al.

🔗 doi.org/10.1093/jxb/...

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Fig. 5 (shortened, full legend in paper): The SlLOXD and SlLOXE transcription is induced by SlERF.E4. (A) A heatmap illustrates the expression patterns of tomato AP2/ERFs transcription factors in ripening fruit treated with various nutrient solutions. The clustering of genes is based on shared expression patterns. Purple corresponds to low gene expression, while orange indicates higher gene expression values. (B) The relative expression of SlLOXD, SlLOXE, and SlERFs during tomato fruit ripening. (C) The G-box binding element (GGACGG) in the SlLOXD and SlLOXE promoter. (D) Yeast one-hybrid assay demonstrates the binding of SlLOXD and SlLOXE promoter by SlERFs (ERF.E4, ERF.E2, ERF.F4, and ERF.H1). (E) Direct binding of SlERF.E4 to the promoters of SlLOXD and SlLOXE in vivo performed by chromatin immunoprecipitation (ChIP)-qPCR. (F) The dual luciferase assay of SlERF.E4 and SlLOXD or SlLOXE promoters. MG, mature green; BR, breaker; BR-nd, n days after breaker.
December 3, 2025 at 2:12 PM
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🧬🍅 SPECIAL ISSUE REVIEW 🍅🧬

Recent breakthroughs in genome sequencing have transformed tomato research, unlocking key wild germplasm traits 🌍
Rose et al. outline how these well-characterized genetic resources can be used to improve tomato research 🔬

🔗 doi.org/10.1093/jxb/...
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Fig. 1.Current stage of tomato and wild relative genome sequencing.
December 3, 2025 at 10:32 AM
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🍅 SPECIAL ISSUE RESEARCH 🍅

Priming with arbuscular mycorrhizal fungi & natural compounds enhances tomato resilience to drought & salinity by remodelling transcriptomes and metabolomes, boosting antioxidant & osmoprotective responses - Giovannini et al.

🔗 doi.org/10.1093/jxb/...
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Fig. 1.Arbuscular mycorrhizal fungal (AMF) colonization assessment in tomato potted plants (Solanum lycopersicum cv. Moneymaker) inoculated with a commercial inoculum (MycAgro, Funneliformis mosseae). (A) Representative images of AMF-inoculated roots. Scale bars 120 µm (Aa), 60 µm (Ab), and 20 µm (Ac). (B) Frequency of mycorrhization in root system. (C) Arbuscule abundance in the colonized root system. Data are means ±SE. Lower case letters above bars denote significant differences as assessed by Tukey’s HSD test (P<0.05) and are reported only when the priming treatment (T)×stress condition (S) interaction is significant. ns, not significant; *, significant at P≤0.05. Analysis of variance on the single variables is reported in Supplementary Table S1. CHI, chitosan; CTRL, control, untreated; MYC, inoculated; NMYC, not inoculated; NS, not stressed; SA, salicylic acid; SS, salt stress; WS, water stress.
December 3, 2025 at 8:02 AM
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🍅🔬 SPECIAL ISSUE REVIEW 🔬🍅

This study highlights how metabolomics unveils key metabolic pathways in tomato ripening, offering insights for breeding strategies aimed at improving flavor, nutrition, and overall fruit quality - Karakas & Fernie

🔗 doi.org/10.1093/jxb/...

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Fig. 2.Flowchart outlining the sample processing pipeline. Starting with the experimental population, sample harvesting and extraction for MS, data analysis for the variation, genome-wide association study (GWAS), and quantitative trait locus (QTL) mapping for genetic associations, biological validation for confirming the findings, and the last step is the observation of the phenotypical changes of knockout (KO) or overexpression (OX) lines. Created in BioRender. Karakas, E. (2025) https://BioRender.com/ufeuy48.
December 2, 2025 at 5:43 PM
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🧬 TECHNICAL INNOVATION 🧬

CRISPR/Cas technology is an emerging tool for identifying nucleic acid sequences.

Hak et al. present a user-friendly, extraction-free, rapid protocol for specific on-site detection of plant viruses using CRISPR/Cas13a.

🔗 doi.org/10.1093/jxb/...
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Fig. 5 (shortened, full legend in paper): Development of a simplified approach for on-site Cas13a-based diagnostics. (A) Cas13a-mediated detection of tomato brown rugose fruit virus (ToBRFV) in serial dilutions of crude RNA samples from ToBRFV-infected plants diluted in RNA from healthy plants. Viral RNA can be detected in a 1:5 dilution using this method. (B) Equipment required for on-site diagnostics includes dry bath, vortex, portable fluorescence viewer, a pipette, and test tubes. (C) Schematic illustration of virus detection using a portable fluorescence viewer and a cellular phone camera. (D) Mobile phone camera image of serial dilutions of crude RNA from ToBRFV-infected plants. (E) Samples are converted to grayscale. (F) Fluorescence intensity is quantified using ImageJ.
December 2, 2025 at 2:11 PM
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🟠🍅 SPECIAL ISSUE EXPERT VIEW 🍅🟠

Tomato carotenoids contribute to photosynthesis, color ripe fruit and produce bioactive signals.
Rodriguez-Concepcion et al. provide an update on how paralogs of key biosynthetic enzymes control carotenoid production.

🔗 doi.org/10.1093/jxb/...
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Box 1. Key developments in understanding the role of enzyme paralogs feeding the carotenoid pathway in tomato The steps catalyzed by DXS, GGPPS, and PSY are shown in a schematic pathway. The relative contribution of individual paralogs to carotenoid biosynthesis in different tomato organs is represented in the lower panel (the paler the color, the weaker the contribution of the corresponding isoform; no color means no contribution). The main findings of the indicated papers are also indicated in the figure.
December 2, 2025 at 11:52 AM
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⬇️ SPECIAL ISSUE RESEARCH ⬇️

🍅 Hypoxia in red tomato fruit enhances glycolysis, fermentation, GABA shunt, & accumulation of alanine & glycine, with columella tissue showing the highest metabolic activity & sensitivity to low oxygen stress- Li et al.

🔗 doi.org/10.1093/jxb/...
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Fig. 1.Heat plot showing the distribution of concentration for identified sugars (A), organic acids (B), and amino acids (C) with more than 2-fold difference between three tissues at the beginning of the incubation period (t=0 h). The scale for each plot ranges from 1/4.5 to 2.5 times the mean of the metabolite concentration in the three tissues. Tissues not measured are marked in grey.
December 2, 2025 at 8:49 AM
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🍅 DARWIN REVIEW 🍅

Jaryal et al. discuss the role of four stress hormones, abscisic acid, ethylene, jasmonates, and salicylic acid, in the orchestration of signaling pathways that mediate tomato resilience and metabolism 📝

🔗 doi.org/10.1093/jxb/...
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Fig. 2.The role of abscisic acid (ABA), ethylene (ET), jasmonic acid (JA), and salicylic acid (SA) in the regulation of tomato resilience and metabolism during different (a)biotic stress conditions. (A) Overview of the effect of different plant stress hormones on tomato resilience. Arrows and blocked arrows represent a positive and negative effect, respectively, and dotted lines represent an unclear effect of the hormone on tomato resilience in the specific stress condition. (B and C) Overview of the effect of different plant stress hormones on tomato metabolism in (B) fruit and (C) vegetative tissues. Upwards and downwards pointing arrows represent positive and negative regulation, respectively. Created in BioRender.Toçilla, S. (2025) https://BioRender.com/k49a446.
December 1, 2025 at 3:23 PM
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📝 SPECIAL ISSUE EDITORIAL 📝

🍅 Tomato 🍅

🔎 Guest editors Gibon, Beckles, Osorio & Ezura dive into the reviews, technical innovations and original research articles in this special issue that address the major challenges facing the tomato industry 🍅

🔗 doi.org/10.1093/jxb/...

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Ripe tomato fruit on its truss (credit: Marine Honoré).
December 1, 2025 at 1:49 PM
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🌊 SPECIAL ISSUE REVIEW 🌊

Flooding stress can severely impact tomato cultivation and productivity. Eerdekens et al. explore low-oxygen stress in tomato, including hypoxia signaling, hormonal regulation, and physiological and morphological responses 🌊🍅

🔗 doi.org/10.1093/jxb/...
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Fig. 2.Schematic overview of the morphological and biochemical responses of tomato towards waterlogging stress. (A) Waterlogging impairs photosynthesis by reducing chlorophyll and carotenoid levels. (B) Plants switch to an anaerobic metabolism induced by the hypoxic conditions. (C) Stomatal closure is induced, lowering transpiration rates. (D) Epinasty, or downward leaf bending, is induced to reduce light interception and thus transpiration and photodamage. (E) Emergence of adventitious roots at the stem base to replace damaged roots and aid in recovery. (F) Aerenchyma formation to enhance internal oxygen diffusion. The role of different hormones and signaling molecules is indicated in each process. ET, ethylene; IAA, auxin; ABA, abscisic acid; CK, cytokinins. Created in Biorender. Vanden Broeck, E. (2025) https://BioRender.com/ymc5n71.
December 1, 2025 at 12:19 PM
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📣 Check out the Journal of Experimental Botany's newest special issue 📣

🍅 Tomato - Issue 21 of 2025 🍅
📘 Guest edited by Yves Gibon, Diane Beckles, Sonia Osorio & Hiroshi Ezura

🔗 academic.oup.com/jxb...

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The cover of Vol 76 | Issue 21 | 2025 of the Journal of Experimental Botany, Special Issue: Tomato. Purple banners border the top and bottom of the page and in the centre is an image of a ripe tomato fruit on its truss (credit: Marine Honoré).
December 1, 2025 at 10:14 AM