Fungal interactions with plant roots, either beneficial or detrimental, have a crucial impact on agriculture and ecosystems. The cosmopolitan plant pathogen Fusarium oxysporum (Fo) provokes vascular wilts in more than a hundred different crops. Isolates of this fungus exhibit host-specific pathogenicity, which is conferred by lineage-specific Secreted In Xylem (SIX) effectors encoded on accessory genomic regions. However, such isolates also can colonize the roots of other plants asymptomatically as endophytes or even protect them against pathogenic strains. The molecular determinants of endophytic multihost compatibility are largely unknown. Here, we characterized a set of Fo candidate effectors from tomato (Solanum lycopersicum) root apoplastic fluid; these early root colonization (ERC) effectors are secreted during early biotrophic growth on main and alternative plant hosts. In contrast to SIX effectors, ERCs have homologs across the entire Fo species complex as well as in other plant-interacting fungi, suggesting a conserved role in fungus\uffe2\uff80\uff93plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence and rapid activation of plant immune responses, while ERC deletion in a nonpathogenic isolate led to impaired root colonization and biocontrol ability. Strikingly, some ERCs contribute to Fo infection on the nonvascular land plant Marchantia polymorpha, revealing an evolutionarily conserved mechanism for multihost colonization by root infecting fungi.
Several studies have investigated soil microbial biodiversity, but understanding of the mechanisms underlying plant responses to soil microbiota remains in its infancy. Here, we focused on tomato (Solanum lycopersicum), testing the hypothesis that plants grown on native soils display different responses to soil microbiotas.
Using transcriptomics, proteomics, and biochemistry, we describe the responses of two tomato genotypes (susceptible or resistant to Fusarium oxysporum f. sp. lycopersici) grown on an artificial growth substrate and two native soils (conducive and suppressive to Fusarium).
Native soils affected tomato responses by modulating pathways involved in responses to oxidative stress, phenol biosynthesis, lignin deposition, and innate immunity, particularly in the suppressive soil. In tomato plants grown on steam\uffe2\uff80\uff90disinfected soils, total phenols and lignin decreased significantly. The inoculation of a mycorrhizal fungus partly rescued this response locally and systemically. Plants inoculated with the fungal pathogen showed reduced disease symptoms in the resistant genotype in both soils, but the susceptible genotype was partially protected from the pathogen only when grown on the suppressive soil.
The \uffe2\uff80\uff98state of alert\uffe2\uff80\uff99 detected in tomatoes reveals novel mechanisms operating in plants in native soils and the soil microbiota appears to be one of the drivers of these plant responses.
", "keywords": ["0301 basic medicine", "Proteome", "Propanols", "Arbuscular mycorrhizal fungi", "arbuscular mycorrhizal fungi", "tomato", "Lignin", "Models", " Biological", "Plant Roots", "defence responses", "Tomato", "Soil", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "microbiota", "Plant Immunity", "Soil Microbiology", "suppressive and conducive soils", "susceptible and resistant genotypes", "2. Zero hunger", "0303 health sciences", "Defence responses", "Microbiota", "15. Life on land", "Lignin biosynthesis", "Gene Ontology", "Susceptible and resistant genotypes", "Arbuscular mycorrhizal fungi; Defence responses; Lignin biosynthesis; Microbiota; Suppressive and conducive soils; Susceptible and resistant genotypes; Tomato; Physiology; Plant Science", "Suppressive and conducive soils", "Transcriptome", "lignin biosynthesis"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1660820/1/Chialva%20et%20al%20Iris.pdf"}, {"href": "https://nph.onlinelibrary.wiley.com/doi/pdf/10.1111/nph.15014"}, {"href": "https://doi.org/10.1111/nph.15014"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/New%20Phytologist", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/nph.15014", "name": "item", "description": "10.1111/nph.15014", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/nph.15014"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-02-09T00:00:00Z"}}, {"id": "10.1186/s12870-018-1411-5", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:19:22Z", "type": "Journal Article", "created": "2018-09-20", "title": "Root inoculation with Azotobacter chroococcum 76A enhances tomato plants adaptation to salt stress under low N conditions", "description": "The emerging roles of rhizobacteria in improving plant nutrition and stress protection have great potential for sustainable use in saline soils. We evaluated the function of the salt-tolerant strain Azotobacter chroococcum 76A as stress protectant in an important horticultural crop, tomato. Specifically we hypothesized that treatment of tomato plants with A. chroococcum 76A could improve plant performance under salinity stress and sub-optimal nutrient regimen.Inoculation of Micro Tom tomato plants with A. chroococcum 76A increased numerous growth parameters and also conferred protective effects under both moderate (50\u00a0mM NaCl) and severe (100\u00a0mM NaCl) salt stresses. These benefits were mostly observed under reduced nutrient regimen and were less appreciable in optimal nitrogen conditions. Therefore, the efficiency of A. chroococcum 76A was found to be dependent on the nutrient status of the rhizosphere. The expression profiles of LEA genes indicated that A. chroococcum 76A treated plants were more responsive to stress stimuli when compared to untreated controls. However, transcript levels of key nitrogen assimilation genes revealed that the optimal nitrogen regimen, in combination with the strain A. chroococcum 76A, may have saturated plant's ability to assimilate nitrogen.Roots inoculation with A. chroococcum 76A tomato promoted tomato plant growth, stress tolerance and nutrient assimilation efficiency under moderate and severe salinity. Inoculation with beneficial bacteria such as A. chroococcum 76A may be an ideal solution for low-input systems, where environmental constraints and limited chemical fertilization may affect the potential yield.", "keywords": ["0301 basic medicine", "Salinity", "Nitrogen", "Physiological", "Plant Science", "Plant Roots", "Tomato", "Micro tom", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Azotobacter chroococcum; Micro tom; Plant nutrition; Rhizobacteria; Salinity; Tomato; Adaptation", " Physiological; Azotobacter; Gene Expression Regulation", " Plant; Lycopersicon esculentum; Nitrogen; Plant Leaves; Plant Roots; Rhizosphere; Salt Tolerance; Symbiosis; Plant Science", "Rhizobacteria", "Adaptation", "Lycopersicon esculentum", "Plant nutrition", "Symbiosis", "2. Zero hunger", "0303 health sciences", "Botany", "Plant", "Salt Tolerance", "15. Life on land", "Adaptation", " Physiological", "6. Clean water", "3. Good health", "Plant Leaves", "Gene Expression Regulation", "QK1-989", "Azotobacter", "Rhizosphere", "Azotobacter chroococcum", "Research Article"]}, "links": [{"href": "https://www.iris.unina.it/bitstream/11588/728072/2/VanOosten2018_Article_RootInoculationWithAzotobacter.pdf"}, {"href": "http://link.springer.com/content/pdf/10.1186/s12870-018-1411-5.pdf"}, {"href": "https://doi.org/10.1186/s12870-018-1411-5"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/BMC%20Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1186/s12870-018-1411-5", "name": "item", "description": "10.1186/s12870-018-1411-5", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1186/s12870-018-1411-5"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-09-20T00:00:00Z"}}, {"id": "10.1038/s41598-021-02302-2", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:17:52Z", "type": "Journal Article", "created": "2021-11-30", "title": "Predicting sensitivity of recently harvested tomatoes and tomato sepals to future fungal infections", "description": "AbstractTomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000\uffe2\uff80\uff931700\uffc2\uffa0nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390\uffe2\uff80\uff931420\uffc2\uffa0nm contributes most to the model\uffe2\uff80\uff99s final decision.A dramatic evolution of fruit size has accompanied the domestication and improvement of fruit-bearing crop species. In tomato (Solanum lycopersicum), naturally occurring cis-regulatory mutations in the genes of the CLAVATA-WUSCHEL signaling pathway have led to a significant increase in fruit size generating enlarged meristems that lead to flowers with extra organs and bigger fruits. In this work, by combining mapping-by-sequencing and CRISPR/Cas9 genome editing methods, we isolatedEXCESSIVE NUMBER OF FLORAL ORGANS(ENO), an AP2/ERF transcription factor which regulates floral meristem activity. Thus, theENOgene mutation gives rise to plants that yield larger multilocular fruits due to an increased size of the floral meristem. Genetic analyses indicate thatenoexhibits synergistic effects with mutations at theLOCULE NUMBER(encodingSlWUS) andFASCIATED(encodingSlCLV3) loci, two central players in the evolution of fruit size in the domestication of cultivated tomatoes. Our findings reveal that anenomutation causes a substantial expansion ofSlWUSexpression domains in a flower-specific manner. In vitro binding results show that ENO is able to interact with the GGC-box cis-regulatory element within theSlWUSpromoter region, suggesting that ENO directly regulatesSlWUSexpression domains to maintain floral stem-cell homeostasis. Furthermore, the study of natural allelic variation of theENOlocus proved that a cis-regulatory mutation in the promoter ofENOhad been targeted by positive selection during the domestication process, setting up the background for significant increases in fruit locule number and fruit size in modern tomatoes.
", "keywords": ["0301 basic medicine", "570", "Floral meristem", "[SPI] Engineering Sciences [physics]", "[SDV]Life Sciences [q-bio]", "Meristem", "Quantitative Trait Loci", "Genes", " Plant", "CLAVATA/WUSCHEL regulatory network", "Domestication", "[SPI]Engineering Sciences [physics]", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "AP2/ERF transcription factor", "Promoter Regions", " Genetic", "Cell Proliferation", "Plant Proteins", "580", "Homeodomain Proteins", "2. Zero hunger", "Tomato (Solanum lycopersicum)", "0303 health sciences", "Stem Cells", "Biological Sciences", "15. Life on land", "fruit size", "Crop Production", "[SDV] Life Sciences [q-bio]", "CLAVATA-WUSCHEL regulatory network", "GENETICA", "Fruit", "Mutation", "Fruit size", "floral meristem", "Transcription Factors"]}, "links": [{"href": "https://pnas.org/doi/pdf/10.1073/pnas.1913688117"}, {"href": "https://doi.org/10.1073/pnas.1913688117"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Proceedings%20of%20the%20National%20Academy%20of%20Sciences", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1073/pnas.1913688117", "name": "item", "description": "10.1073/pnas.1913688117", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1073/pnas.1913688117"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-16T00:00:00Z"}}, {"id": "10.1080/15592324.2018.1464855", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:18:20Z", "type": "Journal Article", "created": "2018-04-27", "title": "Not only priming: Soil microbiota may protect tomato from root pathogens", "description": "An increasing number of studies have investigated soil microbial biodiversity. However, the mechanisms regulating plant responses to soil microbiota are largely unknown. A previous work tested the hypothesis that tomato plants grown on native soils with their complex microbiotas respond differently from tomato growing in a sterile substrate. Two soils, suppressive or conducive to Fusarium oxysporum f. sp. lycopersici (FOL), and two genotypes susceptible and resistant to the same pathogen were considered. The work highlighted that the two tested soil microbiotas, irrespectively of their taxonomic composition, elicit the PAMP-triggered Immunity Pathway, the first level of plant defence, as well as an increased lignin synthesis, leading to an active protection when FOL is present in the soil. Here, we tested the expression of a panel of genes involved in Effector-Triggered Immunity (ETI), demonstrating that soil microbiota, beside genotype, affects plant resistance to FOL also modulating this pathway.", "keywords": ["suppressive and conducive soils", "susceptible and resistant genotypes", "0301 basic medicine", "2. Zero hunger", "0303 health sciences", "defence responses; Fusarium oxysporum f. sp. lycopersici; arbuscular mycorrhizal fungi; gene expression; lignin biosynthesis; microbiota; suppressive and conducive soils; susceptible and resistant genotypes; tomato; Plant Science", "arbuscular mycorrhizal fungi", "tomato", "15. Life on land", "defence responses", "03 medical and health sciences", "Fusarium", "Solanum lycopersicum", "microbiota", "gene expression", "Fusarium oxysporum f. sp. lycopersici", "lignin biosynthesis", "Soil Microbiology", "Plant Diseases"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1677702/2/Chialva_et_al_2018_PostPrint.pdf"}, {"href": "https://www.tandfonline.com/doi/pdf/10.1080/15592324.2018.1464855"}, {"href": "https://doi.org/10.1080/15592324.2018.1464855"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Signaling%20%26amp%3B%20Behavior", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1080/15592324.2018.1464855", "name": "item", "description": "10.1080/15592324.2018.1464855", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1080/15592324.2018.1464855"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2018-04-27T00:00:00Z"}}, {"id": "10.1093/plcell/koac174", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:18:27Z", "type": "Journal Article", "created": "2022-06-11", "title": "Conserved secreted effectors contribute to endophytic growth and multihost plant compatibility in a vascular wilt fungus", "description": "AbstractFungal interactions with plant roots, either beneficial or detrimental, have a crucial impact on agriculture and ecosystems. The cosmopolitan plant pathogen Fusarium oxysporum (Fo) provokes vascular wilts in more than a hundred different crops. Isolates of this fungus exhibit host-specific pathogenicity, which is conferred by lineage-specific Secreted In Xylem (SIX) effectors encoded on accessory genomic regions. However, such isolates also can colonize the roots of other plants asymptomatically as endophytes or even protect them against pathogenic strains. The molecular determinants of endophytic multihost compatibility are largely unknown. Here, we characterized a set of Fo candidate effectors from tomato (Solanum lycopersicum) root apoplastic fluid; these early root colonization (ERC) effectors are secreted during early biotrophic growth on main and alternative plant hosts. In contrast to SIX effectors, ERCs have homologs across the entire Fo species complex as well as in other plant-interacting fungi, suggesting a conserved role in fungus\uffe2\uff80\uff93plant associations. Targeted deletion of ERC genes in a pathogenic Fo isolate resulted in reduced virulence and rapid activation of plant immune responses, while ERC deletion in a nonpathogenic isolate led to impaired root colonization and biocontrol ability. Strikingly, some ERCs contribute to Fo infection on the nonvascular land plant Marchantia polymorpha, revealing an evolutionarily conserved mechanism for multihost colonization by root infecting fungi.To address the challenge of predicting tomato yields in the field, we used whole-plant functional phenotyping to evaluate water relations under well-irrigated and drought conditions. The genotypes tested are known to exhibit variability in their yields in wet and dry fields. The examined lines included two lines with recessive mutations that affect carotenoid biosynthesis, zetaz2083and tangerinet3406, both isogenic to the processing tomato variety M82. The two mutant lines were reciprocally grafted onto M82, and multiple physiological characteristics were measured continuously, before, during and after drought treatment in the greenhouse. A comparative analysis of greenhouse and field yields showed that the whole-canopy stomatal conductance (gsc) in the morning and cumulative transpiration (CT) were strongly correlated with field measurements of total yield (TY:r2= 0.9 and 0.77, respectively) and plant vegetative weight (PW:r2= 0.6 and 0.94, respectively). Furthermore, the minimum CT during drought and the rate of recovery when irrigation was resumed were both found to predict resilience.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "Dehydration", "Genotype", "Genetic Variation", "15. Life on land", "Genes", " Plant", "Adaptation", " Physiological", "6. Clean water", "Droughts", "03 medical and health sciences", "Phenotype", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Mutation", "Plant Physiological Phenomena", "Forecasting"]}, "links": [{"href": "https://doi.org/10.1101/2021.03.18.435447"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1101/2021.03.18.435447", "name": "item", "description": "10.1101/2021.03.18.435447", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1101/2021.03.18.435447"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-03-19T00:00:00Z"}}, {"id": "10.1101/2022.10.10.511665", "type": "Feature", "geometry": null, "properties": {"license": "Open Access", "updated": "2026-07-25T16:18:33Z", "type": "Journal Article", "created": "2022-10-13", "title": "A suberized exodermis is required for tomato drought tolerance", "description": "SUMMARYPlant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.Abstract
Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (
Elevation in atmospheric CO2 concentration broadly affects plant phenology and physiology, and these effects may alter the performance of plant viruses. The effects of elevated CO2 on the susceptibility of tomato plants to Tomato yellow leaf curl virus (TYLCV) were examined for two successive years in open top chambers (OTC) in the field. We experimentally tested the hypothesis that elevated CO2 would reduce the incidence and severity of TYLCV on tomato by altering plant defence strategies. Our results showed that elevated CO2 decreased TYLCV disease incidence (by 14.6% in 2009 and 11.8% in 2010) and decreased disease severity (by 20.0% in 2009 and 10.4% in 2010). Elevated CO2 also decreased the level of TYLCV coat protein in tomato leaves. Regardless of virus infection, elevated CO2 increased plant height and aboveground biomass. Additionally, elevated CO2 increased the leaf C:N ratio of tomato, but decreased soluble protein content in leaves. Notably, elevated CO2 increased the salicylic acid (SA) level in uninfected and infected plants. In contrast, elevated CO2 reduced jasmonic acid (JA) in uninfected plants while it increased JA and abscisic acid (ABA) in virus\uffe2\uff80\uff90infected plants. Furthermore, combined exogenous SA and JA application enhanced resistance to TYLCV more than application of either SA or JA alone. Our results suggest that the modulated antagonistic relationship between SA and JA under elevated CO2 makes a great contribution to increased tomato resistance to TYLCV, and the predicted increases in tomato productivity may be enhanced by reduced plant virus susceptibility under projected rising CO2 conditions.
", "keywords": ["2. Zero hunger", "0301 basic medicine", "0303 health sciences", "Plant Stems", "Cyclopentanes", "Carbon Dioxide", "3. Good health", "Plant Viruses", "Plant Leaves", "03 medical and health sciences", "Solanum lycopersicum", "Capsid Proteins", "Oxylipins", "Salicylic Acid", "Abscisic Acid", "Disease Resistance", "Plant Diseases"], "contacts": [{"organization": "Yuhan Sun, H. Cao, Feng Ge, L. Huang, L. Ye, Q. Ren,", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.1111/j.1438-8677.2012.00582.x"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%20Biology", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/j.1438-8677.2012.00582.x", "name": "item", "description": "10.1111/j.1438-8677.2012.00582.x", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/j.1438-8677.2012.00582.x"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2012-04-18T00:00:00Z"}}, {"id": "10.1111/pce.13758", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:19:07Z", "type": "Journal Article", "created": "2020-03-20", "title": "A novel strigolactone\u2010miR156 module controls stomatal behaviour during drought recovery", "description": "AbstractmiR156 is a conserved microRNA whose role and induction mechanisms under stress are poorly known. Strigolactones are phytohormones needed in shoots for drought acclimation. They promote stomatal closure ABA\uffe2\uff80\uff90dependently and independently; however, downstream effectors for the former have not been identified. Linkage between miR156 and strigolactones under stress has not been reported. We compared ABA accumulation and sensitivity as well as performances of wt and miR156\uffe2\uff80\uff90overexpressing (miR156\uffe2\uff80\uff90oe) tomato plants during drought. We also quantified miR156 levels in wt, strigolactone\uffe2\uff80\uff90depleted and strigolactone\uffe2\uff80\uff90treated plants, exposed to drought stress. Under irrigated conditions, miR156 overexpression and strigolactone treatment led to lower stomatal conductance and higher ABA sensitivity. Exogenous strigolactones were sufficient for miR156 accumulation in leaves, while endogenous strigolactones were required for miR156 induction by drought. The \uffe2\uff80\uff9cafter\uffe2\uff80\uff90effect\uffe2\uff80\uff9d of drought, by which stomata do not completely re\uffe2\uff80\uff90open after rewatering, was enhanced by both strigolactones and miR156. The transcript profiles of several miR156 targets were altered in strigolactone\uffe2\uff80\uff90depleted plants. Our results show that strigolactones act as a molecular link between drought and miR156 in tomato, and identify miR156 as a mediator of ABA\uffe2\uff80\uff90dependent effect of strigolactones on the after\uffe2\uff80\uff90effect of drought on stomata. Thus, we provide insights into both strigolactone and miR156 action on stomata.
", "keywords": ["Osmotic stress", "0301 basic medicine", "Stress-responsive microRNA", "stomata", "hormone signalling", "after-effect of drought", "abscisic acid (ABA); after-effect of drought; hormone signalling; osmotic stress; Solanum lycopersicum; stomata; stress-responsive microRNA", "Lactones", "03 medical and health sciences", "Solanum lycopersicum", "Plant Growth Regulators", "Stomata", "2. Zero hunger", "0303 health sciences", "Dehydration", "After-effect of drought", "15. Life on land", "Abscisic acid (ABA)", "Hormone signalling", "6. Clean water", "MicroRNAs", "RNA", " Plant", "13. Climate action", "Plant Stomata", "abscisic acid (ABA)", "stress-responsive microRNA", "osmotic stress", "Heterocyclic Compounds", " 3-Ring", "Abscisic Acid"]}, "links": [{"href": "https://iris.unito.it/bitstream/2318/1764369/1/Visentin%20et%20al_PCE_R2.pdf"}, {"href": "https://onlinelibrary.wiley.com/doi/pdf/10.1111/pce.13758"}, {"href": "https://doi.org/10.1111/pce.13758"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plant%2C%20Cell%20%26amp%3B%20Environment", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.1111/pce.13758", "name": "item", "description": "10.1111/pce.13758", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.1111/pce.13758"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-03-30T00:00:00Z"}}, {"id": "10.3389/fpls.2021.633957", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:20:50Z", "type": "Journal Article", "created": "2021-04-07", "title": "Variation for Composition and Quality in a Collection of the Resilient Mediterranean \u2018de penjar\u2019 Long Shelf-Life Tomato Under High and Low N Fertilization Levels", "description": "The \uffe2\uff80\uff98de penjar\uffe2\uff80\uff99 tomato (Solanum lycopersicum L.) is a group of local varieties from the Spanish Mediterranean region carrying the alc mutation, which provides long shelf-life. Their evolution under low-input management practices has led to the selection of resilient genotypes to adverse conditions. Here we present the first evaluation on nutritional fruit composition of a collection of 44 varieties of \uffe2\uff80\uff98de penjar\uffe2\uff80\uff99 tomato under two N fertilization levels, provided by doses of manure equivalent to 162 kg N ha\uffe2\uff80\uff931 in the high N treatment and 49 kg N ha\uffe2\uff80\uff931 in the low N treatment. Twenty-seven fruit composition and quality traits, as well as plant yield and SPAD value, were evaluated. A large variation was observed, with lycopene being the composition trait with the highest relative range of variation (over 4-fold) under both N treatments, and significant differences among varieties were detected for all traits. While yield and most quality traits were not affected by the reduction in N fertilization, fruits from the low N treatment had, on average, higher values for hue (5.9%) and lower for fructose (\uffe2\uff88\uff9211.5%), glucose (\uffe2\uff88\uff9215.8%), and total sweetness index (\uffe2\uff88\uff9212.9%). In addition, lycopene and \uffce\uffb2-carotene presented a strongly significant genotype \uffc3\uff97 N input interaction. Local varieties had higher values than commercial varieties for traits related to the ratio of sweetness to acidity and for vitamin C, which reinforces the appreciation for their organoleptic and nutritional quality. Highest-yielding varieties under both conditions displayed wide variation in the composition and quality profiles, which may allow the selection of specific ideotypes with high quality under low N conditions. These results revealed the potential of \uffe2\uff80\uff98de penjar\uffe2\uff80\uff99 varieties as a genetic resource in breeding for low N inputs and improving the organoleptic and nutritional tomato fruit quality.
", "keywords": ["0301 basic medicine", "2. Zero hunger", "nutritional quality", "Plant culture", "Nutritional quality", "Plant Science", "04 agricultural and veterinary sciences", "15. Life on land", "Abiotic stress", "local varieties", "Plant breeding", "SB1-1110", "taste", "Local varieties", "GENETICA", "03 medical and health sciences", "Solanum lycopersicum", "Taste", "plant breeding", "Metabolites", "0401 agriculture", " forestry", " and fisheries", "metabolites"]}, "links": [{"href": "https://doi.org/10.3389/fpls.2021.633957"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Frontiers%20in%20Plant%20Science", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3389/fpls.2021.633957", "name": "item", "description": "10.3389/fpls.2021.633957", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3389/fpls.2021.633957"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-04-07T00:00:00Z"}}, {"id": "10.15835/buasvmcn-hort:2018.0020", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:19:48Z", "type": "Journal Article", "created": "2019-09-29", "title": "Establishment of Technological Stages for Obtaining Some Grafted Tomato Seedlings (Dutch Scion \u00d7 Romanian Rootstocks)", "description": "The tomatoes are valuable vegetables, with highest share in Romanian crops from protected spaces. The grafting is a vegetative multiplication method that induces or improves some qualities of the plants (vigor, resistance to soil diseases and pests, resistance to abiotic factors, quantity and quality of fruit production). The research aim has been to establish the technological stages for producing of Dutch scion and Romanian rootstock seedlings from Solanum lycopersicum L. species, to obtain some compatible phenotypes for grafting. This research has been conducted in a greenhouse of the Horting Institute Bucharest. The experience was carried out on a tomato cultivar collection consisting from a Dutch scion (\uffe2\uff80\uff98Abellus\uffe2\uff80\uff99 F1 hybrid) and three Romanian rootstocks (\uffe2\uff80\uff98L542\uffe2\uff80\uff99, \uffe2\uff80\uff98L543\uffe2\uff80\uff99, \uffe2\uff80\uff98L544\uffe2\uff80\uff99). The scion and rootstock diameters have been correlated for manual grafting, cutting at 45 degrees and using the method of splice in silicone tube. The technological stages for obtaining grafted tomatoes have been established for the researched genotypes. These tomato combinations have been compatible for vegetable crops in protected spaces in the south area of Romania.
", "keywords": ["2. Zero hunger", "S", "Agriculture (General)", "solanum lycopersicum l.", "0401 agriculture", " forestry", " and fisheries", "Agriculture", "04 agricultural and veterinary sciences", "0405 other agricultural sciences", "grafting", "dutch scion", "romanian rootstocks", "S1-972"], "contacts": [{"organization": "SORA, Dorin", "roles": ["creator"]}]}, "links": [{"href": "https://doi.org/10.15835/buasvmcn-hort:2018.0020"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Bulletin%20of%20University%20of%20Agricultural%20Sciences%20and%20Veterinary%20Medicine%20Cluj-Napoca.%20Horticulture", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.15835/buasvmcn-hort:2018.0020", "name": "item", "description": "10.15835/buasvmcn-hort:2018.0020", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.15835/buasvmcn-hort:2018.0020"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2019-06-12T00:00:00Z"}}, {"id": "10.21203/rs.3.rs-25108/v1", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:20:05Z", "type": "Journal Article", "created": "2020-05-01", "title": "Trichomes form genotype-specific microbial hotspots in the phyllosphere of tomato", "description": "Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (
The convenient model Arabidopsis thaliana has allowed tremendous advances in plant genetics and physiology, in spite of only being a weed. It has also unveiled the main molecular networks governing, among others, abiotic stress responses. Through the use of the latest genomic tools, Arabidopsis research is nowadays being translated to agronomically interesting crop models such as tomato, but at a lagging pace. Knowledge transfer has been hindered by invariable differences in plant architecture and behaviour, as well as the divergent direct objectives of research in Arabidopsis vs. crops compromise transferability. In this sense, phenotype translation is still a very complex matter. Here, we point out the challenges of \uffe2\uff80\uff9ctranslational phenotyping\uffe2\uff80\uff9d in the case study of drought stress phenotyping in Arabidopsis and tomato. After briefly defining and describing drought stress and survival strategies, we compare drought stress protocols and phenotyping techniques most commonly used in the two species, and discuss their potential to gain insights, which are truly transferable between species. This review is intended to be a starting point for discussion about translational phenotyping approaches among plant scientists, and provides a useful compendium of methods and techniques used in modern phenotyping for this specific plant pair as a case study.
", "keywords": ["Crops", " Agricultural", "0301 basic medicine", "2. Zero hunger", "9. Industry and infrastructure", "Arabidopsis", "Review", "15. Life on land", "6. Clean water", "Droughts", "03 medical and health sciences", "Phenotype", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Stress", " Physiological", "Arabidopsis; tomato; phenotyping; drought stress; translational phenotyping; osmotic stress; Dehydration; Arabidopsis thaliana; Solanum lycopersicum; Lycopersicon esculentum", "Plant Proteins"]}, "links": [{"href": "https://air.unimi.it/bitstream/2434/898415/2/genes-11-01011-v3.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1757296/1/genes-11-01011-v3.pdf"}, {"href": "https://www.mdpi.com/2073-4425/11/9/1011/pdf"}, {"href": "https://doi.org/10.3390/genes11091011"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Genes", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/genes11091011", "name": "item", "description": "10.3390/genes11091011", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/genes11091011"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-08-27T00:00:00Z"}}, {"id": "10.3390/plants10112419", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:21:05Z", "type": "Journal Article", "created": "2021-11-09", "title": "Legume-Based Mobile Green Manure Can Increase Soil Nitrogen Availability and Yield of Organic Greenhouse Tomatoes", "description": "Information about the availability of soil mineral nitrogen (N) in organic greenhouse tomatoes after the application of mobile green manure (MGM), and its impact on plant nutrient status and yield is scarce. Considering this knowledge gap, the effects of legume biomass from faba beans that are cultivated outdoors (FAB), or from feed-grade alfalfa pellets at two different doses (AAL = 330 g m\uffe2\uff88\uff922; AAH = 660 g m\uffe2\uff88\uff922) that were applied as MGM on the nutrition and yield of an organic greenhouse crop of tomatoes were evaluated. All of the MGM treatments increased the mineral N concentrations in the soil throughout the cropping period, and the total N concentration in tomato leaves when compared to the untreated control. FAB and AAH treatments had a stronger impact than AAL in all of the measured parameters. In addition, AAL, AAH, and FAB treatments increased the yield compared to the control by 19%, 33%, and 36%, respectively. The application of MGM, either as faba bean fresh biomass or as alfalfa dry pellets, in organic greenhouse tomatoes significantly increased the plant available soil N, improved N nutrition, and enhanced the fruit yield. However, the N mineralization rates after the MGM application were excessive during the initial cropping stages, followed by a marked decrease thereafter. This may impose an N deficiency during the late cropping period.
", "keywords": ["2. Zero hunger", "Solanum lycopersicum", "soil nitrogen", "alfalfa pellet", "Botany", "04 agricultural and veterinary sciences", "Alfalfa pellet; Biological nitrogen fixation; Faba bean; Organic tomato; Rhizobia; Soil nitrogen; Solanum lycopersicum", "biological nitrogen fixation", "rhizobia", "faba bean", "Article", "QK1-989", "0401 agriculture", " forestry", " and fisheries", "organic tomato"]}, "links": [{"href": "http://www.mdpi.com/2223-7747/10/11/2419/pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1818902/1/Plants_10_2419.pdf"}, {"href": "https://www.mdpi.com/2223-7747/10/11/2419/pdf"}, {"href": "https://doi.org/10.3390/plants10112419"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Plants", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/plants10112419", "name": "item", "description": "10.3390/plants10112419", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/plants10112419"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2021-11-09T00:00:00Z"}}, {"id": "10.3390/v12060675", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:21:12Z", "type": "Journal Article", "created": "2020-06-23", "title": "Arbuscular Mycorrhizal Symbiosis Primes Tolerance to Cucumber Mosaic Virus in Tomato", "description": "Tomato plants can establish symbiotic interactions with arbuscular mycorrhizal fungi (AMF) able to promote plant nutrition and prime systemic plant defenses against pathogens attack; the mechanism involved is known as mycorrhiza-induced resistance (MIR). However, studies on the effect of AMF on viral infection, still limited and not conclusive, indicate that AMF colonization may have a detrimental effect on plant defenses against viruses, so that the term \uffe2\uff80\uff9cmycorrhiza-induced susceptibility\uffe2\uff80\uff9d (MIS) has been proposed for these cases. To expand the case studies to a not yet tested viral family, that is, Bromoviridae, we investigated the effect of the colonization by the AMF Funneliformis mosseae on cucumber mosaic virus (CMV) infection in tomato by phenotypic, physiological, biochemical, and transcriptional analyses. Our results showed that the establishment of a functional AM symbiosis is able to limit symptoms development. Physiological and transcriptomic data highlighted that AMF mitigates the drastic downregulation of photosynthesis-related genes and the reduction of photosynthetic CO2 assimilation rate caused by CMV infection. In parallel, an increase of salicylic acid level and a modulation of reactive oxygen species (ROS)-related genes, toward a limitation of ROS accumulation, was specifically observed in CMV-infected mycorrhizal plants. Overall, our data indicate that the AM symbiosis influences the development of CMV infection in tomato plants and exerts a priming effect able to enhance tolerance to viral infection.
", "keywords": ["0301 basic medicine", "plant\u2013virus interaction", "arbuscular mycorrhizal symbiosis", "Microbiology", "Cucumovirus", "Plant Roots", "Article", "03 medical and health sciences", "Solanum lycopersicum", "Gene Expression Regulation", " Plant", "Mycorrhizae", "arbuscular mycorrhizal symbiosis", " cucumber mosaic virus", " Funneliformis mosseae", " gene expression", " priming tolerance", " plant-virus interaction", " RNA sequencing", " Solanum lycopersicum L.", "Photosynthesis", "Symbiosis", "Funneliformis mosseae", "Plant Diseases", "2. Zero hunger", "0303 health sciences", "cucumber mosaic virus", "Fungi", "RNA sequencing", "Carbon Dioxide", "QR1-502", "3. Good health", "Solanum lycopersicum L.", "gene expression", "arbuscular mycorrhizal symbiosis; cucumber mosaic virus; Funneliformis mosseae; gene expression; priming tolerance; plant-virus interaction; RNA sequencing; Solanum lycopersicum L.", "priming tolerance", "Arbuscular mycorrhizal symbiosis; Cucumber mosaic virus; Funneliformis mosseae; Gene expression; Plant-virus interaction; Priming tolerance; RNA sequencing; Solanum lycopersicum L", "Reactive Oxygen Species"]}, "links": [{"href": "http://www.mdpi.com/1999-4915/12/6/675/pdf"}, {"href": "https://iris.cnr.it/bitstream/20.500.14243/410166/1/prod_424799-doc_151509.pdf"}, {"href": "https://iris.unito.it/bitstream/2318/1765477/1/Miozzi%20et%20al%20Viruses%202020.pdf"}, {"href": "https://www.mdpi.com/1999-4915/12/6/675/pdf"}, {"href": "https://doi.org/10.3390/v12060675"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Viruses", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10.3390/v12060675", "name": "item", "description": "10.3390/v12060675", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10.3390/v12060675"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2020-06-22T00:00:00Z"}}, {"id": "10261/393730", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:24:46Z", "type": "Journal Article", "created": "2024-10-10", "title": "Macro- and microplastics leachates: Characterization and impact on seed germination", "description": "Although plastic mulch enhances crop yield, its removal and disposal present significant challenges, contributing to macro- and microplastic pollution in agricultural soils. The adverse effects of this pollution on soil and plant health are not fully understood but may stem from the plastic particles or the toxicity of leached chemical additives. This study assessed the impact of macro- and microplastics from nondegradable LDPE-based (LDPEb) and biodegradable PBAT-based (PBATb) mulch films, along with their leachates, on the germination of three plant species. After seven days of incubation, PBAT mulch leached compounds that significantly inhibited Arabidopsis germination, while cotton and tomato exhibited notable tolerance. Notably, PBATb mulch released a higher concentration of compounds, whereas LDPEb mulch exhibited a greater diversity of leached chemicals. Microplastic particles alone did not hinder seed germination, indicating that plastic toxicity primarily arises from the leachates. Many of these leached compounds lack global regulation and hazard information, underscoring the urgent need for further investigation into their environmental impacts and the development of appropriate regulatory frameworks to mitigate the potential toxicity of chemicals from conventional and biodegradable mulches.", "keywords": ["Plastic mulch", "Toxicity", "ddc:550", "Microplastics", "Arabidopsis", "0211 other engineering and technologies", "Germination", "02 engineering and technology", "Plant health", "01 natural sciences", "Solanum lycopersicum", "Contaminants", "Seeds", "Life Science", "Soil Pollutants", "Environmental toxicology", "Plastics", "Water Pollutants", " Chemical", "Plastic additives", "0105 earth and related environmental sciences"]}, "links": [{"href": "https://doi.org/10261/393730"}, {"rel": "related", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/Journal%20of%20Hazardous%20Materials", "name": "related record", "description": "related record", "type": "application/json"}, {"rel": "self", "type": "application/geo+json", "title": "10261/393730", "name": "item", "description": "10261/393730", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main/items/10261/393730"}, {"rel": "collection", "type": "application/json", "title": "Collection", "name": "collection", "description": "Collection", "href": "https://repository.soilwise-he.eu/cat/collections/metadata:main"}], "time": {"date": "2024-12-01T00:00:00Z"}}, {"id": "10261/395709", "type": "Feature", "geometry": null, "properties": {"updated": "2026-07-25T16:24:46Z", "type": "Journal Article", "created": "2022-10-24", "title": "Regulation and Function of a Polarly Localized Lignin Barrier in the Exodermis", "description": "ABSTRACTMulticellular organisms control interactions with their environment through the development of specialized barriers in specific cell types. A conserved barrier in plant roots is the endodermal Casparian strip (CS). The CS is made of polymerized lignin and forms a ring-like structure that seals the apoplastic space between the endodermal cells. Most angiosperms also have another root cell type, the exodermis, that is reported to form a barrier. Our understanding of exodermal developmental and molecular regulation, as well as function, is limited as this cell type is absent from the model speciesArabidopsis thaliana. Using tomato (Solanum lycopersicum) as a model system we demonstrate that in this species, the exodermis does not form a CS. Instead, it forms a polar lignin cap with an equivalent barrier function to the endodermal CS. We demonstrate that although endodermal regulators are conserved between Arabidopsis and tomato, exodermal differentiation occurs by a distinct regulatory pathway involving theSlSCZandSlEXO1transcription factors. Although the exodermis and endodermis both produce barriers that restrict mineral ion uptake, they have unique and overlapping roles in their selectivity. Whether conservation and similarities between the endodermis and exodermis exist in other species remains to be determined. Nonetheless, in tomato, these distinct lignin structures have a convergent function with different genetic regulations.Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.Abstract
Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (
Tomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000\uffe2\uff80\uff931700\uffc2\uffa0nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390\uffe2\uff80\uff931420\uffc2\uffa0nm contributes most to the model\uffe2\uff80\uff99s final decision.Plant roots integrate environmental signals and developmental programs using exquisite spatiotemporal control. This is apparent in the deposition of suberin, an apoplastic diffusion barrier, which regulates the entry and exit of water, solutes and gases, and is environmentally plastic. Suberin is considered a hallmark of endodermal differentiation, but we find that it is absent in the tomato endodermis during normal development. Instead, suberin is present in the exodermis, a cell type that is absent in the model organismArabidopsis thaliana. Here, we uncover genes driving exodermal suberization and describe its effects on drought responses in tomato, unravelling the similarities and differences with the paradigmatic Arabidopsis endodermis. Cellular resolution imaging, gene expression, and mutant analyses reveal loss of this program from the endodermis, and its co-option in the exodermis. Functional genetic analyses of the tomato MYB92 transcription factor and ASFT enzyme demonstrate the importance of exodermal suberin for a plant water-deficit response. Controlling the degree of exodermal suberization could be a new strategy for breeding climate-resilient plants.Abstract
Background The plant phyllosphere is a well-studied habitat characterized by low nutrient availability and high community dynamics. In contrast, plant trichomes, known for their production of a large number of metabolites, are a yet unexplored habitat for microbes. We analyzed the phyllosphere as well as trichomes of two tomato genotypes (
Tomato is an important commercial product which is perishable by nature and highly susceptible to fungal incidence once it is harvested. Not all tomatoes are equally vulnerable to pathogenic fungi, and an early detection of the vulnerable ones can help in taking timely preventive actions, ranging from isolating tomato batches to adjusting storage conditions, but also in making right business decisions like dynamic pricing based on quality or better shelf life estimate. More importantly, early detection of vulnerable produce can help in taking timely actions to minimize potential post-harvest losses. This paper investigates Near-infrared (NIR) hyperspectral imaging (1000\uffe2\uff80\uff931700\uffc2\uffa0nm) and machine learning to build models to automatically predict the susceptibility of sepals of recently harvested tomatoes to future fungal infections. Hyperspectral images of newly harvested tomatoes (cultivar Brioso) from 5 different growers were acquired before the onset of any visible fungal infection. After imaging, the tomatoes were placed under controlled conditions suited for fungal germination and growth for a 4-day period, and then imaged using normal color cameras. All sepals in the color images were ranked for fungal severity using crowdsourcing, and the final severity of each sepal was fused using principal component analysis. A novel hyperspectral data processing pipeline is presented which was used to automatically segment the tomato sepals from spectral images with multiple tomatoes connected via a truss. The key modelling question addressed in this research is whether there is a correlation between the hyperspectral data captured at harvest and the fungal infection observed 4 days later. Using 10-fold and group k-fold cross-validation, XG-Boost and Random Forest based regression models were trained on the features derived from the hyperspectral data corresponding to each sepal in the training set and tested on hold out test set. The best model found a Pearson correlation of 0.837, showing that there is strong linear correlation between the NIR spectra and the future fungal severity of the sepal. The sepal specific predictions were aggregated to predict the susceptibility of individual tomatoes, and a correlation of 0.92 was found. Besides modelling, focus is also on model interpretation, particularly to understand which spectral features are most relevant to model prediction. Two approaches to model interpretation were explored, feature importance and SHAP (SHapley Additive exPlanations), resulting in similar conclusions that the NIR range between 1390\uffe2\uff80\uff931420\uffc2\uffa0nm contributes most to the model\uffe2\uff80\uff99s final decision.