Humic acids (HA) derived from biomass residues are increasingly recognized as biostimulants that enhance nutrient uptake and plant growth. However, genotype-dependent responses under contrasting phosphorus conditions remain insufficiently understood. In this study, HA was extracted from sugarcane filter cake, a by-product of the bioenergy sector, representing a sustainable valorization pathway for agro-industrial residues. Phosphate uptake kinetics, biomass responses, and expression of the high-affinity phosphate transporter gene LePT1 were investigated in four tomato genotypes differing in hormonal background: wild-type (Micro-Tom), auxin-insensitive (MT-dgt), cytokinin-related, and strigolactone-deficient (CCD7). Plants were grown under contrasting phosphorus supply (−P, +P) with or without HA.Kinetic analyses revealed a biphasic phosphate uptake pattern, with a rapid high-affinity phase followed by saturation. HA slightly increased the maximum uptake rate (Vmax) without altering affinity (Km), indicating a transient enhancement of uptake capacity rather than a change in transporter properties. Growth responses were genotype-dependent. In wild-type plants, HA stimulated root biomass under low phosphorus conditions, whereas the auxin-insensitive MT-dgt mutant showed limited responsiveness, indicating that responsiveness to HA differed among genotypes with contrasting hormonal backgrounds. The cytokinin-related genotype exhibited shoot-biased growth under HA, particularly under high phosphorus, while the strigolactone-deficient CCD7 mutant showed shifts in biomass allocation.Factorial ANOVA of LePT1 expression revealed a strong genotype effect, while phosphate supply alone was not significant. A significant genotype × HA interaction indicated genotype-specific differences in LePT1 expression responses. Overall, sugarcane filter cake-derived HA influenced phosphorus acquisition and growth responses in a genotype-dependent manner, supporting its potential use as a bio-based amendment within circular bioeconomy frameworks, supporting its role in sustainable nutrient management within circular bioeconomy frameworks.

Natural variation in SlAMT1.1 among wild tomatoes may influence post-translational regulation, allowing sustained ammonium uptake under high N supply and providing alleles that can be employed to improve N uptake efficiency in crops. Cultivated plants, particularly tomato (Solanum lycopersicum), require substantial nitrogen (N) inputs to achieve high commercial yields. This demand often leads to the excessive application of costly N-based fertilizers during cultivation. Wild tomato species represent valuable genetic resources for enhancing N uptake efficiency. In many plants, ammonium is the preferred N source, transported by proteins of the AMMONIUM TRANSPORTERS (AMT) family. Here, we characterized the extensive genetic diversity of an AMT1.1 ortholog across both cultivated and distantly related wild tomato species. Phylogenetic and diversity analyses revealed marked divergence in the SlAMT1.1 sequence between cultivated tomato accessions and wild Solanum (section Lycopersicon) species. Comparative analyses of SlAMT1.1 alleles from the Arcanum and Neolycopersicon groups showed enhanced uptake of 15N-labeled ammonium in roots under repressive ammonium resupply conditions. Notably, we found that the feedback inhibition of ammonium uptake, typical in domesticated tomato roots, was lost in these wild accessions, indicating the presence of a novel regulatory mechanism that adjusts uptake capacity across a wide range of ammonium availability. Our findings indicate that variation in the SlAMT1.1 gene largely explains the observed differences in ammonium uptake between domesticated tomatoes and their wild relatives. Therefore, the natural genetic variation present in the wild tomato SlAMT1.1 alleles offers valuable potential for genomic-based breeding strategies to sustainably improve ammonium uptake in crops.

Anthocyanins are specialized plant metabolites with significant dietary value due to their anti-inflammatory properties. Research indicates that dietary intake of these phenolic compounds contributes to preventing various chronic diseases. As the most consumed vegetable worldwide, tomato (Solanum lycopersicum) is an excellent candidate for anthocyanin-enrichment strategies. In tomato, the activation of anthocyanin biosynthesis is light-dependent, but this mechanism has yet to be entirely characterized. We investigated the role of light in anthocyanin biosynthesis in purple tomato fruits generated by combining the Anthocyanin fruit (Aft), atroviolacea (atv), and high-pigment 2 (hp2) mutations into cv. Micro-Tom (MT). MT-Aft/atv/hp2 starts accumulating anthocyanins early during fruit development, but this accumulation is restricted to the peel (exocarp and epicarp). By manipulating light incidence in different fruit tissues, we determined that the absence of anthocyanin accumulation in the flesh results from the sun-blocking effect of the cyanic epicarp on the flesh (mesocarp), thus preventing light from penetrating deeper into the fruits. Comparative transcriptional analyses of the fruit peel and flesh indicated that the bHLH transcription factor SlAN1 (Solyc09g065100) may be the limiting factor for light-dependent anthocyanin accumulation in both tissues. This research enhances our comprehension of the genetic and environmental regulation of anthocyanin accumulation in fruit tissues, offering valuable insights into plant breeding for human nutrition.

Anthocyanins are widespread specialized metabolites that provide pigmentation and antioxidant capacity, contributing to pollinator and seed-disperser attraction and to plant resistance to diverse environmental stresses. In human diets, anthocyanins are valued for their antioxidant and health-promoting properties. The biosynthetic pathway of anthocyanins is relatively conserved across plant species and is controlled by structural genes that encode the enzymes of the pathway along with regulatory genes, particularly transcription factors. This network integrates developmental and environmental signals, with light serving as a dominant cue: anthocyanins typically accumulate in light-exposed tissues and are repressed in darkness. A key node in this light-dependent switch is CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase that, in the dark, promotes polyubiquitination and proteasome-mediated turnover of positive regulators of anthocyanin production. Although ELONGATED HYPOCOTYL 5 (HY5) is a canonical COP1 target and major activator of anthocyanin biosynthesis, COP1 control of this pathway extends well beyond HY5. Evidence from Arabidopsis and multiple horticultural crops, including apple, pear, eggplant, and tomato, indicates that COP1 also regulates anthocyanin accumulation through interactions with additional transcription factors and regulatory modules. Here, we synthesize recent advances in COP1-centered regulation of anthocyanin biosynthesis, with an emphasis on post-translational mechanisms and COP1 targets beyond HY5. We also discuss emerging opportunities to leverage this regulatory axis for nutritional improvement in horticultural species.

The Anaphase-Promoting Complex/Cyclosome (APC/C) is an E3 ubiquitin ligase that plays a crucial role in ubiquitin-dependent proteolysis of key cell cycle regulators, which is completed by the 26S proteasome. Previously, SAMBA, a plant-specific regulator of the APC/C, was identified in Arabidopsis as a critical factor controlling organ size through the regulation of cell proliferation. Here, by assessing its role in the crop tomato (Solanum lycopersicum), we confirm that SAMBA is a conserved APC/C regulator in plants and shows additional roles, including the modulation of fruit shape and changes in sugar metabolism. Two slsamba genome-edited lines were produced and characterized, and showed delayed growth, reduced plant size, and altered fruit morphology, which were linked to changes in cell division and expansion. Notably, untargeted metabolomics revealed altered flavonoid profiles, along with elevated Brix values in the fruits, indicating a sweeter taste. Accordingly, transcriptomics uncovered a change in temporal gene expression gradients during early fruit development, correlating with the alterations in sugar metabolism and revealing changes in cell wall biosynthesis genes. This study provides the first evidence of SAMBA's role in regulating fruit development, metabolic content, and ultimately, quality. These important findings offer potential applications for improving the nutritional quality and overall performance of tomatoes.

Timely initiation of fruit ripening is crucial for improving agricultural efficiency and shelf life. While the progression of tomato ripening and the roles of ethylene and its core transcriptional controls are well established from the breaker (BR) stage onwards, the molecular mechanisms that fine-tune the transition from fruit development to ripening remain poorly understood. In this study, we identified a previously uncharacterized NAC transcription factor (TF), Ripening Accelerator (RAR), as a key negative modulator of climacteric ripening onset. In fruit, RAR is highly expressed at the mature green (MG) stage and downregulated at BR stage, preceding the climacteric ethylene burst. Silencing RAR via RNA interference significantly accelerated fruit ripening and ethylene production prior to BR stage, especially under high light conditions. RAR directly represses ACC Synthase 2 (ACS2), a key ethylene biosynthesis gene. Although RAR can form a heterodimer with the ripening-promoting NAC TF Non-Ripening (NOR), this heterodimer exhibits weaker transcriptional activation than the NOR homodimer, indicating a repressive effect of RAR on NOR-mediated activation. Moreover, RAR expression is negatively regulated by ethylene, forming a feedback loop that modulates the timing of ripening onset. Our findings uncover a previously unrecognized regulatory checkpoint in the ripening program, where RAR probably acts as a developmental safeguard to prevent premature ripening. Targeted manipulation of RAR offers a promising strategy for fine-tuning ripening onset and improve postharvest fruit quality across diverse environmental conditions.

Model organisms have been instrumental in advancing discoveries in plant biology. Tomato (Solanum lycopersicum) is distinguished as a prominent model system due to its well-characterized genetics and economic significance as a crop. Micro-Tom (MT), an ornamental dwarf tomato variety, was adopted by the tomato research community as a model plant due to its short stature, fast life cycle, ease of genetic transformation, and ample genomic resources. Over the last 30 years, the use of MT has illuminated various facets of plant development, including the control of growth habit, glandular trichomes, leaf anatomy, and the formation of arbuscular mycorrhizal symbioses. We briefly summarize these contributions and point to further potential advances in the future.

Type-IV glandular trichomes, which only occur in the juvenile phase of tomato development, produce acylsugars (AS) that broadly protect against arthropod herbivory. Previously, we introgressed the capacity to retain type-IV trichomes in the adult phase from Solanum galapagense into the cv. Micro-Tom (MT). The resulting MT- Get line contained five loci associated with enhancing the density of type-IV trichomes in adult plants. We genetically dissected MT- Get and obtained a sub-line containing only the locus on chromosome 2 (MT- Get02 ). This genotype displayed about half the density of type-IV trichomes compared to the wild progenitor. However, when we stacked the gain-of-function allele of WOOLLY , which codes for a HD-ZIP IV transcription factor, MT- Get02/Wo exhibited double the number of type-IV trichomes compared to S. galapagense . This discovery corroborates previous reports positioning WOOLLY as a master regulator of trichome development. AS levels in MT- Get02/Wo were comparable to the wild progenitor, although the composition of AS types differed, especially regarding less AS with medium-length acyl chains. Agronomical parameters of MT- Get02/Wo , including yield, were comparable to MT. Pest resistance assays showed enhanced protection against whitefly, caterpillar, and the fungus Septoria lycopersici . However, resistance levels did not reach that of the wild progenitor, suggesting the specificity of particulars AS types in the pest resistance mechanism. Our findings in trichome-mediated resistance advance the development of robust, naturally resistant tomato varieties, harnessing the potential of natural genetic variation. Moreover, by manipulating only two loci, we achieved exceptional results for a highly complex, polygenic trait, such as herbivory resistance in tomato.

Anthocyanins are specialized plant metabolites with significant dietary value due to their anti-inflammatory properties. Research indicates that dietary intake of these phenolic compounds contributes to preventing various chronic diseases. As the most consumed vegetable worldwide, tomato ( Solanum lycopersicum ) is an excellent candidate for anthocyanin-enrichment strategies. In tomato, activation of anthocyanin biosynthesis is light-dependent, but this mechanism has yet to be entirely characterized. We investigated the role of light in anthocyanin biosynthesis in fruits of the purple tomato, which is a near-isogenic line (NIL) derived from wild accessions into cv. Micro-Tom (MT). MT- Aft/atv/hp2 starts accumulating anthocyanin early during fruit development but is restricted to the peel (exocarp and epicarp). Manipulating light incidence in different fruit tissues determined that the absence of anthocyanin accumulation in the flesh results from the sun-blocking effect of the cyanic epicarp on the mesocarp, thus preventing light from penetrating deeper into the fruit. Transcriptional analyses of the fruit peel and flesh revealed that the bHLH transcription factor SlAN1 (Solyc09g065100) is the limiting factor for light-dependent anthocyanin accumulation in both tissues. This research enhances our comprehension of the genetic and environmental regulation of anthocyanin accumulation in fruit tissues, offering valuable insights into plant breeding for human nutrition.Highlight The expression of the SlAN1 gene is activated in response to light signals, and it is the limiting factor for anthocyanin pigmentation in tomato fruit tissues.### Competing Interest StatementThe authors have declared no competing interest.

Fruit morphogenesis is determined by the coordination of cell division and expansion, which are fundamental processes required for the development of all plant organs. Here, we show that the regulation of TEOSINTE BRANCHED1/CYCLOIDEA/PCF (TCP) LANCEOLATE (TCP2/LA) by miR319 is crucial for tomato fruit morphology. The loss of miR319 regulation in the semi-dominant La mutant led to a premature SlTCP2/LA expression during gynoecium patterning, which results in modified cell division during carpel development. As a consequence, La mutants exhibited elongated ovary and fruit shape, and a reduced number of ovules and seeds. Elongated fruit shape in La may be partially due to the SlTCP2/LA-mediated repression of OVATE activity in young floral buds. Further analysis showed that the de-repression of SlTCP2/LA decreases auxin responses in young floral buds by directly repressing SlYUCCA4 expression, but SlTCP2/LA also acts in parallel with ENTIRE (E) to orchestrate fruit morphology and seed production. Our study defines a novel miRNA-based molecular link between the domestication-associated OVATE gene and auxin responses. Given the striking variation in fruit morphology among members of the Solanaceae family, fine-tuning regulation of gene expression by miRNA coupled with modulation of auxin dynamics may be a common driver in the evolution of fruit shape diversity.

The advent of highly efficient genome editing (GE) tools, coupled with high-throughput genome sequencing, has paved the way for the accelerated domestication of crop wild relatives. New crops could thus be rapidly created that are well adapted to cope with drought, flooding, soil salinity, or insect damage. De novo domestication avoids the complexity of transferring polygenic stress resistance from wild species to crops. Instead, new crops can be created by manipulating major genes in stress-resistant wild species. However, the genetic basis of certain relevant domestication-related traits often involve epistasis and pleiotropy. Furthermore, pan-genome analyses show that structural variation driving gene expression changes has been selected during domestication. A growing body of work suggests that the Solanaceae family, which includes crop species such as tomatoes, potatoes, eggplants, peppers, and tobacco, is a suitable model group to dissect these phenomena and operate changes in wild relatives to improve agronomic traits rapidly with GE. We briefly discuss the prospects of this exciting novel field in the interface between fundamental and applied plant biology and its potential impact in the coming years.

Plants display tremendous chemical diversity. Like all organisms, they possess a core set of metabolites for growth and development. However, plants are notorious for their specialized chemical repertoire. Biologically active specialized metabolites enable plants to interact with their environment and provide humans with diverse medicines. Specialized metabolites are derived from core metabolites, often using enzymes that evolved from core pathways in a lineage-specific manner. Biochemical understanding of plant specialized metabolic pathways provides insight into the evolutionary origins of chemical diversity and tools for engineering the production of biologically active metabolites. Acylsugars are a class of specialized metabolites occurring widely in the Solanaceae and other plant families where they contribute to fitness. Although assembled from simple core metabolic precursors, sugars and acyl chains, tremendous acylsugar structural diversity is observed across the Solanaceae family. Enzymes that catalyze the esterification of acyl chains to sugar cores have been well characterized from phylogenetically diverse species, and their biochemical diversity contributes to acylsugar structural variation. The upstream metabolic pathways that provide the acyl chain precursors also contribute to acylsugar structural variation. Yet, biochemical and genetic understanding of these upstream biosynthetic pathways is less well known. Here, we focus on recent advances in acyl chain biosynthesis and elongation pathways, the subcellular distribution of acylsugar biosynthesis, and how biochemical innovations in acylsugar biosynthesis contribute to structural diversity specifically focusing on Solanaceae-type acylsugars.

Intensive agriculture maintains high crop yields through chemical inputs, which are well known for their adverse effects on environmental quality and human health. Innovative technologies are required to reduce the risk generated by the extensive and harmful use of pesticides. The plant biostimulants made from humic substances isolated from recyclable biomass offer an alternative approach to address the need for replacing conventional agrochemicals without compromising the crop yield. The stimulatory effects of humic substances are commonly associated with plant hormones, particularly auxins. However, jasmonic acid (JA) is crucial metabolite in mediating the defence responses and governing plant growth and development. This work aimed to evaluate the changes in the biosynthesis and signalling pathway of JA in tomato seedlings treated with humic acids (HA) isolated from vermicompost. We use the tomato model system cultivar Micro-Tom (MT) harbouring a reporter gene fused to a synthetic promoter that responds to jasmonic acid (JERE::GUS). The transcript levels of genes involved in JA generation and activity were also determined using qRT-PCR. The application of HA promoted plant growth and altered the JA status, as revealed by both GUS and qRT-PCR assays. Both JA enzymatic synthesis (LOX, OPR3) and JA signalling genes (JAZ and JAR) were found in higher transcription levels in plants treated with HA. In addition, ethylene (ETR4) and auxin (ARF6) signalling components were positively modulated by HA, revealing a hormonal cross-talk. Our results prove that the plant defence system linked to JA can be emulated by HA application without growth inhibition.

BACKGROUND AND AIMS:Gigantism is a key component of the domestication syndrome, a suite of traits that differentiates crops from their wild relatives. Allometric gigantism is strongly marked in horticultural crops, causing disproportionate increases in the size of edible parts such as stems, leaves or fruits. Tomato (Solanum lycopersicum) has attracted attention as a model for fruit gigantism, and many genes have been described controlling this trait. However, the genetic basis of a corresponding increase in size of vegetative organs contributing to isometric gigantism has remained relatively unexplored. METHODS:Here, we identified a 0.4-Mb region on chromosome 7 in introgression lines (ILs) from the wild species Solanum pennellii in two different tomato genetic backgrounds (cv. 'M82' and cv. 'Micro-Tom') that controls vegetative and reproductive organ size in tomato. The locus, named ORGAN SIZE (ORG), was fine-mapped using genotype-by-sequencing. A survey of the literature revealed that ORG overlaps with previously mapped quantitative trait loci controlling tomato fruit weight during domestication. KEY RESULTS:Alleles from the wild species led to lower cell number in different organs, which was partially compensated by greater cell expansion in leaves, but not in fruits. The result was a proportional reduction in leaf, flower and fruit size in the ILs harbouring the alleles from the wild species. CONCLUSIONS:Our findings suggest that selection for large fruit during domestication also tends to select for increases in leaf size by influencing cell division. Since leaf size is relevant for both source-sink balance and crop adaptation to different environments, the discovery of ORG could allow fine-tuning of these parameters.

S-Nitrosoglutathione plays a central role in nitric oxide (NO) homeostasis, and S-nitrosoglutathione reductase (GSNOR) regulates the cellular levels of S-nitrosoglutathione across kingdoms. Here, we investigated the role of endogenous NO in shaping shoot architecture and controlling fruit set and growth in tomato (Solanum lycopersicum). SlGSNOR silencing promoted shoot side branching and led to reduced fruit size, negatively impacting fruit yield. Greatly intensified in slgsnor knockout plants, these phenotypical changes were virtually unaffected by SlGSNOR overexpression. Silencing or knocking out of SlGSNOR intensified protein tyrosine nitration and S-nitrosation and led to aberrant auxin production and signaling in leaf primordia and fruit-setting ovaries, besides restricting the shoot basipetal polar auxin transport stream. SlGSNOR deficiency triggered extensive transcriptional reprogramming at early fruit development, reducing pericarp cell proliferation due to restrictions on auxin, gibberellin, and cytokinin production and signaling. Abnormal chloroplast development and carbon metabolism were also detected in early-developing NO-overaccumulating fruits, possibly limiting energy supply and building blocks for fruit growth. These findings provide new insights into the mechanisms by which endogenous NO fine-tunes the delicate hormonal network controlling shoot architecture, fruit set, and post-anthesis fruit development, emphasizing the relevance of NO-auxin interaction for plant development and productivity.

Phytophthora infestans causes the destructive late blight disease in tomato and its control is achieved mainly by fungicides. Resistance inducers such as potassium phosphite (KPhi) represent an environmentally friendly alternative for control. The effect of KPhi on disease severity and on the activity of antioxidant enzymes was investigated in wild-type (WT) Micro-Tom plants and mutant/transgenic genotypes were used to determine the hormonal pathways required for resistance. KPhi presented a systemic action and reduced disease severity up to 86% depending on the mode (foliar spray or irrigation) and time of application (3 or 7 days before inoculation). The compound reduced the concentration of phenolics and altered the activity of antioxidant enzymes, notably of catalase, whose activity was reduced even before pathogen inoculation, indicating a physiological effect. In addition, KPhi was toxic to the pathogen in an in vitro assay. Disease severity on plants that overproduce ethylene, are insensitive to brassinosteroid (BR) or do not accumulate salicylic acid was higher than in the WT, revealing that these hormonal pathways are involved in the reaction to P. infestans. The results indicate a possible mode of action of KPhi through the early accumulation of H2O2 and interplay with the salicylic acid pathway. This is the first report on the involvement of BR against this pathogen and the results point to a positive effect on resistance. This study extends the understanding of the role of KPhi as a disease control agent, confirming it as a good option to be used in the management of late blight.

ABSTRACT Many developmental processes associated with fruit development take place at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GA) interact to control flowering time, but their interplay in subsequent stages of reproductive development is poorly understood. Here, we show that GA and miR156 function in tomato FM and fruit patterning. High GA responses or overexpression of miR156 (156OE), which leads to low levels of miR156-targeted SQUAMOSA PROMOTER BINDING PROTEIN– LIKE ( SPL/SBP ), resulted in enlarged FMs, defects in FM determinacy and fruits with increased locule number. Conversely, low GA responses reduced fruit indeterminacy and locule number, and overexpression of a miR156-resistant SlSBP15 allele ( rSBP15 ) reduced cell number and size in the FM, as well as locule number. GA responses were partially required for the fruit defects observed in 156OE and rSBP15 plants. Transcriptome analysis and genetic interactions revealed shared and divergent functions of miR156-targeted SlSBPs, PROCERA/DELLA and the classical WUSCHEL/CLAVATA pathway, which has been previously associated with meristem size and determinacy. Our findings reveal that the miR156/ SlSBP /GA regulatory module is deployed differently depending on developmental stage and create novel opportunities to genetically fine-tune aspects of fruit development that have been important for tomato domestication.

Many developmental processes associated with fruit development occur at the floral meristem (FM). Age-regulated microRNA156 (miR156) and gibberellins (GAs) interact to control flowering time, but their interplay in subsequent stages of reproductive development is poorly understood. Here, in tomato (Solanum lycopersicum), we show that GA and miR156-targeted SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL or SBP) genes interact in the tomato FM and ovary patterning. High GA responses or overexpression of miR156 (156OE), which leads to low expression levels of miR156-silenced SBP genes, resulted in enlarged FMs, ovary indeterminacy and fruits with increased locule number. Conversely, low GA responses reduced indeterminacy and locule number, and overexpression of a S. lycopersicum (Sl)SBP15 allele that is miR156 resistant (rSBP15) reduced FM size and locule number. GA responses were partially required for the defects observed in 156OE and rSBP15 fruits. Transcriptome analysis and genetic interactions revealed shared and divergent functions of miR156-targeted SlSBP genes, PROCERA/DELLA and the classical WUSCHEL/CLAVATA pathway, which has been previously associated with meristem size and determinacy. Our findings reveal that the miR156/SlSBP/GA regulatory module is deployed differently depending on developmental stage and create novel opportunities to fine-tune aspects of fruit development that have been important for tomato domestication.