Genetics and control of tomato fruit ripening and quality attributes

Strigolactone (GR24) regulates fruit ripening in yft3 tomatoes by altering ABA biosynthesis

Color development in tomato fruits is a key indicator of ripening, and is driven by complex hormonal and molecular interactions. The present study investigated the effects of exogenous treatment with abscisic acid (ABA), GR24 (a synthetic strigolactone analog), and water (ddH2O as control) on tomato fruit ripening, ethylene emission, carotenoid biosynthesis, ABA metabolism, and chromoplast development in yft3 and wild-type (WT cv. M82) tomato fruits at 35, 47, and 54 days post-anthesis (dpa). Results showed that GR24 significantly accelerated ripening in yft3, transitioning from green to deep orange at 54 dpa, whereas ABA had a moderate effect. In cv. M82, both treatments enhanced color development, leading to a deep red phenotype. GR24 increased ethylene emission and upregulated the expression of ethylene related genes (ACO1, ACS2/4), with yft3 showing increased sensitivity than cv. M82. Carotenoid profiling revealed higher lycopene and β-carotene contents in yft3, with GR24 enhancing β-carotene and lutein, whereas ABA increased lycopene. GR24 and ABA strongly induced the expression of carotenoid-related genes (CRTISO, PSY1, and CYCB), particularly in yft3 at 54 dpa. Moreover, ABA-content and the expression of genes involved in ABA biosynthesis (NCED, AAO), catabolism (CYP707A), conjugation (GT), and activation (BG) were significantly altered by ABA and GR24 treatments. Furthermore, ultrastructural analysis revealed that GR24 promoted plastoglobule formation and chromoplast differentiation, with yft3 exhibiting a stronger response than cv. M82. These findings highlight that GR24 plays vital roles in regulating tomato fruit ripening, ethylene biosynthesis, carotenoids accumulation, as well as ABA-metabolism, with implications for improving fruit quality in tomatoes.

Effect of the overexpression of the GGP1 gene on cell wall remodelling and redox state in the tomato fruit

Tomato fruit ripening is a complex physiological process that involves morphological, anatomical, biochemical, and molecular alterations. One of these changes occurring during ripening is the softening of the fruit, which is attributed to modifications in the biosynthesis and degradation of individual cell wall components, i.e. polysaccharides and proteoglycans. In addition, ripening is affected by redox processes, and interplay of the reactive oxygen species (ROS) and specific antioxidants, enzymes, ascorbate, and phenolic compounds. The present study aims to determine the impact of the overexpression of the GDP-l-galactose phosphorylase (GGP1) gene under the control of two fruit-specific promoters, namely PPC - phosphoenolpyruvate carboxylase and PG - polygalacturonase on cell wall properties, activities of H2O2-regulating enzymes and the abundance of phenolic compounds. PPC-GGP1 and PG-GGP1 transgenic lines revealed significant structural changes in fruit parenchyma, compared to wild type fruit, followed by a disturbance in the spatial distribution and molecular & chemical composition of homogalacturonans. In addition, cell wall-bound monolignol, p-coumaryl alcohol was higher in transgenic fruit compared with wild type ones. Lastly, the catalase and ascorbate peroxidase activities were lower in PPC-GGP1 fruits, indicating changes in the regulation of antioxidative defense during the ripening process of this line. These results suggest that overexpression of the GGP1 gene affects the cell wall remodelling and redox state in the red ripe tomato fruits.

Hydrogen-rich water enhances vegetable growth and fruit quality by regulating ascorbate biosynthesis

Under aerobic conditions, the growth and fruit quality of vegetable crops are significantly influenced by reactive oxygen species (ROS) metabolism. Hydrogen-rich water (HRW) has emerged as a promising tool for enhancing resistance to abiotic stresses and delaying postharvest ripening and senescence. However, the physiological response and adaptation mechanisms of vegetable crops to HRW remain rarely understood. This study explores the effects of low concentrations of HRW on the growth and physiological processes of lettuce, tomato, and cucumber. The results indicate that HRW enhances seedling vigor, boosts photosynthetic efficiency, and promotes biomass accumulation. Additionally, HRW-irrigated cucumber fruit showed a 15-20 % increase in vitamin C (ascorbic acid) content, a 10-15 % rise in soluble sucrose levels, and an increase in fruit weight and diameter by 25-35 % and 8-12 %, respectively. Transcriptomic analyses revealed variations in genes associated with carbon fixation in photosynthesis, glyoxylate and dicarboxylate metabolism, hormonal regulation, and phenylalanine metabolism. These findings illuminate the mechanisms behind improved antioxidant production and L-ascorbate biosynthesis. Notably, this marks the documented case of HRW irrigation enhancing natural antioxidants in fruits. Given the unique properties of hydrogen and the potential of HRW technology in horticultural industry, the findings of this study provide valuable insights into hydrogen's role in biological processes and its impact on vegetable crops production and fruit quality.

Autophagy plays a dual role in chromoplast transition and degradation and is essential for fruit coloration and ripening

The color of tomato fruits is determined by carotenoids. The process involves removing chloroplast-related components and the biogenesis of chromoplast membranes where carotenoids are stored, but how these events are coordinated is unknown. Here, we demonstrated that part of this mechanism involves macroautophagy/autophagy playing dual roles in chromoplast transition and degradation. We have used fluorescence lifetime imaging microscopy (FLIM) to show that autophagosomes containing chloroplast-derived-vesicles increased significantly during early fruit ripening, which is an essential part of a pathway to the formation of chromoplasts. Interestingly, we also showed that autophagy controls the degradation of the chromoplasts containing carotenoids at the late ripening stage through a process we named chromophagy. This affects fruit color and ABA levels, which were higher in autophagy mutants with a slower turnover of chromoplasts. We concluded that autophagy is a determinant of both fruit coloration and ripening through degrading different plastid-related cargo.Abbreviation: ABA: abscisic acid; ATG: autophagy related; AP: autophagosome; BR: breaker stage; BR + 3: 3 days after breaker stage; BR + 7: 7 days after breaker stage; CV: coefficient of variation; FLIM: fluorescence lifetime imaging microscopy; IG: immature green; LR: light red; MG: mature green; PDVs: plastid-derived-vesicles; RhB: rhodamine B; RNAi: RNA interference; RR: ripe red; TEM: transmission electron microscopy; WLL: white-light laser.

ENDOGLUCANASE SlCEL2 and EXPANSIN SlEXP1 synergistically affect cellulose degrading and tomato fruit softening

Delayed fruit softening in tomato (Solanum lycopersicum) is highly desirable for extending shelf life, facilitating long-distance transportation, and reducing post-harvest losses caused by mechanical damage. Fruit softening is a natural ripening process characterized by the increased expression of genes involved in cell wall modification, leading to the breakdown of cell wall polysaccharides and the gradual disintegration of cellular structure. The yft1 mutant (yellow-fruited tomato 1, originally designated n3122) exhibits inhibited ethylene production, preventing normal ripening and resulting in firmer fruit. Concurrently, yft1 shows significant downregulation of several genes associated with cell wall degradation, including endoglucanase SlCEL2 and EXPANSIN SlEXP1. Both genes exhibit similar expression patterns, peaking during ripening, suggesting their importance in fruit softening. To investigate this further, RNAi silencing lines targeting SlCEL2 and SlEXP1 were generated. The double mutant, slcel2 slexp1, displayed increased firmness at the red ripe stage (54 days post-anthesis, dpa), whereas the single mutants showed similar softening to the wild-type M82. Anatomical analysis at 54 dpa revealed enhanced cell wall structure, slightly increased cuticle thickness, and significantly higher pericarp cellulose content in slcel2 slexp1 compared to M82, slcel2, and slexp1. Furthermore, this study found that SlEXP1 expression was significantly upregulated in slcel2 fruit, compared to M82 (wild type), at 54 dpa. This suggests a compensatory transcriptional regulation between these two genes in tomato fruit, potentially aimed at maintaining normal softening during ripening. These findings demonstrate that SlCEL2 and SlEXP1 act synergistically in cellulose degradation during tomato ripening, and promoting fruit softening.

Melatonin suppresses ethylene biosynthesis by inhibiting transcription factor MdREM10 during apple fruit ripening

Ethylene, a plant hormone, is essential for apple (Malus domestica) ripening. The precise molecular mechanism by which melatonin (MT) influences ethylene biosynthesis during apple fruit ripening remains unclear. This study found that exogenous MT treatment inhibited ethylene production and postponed apple fruit ripening. The endogenous MT content of apple fruits exhibited an inverse correlation with ethylene production during fruit ripening, suggesting that MT functions as a ripening suppressor in apple fruits. MT treatment suppressed the expression of key ethylene biosynthesis genes, MdACS1 and MdACO1, during apple fruit ripening. MT treatment decreased the expression levels of transcription factors MdREM10 and MdZF32. MdREM10 binds to the MdERF3 promoter, enhancing its expression and subsequently promoting MdACS1 transcription. Furthermore, MdREM10 directly bound to the MdZF32 promoter, promoting its transcription. MdZF32 directly bound to the MdACO1 promoter, inducing its expression. The findings suggested that MT suppresses ethylene biosynthesis and fruit ripening by inhibiting MdREM10, which indirectly promotes MdACS1 transcription via MdERF3 upregulation, and MdACO1 transcription via MdZF32 upregulation.

Phosphorylation of the strawberry MADS-box CMB1 regulates ripening via the catabolism of abscisic acid

Research on the ripening of fleshy fruits has relied on techniques that measure transcriptional changes. How ripening is linked to posttranslational modifications such as protein phosphorylation remains less studied. Here, we characterize the MADS-box SEPALLATA 4 (SEP4) subfamily transcription factor FaCMB1, a key negative regulator controlling strawberry ripening, whose transcript and protein abundance decrease progressively with fruit development and are repressed by abscisic acid (ABA). Transient RNAi or overexpression of FaCMB1 significantly altered the fruit ripening process and affected the content of endogenous ABA and ripening-related quality. Transcriptome sequencing (RNA-seq) analysis suggested that manipulation of FaCMB1 expression levels affected the transcription of FaASR (ABA-, stress-, ripening-induced), while FaCMB1 can repress the gene expression of FaASR by directly binding to its promoter. Furthermore, FaASR inhibited the transcriptional activity of FaCYP707A4, a key ABA 8'-hydroxylase enzyme involved in ABA catabolism. We show that FaCMB1 can be phosphorylated by the kinase FaSTPK, and Phos-tag assays indicated that the phosphorylation level of FaCMB1 increases during fruit ripening. This phosphorylation of FaCMB1 affects the binding ability of FaCMB1 to the FaASR promoter and alleviates its transcriptional repression. In conclusion, we elucidated a feedback regulatory path involving FaCMB1-FaASR-FaCYP707A4-ABA. During the fruit ripening process, an increase in ABA content led to a decrease in FaCMB1 transcript and protein levels, which, combined with increased phosphorylation levels, collectively impaired the transcriptional repression of FaASR by FaCMB1. Meanwhile, the increased transcriptional level of FaASR further repressed the expression level of FaCYP707A4, leading to ABA accumulation and fruit ripening.

The effects of different light qualities on the growth and nutritional components of Pleurotus citrinopileatus

Light is one of the key factors affecting the flavor of edible fungi. Pleurotus citrinopileatus were planted in a growth chamber in order to investigate the effects of different LED lights on the growth and development. Five treatments were set up in the experiment, namely white light (CK, as control), pure green light (G), pure blue light (B), pure red light (R) and far-red light (Fr). The results showed that: (1) R or Fr treatment caused deformities in Pleurotus citrinopileatus, showing a soft stipe, thin pileus, and shallow color. Compared with the control, the stipe length of Pleurotus citrinopileatus significantly decreased by 12.52% under treatment B, while the stipe diameter, pileus diameter, and fruiting body weight significantly increased by 35.52%, 18.30%, and 23.66%, respectively (P < 0.05). The color of Pleurotus citrinopileatus was more plump under B treatment, among which the spectral color parameters C and Hue increased by 2.72% and 1.64%, respectively. (2) B increased the proportion of umami and sweet amino acids [(UAA+SAA)/TAA] while decreased that of bitter amino acids in total amino acids (BAA/TAA) in Pleurotus citrinopileatus relative to the control. In addition, except for B treatment, other treatments (G, R, Fr) significantly reduced the content of mushroom flavored amino acids (e.g., Asp and Glu). (3) B increased the odor activity value (OAV) of key aroma compounds in Pleurotus citrinopileatus compared with the other light qualities in this study, while R increased the OAV of 1-octen-3-ol and 1-octen-3-one. However, considering that mushrooms cannot grow normally under R treatment, this study recommended blue light as the main light quality for industrial production of Pleurotus citrinopileatus.

Two transcription factors play critical roles in mediating epigenetic regulation of fruit ripening in tomato

DNA methylation regulates fruit ripening in tomato, and disruption of the DNA demethylase DEMETER-LIKE 2 (DML2) results in genome-wide DNA hypermethylation and impaired ripening. We report here that the transcription factors Ripening Inhibitor (RIN) and FRUITFULL 1 (FUL1) play critical roles in mediating the effect of DNA methylation on tomato fruit ripening. RIN and FUL1 are silenced in dml2 mutant plants, and the defective ripening phenotype of dml2 is mimicked by the rin/ful1 double mutant. Restoration of RIN expression in dml2 partially rescues its ripening defects. DNA methylation controls ripening not only by regulating the expression of RIN and FUL1 but also by interfering with the genomic binding of RIN. In dml2 mutant plants, RIN cannot bind to some of its targets in vivo even though DNA methylation does not interfere with RIN binding in vitro; this inhibited binding in vivo is correlated with increased DNA methylation and histone H3 enrichment within 100 bp of the binding site. Our work uncovers the molecular mechanisms underlying DNA methylation control of fruit ripening in tomato.

Comparative Transcriptome Reveals Conserved Gene Expression in Reproductive Organs in Solanaceae

The Solanaceae family, which includes key crops such as tomato, pepper, eggplant, wolfberry, and groundcherry, is distinguished by its diversity of fruit types. However, the conservation of gene expression regulatory networks across different species remains poorly understood. This study utilizes comparative transcriptomics to analyze 293 transcriptome samples from 22 Solanaceae species, focusing on the expression profiles of reproductive organ (flower and fruit)-specific genes. Our results reveal evolutionary conservation in the expression patterns of these genes, particularly within regulatory pathways essential for plant reproduction. A detailed comparative analysis of gene expression patterns between tomato and pepper reveals common regulatory networks governing fruit development. Furthermore, through co-expression network analysis, we identified functional partners of YABBY in flower/fruit development and found that YABBY genes coordinate fruit development through spatiotemporal dynamic expression, shaping its regulatory role. These findings provide valuable insights that can guide future research on fruit development genes in Solanaceae species.

CsMYB1-CwINV6 Module Involves in the Promotion of Soluble Sugar Accumulation in Citrus Fruits Under Drought Stress

Drought can promote soluble sugar accumulation in fruits by increasing the fruit sink strength. Cell wall invertase (CwINV) plays a pivotal role in determining sink strength by regulating sucrose partitioning into the extracellular matrix. Research has demonstrated that drought stress significantly increases the transcript level of citrus CwINV6, but the transcriptional mechanisms governing its regulation under drought conditions remain elusive. In this study, we characterised the MYB transcription factor gene CsMYB1 from the citrus genome. CsMYB1 is localised in the cell nucleus, and CwINV6 is localised in the cell wall. Furthermore, the transcript levels of both CsMYB1 and CwINV6 significantly increased in 'Nanfeng' tangerine fruits (Citrus reticulata) in response to drought or ABA treatment. Transient overexpression of CsMYB1 or CwINV6 promoted the accumulation of glucose and fructose in 'Nanfeng' fruits. Conversely, transient VIGS of CsMYB1 or CwINV6 resulted in the opposite trend. Additionally, stable overexpression of CsMYB1 or CwINV6 significantly increased the soluble sugar content in the fruits of the 'Micro-Tom' tomato lines. Y1H and luciferase assays confirmed that CsMYB1 can bind to the CwINV6 promoter and positively regulate its expression. Taken together, our findings reveal that drought promotes soluble sugar distribution in citrus fruits by increasing sink strength via the CsMYB1-CwINV6 module.

Autophagy positively regulates ethylene-induced colouration in citrus fruits

Autophagy is an evolutionarily conserved process in eukaryotes that regulates metabolic reprogramming and organelle recycling in response to various environmental signals and developmental cues. However, little is known about its regulatory mechanism during fruit colouration and ripening, which also undergo dramatic metabolic and cellular alterations. Here, we demonstrate that the autophagy pathway is activated during citrus fruit colouration, and the colour transition of citrus fruit is significantly delayed when autophagy is blocked. Furthermore, we revealed that ethylene, a plant hormone crucial for citrus fruit colouration, activates the autophagy pathway through the ethylene-responsive factor, CsERF061. Further analysis revealed that CsERF061 directly binds to the promoter of CsATG8h and activates its expression, thereby promoting autophagy and fruit colouration, suggesting autophagy is a key determinant of citrus fruit colouration in response to ethylene. These findings enhance our understanding of fruit colouration and offer a potential method to improve citrus fruit colour and quality for future applications.

Visualizing the spatial distribution of metabolites in tomato fruit at different maturity stages by matrix-assisted laser desorption/ionization mass spectrometry imaging

Tomato is one of the highest-value fruit and vegetable crop worldwide, serving as an important source of micro-nutrients in the human diet. Understanding the spatial distribution changes of critical metabolites during fruit maturation is essential for investigating the physiological roles, nutritional value, and potential functional values of phytochemicals in tomato fruit. However, information on their spatial distribution remains limited. This study aimed to visualize the distribution differences of endogenous metabolites in tomatoes across four maturity stages (from green to red) using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). Relative quantification results showed that as the fruit ripened, levels of soluble sugars, amino acids and volatile organic compounds (VOCs) increased significantly at the red ripening stage, while L-hydroxysuccinic acid exhibited an opposite trend, and citric acid initially decreased, then increased. Mass spectrometry imaging revealed that soluble sugars, organic acids, and amino acids were evenly distributed throughout the fruit across all maturity stages. During maturation, nine VOCs transitioned from a widespread distribution in the flesh tissue to concentrating near the peel, suggesting that aromatic compounds predominantly localize in the fruit's outer regions at full maturity. Additionally, a colocalization phylogenetic tree was constructed based on the spatial distribution imaging of each metabolite. These findings provide a deeper understanding of the changes and distribution of phytochemicals during tomato fruit development, offering a scientific basis for breeding, utilization, and production strategies.

Chlorine Modulates Photosynthetic Efficiency, Chlorophyll Fluorescence in Tomato Leaves, and Carbohydrate Allocation in Developing Fruits

Chlorine (Cl) is an essential nutrient for higher plants, playing a critical role in their growth and development. However, excessive Cl application can be detrimental, leading to its limited use in controlled-environment agriculture. Recently, Cl has been recognized as a beneficial macronutrient, yet studies investigating its impact on plant growth and fruit quality remain scarce. In this study, we determined the optimal Cl concentration in nutrient solutions through a series of cultivation experiments. A comparative analysis of Cl treatments at 1, 2, and 3 mM revealed that 3 mM Cl- significantly enhanced chlorophyll content, biomass accumulation, and yield. Furthermore, we examined the effects of 3 mM Cl- (supplied as 1.5 mM CaCl2 and 3 mM KCl) on leaf photosynthesis, chlorophyll fluorescence, and fruit sugar metabolism. The results demonstrated that Cl- treatments enhanced the activity of Photosystem I (PS I) and Photosystem II (PS II), leading to a 25.53% and 28.37% increase in the net photosynthetic rate, respectively. Additionally, Cl- application resulted in a 12.3% to 16.5% increase in soluble sugar content in mature tomato fruits. During fruit development, Cl- treatments promoted the accumulation of glucose, fructose, and sucrose, thereby enhancing fruit sweetness and overall quality. The observed increase in glucose and fructose levels was attributed to the stimulation of invertase activity. Specifically, acidic invertase (AI) activity increased by 61.6% and 62.6% at the green ripening stage, while neutral invertase (NI) activity was elevated by 56.2% and 32.8% in the CaCl2 and KCl treatments, respectively, at fruit maturity. Furthermore, sucrose synthase (SS-I) activity was significantly upregulated by 1.5- and 1.4-fold at fruit maturity, while sucrose phosphate synthase (SPS) activity increased by 76.4% to 77.8% during the green ripening stage. These findings provide novel insights into the role of Cl- in tomato growth and metabolism, offering potential strategies for optimizing fertilization practices in protected horticulture.

Molecular breeding of tomato: Advances and challenges

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Characterization of a tomato chlh mis-sense mutant reveals a new function of ChlH in fruit ripening

Tomato fruit ripening is a complex developmental process that is important for fruit quality and shelf life. Many factors, including ethylene and several key transcription factors, have been shown to play important roles in the regulation of tomato fruit ripening. However, our understanding of the regulation of tomato fruit ripening is still limited. Here, we describe mut26, an EMS-induced tomato (Solanum lycopersicum) mutant that exhibits chlorophyll-deficient phenotypes in various organs, including fruits. Genetic mapping and functional analyses revealed that a single-nucleotide substitution and a corresponding Pro398->Ser mis-sense mutation in SlChlH (GENOMES UNCOUPLED 5, GUN5), which encodes the H subunit of magnesium chelatase, are responsible for the defects in the mut26 strain. Transcript analyses towards the expression of many SlPhANGs revealed that mut26 is defective in plastid retrograde signalling during tomato fruit ripening initiation, namely the transition from mature green to breaker stage. mut26 exhibits delayed progression of fruit ripening characterized by reduced fruit ethylene emission, increased fruit firmness, reduced carotenoid content and delayed plastid conversion from chloroplast to chromoplast. Given that fruit ripening requires signalling from plastids to nucleus, these data support the hypothesis that GUN5-mediated plastid retrograde signalling promotes tomato fruit ripening. We further showed that the delayed fruit ripening of mut26 is not likely caused by reduced chlorophyll content. Taken together, we identified a new function of SlChlH in the promotion of tomato fruit ripening and ethylene biosynthesis, suggesting that GUN5-mediated plastid retrograde signalling plays a promotive role in tomato fruit ripening.

Detecting the physiological and molecular mechanisms by which abscisic acid (ABA) regulates the consistency of sweet cherry fruit maturity

In the cultivation and production of sweet cherry, the cost of picking fruit is high due to inconsistency in the maturation period, which has affected the development of the cherry industry. In this study, the effects of exogenous abscisic acid (ABA) on the sweet cherry variety 'Luying 3' fruit quality and maturation stage were observed and recorded, and the physiological and molecular mechanisms were explored to systematically analyze the effects of ABA on sweet cherry fruit ripening to promote the development of the cherry industry. Exogenous ABA (400 mg L-1) enhanced the color of 'Luying 3' fruit in the developing stage but had no significant effect on the fruit weight, soluble solid content, titratable acid content, and sugar-acid ratio in the mature stage. The application of ABA significantly promoted the secretion of endogenous ABA, gibberellin (GA) and salicylic acid (SA). A total of 766 differentially expressed genes (DEGs) were obtained between the treatment group and the control group at 47 and 54 d after flowering. The DEGs were significantly enriched in plant hormone signal transduction pathway, MAPK plant signal transduction pathway and glycolysis pathway. Six genes related to the synthesis of endogenous hormones were screened, of which five were upregulated and one was downregulated. Four DEGs related to the sweet cherry fruit metabolic rate were upregulated by ABA, which positively regulated fruit ripening. Eight differentially expressed AP2/ERF transcription factors were identified, of which 5 were upregulated and 3 were downregulated. This study provides a theoretical foundation for the application of ABA in promoting the consistency of cherry fruit maturity.

Detection and comparative analysis of VOCs between tomato and pepper based on GC×GC-TOFMS

This study aimed to identify and compare the flavor substances in mature tomato and pepper fruits using flavoromics based on GC×GC-TOF-MS. A total of 1560 volatile substances were identified, including 627 tomato specific substances and 534 pepper specific substances. Esters were identified as the distinguishing factor in the aroma profiles of the two. ROAV, an effective flavor evaluation criterion, can help identify the main contributors to flavor that can be detected by the taste buds. VOCs with ROAV > 1 are typically regarded as the key flavor contributors. Interestingly, it was found that tomato and pepper shared three common VOCs (2-nonenal, (E)-; 2-octenal, (E)-; and furan, 2-pentyl-.), which exhibited higher ROAV in both. Except for the three common VOCs, heptanal; 2-dodecenal, (E)-; 1-octen-3-one; 2-undecanone in tomato and pyrazine, 2-methoxy-3-(2-methylpropyl)- in pepper were identified to be contributive to their corresponding aromatic flavor (ROVA > 1), respectively. The contents of 138 volatile metabolites differ between tomato and pepper. Among them, acetoin, dodecanal and 1-decanol demonstrated highest fold change (Log2FC > 10). The flavor wheel shows the most obvious flavor characteristic of both tomato and pepper is sweet flavor. In addition, green, fruity, herbal, woody and apple flavors are prominent in pepper, while waxy, citrus and fatty flavors are prominent in tomato.

Ethylene response factor SlERF.D6 promotes ripening in part through transcription factors SlDEAR2 and SlTCP12

Ripening is crucial for the development of fleshy fruits that release their seeds following consumption by frugivores and are important contributors to human health and nutritional security. Many genetic ripening regulators have been identified, especially in the model system tomato, yet more remain to be discovered and integrated into comprehensive regulatory models. Most tomato ripening genes have been studied in pericarp tissue, though recent evidence indicates that locule tissue is a site of early ripening-gene activities. Here, we identified and functionally characterized an Ethylene Response Factor (ERF) gene, SlERF.D6, by investigating tomato transcriptome data throughout plant development, emphasizing genes elevated in the locule during fruit development and ripening. SlERF.D6 loss-of-function mutants resulting from CRISPR/Cas9 gene editing delayed ripening initiation and carotenoid accumulation in both pericarp and locule tissues. Transcriptome analysis of lines altered in SlERF.D6 expression revealed multiple classes of altered genes including ripening regulators, in addition to carotenoid, cell wall, and ethylene pathway genes, suggesting comprehensive ripening control. Distinct regulatory patterns in pericarp versus locule tissues were observed, indicating tissue-specific activity of this transcription factor (TF). Analysis of SlERF.D6 interaction with target promoters revealed an APETALA 2/ETHYLENE RESPONSE FACTOR (AP2/ERF) TF (SlDEAR2) as a target of SlERF.D6. Furthermore, we show that a third TF gene, SlTCP12, is a target of SlDEAR2, presenting a tricomponent module of ripening control residing in the larger SlERF.D6 regulatory network.

Determining the function of ripening associated genes and biochemical changes during tomato (Solanum lycopersicum L.) fruit maturation

This article examines biochemical alterations and gene expression changes during tomato fruit physiology. The chroma index increases from mature green (41.27) to red ripe (48.36) stages, and the texture softens from mature green (43.56 N) to red ripe (24.75 N). Reducing sugar and total carotenoid levels rise at the red ripe stage. Free radical content was elevated in the early stages (7 nM) of ripening and declined at the later stages (4 nM). The specific activity of α-mannosidase and β-N-acetyl hexosaminidase was high at the breaker (0.077 & 0.075 U/mg, respectively) stages, while polygalacturonase activity was high at red ripe (1.173 U/mg) stage. qPCR experiments revealed that the α-mannosidase was upregulated during the breaker (1.2 fold) stages of tomato ripening, the β-N-acetyl Hexosaminidase was upregulated throughout the breaker (2 fold), and pink (1.2 fold) stages of tomato ripening, and the β-xylosidase was upregulated significantly during the breaker stage (3.9 fold) of tomato ripening. The current findings revealed that the α-Mannosidase (0.77), β-N-acetylhexosaminidase (0.99), xylosidase (0.85), ethylene-responsive factors (0.86), aminocylco propane carboxylic oxidase (0.90), and pectin methylesterase (0.83), were significantly associated with textural softening. Polygalacturonase (0.75) positively correlated to reducing sugar formation, aminocylco propane carboxylic synthase 4 (0.96) expression correlates with chroma changes during tomato fruit ripening. These correlations illustrate the complex interplay between gene expression and the physical and biochemical changes occurring during tomato fruit ripening.

The MADS-Box Transcription Factor CaRIN Positively Regulates Chlorophyll Degradation During Pepper (Capsicum annuum L.) Fruit Ripening by Repressing the Expression of CaLhcb-P4

Pepper (Capsicum spp.) is an important global vegetable and spice, with fruit color being a key determinant of its commercial quality. However, the regulatory mechanisms underlying pepper fruit color are still not fully understood. This study focuses on the MADS-RIPENING INHIBITOR (MADS-RIN), a MADS-box transcription factor that regulates various aspects of fruit ripening, including pigmentation. We identified CaRIN, a homolog of tomato's SlRIN, whose expression is closely associated with fruit ripening in pepper. Silencing CaRIN through virus-induced gene silencing (VIGS) resulted in increased chlorophyll and chlorophyll a content, reduced carotenoid accumulation, and uneven fruit coloration. Integrative analysis of the RNA-seq and DAP-seq data identified 77 target genes regulated by CaRIN, which was involved in processes such as chlorophyll metabolism and plant hormone signaling. Yeast one-hybrid (Y1H) and dual-luciferase (LUC) assays demonstrated that CaRIN directly bound to the promoter of CaLhcb-P4, repressing its expression. Downregulation of CaLhcb-P4 in pepper fruits via VIGS accelerated chlorophyll degradation. Additionally, CaRIN indirectly regulated multiple genes associated with chlorophyll and carotenoid metabolism, sugar transport, and cell wall degradation. These findings provide novel insights into the regulatory mechanisms of chlorophyll degradation during pepper fruit ripening, offering a foundation for further research and potential genetic improvement strategies.

A tomato ethylene-resistant mutant displays altered growth and higher β-carotene levels in fruit

The mutants resistant to ethylene are helpful in deciphering the role of ethylene in plant development. We isolated an ethylene-resistant tomato (Solanum lycopersicum) mutant by screening for acetylene-resistant (atr-1) seedlings. The atr-1 mutant displayed resistance to kinetin, suggesting attenuation of the ethylene sensing response. atr-1 also exhibited resistance to ABA- and glucose-mediated inhibition of seed germination. Unlike the Never-ripe (Nr) mutant seedlings that were hypersensitive to glucose, atr-1 seedlings were resistant to glucose, indicating ethylene sensing in atr-1 is compromised in a manner distinct from Nr. Metabolically, atr-1 seedlings had lower levels of amino acids but higher levels of several phytohormones, including ABA. atr-1 plants grew faster and produced more flowers, leading to a higher fruit set. However, the atr-1 fruits took a longer duration to reach the red-ripe (RR) stage. The ripened atr-1 fruits retained high β-carotene and lycopene levels post-RR stage and had longer on-vine longevity. The metabolome profiles of post-RR stage atr-1 fruits revealed increased levels of sugars. The atr-1 had a P279L mutation in the GAF domain of the ETR4, a key ethylene receptor regulating tomato ripening. The atr-1 exhibits phenotypic traits distinct from the Sletr4-1 (G154S) mutant, thus represents a new ETR4 allele named Sletr4-2. Our study highlights that novel alleles in ethylene receptors may aid in enhancing the nutritional quality of tomato.

Moderate salt stress aids in the enhancement of nutritional and flavor quality in tomato (Solanum lycopersicum L.) fruits

Salt stress has been found to enhance the quality of certain plants, yet its influence on fruit flavor remains largely unexplored. Our study probes the impact of salinity on the nutritional and flavor profile of tomatoes. Tomato plants were exposed to 0, 30, 50, 70, 90, and 110 mM of NaCl. Moderate salinity levels (50-70 mM) were found to boost the nutritional value of tomatoes, with increases in soluble solids, protein, and sugar levels. However, the concentration of key minerals such as K, Mg, and Mn declined with escalating salinity. Furthermore, the number of volatile compounds has increased, and the content of different types (alcohols, aldehydes, esters, etc.) has also significantly increased. Salinity stress also significantly influenced the levels of characteristic volatile compounds, especially hexanal, phenylethyl alcohol, and 6-methyl-5-hepten-2-one. Overall, these results will provide valuable strategies for producing high-quality tomatoes.

Cytokinin negatively regulates tomato fruit ripening by influencing the ethylene pathway

KEY MESSAGE

Reducing endogenous CK levels accelerates fruit ripening in tomato by regulating ethylene biosynthesis and signalling pathway. Tomato is a typical climacteric fruit and is recognized as one of the most important horticultural crops globally. The ripening of tomato fruits is a complex process, highly regulated by phytohormones. Cytokinin (CK) is a hormone that primarily impacts the early development of fruit, however its influence on fruit ripening has not been thoroughly investigated. In this study, we used both wild-type Micro-Tom and transgenic tomato plants that overexpress AtCKX2, a CK degradation gene driven by the fruit-specific promoter Tfm7, to investigate the effect of CK on tomato fruit ripening. Our findings revealed that reducing endogenous CK levels in transgenic plants can accelerate the ripening process of tomato fruits. Premature activation of ethylene biosynthetic genes and ripening regulator genes was upregulated in CK-deficient fruits. Moreover, the application of exogenous ethylene inhibitors resulted in delayed fruit ripening in CK-deficient fruits. These results together suggest that CK plays a negative role in tomato fruit ripening by affecting the ethylene pathway.

Ethylene Signaling in Regulating Plant Growth, Development, and Stress Responses

Ethylene is a gaseous plant hormone that plays a crucial role in coordinating various physiological processes in plants. It acts as a key mediator, integrating both endogenous developmental cues and external environmental signals to regulate a wide range of functions, including growth, fruit ripening, leaf abscission, and responses to stress. The signaling pathway is initiated when ethylene binds to its receptor. After decades of research, the key components of ethylene signaling have been identified and characterized. Although the molecular mechanisms of the sensing of ethylene signal and its transduction have been studied extensively, a new area of research is how respiration and epigenetic modifications influence ethylene signaling and ethylene response. Here, we summarize the research progress in recent years and review the function and importance of ethylene signaling in plant growth and stress responses. In addition, we also describe the current understanding of how epigenetic modifications regulate ethylene signaling and the ethylene response. Together, our review sheds light on the new signaling mechanisms of ethylene.

Vacuum-assisted headspace solid phase microextraction for monitoring ripening-induced changes in tomato volatile profile

This work proposes, for the first time, the use of vacuum-assisted headspace solid phase microextraction (Vac-HS-SPME) for studying the free volatiles in tomato fruits. Initially, a comparative optimization between Vac-HS-SPME and regular HS-SPME was conducted, examining the effects of sampling time (15-60 min) and temperature (40 and 60°C) on the extraction of 29 target compounds from tomato puree samples. Compared to regular HS-SPME, sampling under vacuum resulted in the detection of nine additional analytes at 40°C, and an extra three at 60°C. The optimized methods (45 minutes sampling with Vac-HS-SPME at 40°C and regular HS-SPME at 60°C) were then successfully applied for the semi-quantitative comparison of free volatiles during on-plant ripening. These studies revealed an increase in volatiles across the six ripening stages considered (mature green, breaker, turning, pink, light red and red ripe) that was dominated by aldehydes. Compared to HS-SPME, the optimized Vac-HS-SPME showed substantial improvement in extraction efficiencies, and enabled the detection of key volatiles at earlier ripening stages, such as the breaker and turning stages. Overall, compared to the regular method, this study demonstrated that Vac-HS-SPME is a powerful approach that provides additional insights on free volatiles in fruits, even when sampling at lower temperatures.

Overexpression of the persimmon ABA receptor DkPYL3 gene alters fruit development and ripening in transgenic tomato

Abscisic acid (ABA) is a crucial plant hormone that regulates various aspects of plant development. However, the specific function of the ABA receptor PYL in fruit development has not been fully understood. In this study, we focused on DkPYL3, a member of the ABA receptor subfamily Ⅰ in persimmon, which exhibited high expression levels in fruit, particularly during the young fruit and turning stages. Through yeast two-hybrid (Y2H), firefly luciferase complementation imaging (LCI), protein inhibition assays, and RNA-seq techniques, we identified and characterized the DkPYL3 protein, which was found to inhibit the activity of protein phosphatase type 2 C (PP2C). By heterologous overexpressing (OE) persimmon DkPYL3 in tomatoes, we investigated the impact of the DkPYL3 gene on fruit development and ripening. DkPYL3-OE upregulated the expression of genes related to chlorophyll synthesis and development, leading to a significant increase in chlorophyll content in young fruit. Several fruit quality parameters were also affected by DkPYL3 expression, including sugar content, single fruit weight, and photosynthesis rate. Additionally, fruits overexpressing DkPYL3 exhibited earlier ripening and higher levels of carotenoids and flavonoids compared to wild-type fruits. These results demonstrate the pivotal role of DkPYL3 in ABA-mediated young fruit development, ripening onset, and fruit quality in transgenic tomatoes.

Differential impact of impaired steryl ester biosynthesis on the metabolome of tomato fruits and seeds

Steryl esters (SE) are a storage pool of sterols that accumulates in cytoplasmic lipid droplets and helps to maintain plasma membrane sterol homeostasis throughout plant growth and development. Ester formation in plant SE is catalyzed by phospholipid:sterol acyltransferase (PSAT) and acyl-CoA:sterol acyltransferase (ASAT), which transfer long-chain fatty acid groups to free sterols from phospholipids and acyl-CoA, respectively. Comparative mass spectrometry-based metabolomic analysis between ripe fruits and seeds of a tomato (Solanum lycopersicum cv Micro-Tom) mutant lacking functional PSAT and ASAT enzymes (slasat1xslpsat1) shows that disruption of SE biosynthesis has a differential impact on the metabolome of these organs, including changes in the composition of free and glycosylated sterols. Significant perturbations were observed in the fruit lipidome in contrast to the mild effect detected in the lipidome of seeds. A contrasting response was also observed in phenylpropanoid metabolism, which is down-regulated in fruits and appears to be stimulated in seeds. Comparison of global metabolic changes using volcano plot analysis suggests that disruption of SE biosynthesis favours a general state of metabolic activation that is more evident in seeds than fruits. Interestingly, there is an induction of autophagy in both tissues, which may contribute along with other metabolic changes to the phenotypes of early seed germination and enhanced fruit tolerance to Botrytis cinerea displayed by the slasat1xslpsat1 mutant. The results of this study reveal unreported connections between SE metabolism and the metabolic status of plant cells and lay the basis for further studies aimed at elucidating the mechanisms underlying the observed effects.

Chloroplast Vesiculation and Induced Chloroplast Vesiculation and Senescence-Associated Gene 12 Expression During Tomato Flower Pedicel Abscission

Abscission is a tightly regulated process in which plants shed unnecessary, infected, damaged, or aging organs, as well as ripe fruits, through predetermined abscission zones in response to developmental, hormonal, and environmental signals. Despite its importance, the underlying mechanisms remain incompletely understood. This study highlights the deleterious effects of abscission on chloroplast ultrastructure in the cells of the tomato flower pedicel abscission zone, revealing spatiotemporal differential gene expression and key transcriptional networks involved in chloroplast vesiculation during abscission. Significant changes in chloroplast structure and vesicle formation were observed 8 and 14 h after abscission induction, coinciding with the differential expression of vesiculation-related genes, particularly with upregulation of Senescence-Associated Gene 12 (SAG12) and Chloroplast Vesiculation (CV). This suggests a possible vesicle transport of chloroplast degrading material for recycling by autophagy-independent senescence-associated vacuoles (SAVs) and CV-containing vesicles (CCVs). Ethylene signaling appears to be involved in the regulation of these processes, as treatment with a competitive inhibitor of ethylene action, 1-methylcyclopropene, delayed vesiculation, reduced the expression of SAG12, and increased expression of Curvature Thylakoid 1A (CURT1A). In addition, chloroplast vesiculation during abscission was associated with differential expression of photosynthesis-related genes, particularly those involved in light reactions, underscoring the possible functional impact of the observed structural changes. This work provides new insights into the molecular and ultrastructural mechanisms underlying abscission and offers potential new targets for agricultural or biotechnological applications.

DNA Methylation Is Crucial for 1-Methylcyclopropene Delaying Postharvest Ripening and Senescence of Tomato Fruit

DNA methylation is an epigenetic modification process that can alter the functionality of a genome. It has been reported to be a key regulator of fruit ripening. In this study, the DNA methylation changes of CpG islands of ethylene signaling genes regulated by 1-methylcyclopropene (1-MCP) during ripening and senescence of tomato fruit were detected. The results showed that the 1-MCP treatment decreased the accumulation of lycopene, maintained the content of vitamin C, and delayed the ripening and senescence of tomato fruit. The quantitative real-time PCR and bisulfite sequencing analysis showed that 1-MCP treatment changed the expression and the DNA methylation level of CpG islands related to the ethylene signaling pathway genes, among which the DNA methylation change of LeEIN3 was the most significant. Compared with the control, 1-MCP treatment increased the DNA methylation level of the CpG island of the LeEIN3 gene, reduced the expression of LeEIN3 in tomato fruit, and was involved in 1-MCP delaying the postharvest senescence of tomato fruit. The results indicated that DNA methylation changes of ethylene signaling genes were involved in ethylene synthesis and signal transduction and played an important role in the regulation of 1-methylcyclopropene, delaying postharvest ripening and senescence of tomato fruit.

An InDel variant in the promoter of the NAC transcription factor MdNAC18.1 plays a major role in apple fruit ripening

A complex regulatory network governs fruit ripening, but natural variations and functional differentiation of fruit ripening genes remain largely unknown. Utilizing a genome-wide association study (GWAS), we identified the NAC family transcription factor MdNAC18.1, whose expression is closely associated with fruit ripening in apple (Malus × domestica Borkh.). MdNAC18.1 activated the transcription of genes related to fruit softening (Polygalacturonase, PG) and ethylene biosynthesis (1-aminocyclopropane-1-carboxylic acid synthase, ACS), thereby promoting fruit ripening of apple and tomato (Solanum lycopersicum). There were two single-nucleotide polymorphisms (SNP-1,545 and SNP-2,002) and a 58-bp insertion-deletion (InDel-58) in the promoter region of MdNAC18.1. Among these, InDel-58 serves as the main effector in activating the expression of MdNAC18.1 and driving fruit ripening. InDel-58 determines the binding affinity of the class D MADS-box protein AGAMOUS-LIKE 11 (MdAGL11), a negative regulator of fruit ripening. The InDel-58 deletion in the early-ripening genotype reduces the inhibitory effect of MdAGL11 on MdNAC18.1. Moreover, MdNAC18.1 and its homologous genes originated from a common ancestor across 61 angiosperms, with functional diversification attributed to tandem replications that occurred in basal angiosperms. In summary, our study revealed how a set of natural variations influence fruit ripening and explored the functional diversification of MdNAC18.1 during evolution.

Protein phosphatase PP2C2 dephosphorylates transcription factor ZAT5 and modulates tomato fruit ripening

Although C2H2 zinc finger transcription factors are important in plant growth, development, and stress resistance, their specific roles in fruit ripening have been less explored. Here, we demonstrate that the C2H2 zinc finger transcription factor 5 (SlZAT5) regulates fruit ripening in tomato (Solanum lycopersicum L.). Overexpression of SlZAT5 delayed ripening, while its knockout accelerated it, confirming its role as a negative regulator. SlZAT5 functions as a transcriptional repressor by directly inhibiting ripening-related genes, including SlACS4, SlPL8, and SlGRAS38, thereby delaying ripening. Furthermore, SlZAT5 interacts with the type 2C protein phosphatase SlPP2C2, which regulates the repressor activity of SlZAT5 by dephosphorylating SlZAT5 at Ser-65. This interaction is crucial in modulating ethylene production, thereby influencing the ripening process. These findings reveal a regulatory function of SlZAT5 in tomato fruit development, offering insights into the SlZAT5-SlPP2C2 module and potential targets for genetic modification to improve fruit quality and extend fruit shelf life.

Tomato MADS-RIN regulates GAME5 expression to promote non-bitter glycoalkaloid biosynthesis in fruit

A well-known defense-associated steroidal glycoalkaloid (SGA) metabolic shift eliminates the bitterness and toxicity of ripe tomato fruits. This study was conducted to clarify the effects of MADS-RIN (RIN) and its cofactors on SGA metabolism in tomato fruits. Using a CRISPR/Cas9-based gene-editing system, we mutated RIN and two cofactor genes (FUL1 and FUL2). The observed changes to fruit color and size in the mutants reflected the overlapping and distinct effects of RIN, FUL1, and FUL2 on fruit ripening. According to a UPLC-MS/MS analysis, the RIN and cofactor mutants had decreased levels of the relatively non-toxic metabolite esculeoside A, but they accumulated toxic SGA pathway intermediates, suggesting RIN and its cofactors are directly involved in esculeoside A biosynthesis. Transcriptome and qPCR analyses detected the downregulated expression of GAME5, which encodes a key enzyme mediating esculeoside A biosynthesis. ChIP-seq and ChIP-qPCR analyses confirmed GAME5 is targeted by RIN. RIN was observed to activate GAME5 transcription by binding to two non-canonical CArG-boxes in the GAME5 promoter. Additionally, RIN promotes SGA metabolism independently of ethylene. Collectively, these findings enhance our understanding of the molecular mechanism governing tomato fruit ripening and SGA biosynthesis. Furthermore, they may be useful for improving tomato fruit quality and safety.

The variegated canalized-1 tomato mutant is linked to photosystem assembly

The recently described canal-1 tomato mutant, which has a variegated leaf phenotype, has been shown to affect canalization of yield. The corresponding protein is orthologous to AtSCO2 -SNOWY COTYLEDON 2, which has suggested roles in thylakoid biogenesis. Here we characterize the canal-1 mutant through a multi-omics approach, by comparing mutant to wild-type tissues. While white canal-1 leaves are devoid of chlorophyll, green leaves of the mutant appear wild-type-like, despite an impaired protein function. Transcriptomic data suggest that green mutant leaves compensate for this impaired protein function by upregulation of transcription of photosystem assembly and photosystem component genes, thereby allowing adequate photosystem establishment, which is reflected in their wild-type-like proteome. White canal-1 leaves, however, likely fail to reach a certain threshold enabling this overcompensation, and plastids get trapped in an undeveloped state, while additionally suffering from high light stress, indicated by the overexpression of ELIP homolog genes. The metabolic profile of white and to a lesser degree also green tissues revealed upregulation of amino acid levels, that was at least partially mediated by transcriptional and proteomic upregulation. These combined changes are indicative of a stress response and suggest that white tissues behave as carbon sinks. In summary, our work demonstrates the relevance of the SCO2 protein in both photosystem assembly and as a consequence in the canalization of yield.

Abscisic acid and ethylene coordinating fruit ripening under abiotic stress

Fleshy fruit metabolism is intricately influenced by environmental changes, yet the hormonal regulations underlying these responses remain poorly elucidated. ABA and ethylene, pivotal in stress responses across plant vegetative tissues, play crucial roles in triggering fleshy fruit ripening. Their actions are intricately governed by complex mechanisms, influencing key aspects such as nutraceutical compound accumulation, sugar content, and softening parameters. Both hormones are essential orchestrators of significant alterations in fruit development in response to stressors like drought, salt, and temperature fluctuations. These alterations encompass colour development, sugar accumulation, injury mitigation, and changes in cell-wall degradation and ripening progression. This review provides a comprehensive overview of recent research progress on the roles of ABA and ethylene in responding to drought, salt, and temperature stress, as well as the molecular mechanisms controlling ripening in environmental cues. Additionally, we propose further studies aimed at genetic manipulation of ABA and ethylene signalling, offering potential strategies to enhance fleshy fruit resilience in the face of future climate change scenarios.

Low storage temperature affects quality and volatile compounds in fresh tomatoes

To investigate the impact of low temperature on the quality and flavor of ripe red tomatoes, we analyzed transcriptomes and volatile metabolomes of ripe red fruits stored at 0 °C and 20 °C for 8 days. The results showed that 0 °C maintained the sugar content by increasing the expression of sucrose synthetase (SUS) and sucrose transporter (SUT). Low expression of aroma synthesis-related genes, such as alcohol dehydrogenase 1 (ADH1), amino acid decarboxylase 1 A (AADC1A), and branched-chain amino acid aminotransferase 2 (BCAT2), were associated with reduced levels of pentanal, hexanal, 3-methylbutanal, 2-methylbutanal, and 2-phenylethanol. Additionally, the expression of pectinesterase (PE), beta-galactosidase (β-GAL), and beta-glucosidase (β-Glu), as well as phytoene synthase1 (PSY1) involved in carotenoid synthesis, was inhibited, thereby maintaining fruits texture and color. Furthermore, storage at 0 °C induced the expression of numerous genes regulating antioxidant and heat shock proteins, which further preserved the postharvest quality of tomatoes.

Transcription factor PbrERF114 is involved in the regulation of ethylene synthesis during pear fruit ripening

The plant hormone ethylene is indispensable to the ripening of climacteric fruits. Although extensive studies have been conducted on ethylene signaling, the ethylene response factor (ERF)-mediated transcriptional regulation of ethylene biosynthesis in pear fruits remains to be fully elucidated. We here constructed, sequenced, and analyzed transcriptome libraries in ethephon-treated and 1-MCP-treated Cuiguan pear fruits. In total, 721 fruit ripening-associated differentially expressed genes were identified. Among them, two key genes exhibited positive correlations: the 1-aminocyclopropane-1-carboxylic acid synthase (ACS)-encoding gene PbrACS3 and the ERF-encoding gene named PbrERF114. PbrERF114 overexpression increased ethylene production as well as the PbrACS3 expression level. Conversely, virus-induced gene silencing downregulated PbrERF114, thereby decreasing ethylene production and reducing PbrACS3 expression levels. Notably, PbrERF114 could directly interact with PbrACS3 and PbrERF24 promoters, thus inducing their expression. However, it did not result in an enhancement in luciferase activity, which is regulated by the PbrACS1b or PbrACO1 promoter. PbrERF24 could directly bind to PbrACO1 as well as PbrACS3 to promote ethylene synthesis. In conclusion, PbrERF114 can directly and indirectly mediate ethylene biosynthesis by transcriptionally regulating PbrACS3 and PbrERF24, respectively, thereby triggering a signaling cascade that induces the expression of both PbrACS3 and PbrACO1.

An integrated quality, physiological and transcriptomic analysis reveals mechanisms of kiwifruit response to postharvest transport vibrational stress

The 'Xuxiang' kiwifruit, a leading cultivar in China known for its high quality and yield, experiences quality degradation due to vibration stress during postharvest transportation. This study simulated the postharvest transportation vibrations of 'Xuxiang' kiwifruits to investigate the effects on the fruit quality and physiology. Different vibration intensities (0.26, 0.79, and 1.5 m s-2) and durations (0, 24, 48, 72, and 96 h) were applied to analyze the quality, physiological and transcriptomic changes of fruits after vibration stress, as well as the association between quality deterioration, gene networks, and key genes. Results indicated that vibration stress significantly accelerated the deterioration of fruit quality and induced physiological changes. As vibration intensity and duration increased, there was a rapid decrease in fruit firmness and an increase in weight loss, soluble solid content, relative conductivity, ethylene production, respiratory rate, and malondialdehyde levels. The most severe deterioration in fruit quality occurred at a vibration intensity of 1.5 m s-2. Transcriptome sequencing analysis was conducted on samples from different durations of exposure to the 1.5 m s-2 vibration intensity. Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses identified key genes associated with ethylene metabolism and softening. Weighted Gene Co-Expression Network Analysis (WGCNA) and correlation analysis further determined that 24 of these genes were regulated by vibrational stress, impacting ethylene metabolism and cell wall degradation. Vibration stress induced changes in genes related to ethylene metabolism and cell wall degradation, promoting lipid peroxidation and respiratory changes, which compromise cell membrane integrity and lead to quality deterioration. Compared with untreated fruits, vibration stress caused the quality deterioration, physiological changes and transcriptional regulation of kiwifruits, indicating that kiwifruits respond to vibration stress through multiple aspects. It proposes a fresh outlook on the understanding of the mechanism of transport vibration stress and further illustrates the importance of monitoring vibration intensity and duration as well as reducing vibration.

From Regulation to Application: The Role of Abscisic Acid in Seed and Fruit Development and Agronomic Production Strategies

Abscisic acid (ABA) is a crucial plant hormone that plays a decisive role in regulating seed and fruit development and is becoming increasingly important in agricultural applications. This article delves into ABA's regulatory functions in plant growth, particularly during the stages of seed and fruit development. In the seed phase, elevated ABA levels help maintain seed dormancy, aiding seed survival under unfavorable conditions. During fruit development, ABA regulates pigment synthesis and sugar accumulation, influencing the nutritional value and market quality of the fruit. This article highlights three main strategies for applying ABA in agricultural production: the use of ABA analogs, the development of ABA signal modulators, and breeding techniques based on ABA signaling. ABA analogs can mimic the natural functions of ABA, while ABA signal modulators, including enhancers and inhibitors, are used to finely tune plant responses to ABA, optimizing crop performance under specific growth conditions. Furthermore, breeding strategies based on ABA signaling aim to select crop varieties that effectively utilize ABA pathways through genetic engineering and other technologies. ABA is not only a key regulator of plant growth and development but also holds great potential for modern agricultural practices.

Ethylene and its crosstalk with hormonal pathways in fruit ripening: mechanisms, modulation, and commercial exploitation

Ethylene is an important phytohormone that orchestrates a multitude of physiological and biochemical processes regulating fruit ripening, from early maturation to post-harvest. This review offers a comprehensive analysis of ethylene's multifaceted roles in climacteric fruit ripening, characterized by a pronounced increase in ethylene production and respiration rates. It explores potential genetic and molecular mechanisms underlying ethylene's action, focusing on key transcription factors, biosynthetic pathway genes, and signal transduction elements crucial for the expression of ripening-related genes. The varied sensitivity and dependency of ripening traits on ethylene are elucidated through studies employing genetic mutations and ethylene inhibitors such as AVG and 1-MCP. Additionally, the modulation of ripening traits by ethylene is influenced by its interaction with other phytohormones, including auxins, abscisic acid, gibberellins, jasmonates, brassinosteroids, and salicylic acid. Pre-harvest fruit drop is intricately linked to ethylene, which triggers enzyme activity in the abscission zone, leading to cell wall degradation and fruit detachment. This review also highlights the potential for applying ethylene-related knowledge in commercial contexts to enhance fruit quality, control pre-harvest drop, and extend shelf life. Future research directions are proposed, advocating for the integration of physiological, genetic, biochemical, and transcriptional insights to further elucidate ethylene's role in fruit ripening and its interaction with other hormonal pathways.

Histone deacetylase SlHDA7 impacts fruit ripening and shelf life in tomato

Fruit ripening depends on the accurate control of ripening-related genes expression, with histone deacetylases (HDACs) playing crucial roles in transcriptional regulation. However, the functions of HDACs in fruit maturation remain largely unexplored. Here, we show that SlHDA7 acts as a suppressor of fruit ripening and functions as an H4ac HDAC in tomato. Deletion of SlHDA7 accelerated fruit ripening, while overexpression of SlHDA7 delayed the maturation process. Additionally, ethylene production and carotenoid biosynthesis significantly increased in slhda7 mutant fruits but decreased in SlHDA7-overexpressing fruits. Furthermore, SlHDA7 repress the expression of ethylene production and signaling, carotenoid metabolism, cell wall modification, and transcriptional regulation-related genes. RT-qPCR and ChIP-qPCR analyses indicated that SlHDA7 may deacetylate H4ac, leading to reduced transcript levels of ACO1, GGPPS2, Z-ISO, EXP1, and XYL1 mRNA, consequently suppressing fruit ripening. Moreover, SlHDA7 suppresses fruit ripening by targeting specific ripening-associated transcription factors (TFs) like RIN, FUL1, and ERF.E1, ultimately leading to delayed ripening and prolonged fruit shelf life. In summary, our findings indicate that SlHDA7 negatively modulates tomato fruit maturation by adjusting H4ac levels of these ripening-associated genes and key TFs.

Exogenous 5-aminolevulinic acid promotes carotenoid accumulation in tomato fruits by regulating ethylene biosynthesis and signaling

5-Aminolevulinic acid (ALA) can not only improve fruit yield and quality, but also increase the lycopene content in tomato fruits. Furthermore, ALA has been shown to promote system-2 ethylene production in tomato fruits. However, the specific interactions between ALA and ethylene during fruit ripening remain unclear. In this study, we treated tomato fruits with ALA, 1-aminocyclopropane-1-carboxylic acid (ACC), aminooxyacetic acid (AOA) + AgNO3, and AOA + AgNO3 + ALA and analyzed ethylene emissions, carotenoid contents, and the relative gene expression levels related to fruit ripening, carotenoid contents, ethylene synthesis, and signal transduction. The ALA treatment significantly enhanced ethylene bursts and carotenoid accumulation, and significantly upregulated the expression of ethylene and carotenoid-related genes, such as SlACS2, SlACS4, SlACO1, SlPSY1, and SlPDS. We also observed that the gene expression levels associated with carotenoid synthesis were downregulated in fruits treated with a combination of ethylene inhibitors (AOA + AgNO3). However, there was a significant upregulation in the gene expression levels associated with carotenoid synthesis and an increase in carotenoid content when fruits were treated with AOA + AgNO3 + ALA. After silencing SlACO1 expression, the total carotenoid content and SlPSY1 expression decreased significantly, while this effect was reversed after exogenous application of ALA. These results indicated that ALA promotes carotenoid accumulation in tomato fruits by promoting ethylene biosynthesis. In conclusion, our results highlighted the role of ALA in promoting carotenoid accumulation and ripening in tomato fruits by regulating ethylene synthesis, thereby providing a novel strategy for improving fruit quality.

Releasing a sugar brake generates sweeter tomato without yield penalty

In tomato, sugar content is highly correlated with consumer preferences, with most consumers preferring sweeter fruit1-4. However, the sugar content of commercial varieties is generally low, as it is inversely correlated with fruit size, and growers prioritize yield over flavour quality5-7. Here we identified two genes, tomato (Solanum lycopersicum) calcium-dependent protein kinase 27 (SlCDPK27; also known as SlCPK27) and its paralogue SlCDPK26, that control fruit sugar content. They act as sugar brakes by phosphorylating a sucrose synthase, which promotes degradation of the sucrose synthase. Gene-edited SlCDPK27 and SlCDPK26 knockouts increased glucose and fructose contents by up to 30%, enhancing perceived sweetness without fruit weight or yield penalty. Although there are fewer, lighter seeds in the mutants, they exhibit normal germination. Together, these findings provide insight into the regulatory mechanisms controlling fruit sugar accumulation in tomato and offer opportunities to increase sugar content in large-fruited cultivars without sacrificing size and yield.

RNA-protein interactions reveals the pivotal role of lncRNA1840 in tomato fruit maturation

Long non-coding RNAs (lncRNAs) play crucial roles in various biological processes in plants. However, the functional mechanism of lncRNAs in fruit ripening, particularly the transition from unripe to ripe stages, remains elusive. One such lncRNA1840, reported by our group, was found to have important role in tomato fruit ripening. In the present study, we gain insight into its functional role in fruit ripening. CRISPR-Cas9 mediated lncRNA1840 mutants caused the delayed tomato fruit ripening. Notably, loss function of lncRNA1840 did not directly impact ethylene signaling but rather delay ethylene synthesis. Transcriptomic analysis revealed differences in the expression of ripening related genes in lncRNA1840 mutants, suggesting that it is involved in gene regulation of fruit ripening. We used Chromatin Isolation by RNA Purification (ChIRP)-Seq to identify lncRNA1840 binding sites on chromatin. ChIRP-seq suggested that lncRNA1840 had occupancy on 40 genes, but none of them is differentially expressed genes in transcriptomic analysis, which indicated lncRNA1840 might indirectly modulate the gene expression. ChIRP-mass spectrometry analysis identified potential protein interactors of lncRNA1840, Pre-mRNA processing splicing factor 8, highlighting its involvement in post-transcriptional regulatory pathways. In summary, lncRNA1840 is key player in tomato plant growth and fruit ripening, with multifaceted roles in gene expression and regulatory networks.

Genomic variation across distribution of Micro-Tom, a model cultivar of tomato (Solanum lycopersicum)

Micro-Tom is a cultivar of tomato (Solanum lycopersicum), which is known as a major crop and model plant in Solanaceae. Micro-Tom has phenotypic traits such as dwarfism, and substantial EMS-mutagenized lines have been reported. After Micro-Tom was generated in Florida, USA, it was distributed to research institutes worldwide and used as a genetic resource. In Japan, the Micro-Tom lines have been genetically fixed; currently, three lines have been re-distributed from three institutes, but many phenotypes among the lines have been observed. We have determined the genome sequence de novo of the Micro-Tom KDRI line, one of the Micro-Tom lines distributed from Kazusa DNA Research Institute (KDRI) in Japan, and have built chromosome-scale pseudomolecules. Genotypes among six Micro-Tom lines, including three in Japan, one in the United States, one in France, and one in Brazil showed phenotypic alternation. Here, we unveiled the swift emergence of genetic diversity in both phenotypes and genotypes within the Micro-Tom genome sequence during its propagation. These findings offer valuable insights crucial for the management of bioresources.

The underlying molecular mechanisms of hormonal regulation of fruit color in fruit-bearing plants

Fruit color is a key feature of fruit quality, primarily influenced by anthocyanin or carotenoid accumulation or chlorophyll degradation. Adapting the pigment content is crucial to improve the fruit's nutritional and commercial value. Genetic factors along with other environmental components (i.e., light, temperature, nutrition, etc.) regulate fruit coloration. The fruit coloration process is influenced by plant hormones, which also play a vital role in various physiological and biochemical metabolic processes. Additionally, phytohormones play a role in the regulation of a highly conserved transcription factor complex, called MBW (MYB-bHLH-WD40). The MBW complex, which consists of myeloblastosis (MYB), basic helix-loop-helix (bHLH), and WD40 repeat (WDR) proteins, coordinates the expression of downstream structural genes associated with anthocyanin formation. In fruit production, the application of plant hormones may be important for promoting coloration. However, concerns such as improper concentration or application time must be addressed. This article explores the molecular processes underlying pigment formation and how they are influenced by various plant hormones. The ABA, jasmonate, and brassinosteroid increase anthocyanin and carotenoid formation, but ethylene, auxin, cytokinin, and gibberellin have positive as well as negative effects on anthocyanin formation. This article establishes the necessary groundwork for future studies into the molecular mechanisms of plant hormones regulating fruit color, ultimately aiding in their effective and scientific application towards fruit coloration.

The CsDof1.8-CsLIPOXYGENASE09 module regulates C9 aroma production in cucumber

Nine-carbon aldehydes and their relative alcohols (C9 aromas) are the main aroma compounds of cucumber (Cucumis sativus L.) fruits and provide a unique cucumber-like note. However, the key regulators of C9 aroma accumulation in cucumber fruit are poorly characterized. Based on C9 aroma dynamic analysis and transcriptome analysis during fruit development of two different cucumber inbred lines, Q16 and Q24, Lipoxygenase09 (CsLOX09) was identified as a candidate gene for C9 aroma accumulation. Additionally, Q24 with higher CsLOX09 expression accumulated more C9 aromas than Q16. To verify the function of CsLOX09, Cslox09 homozygote knockout lines were created. C9 aroma content decreased by 80.79% to 99.16% in these mutants compared to the wild type. To further explore the reasons for the difference in CsLOX09 expression between Q16 and Q24 fruits, a co-expression network was constructed by integrating the C9 aroma-associated metabolism and transcriptomic data. Eighteen candidate transcription factors were highly correlated with the expression of CsLOX09. DNA binding with One Finger 1.8 (CsDof1.8) was confirmed to bind directly to the A/TAAAG motif of the CsLOX09 promoter through dual-luciferase, yeast one-hybrid, chromatin immunoprecipitation-qPCR and electrophoretic mobility shift assays. Furthermore, C9 aroma content and CsLOX09 expression were significantly increased in the CsDof1.8 overexpression lines. Overall, these data elucidate the metabolic regulation of C9 aromas in cucumber and provide a foundation for facilitating the regulation of flavor in cucumber breeding.

Persulfidation and phosphorylation of transcription factor SlWRKY6 differentially regulate tomato fruit ripening

Cysteine desulfhydrase catalyses the generation of the signaling molecule hydrogen sulfide (H2S) in plants. In this study, we found that H2S can inhibit tomato (Solanum lycopersicum) fruit ripening and SlWRKY6 undergoes differential protein persulfidation in SlLCD1-overexpressing leaves. Then, further study indicated that SlWRKY6 could be persulfidated by H2S at Cys396. By construction of slwrky6 mutants and SlWRKY6-OE lines, we found that SlWRKY6 positively regulates leaf senescence and fruit ripening by activating the transcription of ripening-related genes STAYGREEN 1 (SlSGR1) and Senescence-Associated Gene 12 (SlSAG12). In addition, SlWRKY6 interacted with kinase SlMAPK4 and was phosphorylated at Ser33. Dual-luciferase transient expression assays and electrophoretic mobility shift assays indicated that SlWRKY6 persulfidation attenuated its transcriptional regulation of target genes SlSGR1 and SlSAG12, whereas SlWRKY6 phosphorylation by SlMAPK4 activated the transcription of target genes to promote fruit ripening. Moreover, we provided evidence that SlWRKY6 persulfidation attenuated its SlMAPK4-mediated phosphorylation to inhibit tomato fruit ripening. By transient expression of SlWRKY6, SlWRKY6C396A, SlWRKY6S33A, and SlWRKY6S33D in slwrky6 fruits, we found that SlWRKY6 persulfidation attenuated the expression of SlSGR1 and SlSAG12 thereby delaying tomato fruit ripening, while SlWRKY6 phosphorylation increased the expression of target genes. As tomato fruits ripened, endogenous H2S production decreased, while SlMAPK4 expression increased. Therefore, our findings reveal a model in which SlWRKY6 persulfidation due to higher endogenous H2S levels in un-ripened fruit inhibits its ability to activate SlSGR1 and SlSAG12 expression, while SlWRKY6 phosphorylation by SlMAPK4 activates its transcriptional activity, thereby promoting tomato fruit ripening.

REDUCED CHLOROPLAST COVERAGE proteins are required for plastid proliferation and carotenoid accumulation in tomato

Increasing the amount of cellular space allocated to plastids will lead to increases in the quality and yield of crop plants. However, mechanisms that allocate cellular space to plastids remain poorly understood. To test whether the tomato (Solanum lycopersicum L.) REDUCED CHLOROPLAST COVERAGE (SlREC) gene products serve as central components of the mechanism that allocates cellular space to plastids and contribute to the quality of tomato fruit, we knocked out the 4-member SlREC gene family. We found that slrec mutants accumulated lower levels of chlorophyll in leaves and fruits, accumulated lower levels of carotenoids in flowers and fruits, allocated less cellular space to plastids in leaf mesophyll and fruit pericarp cells, and developed abnormal plastids in flowers and fruits. Fruits produced by slrec mutants initiated ripening later than wild type and produced abnormal levels of ethylene and abscisic acid (ABA). Metabolome and transcriptome analyses of slrec mutant fruits indicated that the SlREC gene products markedly influence plastid-related gene expression, primary and specialized metabolism, and the response to biotic stress. Our findings and previous work with distinct species indicate that REC proteins help allocate cellular space to plastids in diverse species and cell types and, thus, play a central role in allocating cellular space to plastids. Moreover, the SlREC proteins are required for the high-level accumulation of chlorophyll and carotenoids in diverse organs, including fruits, promote the development of plastids and influence fruit ripening by acting both upstream and downstream of ABA biosynthesis in a complex network.

Fruit ripening and postharvest changes in very early-harvested tomatoes

It is well known that if a fruit is harvested extremely early its development and function are interrupted, and it may never attain full maturity and optimal quality. Reports revealing insights regarding the alterations of maturation, ripening and postharvest quality in very early picked fruits are rare. We examined the effects of early harvesting on tomatoes by characterizing different accessions at the molecular, physiological, and biochemical levels. We found that even very early-harvested fruits could achieve postharvest maturation and ripening though with some defects in pigment and cuticle formation, and seeds from very early-harvested fruits could still germinate and develop as normal and healthy plants. One critical regulator of tomato cuticle integrity, SlCER1-2, was shown to contribute to cuticle defects in very early-harvested fruits. Very early fruit harvest still allowing ripening and seed development indicate that the genetic and physiological programs of later maturation and ripening are set into motion early in fruit development and are not dependent on complete fruit expansion nor attachment to the plant.