On the regulation and function of secondary metabolism during fruit development and ripening

The natural variance of Arabidopsis secondary metabolism on extended darkness

In plants due to their sessile nature, secondary metabolites are important components against different abiotic and biotic stress, such as extended darkness. For this reason, the variation of secondary metabolite content of the Arabidopsis thaliana HapMap natural population following 0-and 6-d darkness treatment were detected and the raw data of different accessions at two timepoints were deposited in the Zenodo database. Moreover, the annotated secondary metabolites of these samples are presented in this data descriptor, which we believe will be a usefully re-usable resource for future integrative analysis with dark-treated transcripts, proteins or other phenotypic data in order to comprehensively illustrate the multiomic landscape of Arabidopsis in response to the stresses exerted by extended darkness.

Integration of Metabolomics and Transcriptomics to Explore Dynamic Alterations in Fruit Color and Quality in 'Comte de Paris' Pineapples during Ripening Processes

Pineapple color yellowing and quality promotion gradually manifest as pineapple fruit ripening progresses. To understand the molecular mechanism underlying yellowing in pineapples during ripening, coupled with alterations in fruit quality, comprehensive metabolome and transcriptome investigations were carried out. These investigations were conducted using pulp samples collected at three distinct stages of maturity: young fruit (YF), mature fruit (MF), and fully mature fruit (FMF). This study revealed a noteworthy increase in the levels of total phenols and flavones, coupled with a concurrent decline in lignin and total acid contents as the fruit transitioned from YF to FMF. Furthermore, the analysis yielded 167 differentially accumulated metabolites (DAMs) and 2194 differentially expressed genes (DEGs). Integration analysis based on DAMs and DEGs revealed that the biosynthesis of plant secondary metabolites, particularly the flavonol, flavonoid, and phenypropanoid pathways, plays a pivotal role in fruit yellowing. Additionally, RNA-seq analysis showed that structural genes, such as FLS, FNS, F3H, DFR, ANR, and GST, in the flavonoid biosynthetic pathway were upregulated, whereas the COMT, CCR, and CAD genes involved in lignin metabolism were downregulated as fruit ripening progressed. APX as well as PPO, and ACO genes related to the organic acid accumulations were upregulated and downregulated, respectively. Importantly, a comprehensive regulatory network encompassing genes that contribute to the metabolism of flavones, flavonols, lignin, and organic acids was proposed. This network sheds light on the intricate processes that underlie fruit yellowing and quality alterations. These findings enhance our understanding of the regulatory pathways governing pineapple ripening and offer valuable scientific insight into the molecular breeding of pineapples.

Evaluation of the Harvest Dates for Three Major Cultivars of Blue Honeysuckle (Lonicera caerulea L.) in China

Blue honeysuckle (Lonicera caerulea L.) is an emerging fruit crop; however, determining its proper harvest time in commercial cultivation remains challenging due to its rapid fruit development characteristics. In this study, we investigated 17 agronomic traits of three blue honeysuckle cultivars harvested on 5 successive dates within their respective harvest windows. 'Lanjingling', 'Wulan', and 'Berel' showed solid-acid ratios (SS:TA) ranging from 10.00 to 16.01, 8.13 to 10.23, and 5.77 to 7.11, respectively; anthocyanin contents ranged from 233.85 to 276.83 mg/100 g, 236.38 to 312.23 mg/100 g, and 235.71 to 334.98 mg/100 g, respectively; vitamin C contents ranged from 88.43 to 99.68 mg/100 g, 108.13 to 191.23 mg/100 g, and 89.71 to 120.40 mg/100 g, respectively; phenolic contents ranged from 25.22 to 37.59 mg/g, 25.40 to 36.52 mg/g, and 37.66 to 50.00 mg/g, respectively. The results revealed the SS:TA value consistently increased with delayed harvesting and were significantly negatively correlated with fruit firmness, total acidity, shelf life, and respiration intensity, suggesting it is an ideal maturity indicator for blue honeysuckle berries. The factor analysis suggests that the suitable harvest date for 'Lanjingling' could be either 47 days after flowering (DAF) with an SS:TA value of approximately 10.0, characterized by high firmness, extended shelf life, and elevated levels of anthocyanins and phenolics; or 67 DAF (SS:TA ≈ 16.0), characterized by high vitamin C content and sweetness, and larger size and weight. For 'Wulan', it suggests the suitable harvest date is either 54 DAF (SS:TA ≈ 9.0), yielding fruit with high levels of anthocyanins and vitamin C; or 62 DAF (SS:TA > 10.0), yielding fruit with high sweetness and large size and weight. For 'Berel', it is suggested to be either 52 DAF (SS:TA ≈ 6.5), resulting in fruit with high levels of anthocyanins and vitamin C; or 62 DAF (SS:TA > 7.0), resulting in balanced levels of the fruit quality traits.

How metabolism and development are intertwined in space and time

Developmental transitions, occurring throughout the life cycle of plants, require precise regulation of metabolic processes to generate the energy and resources necessary for the committed growth processes. In parallel, the establishment of new cells, tissues, and even organs, alongside their differentiation provoke profound changes in metabolism. It is increasingly being recognized that there is a certain degree of feedback regulation between the components and products of metabolic pathways and developmental regulators. The generation of large-scale metabolomics datasets during developmental transitions, in combination with molecular genetic approaches has helped to further our knowledge on the functional importance of metabolic regulation of development. In this perspective article, we provide insights into studies that elucidate interactions between metabolism and development at the temporal and spatial scales. We additionally discuss how this influences cell growth-related processes. We also highlight how metabolic intermediates function as signaling molecules to direct plant development in response to changing internal and external conditions.

The MADS-box protein SlTAGL1 regulates a ripening-associated SlDQD/SDH2 involved in flavonoid biosynthesis and resistance against Botrytis cinerea in post-harvest tomato fruit

3-Dehydroquinate dehydratase/shikimate dehydrogenase (DQD/SDH) is a key rate-limiting enzyme that catalyzes the synthesis of the shikimate, which is an important metabolic intermediate in plants and animals. However, the function of SlDQD/SDH family genes in tomato (Solanum lycopersicum) fruit metabolites is still unknown. In the present study, we identified a ripening-associated SlDQD/SDH member, SlDQD/SDH2, that plays a key role in shikimate and flavonoid metabolism. Overexpression of this gene resulted in an increased content of shikimate and flavonoids, while knockout of this gene by CRISPR/Cas9 mediated gene editing led to a significantly lower content of shikimate and flavonoids by downregulation of flavonoid biosynthesis-related genes. Moreover, we showed that SlDQD/SDH2 confers resistance against Botrytis cinerea attack in post-harvest tomato fruit. Dual-luciferase reporter and EMSA assays indicated that SlDQD/SDH2 is a direct target of the key ripening regulator SlTAGL1. In general, this study provided a new insight into the biosynthesis of flavonoid and B. cinerea resistance in fruit tomatoes.

Triazoles as a Potential Threat to the Nutritional Quality of Tomato Fruits

Triazole fungicides can threaten plants as abiotic stressors but can also positively affect plant defense by inducing priming. Thus, plant yield is also both protected and endangered by triazoles that may influence several metabolic pathways during maturation processes, such as the biosynthesis of saccharides or secondary metabolites. Here, Solanum lycopersicum L. plants were exposed to foliar and soil applications of penconazole, tebuconazole, or their combination, and their resulting effect on tomato fruits was followed. The exposure to the equimolar mixture of both triazoles influenced the representation of free proteinogenic amino acids, especially Gln, Glu, Gly, Ile, Lys, Ser and Pro, saccharide content, and led to a significant increase in the contents of total phenolics and flavonoids as well as positive stimulation of the non-enzymatic antioxidant system. Among the identified secondary metabolites, the most abundant was naringenin, followed by chlorogenic acid in tomato peel. In turn, all triazole-treated groups showed a significantly lower content of rosmarinic acid in comparison with the control. Foliar application of penconazole affected the fruit more than other single triazole applications, showing a significant decrease in antioxidant capacity, the total content of secondary metabolites, and the activities of total membrane-bound peroxidases and ascorbate peroxidase.

Aroma profiling of Shine Muscat grape provides detailed insights into the regulatory effect of gibberellic acid and N-(2-chloro-4-pyridinyl)-N-phenylurea applications on aroma quality

As plant growth regulators, gibberellic acid (GA₃) and CPPU [forchlorfenuron, N-(2-chloro-4-pyridinyl)-N-phenylurea] are widely used in the production of table grapes. However, how these compounds regulate the aroma quality remains unclear. By measuring free and bound aroma compounds in Shine Muscat grapes from eight groups during whole growth period, GA₃ and CPPU were both found to significantly promote the synthesis of acyclic monoterpenes and (E)-2-hexenal, and double applications were found to further increase the aroma compound contents. On the other hand, GA₃ and CPPU obviously promoted the expansion of berries, and the effect of promoting the synthesis of aroma compounds was largely diminished. In conclusion, free compound concentrations in berry were almost unaffected by GA₃ and CPPU. From the perspective of aroma compounds, a highly concerted interplay was observed for terpenes, and bound compounds exhibited higher correlations than those of free compounds. In addition, 17 compounds could be used as markers that indicated the developmental timing of berries.

Carbon sufficiency boosts phenylpropanoid biosynthesis early in peach fruit development priming superior fruit quality

Manipulating the crop load in peach trees determines carbon supply and optimum balance between fruit yield and quality potentials. The impact of carbon supply on peach fruit quality was assessed in three development stages (S2, S3, S4) on fruit of equal maturity from trees that were carbon (C) starved (unthinned) and sufficient (thinned). Previous studies determined that primary metabolites of peach fruit mesocarp are mainly linked with developmental processes, thus, the secondary metabolite profile was assessed using non-targeted liquid chromatography mass-spectrometry (LC-MS). Carbon sufficient (C-sufficient) fruit demonstrated superior quality attributes as compared to C-starved fruit. Early metabolic shifts in the secondary metabolome appear to prime quality at harvest. Enhanced C-availability facilitated the increased and consistent synthesis of flavonoids, like catechin, epicatechin and eriodyctiol, via the phenylpropanoid pathway, providing a link between the metabolome and fruit quality, and serving as signatures of C-sufficiency during peach fruit development.

Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways

Plants are the most important sources of food for humans, as well as supplying many ingredients that are of great importance for human health. Developing an understanding of the functional components of plant metabolism has attracted considerable attention. The rapid development of liquid chromatography and gas chromatography, coupled with mass spectrometry, has allowed the detection and characterization of many thousands of metabolites of plant origin. Nowadays, elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding. Recently, the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways. Here, we review the recent research which integrates metabolomic with different omics methods, to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways. Finally, we discuss other novel methods that can accelerate the process of identification of metabolic pathways and, ultimately, identify metabolite function(s).

Genetic and epigenetic control of the plant metabolome

Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.

An Integrated Approach of Hypobaric Pressures and Potassium Permanganate to Maintain Quality and Biochemical Changes in Tomato Fruits

Limited postharvest life of tomato fruit is due to its highly perishable nature. Hypobaric pressure is a new emerging hurdle technology usually used up to a pressure of 100 kPa for the preservation of fruits and vegetables. In this study, an integrated approach of hypobaric pressures (40 kPa and 50 kPa) and sponge-dipping of potassium permanganate (KMnO4) was designed for the postharvest life extension of tomato fruits. Fruits were treated with either 400 ppm of KMnO4, or 40 or 50 kPa hypobaric pressures, or their combination. Fruits without any treatment was considered as a control treatment. All groups were packaged in polypropylene trays as ready to retail and stored at room temperature at 25 ± 1 °C for 21 days. Basic quality parameters such as pH, total soluble solid, percent weight loss, percent spoilage, firmness, ethylene production rate, and color were evaluated at 3-day intervals. Results showed the application of hypobaric pressures and KMnO4, either alone or in combination, provided a synergistic effect in maintaining the quality compared to the control treatment during the 21 days of storage. The highest decay was found in the control compared to the combined treatments of KMnO4 + 40 kPa and KMnO4 + 50 kPa. Similarly, a decrease in firmness and color values was highest in the control treatment followed by the KMnO4 and 50 kPa hypobaric pressure compared to the combined treatment of KMnO4 + 50 kPa. In the same way, a high ethylene production rate was observed in the control, while the lowest ethylene production rate was found in KMnO4 + 50 kpa. Sensory evaluation indicated a highest score of 9 on the 9-point hedonic scale of tomato fruits. Among all groups, the combined application of 50 kPa hypobaric pressure + 400 ppm KMnO4 retained the best overall quality attributes compared to all other treatments throughout the experiment; therefore, this treatment could be applied at a commercial level for tomato fruits.

Application of Exogenous Melatonin Improves Tomato Fruit Quality by Promoting the Accumulation of Primary and Secondary Metabolites

Melatonin plays key roles in improving fruit quality and yield by regulating various aspects of plant growth. However, the effects of how melatonin regulates primary and secondary metabolites during fruit growth and development are poorly understood. In this study, the surfaces of tomato fruit were sprayed with different concentrations of melatonin (0, 50, and 100 µmol·L^-1) on the 20th day after anthesis; we used high-performance liquid chromatography (HPLC) and liquid chromatography/mass spectrometry (LC/MS) to determine the changes in primary and secondary metabolite contents during fruit development and measured the activity of sucrose metabolizing enzymes during fruit development. Our results showed that 100 µmol·L^-1 melatonin significantly promoted the accumulation of soluble sugar in tomato fruit by increasing the activities of sucrose synthase (SS), sucrose phosphate synthase (SPS), and acid convertase (AI). The application of 100 µmol·L^-1 melatonin also increased the contents of ten amino acids in tomato fruit as well as decreased the contents of organic acids. In addition, 100 µmol·L^-1 melatonin application also increased the accumulation of some secondary metabolites, such as six phenolic acids, three flavonoids, and volatile substances (including alcohols, aldehydes, and ketones). In conclusion, melatonin application improves the internal nutritional and flavor quality of tomato fruit by regulating the accumulation of primary and secondary metabolites during tomato fruit ripening. In the future, we need to further understand the molecular mechanism of melatonin in tomato fruit to lay a solid foundation for quality improvement breeding.

Capsicum Leaves under Stress: Using Multi-Omics Analysis to Detect Abiotic Stress Network of Secondary Metabolism in Two Species

The plant kingdom contains an enormous diversity of bioactive compounds which regulate plant growth and defends against biotic and abiotic stress. Some of these compounds, like flavonoids, have properties which are health supporting and relevant for industrial use. Many of these valuable compounds are synthesized in various pepper (Capsicum sp.) tissues. Further, a huge amount of biomass residual remains from pepper production after harvest, which provides an important opportunity to extract these metabolites and optimize the utilization of crops. Moreover, abiotic stresses induce the synthesis of such metabolites as a defense mechanism. Two different Capsicum species were therefore exposed to chilling temperature (24/18 ℃ vs. 18/12 ℃), to salinity (200 mM NaCl), or a combination thereof for 1, 7 and 14 days to investigate the effect of these stresses on the metabolome and transcriptome profiles of their leaves. Both profiles in both species responded to all stresses with an increase over time. All stresses resulted in repression of photosynthesis genes. Stress involving chilling temperature induced secondary metabolism whereas stresses involving salt repressed cell wall modification and solute transport. The metabolome analysis annotated putatively many health stimulating flavonoids (apigetrin, rutin, kaempferol, luteolin and quercetin) in the Capsicum biomass residuals, which were induced in response to salinity, chilling temperature or a combination thereof, and supported by related structural genes of the secondary metabolism in the network analysis.

Modulated Light Dependence of Growth, Flowering, and the Accumulation of Secondary Metabolites in Chilli

Chili is widely used as a food additive and a flavouring and colouring agent and also has great importance in health preservation and therapy due to the abundant presence of many bioactive compounds, such as polyphenols, flavonoids, carotenoids, and capsaicinoids. Most of these secondary metabolites are strong antioxidants. In the present study, the effect of light intensity and spectral composition was studied on the growth, flowering, and yield of chilli together with the accumulation of secondary metabolites in the fruit. Two light intensities (300 and 500 μmol m-2 s-1) were applied in different spectral compositions. A broad white LED spectrum with and without FR application and with blue LED supplement was compared to blue and red LED lightings in different (80/20 and 95/5%) blue/red ratios. High light intensity increased the harvest index (fruit yield vs. biomass production) and reduced the flowering time of the plants. The amount of secondary metabolites in the fruit varied both by light intensity and spectral compositions; phenolic content and the radical scavenging activity were stimulated, whereas capsaicin accumulation was suppressed by blue light. The red colour of the fruit (provided by carotenoids) was inversely correlated with the absolute amount of blue, green, and far-red light. Based on the results, a schematic model was created, representing light-dependent metabolic changes in chilli. The results indicated that the accumulation of secondary metabolites could be modified by the adjustment of light intensity and spectral composition; however, different types of metabolites required different light environments.

The effect of ethylene on squalene and β-sitosterol biosynthesis and its key gene network analysis in Torreya grandis nuts during post-ripening process

Squalene and β-sitosterol are health-benefit compounds due to their nutritional and medicinal properties. It has been reported that the content of these bioactive compounds is relatively high in Torreya grandis nuts. However, it is not yet known what changes in squalene and β-sitosterol accumulation occur during the special post-ripening process of T. grandis nuts and the effect of the well-known ripening hormone ethylene on the regulatory mechanism of their biosynthetic pathways. Thus, we performed transcriptome and metabolite analyses. The results showed that ethylene not only promoted the post-ripening process but also enhanced the accumulation of squalene by inducing gene expression in the mevalonate pathway. At the same time, ethylene treatment also promoted the accumulation of other sterols but inhibited gene expression in the β-sitosterol biosynthesis pathway. In addition, co-expression and correlation analysis suggested a framework for the transcriptional regulation of squalene and β-sitosterol biosynthesis genes under ethylene treatment.

The metabolic changes that effect fruit quality during tomato fruit ripening

As the most valuable organ of tomato plants, fruit has attracted considerable attention which most focus on its quality formation during the ripening process. A considerable amount of research has reported that fruit quality is affected by metabolic shifts which are under the coordinated regulation of both structural genes and transcriptional regulators. In recent years, with the development of the next generation sequencing, molecular and genetic analysis methods, lots of genes which are involved in the chlorophyll, carotenoid, cell wall, central and secondary metabolism have been identified and confirmed to regulate pigment contents, fruit softening and other aspects of fruit flavor quality. Here, both research concerning the dissection of fruit quality related metabolic changes, the transcriptional and post-translational regulation of these metabolic pathways are reviewed. Furthermore, a weighted gene correlation network analysis of representative genes of fruit quality has been carried out and the potential of the combined application of the gene correlation network analysis, fine-mapping strategies and next generation sequencing to identify novel candidate genes determinants of fruit quality is discussed.

Hyperoside regulates its own biosynthesis via MYB30 in promoting reproductive development and seed set in okra

Flavonoids are secondary metabolites that play important roles in fruit and vegetable development. Here, we examined the function of hyperoside, a unique flavonoid in okra (Abelmoschus esculentus), known to promote both flowering and seed set. We showed that the exogenous application of hyperoside significantly improved pollen germination rate and pollen tube growth by almost 50%, resulting in a 42.7% increase in the seed set rate. Of several genes induced by the hyperoside treatment, AeUF3GaT1, which encodes an enzyme that catalyzes the last step of hyperoside biosynthesis, was the most strongly induced. The transcription factor AeMYB30 enhanced AeUFG3aT1 transcription by directly binding to the AeUFG3aT1 promoter. We studied the effect of the hyperoside application on the expression of 10 representative genes at four stages of reproductive development, from pollination to seed maturity. We firstly developed an efficient transformation system that uses seeds as explants to study the roles of AeMYB30 and AeUFG3aT1. Overexpression of AeMYB30 or AeUF3GaT1 promoted seed development. Moreover, exogenous application of hyperoside partially restored the aberrant phenotype of AeUF3GaT1 RNA-interference plants. Thus, hyperoside promotes seed set in okra via a pathway involving AeUF3GaT and AeMYB30, and the exogenous application of this flavonoid is a simple method that can be used to improve seed quality and yield in okra.

The Genetic Basis of Tomato Aroma

Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.

Early metabolic priming under differing carbon sufficiency conditions influences peach fruit quality development

Crop load management is an important preharvest factor to balance yield, quality, and maturation in peach. However, few studies have addressed how preharvest factors impact metabolism on fruit of equal maturity. An experiment was conducted to understand how carbon competition impacts fruit internal quality and metabolism in 'Cresthaven' peach trees by imposing distinct thinning severities. Fruit quality was evaluated at three developmental stages (S2, S3, S4), while controlling for equal maturity using non-destructive visual to near-infrared spectroscopy. Non-targeted metabolite profiling was used to characterize fruit at each developmental stage from trees that were unthinned (carbon starvation) or thinned (carbon sufficiency). Carbon sufficiency resulted in significantly higher fruit dry matter content and soluble solids concentration at harvest when compared to the carbon starved, underscoring the true impact of carbon manipulation on fruit quality. Significant differences in the fruit metabolome between treatments were observed at S2 when phenotypes were similar, while less differences were observed at S4 when the carbon sufficient fruit exhibited a superior phenotype. This suggests a potential metabolic priming effect on fruit quality when carbon is sufficiently supplied during early fruit growth and development. In particular, elevated levels of catechin may suggest a link between secondary/primary metabolism and fruit quality development.

Secondary metabolites in a neotropical shrub: spatiotemporal allocation and role in fruit defense and dispersal

Deciphering the ecological roles of plant secondary metabolites requires integrative studies that assess both the allocation patterns of compounds and their bioactivity in ecological interactions. Secondary metabolites have been primarily studied in leaves, but many are unique to fruits and can have numerous potential roles in interactions with both mutualists (seed dispersers) and antagonists (pathogens and predators). We described 10 alkenylphenol compounds from the plant species Piper sancti-felicis (Piperaceae), quantified their patterns of intraplant allocation across tissues and fruit development, and examined their ecological role in fruit interactions. We found that unripe and ripe fruit pulp had the highest concentrations and diversity of alkenylphenols, followed by flowers; leaves and seeds had only a few compounds at detectable concentrations. We observed a nonlinear pattern of alkenylphenol allocation across fruit development, increasing as flowers developed into unripe pulp then decreasing as pulp ripened. This pattern is consistent with the hypothesis that alkenylphenols function to defend fruits from pre-dispersal antagonists and are allocated based on the contribution of the tissue to the plant's fitness, but could also be explained by non-adaptive constraints. To assess the impacts of alkenylphenols in interactions with antagonists and mutualists, we performed fungal bioassays, field observations, and vertebrate feeding experiments. In fungal bioassays, we found that alkenylphenols had a negative effect on the growth of most fungal taxa. In field observations, nocturnal dispersers (bats) removed the majority of infructescences, and diurnal dispersers (birds) removed a larger proportion of unripe infructescences. In feeding experiments, bats exhibited an aversion to alkenylphenols, but birds did not. This observed behavior in bats, combined with our results showing a decrease in alkenylphenols during ripening, suggests that alkenylphenols in fruits represent a trade-off (defending against pathogens but reducing disperser preference). These results provide insight into the ecological significance of a little studied class of secondary metabolites in seed dispersal and fruit defense. More generally, documenting intraplant spatiotemporal allocation patterns in angiosperms and examining mechanisms behind these patterns with ecological experiments is likely to further our understanding of the evolutionary ecology of plant chemical traits.

Optogenetic Control of Heterologous Metabolism in E. coli

Multiobjective optimization of microbial chassis for the production of xenobiotic compounds requires the implementation of metabolic control strategies that permit dynamic distribution of cellular resources between biomass and product formation. We addressed this need in a previous study by engineering the T7 RNA polymerase to be thermally responsive. The modified polymerase is activated only after the temperature of the host cell falls below 18 °C, and Escherichia coli cells that employ the protein to transcribe the heterologous lycopene biosynthetic pathway exhibit impressive improvements in productivity. We have expanded our toolbox of metabolic switches in the current study by engineering a version of the T7 RNA polymerase that drives the transition between biomass and product formation upon stimulation with red light. The engineered polymerase is expressed as two distinct polypeptide chains. Each chain comprises one of two photoactive components from Arabidopsis thaliana, phytochrome B (PhyB) and phytochrome-integrating factor 3 (PIF3), as well as the N- or C-terminus domains of both, the vacuolar ATPase subunit (VMA) intein of Saccharomyces cerevisiae and the polymerase. Red light drives photodimerization of PhyB and PIF3, which then brings together the N- and C-terminus domains of the VMA intein. Trans-splicing of the intein follows suit and produces an active form of the polymerase that subsequently transcribes any sequence that is under the control of a T7 promoter. The photodimerization also involves a third element, the cyanobacterial chromophore phycocyanobilin (PCB), which too is expressed heterologously by E. coli. We deployed this version of the T7 RNA polymerase to control the production of lycopene in E. coli and observed tight control of pathway expression. We tested a variety of expression configurations to identify one that imposes the lowest metabolic burden on the strain, and we subsequently optimized key parameters such as the source, moment, and duration of photostimulation. We also identified targets for future refinement of the circuit. In summary, our work is a significant advance for the field and greatly expands on previous work by other groups that have used optogenetic circuits to control heterologous metabolism in prokaryotic hosts.

NMR Metabolomics Applied on the Discrimination of Variables Influencing Tomato (Solanum lycopersicum)

Tomato composition and nutritional value are attracting increasing attention and interest from both consumers and producers. The interest in enhancing fruits' quality with respect to beneficious nutrients and flavor/aroma components is based not only in their economic added value but also in their implications involving organoleptic and healthy properties and has generated considerable research interest among nutraceutical and horticultural industries. The present article reviews up to March 2020 some of the most relevant studies based on the application of NMR coupled to multivariate statistical analysis that have addressed the investigation on tomato (Solanum lycopersicum). Specifically, the NMR untargeted technique in the agri-food sector can generate comprehensive data on metabolic networks and is paving the way towards the understanding of variables affecting tomato crops and composition such as origin, variety, salt-water irrigation, cultivation techniques, stage of development, among many others. Such knowledge is helpful to improve fruit quality through cultural practices that divert the metabolism towards the desired pathways and, probably more importantly, drives further efforts towards the differentiation of those crops developed under controlled and desired agronomical conditions.

Within- and cross-species predictions of plant specialized metabolism genes using transfer learning

Plant specialized metabolites mediate interactions between plants and the environment and have significant agronomical/pharmaceutical value. Most genes involved in specialized metabolism (SM) are unknown because of the large number of metabolites and the challenge in differentiating SM genes from general metabolism (GM) genes. Plant models like Arabidopsis thaliana have extensive, experimentally derived annotations, whereas many non-model species do not. Here we employed a machine learning strategy, transfer learning, where knowledge from A. thaliana is transferred to predict gene functions in cultivated tomato with fewer experimentally annotated genes. The first tomato SM/GM prediction model using only tomato data performs well (F-measure = 0.74, compared with 0.5 for random and 1.0 for perfect predictions), but from manually curating 88 SM/GM genes, we found many mis-predicted entries were likely mis-annotated. When the SM/GM prediction models built with A. thaliana data were used to filter out genes where the A. thaliana-based model predictions disagreed with tomato annotations, the new tomato model trained with filtered data improved significantly (F-measure = 0.92). Our study demonstrates that SM/GM genes can be better predicted by leveraging cross-species information. Additionally, our findings provide an example for transfer learning in genomics where knowledge can be transferred from an information-rich species to an information-poor one.

Flux balance analysis of metabolism during growth by osmotic cell expansion and its application to tomato fruits

Cell expansion is a significant contributor to organ growth and is driven by the accumulation of osmolytes to increase cell turgor pressure. Metabolic modelling has the potential to provide insights into the processes that underpin osmolyte synthesis and transport, but the main computational approach for predicting metabolic network fluxes, flux balance analysis, often uses biomass composition as the main output constraint and ignores potential changes in cell volume. Here we present growth-by-osmotic-expansion flux balance analysis (GrOE-FBA), a framework that accounts for both the metabolic and ionic contributions to the osmotica that drive cell expansion, as well as the synthesis of protein, cell wall and cell membrane components required for cell enlargement. Using GrOE-FBA, the metabolic fluxes in dividing and expanding cells were analysed, and the energetic costs for metabolite biosynthesis and accumulation in the two scenarios were found to be surprisingly similar. The expansion phase of tomato fruit growth was also modelled using a multiphase single-optimization GrOE-FBA model and this approach gave accurate predictions of the major metabolite levels throughout fruit development, as well as revealing a role for transitory starch accumulation in ensuring optimal fruit development.

The style and substance of plant flavonoid decoration; towards defining both structure and function

Over 8000 different flavonoids have been described and a considerable number of new flavonoid structures are being elucidated every year. The advent of metabolomics alongside the development of phytochemical genetics - wherein the genetic basis underlying the regulation of the levels of plant metabolites is determined - has provided a massive boost to such efforts. That said our understanding of the individual function(s) of the vast majority of the metabolites that constitute this important class of phytochemicals remains unknown. Here we review what is known concerning the major decorative modifications of flavonoids in plants, namely hydroxylation, glycosylation, methylation and acylation. Our major focus is with regard to the in planta function of these modified compounds, however, we also highlight the demonstrated bioactive roles which they possess. We additionally performed a comprehensive survey of the flavonoids listed in the KNApSAcK database in order to assess the frequency of occurrence of each type of flavonoid modification. We conclude that whilst considerable research has been carried out regarding the biological roles of flavonoids most studies to date have merely provided information on the compound class or sub-classes thereof as a whole with too little currently known on the specific role of individual metabolites. We, therefore, finally suggest a framework based on currently available tools by which the relative importance of the individual compounds can be assessed under various biological conditions in order to fill this knowledge-gap.

Cross-Species Comparison of Fruit-Metabolomics to Elucidate Metabolic Regulation of Fruit Polyphenolics Among Solanaceous Crops

Many solanaceous crops are an important part of the human daily diet. Fruit polyphenolics are plant specialized metabolites that are recognized for their human health benefits and their defensive role against plant abiotic and biotic stressors. Flavonoids and chlorogenates are the major polyphenolic compounds found in solanaceous fruits that vary in quantity, physiological function, and structural diversity among and within plant species. Despite their biological significance, the elucidation of metabolic shifts of polyphenols during fruit ripening in different fruit tissues, has not yet been well-characterized in solanaceous crops, especially at a cross-species and cross-cultivar level. Here, we performed a cross-species comparison of fruit-metabolomics to elucidate the metabolic regulation of fruit polyphenolics from three representative crops of Solanaceae (tomato, eggplant, and pepper), and a cross-cultivar comparison among different pepper cultivars (Capsicum annuum cv.) using liquid chromatography-mass spectrometry (LC-MS). We observed a metabolic trade-off between hydroxycinnamates and flavonoids in pungent pepper and anthocyanin-type pepper cultivars and identified metabolic signatures of fruit polyphenolics in each species from each different tissue-type and fruit ripening stage. Our results provide additional information for metabolomics-assisted crop improvement of solanaceous fruits towards their improved nutritive properties and enhanced stress tolerance.

De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism

Background

Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species.

Results

Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage).

Conclusions

The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.

Impact of scion/rootstock reciprocal effects on metabolomics of fruit juice and phloem sap in grafted Citrus reticulata

Background

Rootstock has a significant impact on plant growth and development, including fruit maturation. However, the existence of mutual interaction between scion and rootstock is often neglected. To explore the origin of different fruit quality traits in citrus, we studied the effect of rootstock and the reciprocal interaction between scion and rootstock of nine combinations; three mandarin varieties grafted on three different rootstocks. We analyzed the metabolic profile of juice via gas and liquid chromatography-mass spectrometry (GC-MS and LC-MS, respectively). Additionally, we profiled phloem sap composition in the scion and the rootstock. Quality traits of fruit and their physio-chemical characteristics were also evaluated.

Results

For all three cultivars, rootstock was found to affect fruit yield and biochemical fruit quality parameters (sugar and acidity) in interactions with the scions. In mandarin juice, eight of 48 compounds (two primary and six secondary) were related directly to the rootstock, and another seven (one primary and six secondary) were interactively affected by scion and rootstock. In scion and rootstock sap, six and 14 of 53 and 55 primary metabolites, respectively, were directly affected by the rootstock, while 42 and 33 were affected by rootstock interactively with scion, respectively.

Conclusion

In this work, we show for the first time a reciprocal effect between rootstock and scion. Based on our results, the scion and rootstock interaction might be organ, distance or time dependent.

Proteome Analysis of 14-3-3 Targets in Tomato Fruit Tissues

Tomato is a major crop plant and an important constituent of the human diet. Exclusive features such as bearing fleshy fruits and undergoing a phase transition from partially photosynthetic to fully heterotrophic metabolism make tomato fruit a model system for fruit development studies. Although the tomato genome has been completely sequenced, functional proteomics studies are still at their starting stage. Proteomics technologies, especially the combination of multiple approaches, provide a very powerful tool to accurately identify functional proteins and investigate certain sets of proteins in more detail. The direct binding of plant 14-3-3 proteins to their multiple target proteins modulates the functions of the latter, suggesting that these 14-3-3 proteins are directly involved in various physiological pathways. This chapter outline methods for the identification of 14-3-3 protein complexes in tomato fruit tissues. These methods include detailed protocols for protein extraction, coimmunoprecipitation, SDS-PAGE, SYPRO Ruby staining, in-gel trypsin digestion, and LC-MS/MS analysis for 14-3-3 interactomics.

Annotation of Specialized Metabolites from High-Throughput and High-Resolution Mass Spectrometry Metabolomics

High-throughput mass spectrometry (MS) metabolomics profiling of highly complex samples allows the comprehensive detection of hundreds to thousands of metabolites under a given condition and point in time and produces information-rich data sets on known and unknown metabolites. One of the main challenges is the identification and annotation of metabolites from these complex data sets since the number of authentic standards available for specialized metabolites is far lower than an account for the number of mass spectral features. Previously, we reported two novel tools, MetNet and MetCirc, for putative annotation and structural prediction on unknown metabolites using known metabolites as baits. MetNet employs differences between m/z values of MS1 features, which correspond to metabolic transformations, and statistical associations, while MetCirc uses MS/MS features as input and calculates similarity scores of aligned spectra between features to guide the annotation of metabolites. Here, we showcase the use of MetNet and MetCirc to putatively annotate metabolites and provide detailed instructions as to how those can be used. While our case studies are from plants, the tools find equal utility in studies on bacterial, fungal, or mammalian xenobiotic samples.

Genetic and metabolic effects of ripening mutations and vine detachment on tomato fruit quality

Tomato (Solanum lycopersicum) fruit ripening is regulated co-operatively by the action of ethylene and a hierarchy of transcription factors, including RIPENING INHIBITOR (RIN) and NON-RIPENING (NOR). Mutations in these two genes have been adopted commercially to delay ripening, and accompanying textural deterioration, as a means to prolong shelf life. However, these mutations also affect desirable traits associated with colour and nutritional value, although the extent of this trade-off has not been assessed in detail. Here, we evaluated changes in tomato fruit pericarp primary metabolite and carotenoid pigment profiles, as well as the dynamics of specific associated transcripts, in the rin and nor mutants during late development and postharvest storage, as well of those of the partially ripening delayed fruit ripening (dfd) tomato genotype. These profiles were compared with those of the wild-type tomato cultivars Ailsa Craig (AC) and M82. We also evaluated the metabolic composition of M82 fruit ripened on or off the vine over a similar period. In general, the dfd mutation resulted in prolonged firmness and maintenance of quality traits without compromising key metabolites (sucrose, glucose/fructose and glucose) and sectors of intermediary metabolism, including tricarboxylic acid cycle intermediates. Our analysis also provided insights into the regulation of carotenoid formation and highlighted the importance of the polyamine, putrescine, in extending fruit shelf life. Finally, the metabolic composition analysis of M82 fruit ripened on or off the vine provided insights into the import into fruit of compounds, such as sucrose, during ripening.

The dynamic mosaic phenotypes of flowering plants

Ecological interaction and adaptation both depend on phenotypic characteristics. In contrast with the common conception of the 'adult' phenotype, plant bodies develop continuously during their lives. Furthermore, the different units (metamers) that comprise plant bodies are not identical copies, but vary extensively within individuals. These characteristics foster recognition of plant phenotypes as dynamic mosaics. We elaborate this conception based largely on a wide-ranging review of developmental, ecological and evolutionary studies of plant reproduction, and identify its utility in the analysis of plant form, function and diversification. An expanded phenotypic conception is warranted because dynamic mosaic features affect plant performance and evolve. Evidence demonstrates that dynamic mosaic phenotypes enable functional ontogeny, division of labour, resource and mating efficiency. In addition, dynamic mosaic features differ between individuals and experience phenotypic selection. Investigation of the characteristics and roles of dynamic and mosaic features of plant phenotypes benefits from considering within-individual variation as a function-valued trait that can be analysed with functional data methods. Phenotypic dynamics and within-individual variation arise despite an individual's genetic uniformity, and develop largely by heterogeneous gene expression and associated hormonal control. These characteristics can be heritable, so that dynamic mosaic phenotypes can evolve and diversify by natural selection.

Nitric oxide in the physiology and quality of fleshy fruits

Fruits are unique to flowering plants and confer a selective advantage as they facilitate seed maturation and dispersal. In fleshy fruits, development and ripening are associated with numerous structural, biochemical, and physiological changes, including modifications in the general appearance, texture, flavor, and aroma, which ultimately convert the immature fruit into a considerably more attractive and palatable structure for seed dispersal by animals. Treatment with exogenous nitric oxide (NO) delays fruit ripening, prevents chilling damage, promotes disease resistance, and enhances the nutritional value. The ripening process is influenced by NO, which operates antagonistically to ethylene, but it also interacts with other regulatory molecules such as abscisic acid, auxin, jasmonic acid, salicylic acid, melatonin, and hydrogen sulfide. NO content progressively declines during fruit ripening, with concomitant increases in protein nitration and nitrosation, two post-translational modifications that are promoted by reactive nitrogen species. Dissecting the intimate interactions of NO with other ripening-associated factors, including reactive oxygen species, antioxidants, and the aforementioned phytohormones, remains a challenging subject of research. In this context, integrative 'omics' and gene-editing approaches may provide additional knowledge of the impact of NO in the regulatory processes involved in controlling physiology and quality traits in both climacteric and non-climacteric fruits.

Phenolic composition and antioxidant properties of ex-situ conserved tomato (Solanum lycopersicum L.) germplasm

Tomato (Solanum lycopersicum L.) local varieties represent a reservoir of genetic diversity for desirable quality traits. In this study, a representative collection of table tomato germplasm conserved ex-situ in the Portuguese Gene Bank was characterized for its polyphenols composition and antioxidant capacity. Phenolic acids, such as caffeic and p-coumaric acids bounded to a hexose and 5-O-caffeoylquinic acid, corresponded to 71-98% of the identified phenolic compounds; while the remaining fraction consisted of quercetin and kaempferol glycoside derivatives. Among the studied tomato accessions, it was possible to identify those that stand out for the analysed bioactive traits. These findings highlighted the interest of using Portuguese tomato germplasm in breeding programs or of reintroducing into cultivation these local varieties used for fresh consumption.

Genetic engineering of the biosynthesis of glycinebetaine enhances the fruit development and size of tomato

Glycinebetaine has been widely considered as an effective protectant against abiotic stress in plants, and also found to promote plant growth under normal growing conditions, especially during the reproductive stage. Betaine aldehyde dehydrogenase (BADH) and choline oxidase (COD) are two key enzymes which have been used to confer glycinebetaine synthesis in plant which normally does not synthesis glycinebetaine. In this study, we used the tomato (Solanum lycopersicum, cv 'Moneymaker') plants of wild-type and the transgenic lines codA (L1, L2) and BADH (2, 46), which were transformed with codA and BADH, respectively, to study the impact of glycinebetaine on tomato fruit development. Our results showed that the codA and BADH transgenes induced the formation of enlarged flowers and fruits in transgenic tomato plants. In addition, the transgenic tomato plants had a higher photosynthetic rate, higher assimilates content, and higher leaf chlorophyll content than the wild-type plants. We also found that the enlargement of fruit size was related to the contents of phytohormones, such as auxin, brassinolide, gibberellin, and cytokinin. Additionally, qPCR results indicated that the expressions levels of certain genes related to fruit growth and development were also elevated in transgenic plants. Finally, transcriptome sequencing results revealed that the differences in the levels of gene expression in tomato fruit between the transgenic and wild-type plants were observed in multiple pathways, predominantly those of photosynthesis, DNA replication, plant hormone signal transduction, and biosynthesis. Taken together, our results suggest that glycinebetaine promotes tomato fruit development via multiple pathways. We propose that genetic engineering of glycinebetaine synthesis offers a novel approach to enhance the productivity of tomato and other crop plants.

Untargeted and Targeted Metabolomics and Tryptophan Decarboxylase In Vivo Characterization Provide Novel Insight on the Development of Kiwifruits (Actinidia deliciosa)

Kiwifruit (Actinidia deliciosa cv. Hayward) is a commercially important crop with highly nutritional green fleshy fruits. The post-harvest maturation of the fruits is well characterized, but little is known about the metabolic changes that occur during fruit development. Here we used untargeted metabolomics to characterize the non-volatile metabolite profile of kiwifruits collected at different time points after anthesis, revealing profound metabolic changes before the onset of ripening including the depletion of many classes of phenolic compounds. In contrast, the phytohormone abscisic acid accumulated during development and ripening, along with two indolamines (serotonin and its precursor tryptamine), and these were monitored in greater detail by targeted metabolomics. The role of indolamines in kiwifruit development is completely unknown, so we also characterized the identity of genes encoding tryptophan decarboxylase in A. deliciosa and its close relative A. chinensis to provide insight into the corresponding biological processes. Our results indicate that abscisic acid and indolamines fulfill unrecognized functions in the development and ripening of kiwifruits.

Identification of quantitative trait loci and candidate genes for primary metabolite content in strawberry fruit

Improvement of nutritional and organoleptic quality of fruits is a key goal in current strawberry breeding programs. The ratio of sugars to acids is a determinant factor contributing to fruit liking, although different sugars and acids contribute in varying degrees to this complex trait. A segregating F1 population of 95 individuals, previously characterized for several fruit quality characters, was used to map during 2 years quantitative trait loci (QTL) for 50 primary metabolites, l-ascorbic acid (L-AA) and other related traits such as soluble solid content (SSC), titratable acidity (TA), and pH. A total of 133 mQTL were detected above the established thresholds for 44 traits. Only 12.9% of QTL were detected in the 2 years, suggesting a large environmental influence on primary metabolite content. An objective of this study was the identification of key metabolites that were associated to the overall variation in SSC and acidity. As it was observed in previous studies, a number of QTL controlling several metabolites and traits were co-located in homoeology group V (HG V). mQTL controlling a large variance in raffinose, sucrose, succinic acid, and L-AA were detected in approximate the same chromosomal regions of different homoeologous linkage groups belonging to HG V. Candidate genes for selected mQTL are proposed based on their co-localization, on the predicted function, and their differential gene expression among contrasting F1 progeny lines. RNA-seq analysis from progeny lines contrasting in L-AA content detected 826 differentially expressed genes and identified Mannose-6-phosphate isomerase, FaM6PI1, as a candidate gene contributing to natural variation in ascorbic acid in strawberry fruit.

The Chemistry behind Tomato Quality

Tomato is one of the most widely consumed fresh vegetables in the industrialized world and an important source of healthy constituents of the human diet. Despite the unique flavor characteristics of tomatoes, which make them extremely valuable in cooking, and their recognized beneficial role in the diet, the quality of tomato was traditionally only considered in connection to external appearances. As it happened with other highly requested crops, breeding programs of tomato focused their efforts on developing new varieties with higher yields and stress resistance, with better uniformity in fruit size, brighter color and prolonged shelf life. The downside of these strategies was that organoleptic features and nutritional value were often neglected, with a detrimental effect on commercial tomatoes. Over the last years, there has been an increase in consumers’ demand for tasty and healthy products. This aspect, paired with novel and multidisciplinary approaches to tomato research, allowed both sensory and nutritional qualities to be reconsidered as valuable parameters in breeding. In this review we describe the main chemical constituents of tomato, focusing on the flavor compounds (both volatile and non-volatile compounds) and secondary metabolites. Particular attention is paid to their beneficial effects on human health and their relevance to the overall quality of tomato.

Metabolomics 20 years on: what have we learned and what hurdles remain?

The term metabolome was coined in 1998, by analogy to genome, transcriptome and proteome. The first research papers using the terms metabolomics, metabonomics, metabolic profiling or metabolite profiling were published shortly thereafter. In this short review we reflect on the major achievements brought about by the use of these approaches, and document the knowledge and technology gaps that are currently constraining its further development. Finally, we detail why we think that the time is ripe to refocus our efforts on the understanding of metabolic function.

Influence of Fruit Ripening on Color, Organic Acid Contents, Capsaicinoids, Aroma Compounds, and Antioxidant Capacity of Shimatogarashi (Capsicum frutescens)

Shimatogarashi (Capsicum frutescens) is a typical chili pepper domesticated in southern Japan. Important traits of Shimatogarashi peppers, such as color; proportion of organic acids, capsaicinoids, and aromatic compounds; and antioxidant activity in three stages of maturity (green (immature), orange (turning), and red (mature) stages) were characterized. The results indicated that the concentration of organic acids, including ascorbic, citric, and malic acid, increased during ripening. In addition, the amount of capsaicinoids, which are responsible for the pungent taste of chili peppers, increased as the fruit matured to the orange and red stages. The volatile compound profile of Shimatogarashi was dominated by the presence of esters, which mainly contributed to fruity notes. The total amount of volatile compounds analyzed by gas chromatography-headspace solid-phase microextraction (GC-HS-SPME), especially esters, decreased as the fruit changed in color from green to red. This was in contrast to the amount of terpenoids, especially limonene, which increased at the red stage, denoting a change in flavor from fruity to a more citrus-like aroma. Based on the total phenolic content (TPC), the oxygen radical absorbance capacity (ORAC) and the diphenylpicrylhydrazyl (DPPH) free radical method, the antioxidant capacity of Shimatogarashi showed an increase at the mature red stage. However, while the red stage showed higher pungency and antioxidant capacity as well as an attractive color, the results of aromatic compound analysis revealed that the immature green stage had the advantages of having pleasant fruity smell, making it suitable for use in condiments.

Unraveling the complexity of transcriptomic, metabolomic and quality environmental response of tomato fruit

BACKGROUND

The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sensorial attributes. We used a systems biology approach to elucidate the complex interacting mechanisms regulating the plasticity of sensorial traits. To investigate environmentally challenged transcriptomic and metabolomic remodeling and evaluate the organoleptic consequences of such variations we grown three tomato varieties, Heinz 1706, whose genome was sequenced as reference and two "local" ones, San Marzano and Vesuviano in two different locations of Campania region (Italy).

RESULTS

Responses to environment were more pronounced in the two "local" genotypes, rather than in the Heinz 1706. The overall genetic composition of each genotype, acting in trans, modulated the specific response to environment. Duplicated genes and transcription factors, establishing different number of network connections by gaining or losing links, play a dominant role in shaping organoleptic profile. The fundamental role of cell wall metabolism in tuning all the quality attributes, including the sensorial perception, was also highlighted.

CONCLUSIONS

Although similar fruit-related quality processes are activated in the same environment, different tomato genotypes follow distinct transcriptomic, metabolomic and sensorial trajectories depending on their own genetic makeup.

Effects of Al3+ and La3+ Trivalent Metal Ions on Tomato Fruit Proteomes

The tomato (Solanum lycopersicum) ripening process from mature green (MG) to turning and then to red stages is accompanied by the occurrences of physiological and biochemical reactions, which ultimately result in the formation of the flavor, color and texture of ripe fruits. The two trivalent metal ions Al³⁺ and La³⁺ are known to induce different levels of phytotoxicity in suppressing root growth. This paper aims to understand the impacts of these two metal ions on tomato fruit proteomes. Tomato ‘Micro-Tom’ plants were grown in a hydroponic culture system supplemented with 50 μM aluminum sulfate (Al₂ (SO4)₃.18H₂O) for Al³⁺ or La₂(SO₄)₃ for La³⁺. Quantitative proteomics analysis, using isobaric tags for relative and absolute quantitation, were performed for fruits at MG, turning and red stages. Results show that in MG tomatoes, proteins involved in protein biosynthesis, photosynthesis and primary carbohydrate metabolisms were at a significantly lower level in Al-treated compared to La-treated plants. For the turning and red tomatoes, only a few proteins of significant differences between the two metal treatments were identified. Results from this study indicate that compared to La³⁺, Al³⁺ had a greater influence on the basic biological activities in green tomatoes, but such an impact became indistinguishable as tomatoes matured into the late ripening stages.

Abiotic Stress Response to As and As+Si, Composite Reprogramming of Fruit Metabolites in Tomato Cultivars

The toxic element arsenic interacts with the beneficial element silicon at many levels of the plant metabolism. The ability of the tomato plant to take up and translocate As into its fruit has risen concerns that it could facilitate the entry of this element into the human food chain above the admitted level. Here, the fruit of two contrasting tomato cultivars, Aragon and Gladis, were evaluated following exposures of either 48 h or 14 days to As-contaminated irrigation water, with or without supplementary Si. The focus was on selected biochemical stress response indicators to dissect metabolic fruit reprogramming induced by As and Si. A multivariate statistical approach was utilized to establish the relationship between tissue As and Si concentrations and selected biochemical aspects of the stress response mechanisms to identify a set of relevant stress response descriptors. This resulted in the recognition of strong cultivar and temporal effects on metabolic and biochemical stress parameters following the treatments. In this paper the metabolic changes in H₂O₂ content, lipid peroxidation, lycopene and carotenoids content, ascorbate and GSH redox state, total phenolics, ABTS and DPPH radicals inhibition were in favor of an oxidative stress. The significance of some of these parameters as reliable arsenic exposition biomarkers is discussed in the context of the limited knowledge on the As-induced stress response mechanisms at the level of the ripening fruit which presents a distinctive molecular background dissimilar from roots and shoots.

Interference with ethylene perception at receptor level sheds light on auxin and transcriptional circuits associated with the climacteric ripening of apple fruit (Malus x domestica Borkh.)

Apple (Malus x domestica Borkh.) is a model species for studying the metabolic changes that occur at the onset of ripening in fruit crops, and the physiological mechanisms that are governed by the hormone ethylene. In this study, to dissect the climacteric interplay in apple, a multidisciplinary approach was employed. To this end, a comprehensive analysis of gene expression together with the investigation of several physiological entities (texture, volatilome and content of polyphenolic compounds) was performed throughout fruit development and ripening. The transcriptomic profiling was conducted with two microarray platforms: a dedicated custom array (iRIPE) and a whole genome array specifically enriched with ripening-related genes for apple (WGAA). The transcriptomic and phenotypic changes following the application of 1-methylcyclopropene (1-MCP), an ethylene inhibitor leading to important modifications in overall fruit physiology, were also highlighted. The integrative comparative network analysis showed both negative and positive correlations between ripening-related transcripts and the accumulation of specific metabolites or texture components. The ripening distortion caused by the inhibition of ethylene perception, in addition to affecting the ethylene pathway, stimulated the de-repression of auxin-related genes, transcription factors and photosynthetic genes. Overall, the comprehensive repertoire of results obtained here advances the elucidation of the multi-layered climacteric mechanism of fruit ripening, thus suggesting a possible transcriptional circuit governed by hormones and transcription factors.

Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development

Development and ripening of tomato fruit are precisely controlled by transcriptional regulation, which depends on the orchestrated accessibility of regulatory proteins to promoters and other cis-regulatory DNA elements. This accessibility and its effect on gene expression play a major role in defining the developmental process. To understand the regulatory mechanism and functional elements modulating morphological and anatomical changes during fruit development, we generated genome-wide high-resolution maps of DNase I hypersensitive sites (DHSs) from the fruit tissues of the tomato cultivar "Moneymaker" at 20 days post anthesis as well as break stage. By exploring variation of DHSs across fruit development stages, we pinpointed the most likely hypersensitive sites related to development-specific genes. By detecting binding motifs on DHSs of these development-specific genes or genes in the ascorbic acid biosynthetic pathway, we revealed the common regulatory elements contributing to coordinating gene transcription of plant ripening and specialized metabolic pathways. Our results contribute to a better understanding of the regulatory dynamics of genes involved in tomato fruit development and ripening.