Tomato fruit photosynthesis is seemingly unimportant in primary metabolism and ripening but plays a considerable role in seed development

Evaluation of high temperature impacts and nanotechnology as a shield against temperature stress on tomatoes - A review

Rising temperature due to changing climate significantly impacts the production of tomato. The morpho-physiological functions of tomato such as gas exchange, growth and development, flowering, fruit setting, quality, fruit size, weight that can influence the yield and production is drastically affected by higher temperatures. Among the growth stages of tomato, flowering and fruit setting stage is highly vulnerable to high temperature resulting in reduced flower numbers, increased flower abortion, stigma exertion, abnormal ovule, reduced pollen germination, pollen numbers, pollen tube development, pollen viability and increased male sterility. The flower to fruit ratio and duration also highly influenced by higher temperatures. It significantly reduced fruit set, fruit number, weight and quality (Lycopene, carotenoids), changing sugars and acids ratio. Apart from day temperature, the asymmetrically rising night temperature and difference in day and night temperature pattern plays a considerable role in physiological and biochemical processes of tomato. Nanotechnology proves to be a successful tool for sustainable production of tomato than many other alternative mitigation strategies due to its localized action, low quantity requirement, minimal wastage, less residues, eco friendliness, biodegradability, multifunctionality, synergistic capabilities and higher plant productivity. It imitates the antioxidant enzymes playing active role in physiological functions in tomato thereby inducing tolerance mechanisms for managing high temperature stress. Further research should focus on use of several other nanoparticles that have potential but not yet experimented on tomato to mitigate heat stress and producing biodegradable, green synthesized nanoparticles that are cost effective and affordable to farmers.

Non-Foliar Photosynthesis in Pea (Pisum sativum L.) Plants: Beyond the Leaves to Inside the Seeds

In addition to leaves, photosynthesis can occur in other green plant organs, including developing seeds of many crops. While the majority of studies examining photosynthesis are concentrated on the leaf level, the role of other green tissues in the production of total photoassimilates has been largely overlooked. The present work studies the photosynthetic behavior of leaves and non-foliar (pericarps, coats, and cotyledons) organs of pea (Pisum sativum L.) plants at the middle stage of seed maturation. The Chl a fluorescence transient was examined based on OJIP kinetics using the FluorPen FP 110. A discrepancy was observed between the performance index (PIABS) for foliar and non-foliar plant tissues, with the highest level noted in the leaves. The number of absorbed photons (ABS) and captured energy flow (TRo) per reaction center (RC) were elevated in the non-foliar tissues, which resulted in a faster reduction in QA. Conversely, the energy dissipation flux per RC (DIo/RC and PHI_Do) indicated an increase in the overall dissipation potential of active reaction centers of photosystem II. This phenomenon was attributed to the presence of a higher number of inactive RCs in tissues that had developed under low light intensity. Furthermore, the expression of genes associated with proteins and enzymes that regulate ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCo) activity was observed, including chaperonins Cpn60α and Cpn60β, RuBisCO activase, as well as phosphoribulokinase. The expression of these genes was found to differ between foliar and non-foliar tissues, indicating that the activation state of RuBisCO may be modified in response to light intensity. Overall, the present study provides insights into the mechanisms by which non-foliar green tissues of plants adapt to efficient light capture and utilization under low light conditions.

Integrative analysis of the methylome and transcriptome of tomato fruit (Solanum lycopersicum L.) induced by postharvest handling

Tomato fruit ripening is triggered by the demethylation of key genes, which alters their transcriptional levels thereby initiating and propagating a cascade of physiological events. What is unknown is how these processes are altered when fruit are ripened using postharvest practices to extend shelf-life, as these practices often reduce fruit quality. To address this, postharvest handling-induced changes in the fruit DNA methylome and transcriptome, and how they correlate with ripening speed, and ripening indicators such as ethylene, abscisic acid, and carotenoids, were assessed. This study comprehensively connected changes in physiological events with dynamic molecular changes. Ripening fruit that reached 'Turning' (T) after dark storage at 20°C, 12.5°C, or 5°C chilling (followed by 20°C rewarming) were compared to fresh-harvest fruit 'FHT'. Fruit stored at 12.5°C had the biggest epigenetic marks and alterations in gene expression, exceeding changes induced by postharvest chilling. Fruit physiological and chronological age were uncoupled at 12.5°C, as the time-to-ripening was the longest. Fruit ripening to Turning at 12.5°C was not climacteric; there was no respiratory or ethylene burst, rather, fruit were high in abscisic acid. Clear differentiation between postharvest-ripened and 'FHT' was evident in the methylome and transcriptome. Higher expression of photosynthetic genes and chlorophyll levels in 'FHT' fruit pointed to light as influencing the molecular changes in fruit ripening. Finally, correlative analyses of the -omics data putatively identified genes regulated by DNA methylation. Collectively, these data improve our interpretation of how tomato fruit ripening patterns are altered by postharvest practices, and long-term are expected to help improve fruit quality.

Ethylene promotes fruit ripening initiation by downregulating photosynthesis, enhancing abscisic acid and suppressing jasmonic acid in blueberry (Vaccinium ashei)

BACKGROUND

Blueberry fruit exhibit atypical climacteric ripening with a non-auto-catalytic increase in ethylene coincident with initiation of ripening. Further, application of ethephon, an ethylene-releasing plant growth regulator, accelerates ripening by increasing the proportion of ripe (blue) fruit as compared to the control treatment. To investigate the mechanistic role of ethylene in regulating blueberry ripening, we performed transcriptome analysis on fruit treated with ethephon, an ethylene-releasing plant growth regulator.

RESULTS

RNA-Sequencing was performed on two sets of rabbiteye blueberry ('Powderblue') fruit: (1) fruit from divergent developmental stages; and (2) fruit treated with ethephon, an ethylene-releasing compound. Differentially expressed genes (DEGs) from divergent developmental stages clustered into nine groups, among which cluster 1 displayed reduction in expression during ripening initiation and was enriched with photosynthesis related genes, while cluster 7 displayed increased expression during ripening and was enriched with aromatic-amino acid family catabolism genes, suggesting stimulation of anthocyanin biosynthesis. More DEGs were apparent at 1 day after ethephon treatment suggesting its early influence during ripening initiation. Overall, a higher number of genes were downregulated in response to ethylene. Many of these overlapped with cluster 1 genes, indicating that ethylene-mediated downregulation of photosynthesis is an important developmental event during the ripening transition. Analyses of DEGs in response to ethylene also indicated interplay among phytohormones. Ethylene positively regulated abscisic acid (ABA), negatively regulated jasmonates (JAs), and influenced auxin (IAA) metabolism and signaling genes. Phytohormone quantification supported these effects of ethylene, indicating coordination of blueberry fruit ripening by ethylene.

CONCLUSION

This study provides insights into the role of ethylene in blueberry fruit ripening. Ethylene initiates blueberry ripening by downregulating photosynthesis-related genes. Also, ethylene regulates phytohormone-metabolism and signaling related genes, increases ABA, and decreases JA concentrations. Together, these results indicate that interplay among multiple phytohormones regulates the progression of ripening, and that ethylene is an important coordinator of such interactions during blueberry fruit ripening.

Physiology, genomics, and evolutionary aspects of desert plants

BACKGROUND

Despite the exposure to arid environmental conditions across the globe ultimately hampering the sustainability of the living organism, few plant species are equipped with several unique genotypic, biochemical, and physiological features to counter such harsh conditions. Physiologically, they have evolved with reduced leaf size, spines, waxy cuticles, thick leaves, succulent hydrenchyma, sclerophyll, chloroembryo, and photosynthesis in nonfoliar and other parts. At the biochemical level, they are evolved to perform efficient photosynthesis through Crassulacean acid metabolism (CAM) and C4 pathways with the formation of oxaloacetic acid (Hatch-Slack pathway) instead of the C3 pathway. Additionally, comparative genomics with existing data provides ample evidence of the xerophytic plants' positive selection to adapt to the arid environment. However, adding more high-throughput sequencing of xerophyte plant species is further required for a comparative genomic study toward trait discovery related to survival. Learning from the mechanism to survive in harsh conditions could pave the way to engineer crops for future sustainable agriculture.

AIM OF THE REVIEW

The distinct physiology of desert plants allows them to survive in harsh environments. However, the genomic composition also contributes significantly to this and requires great attention. This review emphasizes the physiological and genomic adaptation of desert plants. Other important parameters, such as desert biodiversity and photosynthetic strategy, are also discussed with recent progress in the field. Overall, this review discusses the different features of desert plants, which prepares them for harsh conditions intending to translate knowledge to engineer plant species for sustainable agriculture.

KEY SCIENTIFIC CONCEPTS OF REVIEW

This review comprehensively presents the physiology, molecular mechanism, and genomics of desert plants aimed towards engineering a sustainable crop.

The SlGRAS9-SlZHD17 transcriptional cascade regulates chlorophyll and carbohydrate metabolism contributing to fruit quality traits in tomato

Some essential components of fleshy fruits are dependent on photosynthetic activity and carbohydrate metabolism. Nevertheless, the regulatory mechanisms linking chlorophyll and carbohydrate metabolism remain partially understood. Here, we uncovered the role of SlGRAS9 and SlZHD17 transcription factors in controlling chlorophyll and carbohydrate accumulation in tomato fruit. Knockout or knockdown of SlGRAS9 or SlZHD17 resulted in marked increase in chlorophyll content, reprogrammed chloroplast biogenesis and enhanced accumulation of starch and soluble sugars. Combined genome-wide transcriptomic profiling and promoter-binding experiments unveiled a complex mechanism in which the SlGRAS9/SlZHD17 regulatory module modulates the expression of chloroplast and sugar metabolism either via a sequential transcriptional cascade or through binding of both TFs to the same gene promoters, or, alternatively, via parallel pathways where each of the TFs act on different target genes. For instance, the regulation of SlAGPaseS1 and SlSUS1 is mediated by SlZHD17 whereas that of SlVI and SlGLK1 occurs only through SlGRAS9 without the intervention of SlZHD17. Both SlGRAS9 and SlZHD17 can also directly bind the promoter of SlPOR-B to regulate its expression. Taken together, our findings uncover two important regulators acting synergistically to manipulate chlorophyll and carbohydrate accumulation and provide new potential breeding targets for improving fruit quality in fleshy fruits.

Ketocarotenoid production in tomato triggers metabolic reprogramming and cellular adaptation: The quest for homeostasis

Plants are sessile and therefore have developed an extraordinary capacity to adapt to external signals. Here, the focus is on the plasticity of the plant cell to respond to new intracellular cues. Ketocarotenoids are high-value natural red pigments with potent antioxidant activity. In the present study, system-level analyses have revealed that the heterologous biosynthesis of ketocarotenoids in tomato initiated a series of cellular and metabolic mechanisms to cope with the formation of metabolites that are non-endogenous to the plant. The broad multilevel changes were linked to, among others, (i) the remodelling of the plastidial membrane, where the synthesis and storage of ketocarotenoids occurs; (ii) the recruiting of core metabolic pathways for the generation of metabolite precursors and energy; and (iii) redox control. The involvement of the metabolites as regulators of cellular processes shown here reinforces their pivotal role suggested in the remodelled 'central dogma' concept. Furthermore, the role of metabolic reprogramming to ensure cellular homeostasis is proposed.

Novel transcriptome networks are associated with adaptation of capsicum fruit development to a light-blocking glasshouse film

Light-blocking films (LBFs) can contribute to significant energy savings for protected cropping via altering light transmitting, such as UVA, photosynthetically active radiation, blue and red spectra affecting photosynthesis, and capsicum yield. Here, we investigated the effects of LBF on orange color capsicum (O06614, Capsicum annuum L.) fruit transcriptome at 35 (mature green) and 65 (mature ripe) days after pollination (DAP) relative to untreated control in a high-technology glasshouse. The results of targeted metabolites showed that LBF significantly promotes the percentage of lutein but decreased the percentage of zeaxanthin and neoxanthin only at 35 DAP. At 35 DAP, fruits were less impacted by LBF treatment (versus control) with a total of 1,192 differentially expressed genes (DEGs) compared with that at 65 DAP with 2,654 DEGs. Response to stress and response to light stimulus in biological process of Gene Ontology were found in 65-DAP fruits under LBF vs. control, and clustering analysis revealed a predominant role of light receptors and phytohormone signaling transduction as well as starch and sucrose metabolism in LBF adaptation. The light-signaling DEGs, UV light receptor UVR8, transcription factors phytochrome-interacting factor 4 (PIF4), and an E3 ubiquitin ligase (COP1) were significantly downregulated at 65 DAP. Moreover, key DEGs in starch and sucrose metabolism (SUS, SUC, and INV), carotenoid synthesis (PSY2 and BCH1), ascorbic acid biosynthesis (VTC2, AAO, and GME), abscisic acid (ABA) signaling (NCED3, ABA2, AO4, and PYL2/4), and phenylpropanoid biosynthesis (PAL and DFR) are important for the adaptation of 65-DAP fruits to LBF. Our results provide new candidate genes for improving quality traits of low-light adaptation of capsicum in protected cropping.

Loss of S-nitrosoglutathione reductase disturbs phytohormone homeostasis and regulates shoot side branching and fruit growth in tomato

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

Transcriptome and Metabolome Provide Insights into Fruit Ripening of Cherry Tomato (Solanum lycopersicum var. cerasiforme)

Insights into flavor formation during fruit ripening can guide the development of breeding strategies that balance consumer and producer needs. Cherry tomatoes possess a distinctive taste, yet research on quality formation is limited. Here, metabolomic and transcriptomic analyses were conducted on different ripening stages. The results revealed differentially accumulated metabolites during fruit ripening, providing candidate metabolites related to flavor. Interestingly, several key flavor-related metabolites already reached a steady level at the mature green stage. Transcriptomic analysis revealed that the expression levels of the majority of genes tended to stabilize after the pink stage. Enrichment analysis demonstrated that changes in metabolic and biosynthetic pathways were evident throughout the entire process of fruit ripening. Compared to disease resistance and fruit color genes, genes related to flavor and firmness may have a broader impact on the accumulation of metabolites. Furthermore, we discovered the interconversion patterns between glutamic acid and glutamine, as well as the biosynthesis patterns of flavonoids. These findings contribute to our understanding of fruit quality formation mechanisms and support breeding programs aimed at improving fruit quality traits.

Fruit Photosynthesis: More to Know about Where, How and Why

Not only leaves but also other plant organs and structures typically considered as carbon sinks, including stems, roots, flowers, fruits and seeds, may exhibit photosynthetic activity. There is still a lack of a coherent and systematized body of knowledge and consensus on the role(s) of photosynthesis in these "sink" organs. With regard to fruits, their actual photosynthetic activity is influenced by a range of properties, including fruit anatomy, histology, physiology, development and the surrounding microclimate. At early stages of development fruits generally contain high levels of chlorophylls, a high density of functional stomata and thin cuticles. While some plant species retain functional chloroplasts in their fruits upon subsequent development or ripening, most species undergo a disintegration of the fruit chloroplast grana and reduction in stomata functionality, thus limiting gas exchange. In addition, the increase in fruit volume hinders light penetration and access to CO₂, also reducing photosynthetic activity. This review aimed to compile information on aspects related to fruit photosynthesis, from fruit characteristics to ecological drivers, and to address the following challenging biological questions: why does a fruit show photosynthetic activity and what could be its functions? Overall, there is a body of evidence to support the hypothesis that photosynthesis in fruits is key to locally providing: ATP and NADPH, which are both fundamental for several demanding biosynthetic pathways (e.g., synthesis of fatty acids); O₂, to prevent hypoxia in its inner tissues including seeds; and carbon skeletons, which can fuel the biosynthesis of primary and secondary metabolites important for the growth of fruits and for spreading, survival and germination of their seed (e.g., sugars, flavonoids, tannins, lipids). At the same time, both primary and secondary metabolites present in fruits and seeds are key to human life, for instance as sources for nutrition, bioactives, oils and other economically important compounds or components. Understanding the functions of photosynthesis in fruits is pivotal to crop management, providing a rationale for manipulating microenvironmental conditions and the expression of key photosynthetic genes, which may help growers or breeders to optimize development, composition, yield or other economically important fruit quality aspects.

Investigating the Physiological and Molecular Responses of Solanum lycopersicum hp Mutants to Light of Different Quality for Biotechnological Applications

The effect of the light of different spectral compositions, white fluorescent light (WFL), red light (RL, 660 nm), blue light (BL, 450 nm), green light (GL, 525 nm), and white LED light (WL, 450 + 580 nm), on the physiological parameters of Solanum lycopersicum 3005 hp-2 (defective for a DET1 gene) and 4012 hp-1w; 3538 hp-1; 0279 hp-1.2 (defective for a DDB1a gene) photomorphogenetic mutants was studied. The parameters of the primary photochemical processes of photosynthesis, photosynthetic and transpiration rates, the antioxidant capacity of low-molecular weight antioxidants, the content of the total phenolic compounds, including flavonoids, and the expression of the genes involved in light signaling and biosynthesis of secondary metabolites were determined. Under BL, the 3005 hp-2 mutant showed the highest nonenzymatic antioxidant activity, which occurred to a greater extent due to the increase in flavonoid content. At the same time, under BL, the number of secretory trichomes on the surface of the leaves of all mutants increased equally. This suggests the accumulation of flavonoids inside leaf cells rather than in trichomes on the leaf surface. The data obtained indicate the possibility of using the hp-2 mutant for biotechnology to increase its nutritional value by enhancing the content of flavonoids and other antioxidants by modulating the spectral composition of light.

Intra-Specific Variation in Desiccation Tolerance of Citrus sinensis 'bingtangcheng' (L.) Seeds under Different Environmental Conditions in China

Intra-specific variation in seed storage behaviour observed in several species has been related to different maternal environments. However, the particular environmental conditions and molecular processes involved in intra-specific variation of desiccation tolerance remain unclear. We chose Citrus sinensis 'bingtangcheng' for the present study due to its known variability in desiccation tolerance amongst seed lots. Six seed lots of mature fruits were harvested across China and systematically compared for drying sensitivity. Annual sunshine hours and average temperature from December to May showed positive correlations with the level of seed survival of dehydration. Transcriptional analysis indicated significant variation in gene expression between relatively desiccation-tolerant (DT) and -sensitive (DS) seed lots after harvest. The major genes involved in late seed maturation, such as heat shock proteins, showed higher expression in the DT seed lot. Following the imposition of drying, 80% of stress-responsive genes in the DS seed lot changed to the stable levels seen in the DT seed lot prior to and post-desiccation. However, the changes in expression of stress-responsive genes in DS seeds did not improve their tolerance to desiccation. Thus, higher desiccation tolerance of Citrus sinensis 'bingtangcheng' seeds is modulated by the maternal environment (e.g., higher annual sunshine hours and seasonal temperature) during seed development and involves stable expression levels of stress-responsive genes.

Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress

Water availability influences all aspects of plant growth and development; however, most studies of plant responses to drought have focused on vegetative organs, notably roots and leaves. Far less is known about the molecular bases of drought acclimation responses in fruits, which are complex organs with distinct tissue types. To obtain a more comprehensive picture of the molecular mechanisms governing fruit development under drought, we profiled the transcriptomes of a spectrum of fruit tissues from tomato (Solanum lycopersicum), spanning early growth through ripening and collected from plants grown under varying intensities of water stress. In addition, we compared transcriptional changes in fruit with those in leaves to highlight different and conserved transcriptome signatures in vegetative and reproductive organs. We observed extensive and diverse genetic reprogramming in different fruit tissues and leaves, each associated with a unique response to drought acclimation. These included major transcriptional shifts in the placenta of growing fruit and in the seeds of ripe fruit related to cell growth and epigenetic regulation, respectively. Changes in metabolic and hormonal pathways, such as those related to starch, carotenoids, jasmonic acid, and ethylene metabolism, were associated with distinct fruit tissues and developmental stages. Gene coexpression network analysis provided further insights into the tissue-specific regulation of distinct responses to water stress. Our data highlight the spatiotemporal specificity of drought responses in tomato fruit and indicate known and unrevealed molecular regulatory mechanisms involved in drought acclimation, during both vegetative and reproductive stages of development.

Glutamate 1-semialdehyde aminotransferase is connected to GluTR by GluTR-binding protein and contributes to the rate-limiting step of 5-aminolevulinic acid synthesis

Tetrapyrroles play fundamental roles in crucial processes including photosynthesis, respiration, and catalysis. In plants, 5-aminolevulinic acid (ALA) is the common precursor of tetrapyrroles. ALA is synthesized from activated glutamate by the enzymes glutamyl-tRNA reductase (GluTR) and glutamate-1-semialdehyde aminotransferase (GSAAT). ALA synthesis is recognized as the rate-limiting step in this pathway. We aimed to explore the contribution of GSAAT to the control of ALA synthesis and the formation of a protein complex with GluTR. In Arabidopsis thaliana, two genes encode GSAAT isoforms: GSA1 and GSA2. A comparison of two GSA knockout mutants with the wild-type revealed the correlation of reduced GSAAT activity and ALA-synthesizing capacity in leaves with lower chlorophyll content. Growth and green pigmentation were more severely impaired in gsa2 than in gsa1, indicating the predominant role of GSAAT2 in ALA synthesis. Interestingly, GluTR accumulated to higher levels in gsa2 than in the wild-type and was mainly associated with the plastid membrane. We propose that the GSAAT content modulates the amount of soluble GluTR available for ALA synthesis. Several different biochemical approaches revealed the GSAAT-GluTR interaction through the assistance of GluTR-binding protein (GBP). A modeled structure of the tripartite protein complex indicated that GBP mediates the stable association of GluTR and GSAAT for adequate ALA synthesis.

Whole Transcriptome Analyses of Apricots and Japanese Plum Fruits after 1-MCP (Ethylene-Inhibitor) and Ethrel (Ethylene-Precursor) Treatments Reveal New Insights into the Physiology of the Ripening Process

The physiology of Prunus fruit ripening is a complex and not completely understood process. To improve this knowledge, postharvest behavior during the shelf-life period at the transcriptomic level has been studied using high-throughput sequencing analysis (RNA-Seq). Monitoring of fruits has been analyzed after different ethylene regulator treatments, including 1-MCP (ethylene-inhibitor) and Ethrel (ethylene-precursor) in two contrasting selected apricot (Prunus armeniaca L.) and Japanese plum (P. salicina L.) cultivars, ‘Goldrich’ and ‘Santa Rosa’. KEEG and protein–protein interaction network analysis unveiled that the most significant metabolic pathways involved in the ripening process were photosynthesis and plant hormone signal transduction. In addition, previously discovered genes linked to fruit ripening, such as pectinesterase or auxin-responsive protein, have been confirmed as the main genes involved in this process. Genes encoding pectinesterase in the pentose and glucuronate interconversions pathway were the most overexpressed in both species, being upregulated by Ethrel. On the other hand, auxin-responsive protein IAA and aquaporin PIP were both upregulated by 1-MCP in ‘Goldrich’ and ‘Santa Rosa’, respectively. Results also showed the upregulation of chitinase and glutaredoxin 3 after Ethrel treatment in ‘Goldrich’ and ‘Santa Rosa’, respectively, while photosystem I subunit V psaG (photosynthesis) was upregulated after 1-MCP in both species. Furthermore, the overexpression of genes encoding GDP-L-galactose and ferredoxin in the ascorbate and aldarate metabolism and photosynthesis pathways caused by 1-MCP favored antioxidant activity and therefore slowed down the fruit senescence process.

Anatomy and development of the edible fruits of Cordiera concolor (Rubiaceae)

A comprehensive study on the fruit anatomy and development of Cordiera concolor was carried out to establish the origin of the gelatinous tissue surrounding the seeds at maturity. Cordiera currently belongs to tribe Cordiereae, forming part of the species-rich lineage called Gardenieae complex. Most genera of Gardenieae complex has many-seeded fleshy fruits, with seeds usually imbedded in a pulp, which historically was considered of a placental nature. For the histological analyses, fruits at different stages of development were fixed in formalin-acetic acid-alcohol and examined with light microscopy. The endocarp has no woody consistency, it is what classifies a fruit as berry. The pericarp is differentiated into three histological zones: 1) the exocarp, formed of the epidermis and the sub-epidermal tannin cells, 2) the mesocarp, consisting of parenchyma with tannins and druses, and 3) the endocarp, derived from the internal epidermis of the ovary. The placental tissue has little development during the formation of the pericarp. We concluded that the gelatinous tissue surrounding the seeds in the ripe fruit is formed of the mesocarp and endocarp. The present results disagree with the widely accepted conception of the placental origin of the gelatinous pulp surrounding the seeds in Gardenieae Complex species.

Reduced auxin signalling through the cyclophilin gene DIAGEOTROPICA impacts tomato fruit development and metabolism during ripening

Auxin is an important hormone playing crucial roles during fruit growth and ripening; however, the metabolic impact of changes in auxin signalling during tomato (Solanum lycopersicum L.) ripening remains unclear. Here, we investigated the significance of changes in auxin signalling during different stages of fruit development by analysing changes in tomato fruit quality and primary metabolism using mutants with either lower or higher auxin sensitivity [diageotropica (dgt) and entire mutants, respectively]. Altered auxin sensitivity modifies metabolism, through direct impacts on fruit respiration and fruit growth. We verified that the dgt mutant plants exhibit reductions in fruit set, total fruit dry weight, fruit size, number of seeds per fruit, and fresh weight loss during post-harvest. Sugar accumulation was associated with delayed fruit ripening in dgt, probably connected with reduced ethylene levels and respiration, coupled with a lower rate of starch degradation. In contrast, despite exhibiting parthenocarpy, increased auxin perception (entire) did not alter fruit ripening, leading to only minor changes in primary metabolism. By performing a comprehensive analysis, our results connect auxin signalling and metabolic changes during tomato fruit development, indicating that reduced auxin signalling led to extensive changes in sugar concentration and starch metabolism during tomato fruit ripening.

Autophagy modulates the metabolism and growth of tomato fruit during development

Although autophagy is a conserved mechanism operating across eukaryotes, its effects on crops and especially their metabolism has received relatively little attention. Indeed, whilst a few recent studies have used systems biology tools to look at the consequences of lack of autophagy in maize these focused on leaf tissues rather than the kernels. Here we utilized RNA interference (RNAi) to generate tomato plants that were deficient in the autophagy-regulating protease ATG4. Plants displayed an early senescence phenotype yet relatively mild changes in the foliar metabolome and were characterized by a reduced fruit yield phenotype. Metabolite profiling indicated that metabolites of ATG4-RNAi tomato leaves just exhibited minor alterations while that of fruit displayed bigger difference compared to the WT. In detail, many primary metabolites exhibited decreases in the ATG4-RNAi lines, such as proline, tryptophan and phenylalanine, while the representative secondary metabolites (quinic acid and 3-trans-caffeoylquinic acid) were present at substantially higher levels in ATG4-RNAi green fruits than in WT. Moreover, transcriptome analysis indicated that the most prominent differences were in the significant upregulation of organelle degradation genes involved in the proteasome or chloroplast vesiculation pathways, which was further confirmed by the reduced levels of chloroplastic proteins in the proteomics data. Furthermore, integration analysis of the metabolome, transcriptome and proteome data indicated that ATG4 significantly affected the lipid metabolism, chlorophyll binding proteins and chloroplast biosynthesis. These data collectively lead us to propose a more sophisticated model to explain the cellular co-ordination of the process of autophagy.

DNA and Histone Methylation Regulates Different Types of Fruit Ripening by Transcriptome and Proteome Analyses

Methylation affects different aspects of genetic material stability, gene expression regulation, and histone modification. The previous reports depicted that DNA and histone methylation regulates plant growth and development. In this study, we evaluated the effects of DNA and histone methylation on 'Hongjia' strawberry and 'Lichun' tomato. We investigated the transient transformation system for arginine methyltransferase (FvPRMT1.5) overexpression and interference and assessed the phenotypic appearance and mRNA and protein expression levels. Results depicted that changes in methylation levels caused inhibition of carotenoids and anthocyanins. Furthermore, the profiling of aroma components was altered in response to 5-azacytidine. DNA hypomethylation induced the expression levels of genes involved in photosynthesis, flavonoid biosynthesis, and hormone signal transduction pathways, while the expression levels of related proteins showed a downward trend. Overall, we proposed a model that reveals the possible regulatory effects of DNA and histone methylation during fruit ripening.

Comparative transcriptomic analysis of apple and peach fruits: insights into fruit type specification

Fruits represent key evolutionary innovations in angiosperms and exhibit diverse types adapted for seed dissemination. However, the mechanisms that underlie fruit type diversity are not understood. The Rosaceae family comprises many different fruit types, including 'pome' and 'drupe' fruits, and hence is an excellent family for investigating the genetic basis of fruit type specification. Using comparative transcriptomics, we investigated the molecular events that correlate with pome (apple) and drupe (peach) fleshy fruit development, focusing on the earliest stages of fruit initiation. We identified PI and TM6, MADS box genes whose expression negatively correlates with fruit flesh-forming tissues irrespective of fruit type. In addition, the MADS box gene FBP9 is expressed in fruit-forming tissues in both species, and was lost multiple times in the genomes of dry-fruit-forming eudicots including Arabidopsis. Network analysis reveals co-expression between FBP9 and photosynthesis genes in both apple and peach, suggesting that FBP9 and photosynthesis may both promote fleshy fruit development. The large transcriptomic datasets at the earliest stages of pome and drupe fruit development provide rich resources for comparative studies, and the work provides important insights into fruit-type specification.

The Halophyte Species Solanum chilense Dun. Maintains Its Reproduction despite Sodium Accumulation in Its Floral Organs

Salinity is a growing global concern that affects the yield of crop species, including tomato (Solanum lycopersicum). Its wild relative Solanum chilense was reported to have halophyte properties. We compared salt resistance of both species during the reproductive phase, with a special focus on sodium localization in the flowers. Plants were exposed to NaCl from the seedling stage. Salinity decreased the number of inflorescences in both species but the number of flowers per inflorescence and sepal length only in S. lycopersicum. External salt supply decreased the stamen length in S. chilense, and it was associated with a decrease in pollen production and an increase in pollen viability. Although the fruit set was not affected by salinity, fruit weight and size decreased in S. lycopersicum. Concentrations and localization of Na, K, Mg, and Ca differed in reproductive structures of both species. Inflorescences and fruits of S. chilense accumulated more Na than S. lycopersicum. Sodium was mainly located in male floral organs of S. chilense but in non-reproductive floral organs in S. lycopersicum. The expression of Na transporter genes differed in flowers of both species. Overall, our results indicated that S. chilense was more salt-resistant than S. lycopersicum during the reproductive phase and that differences could be partly related to dissimilarities in element distribution and transport in flowers.

A proteomic analysis shows the stimulation of light reactions and inhibition of the Calvin cycle in the skin chloroplasts of ripe red grape berries

The role of photosynthesis in fruits still challenges scientists. This is especially true in the case of mature grape berries of red varieties lined by an anthocyanin-enriched exocarp (skin) almost impermeable to gases. Although chlorophylls are degraded and replaced by carotenoids in several fruits, available evidence suggests that they may persist in red grapes at maturity. In the present study, chloroplasts were isolated from the skin of red grape berries (cv. Vinhão) to measure chlorophyll levels and the organelle proteome. The results showed that chloroplasts (and chlorophylls) are maintained in ripe berries masked by anthocyanin accumulation and that the proteome of chloroplasts from green and mature berries is distinct. Several proteins of the light reactions significantly accumulated in chloroplasts at the mature stage including those of light-harvesting complexes of photosystems I (PSI) and II (PSII), redox chain, and ATP synthase, while chloroplasts at the green stage accumulated more proteins involved in the Calvin cycle and the biosynthesis of amino acids, including precursors of secondary metabolism. Taken together, results suggest that although chloroplasts are more involved in biosynthetic reactions in green berries, at the mature stage, they may provide ATP for cell maintenance and metabolism or even O2 to feed the respiratory demand of inner tissues.

Transcriptome analysis and identification of genes associated with floral transition and fruit development in rabbiteye blueberry (Vaccinium ashei)

Flowering and fruit set are important traits affecting fruit quality and yield in rabbiteye blueberry (Vaccinium ashei). Intense efforts have been made to elucidate the influence of vernalization and phytohormones on flowering, but the molecular mechanisms of flowering and fruit set remain unclear. To unravel these mechanisms, we performed transcriptome analysis to explore blueberry transcripts from flowering to early fruit stage. We divided flowering and fruit set into flower bud (S2), initial flower (S3), bloom flower (S4), pad fruit (S5), and cup fruit (S6) based on phenotype and identified 1,344, 69, 658, and 189 unique differentially expressed genes (DEGs) in comparisons of S3/S2, S4/S3, S5/S4, and S6/S5, respectively. There were obviously more DEGs in S3/S2 and S5/S4 than in S4/S3, and S6/S5, suggesting that S3/S2 and S5/S4 represent major transitions from buds to fruit in blueberry. GO and KEGG enrichment analysis indicated these DEGs were mostly enriched in phytohormone biosynthesis and signaling, transporter proteins, photosynthesis, anthocyanins biosynthesis, disease resistance protein and transcription factor categories, in addition, transcript levels of phytohormones and transporters changed greatly throughout the flowering and fruit set process. Gibberellic acid and jasmonic acid mainly acted on the early stage of flowering development like expression of the florigen gene FT, while the expression of auxin response factor genes increased almost throughout the process from bud to fruit development. Transporter proteins were mainly associated with minerals during the early flowering development stage and sugars during the early fruit stage. At the early fruit stage, anthocyanins started to accumulate, and the fruit was susceptible to diseases such as fungal infection. Expression of the transcription factor MYB86 was up-regulated during initial fruit development, which may promote anthocyanin accumulation. These results will aid future studies exploring the molecular mechanism underlying flowering and fruit set of rabbiteye blueberry.

Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits

The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.

Molecular basis for optimizing sugar metabolism and transport during fruit development

Sugars are fundamental metabolites synthesized in leaves and further delivered to fruit in fruit crops. They not only provide "sweetness" as fruit quality traits, but also function as signaling molecules to modulate the responses of fruit to environmental stimuli. Therefore, the understanding to the molecular basis for sugar metabolism and transport is crucial for improving fruit quality and dissecting responses to abiotic/biotic factors. Here, we provide a review for molecular components involved in sugar metabolism and transport, crosstalk with hormone signaling, and the roles of sugars in responses to abiotic and biotic stresses. Moreover, we also envisage the strategies for optimizing sugar metabolism during fruit quality maintenance.

A Single Nucleotide Substitution of GSAM Gene Causes Massive Accumulation of Glutamate 1-Semialdehyde and Yellow Leaf Phenotype in Rice

BACKGROUND

Tetrapyrroles play indispensable roles in various biological processes. In higher plants, glutamate 1-semialdehyde 2,1-aminomutase (GSAM) converts glutamate 1-semialdehyde (GSA) to 5-aminolevulinic acid (ALA), which is the rate-limiting step of tetrapyrrole biosynthesis. Up to now, GSAM genes have been successively identified from many species. Besides, it was found that GSAM could form a dimeric protein with itself by x-ray crystallography. However, no mutant of GSAM has been identified in monocotyledonous plants, and no experiment on interaction of GSAM protein with itself has been reported so far.

RESULT

We isolated a yellow leaf mutant, ys53, in rice (Oryza sativa). The mutant showed decreased photosynthetic pigment contents, suppressed chloroplast development, and reduced photosynthetic capacity. In consequence, its major agronomic traits were significantly affected. Map-based cloning revealed that the candidate gene was LOC_Os08g41990 encoding GSAM protein. In ys53 mutant, a single nucleotide substitution in this gene caused an amino acid change in the encoded protein, so its ALA-synthesis ability was significantly reduced and GSA was massively accumulated. Complementation assays suggested the mutant phenotype of ys53 could be rescued by introducing wild-type OsGSAM gene, confirming that the point mutation in OsGSAM is the cause of the mutant phenotype. OsGSAM is mainly expressed in green tissues, and its encoded protein is localized to chloroplast. qRT-PCR analysis indicated that the mutation of OsGSAM not only affected the expressions of tetrapyrrole biosynthetic genes, but also influenced those of photosynthetic genes in rice. In addition, the yeast two-hybrid experiment showed that OsGSAM protein could interact with itself, which could largely depend on the two specific regions containing the 81th-160th and the 321th-400th amino acid residues at its N- and C-terminals, respectively.

CONCLUSIONS

We successfully characterized rice GSAM gene by a yellow leaf mutant and map-based cloning approach. Meanwhile, we verified that OsGSAM protein could interact with itself mainly by means of the two specific regions of amino acid residues at its N- and C-terminals, respectively.

Hormonal impact on photosynthesis and photoprotection in plants

Photosynthesis is not only essential for plants, but it also sustains life on Earth. Phytohormones play crucial roles in developmental processes, from organ initiation to senescence, due to their role as growth and developmental regulators, as well as their central role in the regulation of photosynthesis. Furthermore, phytohormones play a major role in photoprotection of the photosynthetic apparatus under stress conditions. Here, in addition to discussing our current knowledge on the role of the phytohormones auxin, cytokinins, gibberellins, and strigolactones in promoting photosynthesis, we will also highlight the role of abscisic acid beyond stomatal closure in modulating photosynthesis and photoprotection under various stress conditions through crosstalk with ethylene, salicylates, jasmonates, and brassinosteroids. Furthermore, the role of phytohormones in controlling the production and scavenging of photosynthesis-derived reactive oxygen species, the duration and extent of photo-oxidative stress and redox signaling under stress conditions will be discussed in detail. Hormones have a significant impact on the regulation of photosynthetic processes in plants under both optimal and stress conditions, with hormonal interactions, complementation, and crosstalk being important in the spatiotemporal and integrative regulation of photosynthetic processes during organ development at the whole-plant level.

Metabolomics of Photosynthetically Active Tissues in White Grapes: Effects of Light Microclimate and Stress Mitigation Strategies

The effects of climate change are becoming a real concern for the viticulture sector, with impacts on both grapevine physiology and the quality of the fresh berries and wine. Short-term mitigation strategies, like foliar kaolin application and smart irrigation regimes, have been implemented to overcome these problems. We previously showed that these strategies also influence the photosynthetic activity of the berries themselves, specifically in the exocarp and seed. In the present work, we assessed the modulating effects of both canopy-light microclimate, kaolin and irrigation treatments on the metabolic profiles of the exocarp and seed, as well as the potential role of berry photosynthesis herein. Berries from the white variety Alvarinho were collected at two contrasting light microclimate positions within the vine canopy (HL—high light and LL—low light) from both irrigated and kaolin-treated plants, and their respective controls, at three fruit developmental stages (green, véraison and mature). Untargeted liquid chromatography mass spectrometry (LCMS) profiling of semi-polar extracts followed by multivariate statistical analysis indicate that both the light microclimate and irrigation influenced the level of a series of phenolic compounds, depending on the ripening stage of the berries. Moreover, untargeted gas chromatography mass spectrometry (GCMS) profiling of polar extracts show that amino acid and sugar levels were influenced mainly by the interaction of irrigation and kaolin treatments. The results reveal that both photosynthetically active berry tissues had a distinct metabolic profile in response to the local light microclimate, which suggests a specific role of photosynthesis in these tissues. A higher light intensity within the canopy mainly increased the supply of carbon precursors to the phenylpropanoid/flavonoid pathway, resulting in increased levels of phenolic compounds in the exocarp, while in seeds, light mostly influenced compounds related to carbon storage and seed development. In addition, our work provides new insights into the influence of abiotic stress mitigation strategies on the composition of exocarps and seeds, which are both important tissues for the quality of grape-derived products.

Multi-gene metabolic engineering of tomato plants results in increased fruit yield up to 23%

The capacity to assimilate carbon and nitrogen, to transport the resultant sugars and amino acids to sink tissues, and to convert the incoming sugars and amino acids into storage compounds in the sink tissues, are key determinants of crop yield. Given that all of these processes have the potential to co-limit growth, multiple genetic interventions in source and sink tissues, plus transport processes may be necessary to reach the full yield potential of a crop. We used biolistic combinatorial co-transformation (up to 20 transgenes) for increasing C and N flows with the purpose of increasing tomato fruit yield. We observed an increased fruit yield of up to 23%. To better explore the reconfiguration of metabolic networks in these transformants, we generated a dataset encompassing physiological parameters, gene expression and metabolite profiling on plants grown under glasshouse or polytunnel conditions. A Sparse Partial Least Squares regression model was able to explain the combination of genes that contributed to increased fruit yield. This combinatorial study of multiple transgenes targeting primary metabolism thus offers opportunities to probe the genetic basis of metabolic and phenotypic variation, providing insight into the difficulties in choosing the correct combination of targets for engineering increased fruit yield.

The Impact of Fruit Etiolation on Quality of Seeds in Tobacco

Seed's maturity and integrity are essential requirements for germination, and they rely on nutrients availability and a correct phytohormones' balance. These aspects are prerequisites for prompt germination at the end of the dormancy period and strictly depend on chloroplast metabolism and photosynthesis. In the present work, capsules of Nicotiana tabacum were grown in dark during the whole post-anthesis period. Among others, photosynthetic rates, dormancy, and phytohormones levels in seeds were found to be significantly different with respect to controls. In particular, etiolated capsules had expectedly reduced photosynthetic rates and, when compared to controls, their seeds had an increased mass and volume, an alteration in hormones level, and a consequently reduced dormancy. The present findings show how, during fruit development, the presence of light and the related fruit's photosynthetic activity play an indirect but essential role for reaching seeds maturity and dormancy. Results highlight how unripe fruits are versatile organs that, depending on the environmental conditions, may facultatively behave as sink or source/sink with associated variation in seed's reserves and phytohormone levels.

Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L

Impatiens balsamina L. is a tropical ornamental and traditional medicinal herb rich in natural compounds, especially 2-methoxy-1,4-naphthoquinone (MNQ) which is a bioactive compound with tested anticancer activities. Characterization of key genes involved in the shikimate and 1,4-dihydroxy-2-naphthoate (DHNA) pathways responsible for MNQ biosynthesis and their expression profiles in I. balsamina will facilitate adoption of genetic/metabolic engineering or synthetic biology approaches to further increase production for pre-commercialization. In this study, HPLC analysis showed that MNQ was present in significantly higher quantities in the capsule pericarps throughout three developmental stages (early-, mature- and postbreaker stages) whilst its immediate precursor, 2-hydroxy-1,4-naphthoquinone (lawsone) was mainly detected in mature leaves. Transcriptomes of I. balsamina derived from leaf, flower, and three capsule developmental stages were generated, totalling 59.643 Gb of raw reads that were assembled into 94,659 unigenes (595,828 transcripts). A total of 73.96% of unigenes were functionally annotated against seven public databases and 50,786 differentially expressed genes (DEGs) were identified. Expression profiles of 20 selected genes from four major secondary metabolism pathways were studied and validated using qRT-PCR method. Majority of the DHNA pathway genes were found to be significantly upregulated in early stage capsule compared to flower and leaf, suggesting tissue-specific synthesis of MNQ. Correlation analysis identified 11 candidate unigenes related to three enzymes (NADH-quinone oxidoreductase, UDP-glycosyltransferases and S-adenosylmethionine-dependent O-methyltransferase) important in the final steps of MNQ biosynthesis based on genes expression profiles consistent with MNQ content. This study provides the first molecular insight into the dynamics of MNQ biosynthesis and accumulation across different tissues of I. balsamina and serves as a valuable resource to facilitate further manipulation to increase production of MNQ.

Global transcriptome analysis of subterranean pod and seed in peanut (Arachis hypogaea L.) unravels the complexity of fruit development under dark condition

Peanut pods develop underground, which is the most salient characteristic in peanut. However, its developmental transcriptome remains largely unknown. In the present study, we sequenced over one billion transcripts to explore the developmental transcriptome of peanut pod using Illumina sequencing. Moreover, we identified and quantified the abundances of 165,689 transcripts in seed and shell tissues along with a pod developmental gradient. The dynamic changes of differentially expressed transcripts (DETs) were described in seed and shell. Additionally, we found that photosynthetic genes were not only pronouncedly enriched in aerial pod, but also played roles in developing pod under dark condition. Genes functioning in photomorphogenesis showed distinct expression profiles along subterranean pod development. Clustering analysis unraveled a dynamic transcriptome, in which transcripts for DNA synthesis and cell division during pod expansion were transitioning to transcripts for cell expansion and storage activity during seed filling. Collectively, our study formed a transcriptional baseline for peanut fruit development under dark condition.

Decoding altitude-activated regulatory mechanisms occurring during apple peel ripening

Apple (Malus domestica Borkh) is an important fruit crop cultivated in a broad range of environmental conditions. Apple fruit ripening is a physiological process, whose molecular regulatory network response to different environments is still not sufficiently investigated and this is particularly true of the peel tissue. In this study, the influence of environmental conditions associated with low (20 m) and high (750 m) altitude on peel tissue ripening was assessed by physiological measurements combined with metabolomic and proteomic analyses during apple fruit development and ripening. Although apple fruit ripening was itself not affected by the different environmental conditions, several key color parameters, such as redness and color index, were notably induced by high altitude. Consistent with this observation, increased levels of anthocyanin and other phenolic compounds, including cyanidin-3-O-galactoside, quercetin-3-O-rhamnoside, quercetin-3-O-rutinoside, and chlorogenic acid were identified in the peel of apple grown at high altitude. Moreover, the high-altitude environment was characterized by elevated abundance of various carbohydrates (e.g., arabinose, xylose, and sucrose) but decreased levels of glutamic acid and several related proteins, such as glycine hydroxymethyltransferase and glutamate-glyoxylate aminotransferase. Other processes affected by high altitude were the TCA cycle, the synthesis of oxidative/defense enzymes, and the accumulation of photosynthetic proteins. From the obtained data we were able to construct a metabolite-protein network depicting the impact of altitude on peel ripening. The combined analyses presented here provide new insights into physiological processes linking apple peel ripening with the prevailing environmental conditions.

Leaf shape is a predictor of fruit quality and cultivar performance in tomato

Commercial tomato (Solanum lycopersicum) is one of the most widely grown vegetable crops worldwide. Heirloom tomatoes retain extensive genetic diversity and a considerable range of fruit quality and leaf morphological traits. Here the role of leaf morphology was investigated for its impact on fruit quality. Heirloom cultivars were grown in field conditions, and BRIX by yield (BY) and other traits were measured over a 14-wk period. The complex relationships among these morphological and physiological traits were evaluated using partial least-squares path modeling, and a consensus model was developed. Photosynthesis contributed strongly to vegetative biomass and sugar content of fruits but had a negative impact on yield. Conversely leaf shape, specifically rounder leaves, had a strong positive impact on both fruit sugar content and yield. Cultivars such as Stupice and Glacier, with very round leaves, had the highest performance in both fruit sugar and yield. Our model accurately predicted BY for two commercial cultivars using leaf shape data as input. This study revealed the importance of leaf shape to fruit quality in tomato, with rounder leaves having significantly improved fruit quality. This correlation was maintained across a range of diverse genetic backgrounds and shows the importance of leaf morphology in tomato crop improvement.

Network Analysis Provides Insight into Tomato Lipid Metabolism

Metabolic correlation networks have been used in several instances to obtain a deeper insight into the complexity of plant metabolism as a whole. In tomato (Solanum lycopersicum), metabolites have a major influence on taste and overall fruit quality traits. Previously a broad spectrum of metabolic and phenotypic traits has been described using a Solanum pennellii introgression-lines (ILs) population. To obtain insights into tomato fruit metabolism, we performed metabolic network analysis from existing data, covering a wide range of metabolic traits, including lipophilic and volatile compounds, for the first time. We provide a comprehensive fruit correlation network and show how primary, secondary, lipophilic, and volatile compounds connect to each other and how the individual metabolic classes are linked to yield-related phenotypic traits. Results revealed a high connectivity within and between different classes of lipophilic compounds, as well as between lipophilic and secondary metabolites. We focused on lipid metabolism and generated a gene-expression network with lipophilic metabolites to identify new putative lipid-related genes. Metabolite–transcript correlation analysis revealed key putative genes involved in lipid biosynthesis pathways. The overall results will help to deepen our understanding of tomato metabolism and provide candidate genes for transgenic approaches toward improving nutritional qualities in tomato.

Photosynthesis in non-foliar tissues: implications for yield

Photosynthesis is currently a focus for crop improvement. The majority of this work has taken place and been assessed in leaves, and limited consideration has been given to the contribution that other green tissues make to whole-plant carbon assimilation. The major focus of this review is to evaluate the impact of non-foliar photosynthesis on carbon-use efficiency and total assimilation. Here we appraise and summarize past and current literature on the substantial contribution of different photosynthetically active organs and tissues to productivity in a variety of different plant types, with an emphasis on fruit and cereal crops. Previous studies provide evidence that non-leaf photosynthesis could be an unexploited potential target for crop improvement. We also briefly examine the role of stomata in non-foliar tissues, gas exchange, maintenance of optimal temperatures and thus photosynthesis. In the final section, we discuss possible opportunities to manipulate these processes and provide evidence that Triticum aestivum (wheat) plants genetically manipulated to increase leaf photosynthesis also displayed higher rates of ear assimilation, which translated to increased grain yield. By understanding these processes, we can start to provide insights into manipulating non-foliar photosynthesis and stomatal behaviour to identify novel targets for exploitation in continuing breeding programmes.

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.

Tomato Fruit Development and Metabolism

Tomato (Solanum lycopersicum L.) belongs to the Solanaceae family and is the second most important fruit or vegetable crop next to potato (Solanum tuberosum L.). It is cultivated for fresh fruit and processed products. Tomatoes contain many health-promoting compounds including vitamins, carotenoids, and phenolic compounds. In addition to its economic and nutritional importance, tomatoes have become the model for the study of fleshy fruit development. Tomato is a climacteric fruit and dramatic metabolic changes occur during its fruit development. In this review, we provide an overview of our current understanding of tomato fruit metabolism. We begin by detailing the genetic and hormonal control of fruit development and ripening, after which we document the primary metabolism of tomato fruits, with a special focus on sugar, organic acid, and amino acid metabolism. Links between primary and secondary metabolic pathways are further highlighted by the importance of pigments, flavonoids, and volatiles for tomato fruit quality. Finally, as tomato plants are sensitive to several abiotic stresses, we briefly summarize the effects of adverse environmental conditions on tomato fruit metabolism and quality.

NTRC Plays a Crucial Role in Starch Metabolism, Redox Balance, and Tomato Fruit Growth

NADPH-thioredoxin reductase C (NTRC) forms a separate thiol-reduction cascade in plastids, combining both NADPH-thioredoxin reductase and thioredoxin activities on a single polypeptide. While NTRC is an important regulator of photosynthetic processes in leaves, its function in heterotrophic tissues remains unclear. Here, we focus on the role of NTRC in developing tomato (Solanum lycopersicum) fruits representing heterotrophic storage organs important for agriculture and human diet. We used a fruit-specific promoter to decrease NTRC expression by RNA interference in developing tomato fruits by 60% to 80% compared to the wild type. This led to a decrease in fruit growth, resulting in smaller and lighter fully ripe fruits containing less dry matter and more water. In immature fruits, NTRC downregulation decreased transient starch accumulation, which led to a subsequent decrease in soluble sugars in ripe fruits. The inhibition of starch synthesis was associated with a decrease in the redox-activation state of ADP-Glc pyrophosphorylase and soluble starch synthase, which catalyze the first committed and final polymerizing steps, respectively, of starch biosynthesis. This was accompanied by a decrease in the level of ADP-Glc. NTRC downregulation also led to a strong increase in the reductive states of NAD(H) and NADP(H) redox systems. Metabolite profiling of NTRC-RNA interference lines revealed increased organic and amino acid levels, but reduced sugar levels, implying that NTRC regulates the osmotic balance of developing fruits. These results indicate that NTRC acts as a central hub in regulating carbon metabolism and redox balance in heterotrophic tomato fruits, affecting fruit development as well as final fruit size and quality.

Regulation of Pyridine Nucleotide Metabolism During Tomato Fruit Development Through Transcript and Protein Profiling

Central metabolism is the engine of plant biomass, supplying fruit growth with building blocks, energy, and biochemical cofactors. Among metabolic cornerstones, nicotinamide adenine dinucleotide (NAD) is particularly pivotal for electron transfer through reduction-oxidation (redox) reactions, thus participating in a myriad of biochemical processes. Besides redox functions, NAD is now assumed to act as an integral regulator of signaling cascades involved in growth and environmental responses. However, the regulation of NAD metabolism and signaling during fruit development remains poorly studied and understood. Here, we benefit from RNAseq and proteomic data obtained from nine growth stages of tomato fruit (var. Moneymaker) to dissect mRNA and protein profiles that link to NAD metabolism, including de novo biosynthesis, recycling, utilization, and putative transport. As expected for a cofactor synthesis pathway, protein profiles failed to detect enzymes involved in NAD synthesis or utilization, except for nicotinic acid phosphoribosyltransferase (NaPT) and nicotinamidase (NIC), which suggested that most NAD metabolic enzymes were poorly represented quantitatively. Further investigations on transcript data unveiled differential expression patterns during fruit development. Interestingly, among specific NAD metabolism-related genes, early de novo biosynthetic genes were transcriptionally induced in very young fruits, in association with NAD kinase, while later stages of fruit growth rather showed an accumulation of transcripts involved in later stages of de novo synthesis and in NAD recycling, which agreed with augmented NAD(P) levels. In addition, a more global overview of 119 mRNA and 78 protein significant markers for NAD(P)-dependent enzymes revealed differential patterns during tomato growth that evidenced clear regulations of primary metabolism, notably with respect to mitochondrial functions. Overall, we propose that NAD metabolism and signaling are very dynamic in the developing tomato fruit and that its differential regulation is certainly critical to fuel central metabolism linking to growth mechanisms.

The zinc-finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato

Chloroplast development and chlorophyll content in the immature fruit has a major impact on the morphology and quality in pepper (Capsicum spp.) fruit. Two major quantitative trait loci (QTLs), pc1 and pc10 that affect chlorophyll content in the pepper fruit by modulation of chloroplast compartment size were previously identified in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2-LIKE transcription factor (CaGLK2) has been found as underlying pc10, similar to its effect on tomato chloroplast development. In the present study, we identified the pepper homolog of the zinc-finger transcription factor LOL1 (LSD ONE LIKE1; CcLOL1) as the gene underlying pc1. LOL1 has been identified in Arabidopsis as a positive regulator of programmed cell death and we report here on its role in controlling fruit development in the Solanaceae in a fruit-specific manner. The light-green C. chinense parent used for QTL mapping was found to carry a null mutation in CcLOL1. Verification of the function of the gene was done by generating CRISPR/Cas9 knockout mutants of the orthologous tomato gene resulting in light-green tomato fruits, indicating functional conservation of the orthologous genes in controlling chlorophyll content in the Solanaceae. Transcriptome profiling of light and dark-green bulks differing for pc1, showed that the QTL affects multiple photosynthesis and oxidation-reduction associated genes in the immature green fruit. Allelic diversity of three known genes CcLOL1, CaGLK2, and CcAPRR2 that influence pepper immature fruit color, was found to be associated with variation in chlorophyll content primarily in C. chinense.

Peach Fruit Development: A Comparative Proteomic Study Between Endocarp and Mesocarp at Very Early Stages Underpins the Main Differential Biochemical Processes Between These Tissues

Peach (Prunus persica) is an important economically temperate fruit. The development follows double sigmoid curve with four phases (S1-S4). We centered our work in the early development. In addition to S1, we studied the very early stage (E) characterized by the lag zone of the exponential growing phase S1, and the second stage (S2) when the pit starts hardening. "Dixiland" peach fruit were collected at 9 (E), 29 (S1), and 53 (S2) days after flowering (DAF) and endocarp and mesocarp were separated. There was a pronounced decrease in total protein content along development in both tissues. Quantitative proteomic allowed the identification of changes in protein profiles across development and revealed the main biochemical pathways sustaining tissue differentiation. Protein metabolism was the category most represented among differentially proteins in all tissues and stages. The decrease in protein synthesis machinery observed during development would be responsible of the protein fall, rather than a proteolytic process; and reduced protein synthesis during early development would reroute cell resources to lignin biosynthesis. These changes were accompanied by net decrease in total amino acids in E1-S1 and increase in S1-S2 transitions. Amino acid profiling, showed Asn parallels this trend. Concerted changes in Asn and in enzymes involved in its metabolism reveal that increased synthesis and decreased catabolism of Asn may conduct to an Asn increase during very early development and that the β-Cyano-Alanine synthase/β-Cyano-Alanine hydratase could be the pathway for Asn synthesis in "Dixiland" peach fruit. Additionally, photosynthetic machinery decays during early development in mesocarp and endocarp. Proteins related to photosynthesis are found to a higher extent in mesocarp than in endocarp. We conclude mesocarpic photosynthesis is possible to occur early on the development, first providing both carbon and reductive power and latter only reductive power. Together with proteomic, histological tests and anatomical analysis help to provide information about changes and differences in cells and cell-walls in both tissues. Collectively, this work represents the first approach in building protein databases during peach fruit development focusing on endocarp and mesocarp tissues and provides novel insights into the biology of peach fruit development preceding pit hardening.

Photosynthetic activity of reproductive organs

During seed development, carbon is reallocated from maternal tissues to support germination and subsequent growth. As this pool of resources is depleted post-germination, the plant begins autotrophic growth through leaf photosynthesis. Photoassimilates derived from the leaf are used to sustain the plant and form new organs, including other vegetative leaves, stems, bracts, flowers, fruits, and seeds. In contrast to the view that reproductive tissues act only as resource sinks, many studies demonstrate that flowers, fruits, and seeds are photosynthetically active. The photosynthetic contribution to development is variable between these reproductive organs and between species. In addition, our understanding of the developmental control of photosynthetic activity in reproductive organs is vastly incomplete. A further complication is that reproductive organ photosynthesis (ROP) appears to be particularly important under suboptimal growth conditions. Therefore, the topic of ROP presents the community with a challenge to integrate the fields of photosynthesis, development, and stress responses. Here, we attempt to summarize our understanding of the contribution of ROP to development and the molecular mechanisms underlying its control.

Identification and characterization of metabolite quantitative trait loci in tomato leaves and comparison with those reported for fruits and seeds

INTRODUCTION

To date, most studies of natural variation and metabolite quantitative trait loci (mQTL) in tomato have focused on fruit metabolism, leaving aside the identification of genomic regions involved in the regulation of leaf metabolism.

OBJECTIVE

This study was conducted to identify leaf mQTL in tomato and to assess the association of leaf metabolites and physiological traits with the metabolite levels from other tissues.

METHODS

The analysis of components of leaf metabolism was performed by phenotypying 76 tomato ILs with chromosome segments of the wild species Solanum pennellii in the genetic background of a cultivated tomato (S. lycopersicum) variety M82. The plants were cultivated in two different environments in independent years and samples were harvested from mature leaves of non-flowering plants at the middle of the light period. The non-targeted metabolite profiling was obtained by gas chromatography time-of-flight mass spectrometry (GC-TOF-MS). With the data set obtained in this study and already published metabolomics data from seed and fruit, we performed QTL mapping, heritability and correlation analyses.

RESULTS

Changes in metabolite contents were evident in the ILs that are potentially important with respect to stress responses and plant physiology. By analyzing the obtained data, we identified 42 positive and 76 negative mQTL involved in carbon and nitrogen metabolism.

CONCLUSIONS

Overall, these findings allowed the identification of S. lycopersicum genome regions involved in the regulation of leaf primary carbon and nitrogen metabolism, as well as the association of leaf metabolites with metabolites from seeds and fruits.

Solanum lycopersicum GOLDEN 2-LIKE 2 transcription factor affects fruit quality in a light- and auxin-dependent manner

Plastids are organelles responsible for essential aspects of plant development, including carbon fixation and synthesis of several secondary metabolites. Chloroplast differentiation and activity are highly regulated by light, and several proteins involved in these processes have been characterised. Such is the case of the GOLDEN 2-LIKE (GLK) transcription factors, which induces the expression of genes related to chloroplast differentiation and photosynthesis. The tomato (Solanum lycopersicum) genome harbours two copies of this gene, SlGLK1 and SlGLK2, each with distinct expression patterns. While the former predominates in leaves, the latter is mainly expressed in fruits, precisely at the pedicel region. During tomato domestication, the selection of fruits with uniform ripening fixed the mutation Slglk2, nowadays present in most cultivated varieties, what penalised fruit metabolic composition. In this study, we investigated how SlGLK2 is regulated by light, auxin and cytokinin and determined the effect of SlGLK2 on tocopherol (vitamin E) and sugar metabolism, which are components of the fruit nutritional and industrial quality. To achieve this, transcriptional profiling and biochemical analysis were performed throughout fruit development and ripening from SlGLK2, Slglk2, SlGLK2-overexpressing genotypes, as well as from phytochrome and hormonal deficient mutants. The results revealed that SlGLK2 expression is regulated by phytochrome-mediated light perception, yet this gene can induce chloroplast differentiation even in a phytochrome-independent manner. Moreover, auxin was found to be a negative regulator of SlGLK2 expression, while SlGLK2 enhances cytokinin responsiveness. Additionally, SlGLK2 enhanced chlorophyll content in immature green fruits, leading to an increment in tocopherol level in ripe fruits. Finally, SlGLK2 overexpression resulted in higher total soluble solid content, possibly by the regulation of sugar metabolism enzyme-encoding genes. The results obtained here shed light on the regulatory network that interconnects SlGLK2, phytohormones and light signal, promoting the plastidial activity and consequently, influencing the quality of tomato fruit.

The Role of Carotenogenic Metabolic Flux in Carotenoid Accumulation and Chromoplast Differentiation: Lessons From the Melon Fruit

Carotenoids have various roles in plant physiology. Plant carotenoids are synthesized in plastids and are highly abundant in the chromoplasts of ripening fleshy fruits. Considerable research efforts have been devoted to elucidating mechanisms that regulate carotenoid biosynthesis, yet, little is known about the mechanism that triggers storage capacity, mainly through chromoplast differentiation. The Orange gene (OR) product stabilizes phytoene synthase protein (PSY) and triggers chromoplast differentiation. OR underlies carotenoid accumulation in orange cauliflower and melon. The OR's 'golden SNP', found in melon, alters the highly evolutionary conserved Arginine¹⁰⁸ to Histidine and controls β-carotene accumulation in melon fruit, in a mechanism yet to be elucidated. We have recently shown that similar carotenogenic metabolic flux is active in non-orange and orange melon fruit. This flux probably leads to carotenoid turnover but known carotenoid turnover products are not detected in non-orange fruit. Arrest of this metabolic flux, using chemical inhibitors or mutations, induces carotenoid accumulation and biogenesis of chromoplasts, regardless of the allelic state of OR. We suggest that the 'golden SNP' induces β-carotene accumulation probably by negatively affecting the capacity to synthesize downstream compounds. The accumulation of carotenoids induces chromoplast biogenesis through a metabolite-induced mechanism. Carotenogenic turnover flux can occur in non-photosynthetic tissues, which do not accumulate carotenoids. Arrest of this flux by the 'golden SNP' or other flux-arrest mutations is a potential tool for the biofortification of agricultural products with carotenoids.

The tomato HIGH PIGMENT1/DAMAGED DNA BINDING PROTEIN 1 gene contributes to regulation of fruit ripening

Fleshy fruit ripening is governed by multiple external and internal cues and accompanied by changes in color, texture, volatiles, and nutritional quality traits. While extended shelf-life and increased phytonutrients are desired, delaying ripening via genetic or postharvest means can be accompanied by reduced nutritional value. Here we report that the high pigment 1 (hp1) mutation at the UV-DAMAGED DNA BINDING PROTEIN 1 (DDB1) locus, previously shown to influence carotenoid and additional phytonutrient accumulation via altered light signal transduction, also results in delayed ripening and firmer texture, resulting at least in part from decreased ethylene evolution. Transcriptome analysis revealed multiple ethylene biosynthesis and signaling-associated genes downregulated in hp1. Furthermore, the hp1 mutation impedes softening of the pericarp, placenta, columella as well as the whole fruit, in addition to reduced expression of the FRUITFUL2 (FUL2) MADS-box transcription factor and xyloglucan endotransglucosylase/hydrolase 5 (XTH5). These results indicate that DDB1 influences a broader range of fruit development and ripening processes than previously thought and present an additional genetic target for increasing fruit quality and shelf-life.

A Systems Analysis With "Simplified Source-Sink Model" Reveals Metabolic Reprogramming in a Pair of Source-to-Sink Organs During Early Fruit Development in Tomato by LED Light Treatments

Tomato (Solanum lycopersicum) is a model crop for studying development regulation and ripening in flesh fruits and vegetables. Supplementary light to maintain the optimal light environment can lead to the stable growth of tomatoes in greenhouses and areas without sufficient daily light integral. Technological advances in genome-wide molecular phenotyping have dramatically enhanced our understanding of metabolic shifts in the plant metabolism across tomato fruit development. However, comprehensive metabolic and transcriptional behaviors along the developmental process under supplementary light provided by light-emitting diodes (LEDs) remain to be fully elucidated. We present integrative omic approaches to identify the impact on the metabolism of a single tomato plant leaf exposed to monochromatic red LEDs of different intensities during the fruit development stage. Our special light delivery system, the "simplified source-sink model," involves the exposure of a single leaf below the second truss to red LED light of different intensities. We evaluated fruit-size- and fruit-shape variations elicited by different light intensities. Our findings suggest that more than high-light treatment (500 μmol m-2 s-1) with the red LED light is required to accelerate fruit growth for 2 weeks after anthesis. To investigate transcriptomic and metabolomic changes in leaf- and fruit samples we used microarray-, RNA sequencing-, and gas chromatography-mass spectrometry techniques. We found that metabolic shifts in the carbohydrate metabolism and in several key pathways contributed to fruit development, including ripening and cell-wall modification. Our findings suggest that the proposed workflow aids in the identification of key metabolites in the central metabolism that respond to monochromatic red-LED treatment and contribute to increase the fruit size of tomato plants. This study expands our understanding of systems-level responses mediated by low-, appropriate-, and high levels of red light irradiation in the fruit growth of tomato plants.