Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta

Genome-wide association studies in lettuce reveal the interplay of seed age, color, and germination under high temperatures

Thermoinhibition, the suppression of seed germination by high temperatures, is an adaptive trait that ensures successful seedling establishment in natural environments. While beneficial for wild plants, thermoinhibition can adversely affect crop yields due to uneven and reduced germination rates, particularly in the face of climate change. To understand the genetic basis of thermoinhibition, we conducted a comprehensive genetic analysis of a diverse panel of Lactuca spp. accessions. Our findings revealed that L. serriola, a wild ancestor of cultivated lettuce, showed relaxed thermoinhibition response compared to cultivated lettuce, suggesting that this trait may have been positively selected during early domestication in the Mediterranean region with hot, dry summers. Additionally, we found that thermoinhibition intensified with seed age but was less pronounced in dark-colored seeds, which showed increased germination under high temperatures. Genome-wide association studies identified genomic regions associated with thermoinhibition, including genes involved in ethylene and ABA signaling. Interestingly, some of these regions were also linked to seed color, suggesting a potential genetic coupling between black seed color and reduced thermoinhibition. These results highlighted the complex interplay between thermoinhibition, seed color, and domestication in lettuce, indicating a complicated nature of thermoinhibition regulation. By elucidating the genetic architecture of thermoinhibition, our study provides a valuable foundation for breeding strategies to enhance lettuce resilience to climate change.

Low storage temperature affects quality and volatile compounds in fresh tomatoes

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

Mutation of YFT3, an isomerase in the isoprenoid biosynthetic pathway, impairs its catalytic activity and carotenoid accumulation in tomato fruit

Tomato fruit colors are directly associated with their appearance quality and nutritional value. However, tomato fruit color formation is an intricate biological process that remains elusive. In this work we characterized a tomato yellow fruited tomato 3 (yft3, e9292, Solanum lycopersicum) mutant with yellow fruits. By the map-based cloning approach, we identified a transversion mutation (A2117C) in the YFT3 gene encoding a putative isopentenyl diphosphate isomerase (SlIDI1) enzyme, which may function in the isoprenoid biosynthetic pathway by catalyzing conversion between isopentenyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). The mutated YFT3 (A2117C) (designated YFT3 allele) and the YFT3 genes did not show expression difference at protein level, and their encoded YFT3 allelic (S126R) and YFT3 proteins were both localized in plastids. However, the transcript levels of eight genes (DXR, DXS, HDR, PSY1, CRTISO, CYCB, CYP97A, and NCED) associated with carotenoid synthesis were upregulated in fruits of both yft3 and YFT3 knockout (YFT3-KO) lines at 35 and 47 days post-anthesis compared with the red-fruit tomato cultivar (M82). In vitro and in vivo biochemical analyses indicated that YFT3 (S126R) possessed much lower enzymatic activities than the YFT3 protein, indicating that the S126R mutation can impair YFT3 activity. Molecular docking analysis showed that the YFT3 allele has higher ability to recruit isopentenyl pyrophosphate (IPP), but abolishes attachment of the Mg2+ cofactor to IPP, suggesting that Ser126 is a critical residue for YTF3 biochemical and physiological functions. As a result, the yft3 mutant tomato line has low carotenoid accumulation and abnormal chromoplast development, which results in yellow ripe fruits. This study provides new insights into molecular mechanisms of tomato fruit color formation and development.

Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit

Knotted1-like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA-seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein-protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1-clade of BEL1-like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9-mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5-SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast- and chlorophyll-related genes, including SlAPRR2-like1, SlCAB-1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5-SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine-tuning the color transition from immature green fruit to mature red fruit.

Molecular approaches to enhance astaxanthin biosynthesis; future outlook: engineering of transcription factors in Haematococcus pluvialis

Microalgae are the preferred species for producing astaxanthin because they pose a low toxicity risk than chemical synthesis. Astaxanthin has multiple health benefits and is being used in: medicines, nutraceuticals, cosmetics, and functional foods. Haematococcus pluvialis is a model microalga for astaxanthin biosynthesis; however, its natural astaxanthin content is low. Therefore, it is necessary to develop methods to improve the biosynthesis of astaxanthin to meet industrial demands, making its commercialization cost-effective. Several strategies related to cultivation conditions are employed to enhance the biosynthesis of astaxanthin in H. pluvialis. However, the mechanism of its regulation by transcription factors is unknown. For the first time, this study critically reviewed the studies on identifying transcription factors, progress in H. pluvialis genetic transformation, and use of phytohormones that increase the gene expression related to astaxanthin biosynthesis. In addition, we propose future approaches, including (i) Cloning and characterization of transcription factors, (ii) Transcriptional engineering through overexpression of positive regulators or downregulation/silencing of negative regulators, (iii) Gene editing for enrichment or deletion of transcription factors binding sites, (iv) Hormonal modulation of transcription factors. This review provides considerable knowledge about the molecular regulation of astaxanthin biosynthesis and the existing research gap. Besides, it provides the basis for transcription factors mediated metabolic engineering of astaxanthin biosynthesis in H. pluvialis.

Differential content of leaf and fruit pigment in tomatoes culminate in a complex metabolic reprogramming without growth impacts

Although significant efforts to produce carotenoid-enriched foods either by biotechnology or traditional breeding strategies have been carried out, our understanding of how changes in the carotenoid biosynthesis might affect overall plant performance remains limited. Here, we investigate how the metabolic machinery of well characterized tomato carotenoid mutant plants [namely crimson (old gold-og), Delta carotene (Del) and tangerine (t)] adjusts itself to varying carotenoid biosynthesis and whether these adjustments are supported by a reprogramming of photosynthetic and central metabolism in the source organs (leaves). We observed that mutations og, Del and t did not greatly affect vegetative growth, leaf anatomy and gas exchange parameters. However, an exquisite metabolic reprogramming was recorded on the leaves, with an increase in levels of amino acids and reduction of organic acids. Taken together, our results show that despite minor impacts on growth and gas exchange, carbon flux is extensively affected, leading to adjustments in tomato leaves metabolism to support changes in carotenoid biosynthesis on fruits (sinks). We discuss these data in the context of our current understanding of metabolic adjustments and carotenoid biosynthesis as well as regarding to improving human nutrition.

The sources, properties, extraction, biosynthesis, pharmacology, and application of lycopene

Lycopene is an important pigment with an alkene skeleton from Lycopersicon esculentum, which is also obtained from some red fruits and vegetables. Lycopene is used in the food field with rich functions and serves in the medical field with multiple clinical values because it has dual functions of both medicine and food. It was found that lycopene was mainly isolated by solvent extraction, ultrasonic-assisted extraction, supercritical fluid extraction, high-intensity pulsed electric field-assisted extraction, enzymatic-assisted extraction, and microwave-assisted extraction. Meanwhile, it was also obtained via 2 synthetic pathways: chemical synthesis and biosynthesis. Pharmacological studies revealed that lycopene has anti-oxidant, hypolipidemic, anti-cancer, immunity-enhancing, hepatoprotective, hypoglycemic, cardiovascular-protective, anti-inflammatory, neuroprotective, and osteoporosis-inhibiting effects. The application of lycopene mainly includes food processing, animal breeding, and medical cosmetology fields. It is hoped that this review will provide some useful information and guidance for future study and exploitation of lycopene.

Fruits from tomato carotenoid mutants have altered susceptibility to grey mold

The necrotrophic fungus Botritys cinerea takes advantage of the oxidative burst to facilitate tissue infection, leading to substantial losses during tomato postharvest. Tomato fruit is a source of carotenoids, pigments with a wide variety of isomeric configurations that determine their antioxidant capacity. Here, fruit susceptibility to B. cinerea was assessed in Micro-Tom Near Isogenic lines harboring mutations that alter the profile of carotenoids. Wound-inoculated fruit of the mutants Delta carotene (Del) and tangerine (t), which show large variety of carotenoids rather than the major accumulation of trans-lycopene, were less susceptible to the pathogen. Differences in susceptibility between the mutants were only observed in ripe fruit, after the formation of carotenoids, and they were associated with attenuation of damage caused by reactive oxygen species. The greater variety of carotenoid isomers, which in turn contributed to the greater lipophilic antioxidant capacity of fruit, was associated with the less susceptible mutants, Del and t. Together, our data reveals a potential activity of carotenoids in fruit defense, in addition to the well-known and widespread ecological role as attractors of seed dispersers.

Trihelix transcription factor SlGT31 regulates fruit ripening mediated by ethylene in tomato

Trihelix proteins are plant-specific transcription factors that are classified as GT factors due to their binding specificity for GT elements, and they play crucial roles in development and stress responses. However, their involvement in fruit ripening and transcriptional regulatory mechanisms remains largely unclear. In this study, we cloned SlGT31, encoding a trihelix protein in tomato (Solanum lycopersicum), and determined that its relative expression was significantly induced by the application of exogenous ethylene whereas it was repressed by the ethylene-inhibitor 1-methylcyclopropene. Suppression of SlGT31 expression resulted in delayed fruit ripening, decreased accumulation of total carotenoids, and reduced ethylene content, together with inhibition of expression of genes related to ethylene and fruit ripening. Conversely, SlGT31-overexpression lines showed opposite results. Yeast one-hybrid and dual-luciferase assays indicated that SlGT31 can bind to the promoters of two key ethylene-biosynthesis genes, ACO1 and ACS4. Taken together, our results indicate that SlGT31 might act as a positive modulator during fruit ripening.

Regulation of Tomato Fruit Autophagic Flux and Promotion of Fruit Ripening by the Autophagy-Related Gene SlATG8f

Autophagy is a highly conserved self-degradation process that involves the degradation and recycling of cellular components and organelles. Although the involvement of autophagy in metabolic changes during fruit ripening has been preliminarily demonstrated, the variations in autophagic flux and specific functional roles in tomato fruit ripening remain to be elucidated. In this study, we analyzed the variations in autophagic flux during tomato fruit ripening. The results revealed differential expression of the SlATG8 family members during tomato fruit ripening. Transmission electron microscopy observations and dansylcadaverine (MDC) staining confirmed the presence of autophagy at the cellular level in tomato fruits. Furthermore, the overexpression of SlATG8f induced the formation of autophagosomes, increased autophagic flux within tomato fruits, and effectively enhanced the expression of ATG8 proteins during the color-transition phase of fruit ripening, thus promoting tomato fruit maturation. SlATG8f overexpression also led to the accumulation of vitamin C (VC) and soluble solids while reducing acidity in the fruit. Collectively, our findings highlight the pivotal role of SlATG8f in enhancing tomato fruit ripening, providing insights into the mechanistic involvement of autophagy in this process. This research contributes to a better understanding of the key factors that regulate tomato fruit quality and offers a theoretical basis for tomato variety improvement.

Integrative Analysis of Metabolome and Transcriptome Revealed Lutein Metabolism Contributed to Yellow Flower Formation in Prunus mume

Prunus mume is a famous ornamental woody tree with colorful flowers. P. mume with yellow flowers is one of the most precious varieties. Regretfully, metabolites and regulatory mechanisms of yellow flowers in P. mume are still unclear. This hinders innovation of flower color breeding in P. mume. To elucidate the metabolic components and molecular mechanisms of yellow flowers, we analyzed transcriptome and metabolome between 'HJH' with yellow flowers and 'ZLE' with white flowers. Comparing the metabolome of the two varieties, we determined that carotenoids made contributions to the yellow flowers rather than flavonoids. Lutein was the key differential metabolite to cause yellow coloration of 'HJH'. Transcriptome analysis revealed significant differences in the expression of carotenoid cleavage dioxygenase (CCD) between the two varieties. Specifically, the expression level of PmCCD4 was higher in 'ZLE' than that in 'HJH'. Moreover, we identified six major transcription factors that probably regulated PmCCD4 to affect lutein accumulation. We speculated that carotenoid cleavage genes might be closely related to the yellow flower phenotype in P. mume. Further, the coding sequence of PmCCD4 has been cloned from the 'HJH' petals, and bioinformatics analysis revealed that PmCCD4 possessed conserved histidine residues, ensuring its enzymatic activity. PmCCD4 was closely related to PpCCD4, with a homology of 98.16%. Instantaneous transformation analysis in petal protoplasts of P. mume revealed PmCCD4 localization in the plastid. The overexpression of PmCCD4 significantly reduced the carotenoid content in tobacco plants, especially the lutein content, indicating that lutein might be the primary substrate for PmCCD4. We speculated that PmCCD4 might be involved in the cleavage of lutein in plastids, thereby affecting the formation of yellow flowers in P. mume. This work could establish a material and molecular basis of molecular breeding in P. mume for improving the flower color.

An unexpected hydratase synthesizes the green light-absorbing pigment fucoxanthin

The ketocarotenoid fucoxanthin and its derivatives can absorb blue-green light enriched in marine environments. Fucoxanthin is widely adopted by phytoplankton species as a main light-harvesting pigment, in contrast to land plants that primarily employ chlorophylls. Despite its supreme abundance in the oceans, the last steps of fucoxanthin biosynthesis have remained elusive. Here, we identified the carotenoid isomerase-like protein CRTISO5 as the diatom fucoxanthin synthase that is related to the carotenoid cis-trans isomerase CRTISO from land plants but harbors unexpected enzymatic activity. A crtiso5 knockout mutant in the model diatom Phaeodactylum tricornutum completely lacked fucoxanthin and accumulated the acetylenic carotenoid phaneroxanthin. Recombinant CRTISO5 converted phaneroxanthin into fucoxanthin in vitro by hydrating its carbon-carbon triple bond, instead of functioning as an isomerase. Molecular docking and mutational analyses revealed residues essential for this activity. Furthermore, a photophysiological characterization of the crtiso5 mutant revealed a major structural and functional role of fucoxanthin in photosynthetic pigment-protein complexes of diatoms. As CRTISO5 hydrates an internal alkyne physiologically, the enzyme has unique potential for biocatalytic applications. The discovery of CRTISO5 illustrates how neofunctionalization leads to major diversification events in evolution of photosynthetic mechanisms and the prominent brown coloration of most marine photosynthetic eukaryotes.

Lycopene ε-cyclase mediated transition of α-carotene and β-carotene metabolic flow in carrot fleshy root

The accumulation of carotenoids, such as xanthophylls, lycopene, and carotenes, is responsible for the color of carrot (Daucus carota subsp. sativus) fleshy roots. The potential role of DcLCYE, encoding a lycopene ε-cyclase associated with carrot root color, was investigated using cultivars with orange and red roots. The expression of DcLCYE in red carrot varieties was significantly lower than that in orange carrots at the mature stage. Furthermore, red carrots accumulated larger amounts of lycopene and lower levels of α-carotene. Sequence comparison and prokaryotic expression analysis revealed that amino acid differences in red carrots did not affect the cyclization function of DcLCYE. Analysis of the catalytic activity of DcLCYE revealed that it mainly formed ε-carotene, while a side activity on α-carotene and γ-carotene was also observed. Comparative analysis of the promoter region sequences indicated that differences in the promoter region may affect the transcription of DcLCYE. DcLCYE was overexpressed in the red carrot 'Benhongjinshi' under the control of the CaMV35S promoter. Lycopene in transgenic carrot roots was cyclized, resulting in the accumulation of higher levels of α-carotene and xanthophylls, while the β-carotene content was significantly decreased. The expression levels of other genes in the carotenoid pathway were simultaneously upregulated. Knockout of DcLCYE in the orange carrot 'Kurodagosun' by CRISPR/Cas9 technology resulted in a decrease in the α-carotene and xanthophyll contents. The relative expression levels of DcPSY1, DcPSY2, and DcCHXE were sharply increased in DcLCYE knockout mutants. The results of this study provide insights into the function of DcLCYE in carrots, which could serve as a basis for creating colorful carrot germplasms.

Genomic basis of selective breeding from the closest wild relative of large-fruited tomato

The long and intricate domestication history of the tomato (Solanum lycopersicum) includes selection sweeps that have not been fully explored, and these sweeps show significant evolutionary trajectories of domestication traits. Using three distinct selection strategies, we represented comprehensive selected sweeps from 53 Solanum pimpinellifolium (PIM) and 166 S. lycopersicum (BIG) accessions, which are defined as pseudo-domestication in this study. We identified 390 potential selection sweeps, some of which had a significant impact on fruit-related traits and were crucial to the pseudo-domestication process. During tomato pseudo-domestication, we discovered a minor-effect allele of the SlLEA gene related to fruit weight (FW), as well as the major haplotypes of fw2.2/cell number regulator (CNR), fw3.2/SlKLUH, and fw11.3/cell size regulator (CSR) in cultivars. Furthermore, 18 loci were found to be significantly associated with FW and six fruit-related agronomic traits in genome-wide association studies. By examining population differentiation, we identified the causative variation underlying the divergence of fruit flavonoids across the large-fruited tomatoes and validated BRI1-EMS-SUPPRESSOR 1.2 (SlBES1.2), a gene that may affect flavonoid content by modulating the MYB12 expression profile. Our results provide new research routes for the genetic basis of fruit traits and excellent genomic resources for tomato genomics-assisted breeding.

Genetic Mechanisms for Hybrid Breeding in Vegetable Crops

To address the complex challenges faced by our planet such as rapidly changing climate patterns, food and nutritional insecurities, and the escalating world population, the development of hybrid vegetable crops is imperative. Vegetable hybrids could effectively mitigate the above-mentioned fundamental challenges in numerous countries. Utilizing genetic mechanisms to create hybrids not only reduces costs but also holds significant practical implications, particularly in streamlining hybrid seed production. These mechanisms encompass self-incompatibility (SI), male sterility, and gynoecism. The present comprehensive review is primarily focused on the elucidation of fundamental processes associated with floral characteristics, the genetic regulation of floral traits, pollen biology, and development. Specific attention is given to the mechanisms for masculinizing and feminizing cucurbits to facilitate hybrid seed production as well as the hybridization approaches used in the biofortification of vegetable crops. Furthermore, this review provides valuable insights into recent biotechnological advancements and their future utilization for developing the genetic systems of major vegetable crops.

Advances in engineering the production of the natural red pigment lycopene: A systematic review from a biotechnology perspective

BACKGROUND

Lycopene is a natural red compound with potent antioxidant activity that can be utilized both as pigment and as a raw material in functional food, and so possesses good commercial prospects. The biosynthetic pathway has already been documented, which provides the foundation for lycopene production using biotechnology.

AIM OF REVIEW

Although lycopene production has begun to take shape, there is still an urgent need to alleviate the yield of lycopene. Progress in this area can provide useful reference for metabolic engineering of lycopene production utilizing multiple approaches.

KEY SCIENTIFIC CONCEPTS OF REVIEW

Using conventional microbial fermentation approaches, biotechnologists have enhanced the yield of lycopene by selecting suitable host strains, utilizing various additives, and optimizing culture conditions. With the development of modern biotechnology, genetic engineering, protein engineering, and metabolic engineering have been applied for lycopene production. Extraction from natural plants is the main way for lycopene production at present. Based on the molecular mechanism of lycopene accumulation, the production of lycopene by plant bioreactor through genetic engineering has a good prospect. Here we summarized common strategies for optimizing lycopene production engineering from a biotechnology perspective, which are mainly carried out by microbial cultivation. We reviewed the challenges and limitations of this approach, summarized the critical aspects, and provided suggestions with the aim of potential future breakthroughs for lycopene production in plants.

A xanthophyll-derived apocarotenoid regulates carotenogenesis in tomato chromoplasts

Carotenoids possess important biological functions that make them essential components of the human diet. β-Carotene and some other carotenoids have vitamin A activity while lutein and zeaxanthin, typically referred to as the macular pigments, are involved in good vision and in delaying the onset of age-related eye diseases. In order to create a zeaxanthin-producing tomato fruit, two transgenic lines, one with a high β-carotene cyclase activity and the other with a high β-carotene hydroxylase activity, have been genetically crossed. Ripe fruits from the resulting progeny contained significant levels of violaxanthin, antheraxanthin, and xanthophyll esters. However, their zeaxanthin content was not as high as expected, and the total level of carotenoids was only 25% of the carotenoids found in ripe fruits of the comparator line. Targeted transcript analysis and apocarotenoids determinations indicated that transcriptional regulation of the pathway or degradation of synthesized carotenoids were not responsible for the low carotenoid content of hybrid fruits which instead appeared to result from a substantial reduction of carotenoid biosynthesis. Notably, the content of an unidentified hydroxylated cyclic (C13) apocarotenoid was 13 times higher in the hybrid fruits than in the control fruits. Furthermore, a GC-MS-based metabolite profiling demonstrated a perturbation of carotenogenesis in ripening hybrid fruits compatible with a block of the pathway. Moreover, carotenoid profiling on leaf, fruit, and petal samples from a set of experimental lines carrying the hp3 mutation, in combination with the two transgenes, indicated that the carotenoid biosynthesis in petal and fruit chromoplasts could be regulated. Altogether the data were consistent with the hypothesis of the regulation of the carotenoid pathway in tomato chromoplasts through a mechanism of feedback inhibition mediated by a xanthophyll-derived apocarotenoid. This chromoplast-specific post-transcriptional mechanism was disclosed in transgenic fruits of HU hybrid owing to the abnormal production of zeaxanthin and antheraxanthin, the more probable precursors of the apocarotenoid signal. A model describing the regulation of carotenoid pathway in tomato chromoplasts is presented.

SlBEL11 affects tomato carotenoid accumulation by regulating SlLCY-b2

Extensive data have demonstrated that carotenoid accumulation in tomato fruit is influenced by environmental cues and hormonal signals. However, there is insufficient information on the mechanism of its transcriptional regulation, as many molecular roles of carotenoid biosynthetic pathways remain unknown. In this work, we found that the silence of the BEL1-like family transcription factor (TF) BEL1-LIKE HOMEODOMAIN 11 (SlBEL11) enhanced carotenoid accumulation in virus induced gene silencing (VIGS) analysis. In its RNA interference (RNAi) transgenic lines, a significant increase in the transcription level for the lycopene beta cyclase 2 (SlLCY-b2) gene was detected, which encoded a key enzyme located at the downstream branch of the carotenoid biosynthetic pathway. In Electrophoretic mobility shift assay (EMSA), SlBEL11 protein was confirmed to bind to the promoter of SlLCY-b2 gene. In addition, the dual-luciferase reporter assay showed its intrinsic transcriptional repression activity. Collectively, our findings added a new member to the carotenoid transcriptional regulatory network and expanded the functions of the SlBEL11 transcription factor.

Biochemical Characterization of Orange-Colored Rice Calli Induced by Target Mutagenesis of OsOr Gene

We generated an orange-colored (OC) rice callus line by targeted mutagenesis of the orange gene (OsOr) using the CRISPR-Cas9 system. The OC line accumulated more lutein, β-carotene, and two β-carotene isomers compared to the WT callus line. We also analyzed the expression levels of carotenoid biosynthesis genes by qRT-PCR. Among the genes encoding carotenoid metabolic pathway enzymes, the number of transcripts of the PSY2, PSY3, PDS, ZDS and β-LCY genes were higher in the OC line than in the WT line. In contrast, transcription of the ε-LCY gene was downregulated in the OC line compared to the WT line. In addition, we detected increases in the transcript levels of two genes involved in carotenoid oxidation in the OC lines. The developed OC lines also showed increased tolerance to salt stress. Collectively, these findings indicate that targeted mutagenesis of the OsOr gene via CRISPR/Cas9-mediated genome editing results in β-carotene accumulation in rice calli. Accordingly, we believe that this type of genome-editing technology could represent an effective alternative approach for enhancing the β-carotene content of plants.

Transcriptome and Metabolite Profiling of Tomato SGR-Knockout Null Lines Using the CRISPR/Cas9 System

Stay-green 1 (SGR1) protein is a critical regulator of chlorophyll degradation and senescence in plant leaves; however, the functions of tomato SGR1 remain ambiguous. Here, we generated an SGR1-knockout (KO) null line via clustered regularly interspaced palindromic repeat (CRISPR)/CRISPR-associated protein 9-mediated gene editing and conducted RNA sequencing and gas chromatography−tandem mass spectrometry analysis to identify the differentially expressed genes (DEGs). Solanum lycopersicum SGR1 (SlSGR1) knockout null line clearly showed a turbid brown color with significantly higher chlorophyll and carotenoid levels than those in the wild-type (WT) fruit. Differential gene expression analysis revealed 728 DEGs between WT and sgr#1-6 line, including 263 and 465 downregulated and upregulated genes, respectively, with fold-change >2 and adjusted p-value < 0.05. Most of the DEGs have functions related to photosynthesis, chloroplasts, and carotenoid biosynthesis. The strong changes in pigment and carotenoid content resulted in the accumulation of key primary metabolites, such as sucrose and its derivatives (fructose, galactinol, and raffinose), glycolytic intermediates (glucose, glucose-6-phosphate, and fructose-6-phosphate), and tricarboxylic acid cycle intermediates (malate and fumarate) in the leaves and fruit of the SGR-KO null lines. Overall, the SGR1-KO null lines developed here provide new evidence for the mechanisms underlying the roles of SGR1 as well as the molecular pathways involved in photosynthesis, chloroplasts, and carotenoid biosynthesis.

G2-LIKE CAROTENOID REGULATOR (SlGCR) is a positive regulator of lutein biosynthesis in tomato

Lutein is an oxygen-containing carotenoid synthesized in plant chloroplasts and chromoplasts. It plays an indispensable role in promoting plant growth and maintaining eye health in humans. The rate-limiting step of lutein biosynthesis is catalyzed by the lycopene ε-cyclase enzyme (LCYE). Although great progress has been made in the identification of transcription factors involved in the lutein biosynthetic pathway, many systematic molecular mechanisms remain to be elucidated. Here, using co-expression analysis, we identified a gene, G2-LIKE CAROTENOID REGULATOR (SlGCR), encoding a GARP G2-like transcription factor, as the potential regulator of SlLCYE in tomato. Silencing of SlGCR reduced the expression of carotenoid biosynthetic genes and the accumulation of carotenoids in tomato leaves. By contrast, overexpression of SlGCR in tomato fruit significantly increased the expression of relevant genes and enhanced the accumulation of carotenoids. SlGCR can directly bind to the SlLCYE promoter and activate its expression. In addition, we also discovered that expression of SlGCR was negatively regulated by the master regulator SlRIN, thereby inhibiting lutein synthesis during tomato fruit ripening. Taken together, we identified SlGCR as a novel regulator involved in tomato lutein biosynthesis, elucidated the regulatory mechanism, and provided a potential tool for tomato lutein metabolic engineering.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-022-00088-z.

Enrichment of health-promoting lutein and zeaxanthin in tomato fruit through metabolic engineering

Carotenoids constitute a large group of natural pigments widely distributed in nature. These compounds not only provide fruits and flowers with distinctive colors, but also have significant health benefits for humans. Lutein and zeaxanthin, both oxygen-containing carotenoids, are considered to play vital roles in promoting ocular development and maintaining eye health. However, humans and mammals cannot synthesize these carotenoid derivatives, which can only be taken from certain fruits or vegetables. Here, by introducing four endogenous synthetic genes, SlLCYE, SlLCYB, SlHYDB, and SlHYDE under fruit-specific promoters, we report the metabolic engineering of lutein/zeaxanthin biosynthesis in tomato fruit. Transgenic lines overexpression of one (SlLCYE), two (SlLCYE and SlLCYB; SlLCYB and SlHYDB), and all these four synthetic genes re-established the lutein/zeaxanthin biosynthetic pathways in the ripe tomato fruit and thus resulted in various types of carotenoid riched lines. Metabolic analyses of these engineered tomato fruits showed the strategy involved expression of SlLCYE tends to produce α-carotene and lutein, as well as a higher content of β-carotene and zeaxanthin was detected in lines overexpressing SlLCYB. In addition, the different combinations of engineered tomatoes with riched carotenoids showed higher antioxidant capacity and were associated with a significantly extended shelf life during postharvest storage. This work provides a successful example of accurate metabolic engineering in tomato fruit, suggesting the potential utility for synthetic biology to improve agronomic traits in crops. These biofortified tomato fruits could be also exploited as new research subjects for studying the health benefits of carotenoid derivatives.

Mapping and Validation of BrGOLDEN: A Dominant Gene Regulating Carotenoid Accumulation in Brassica rapa

In plants, the accumulation of carotenoids can maintain the balance of the photosystem and improve crop nutritional quality. Therefore, the molecular mechanisms underlying carotenoid synthesis and accumulation should be further explored. In this study, carotenoid accumulation differed significantly among parental Brassica rapa. Genetic analysis was carried out using the golden inner leaf ‘1900264′ line and the light−yellow inner leaf ‘1900262′ line, showing that the golden inner leaf phenotype was controlled by a single dominant gene. Using bulked−segregant analysis sequencing, BraA09g007080.3C encoding the ORANGE protein was selected as a candidate gene. Sequence alignment revealed that a 4.67 kb long terminal repeat insertion in the third exon of the BrGOLDEN resulted in three alternatively spliced transcripts. The spatiotemporal expression results indicated that BrGOLDEN might regulate the expression levels of carotenoid−synthesis−related genes. After transforming BrGOLDEN into Arabidopsis thaliana, the seed−derived callus showed that BrGOLDEN_Ins and BrGOLDEN_Del lines presented a yellow color and the BrGOLDEN_Ldel line presented a transparent phenotype. In addition, using the yeast two−hybrid assay, BrGOLDEN_Ins, BrGOLDEN_Ldel, and Brgolden_wt exhibited strong interactions with BrPSY1, but BrGOLDEN_Del did not interact with BrPSY1 in the split−ubiquitin membrane system. In the secondary and 3D structure analysis, BrGOLDEN_Del was shown to have lost the PNFPSFIPFLPPL sequences at the 125 amino acid position, which resulted in the α−helices of BrGOLDEN_Del being disrupted, restricting the formation of the 3D structure and affecting the functions of the protein. These findings may provide new insights into the regulation of carotenoid synthesis in B. rapa.

Development and carotenoid synthesis in dark-grown carrot taproots require PHYTOCHROME RAPIDLY REGULATED1

Light stimulates carotenoid synthesis in plants during photomorphogenesis through the expression of PHYTOENE SYNTHASE (PSY), a key gene in carotenoid biosynthesis. The orange carrot (Daucus carota) synthesizes and accumulates high amounts of carotenoids in the taproot that grows underground. Contrary to other organs, light impairs carrot taproot development and represses the expression of carotenogenic genes, such as DcPSY1 and DcPSY2, reducing carotenoid accumulation. By means of RNA sequencing, in a previous analysis, we observed that carrot PHYTOCHROME RAPIDLY REGULATED1 (DcPAR1) is more highly expressed in the underground grown taproot compared with those grown in light. PAR1 is a transcriptional cofactor with a negative role in shade avoidance syndrome regulation in Arabidopsis (Arabidopsis thaliana) through the dimerization with PHYTOCHROME-INTERACTING FACTORs (PIFs), allowing a moderate synthesis of carotenoids. Here, we show that overexpressing AtPAR1 in carrot increases carotenoid production in taproots grown underground as well as DcPSY1 expression. The high expression of AtPAR1 and DcPAR1 led us to hypothesize a functional role of DcPAR1 that was verified through in vivo binding to AtPIF7 and overexpression in Arabidopsis, where AtPSY expression and carotenoid accumulation increased together with a photomorphogenic phenotype. Finally, DcPAR1 antisense carrot lines presented a dramatic decrease in carotenoid levels and in relative expression of key carotenogenic genes as well as impaired taproot development. These results suggest that DcPAR1 is a key factor for secondary root development and carotenoid synthesis in carrot taproot grown underground.

Coordinated transcriptional regulation of the carotenoid biosynthesis contributes to fruit lycopene content in high-lycopene tomato genotypes

Lycopene content in tomato fruit is largely under genetic control and varies greatly among genotypes. Continued improvement of lycopene content in elite varieties with conventional breeding has become challenging, in part because little is known about the underlying molecular mechanisms in high-lycopene tomatoes (HLYs). We collected 42 HLYs with different genetic backgrounds worldwide. High-performance liquid chromatography (HPLC) analysis revealed lycopene contents differed among the positive control wild tomato Solanum pimpinellifolium, HLYs, the normal lycopene cultivar "Moneymaker", and the non-lycopene cultivar NC 1Y at the pink and red ripe stages. Real-time RT-PCR analysis of expression of the 25 carotenoid biosynthesis pathway genes of each genotype showed a significantly higher expression in nine upstream genes (GGPPS1, GGPPS2, GGPPS3, TPT1, SSU II, PSY2, ZDS, CrtISO and CrtISO-L1 but not the well-studied PSY1, PDS and Z-ISO) at the breaker and/or red ripe stages in HLYs compared to Moneymaker, indicating a higher metabolic flux flow into carotenoid biosynthesis pathway in HLYs. Further conversion of lycopene to carotenes may be prevented via the two downstream genes (β-LCY2 and ε-LCY), which had low-abundance transcripts at either or both stages. Additionally, the significantly higher expression of four downstream genes (BCH1, ZEP, VDE, and CYP97C11) at either or both ripeness stages leads to significantly lower fruit lycopene content in HLYs than in the wild tomato. This is the first systematic investigation of the role of the complete pathway genes in regulating fruit lycopene biosynthesis across many HLYs, and enables tomato breeding and gene editing for increased fruit lycopene content.

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (Solanum lycopersicum). Several, including Solanum lycopersicoides, have been crossed to S. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome-scale genome assembly for S. lycopersicoides LA2951, which contains 37 938 predicted protein-coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of the S. lycopersicoides introgressions in a set of S. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity-associated function of the clustered Pto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of the Aubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild species S. lycopersicoides, which we use to shed light on the Aubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β-cyclase whose function we demonstrate.

Correlation of Carotenoids Content and ASTA Values of Pepper (Capsicum chinense) Genetic Resources

In this study, 226 Capsicum chinense genetic resources were analyzed using high-performance liquid chromatography and a spectrophotometer to measure and compare their carotenoid content and American Spice Trade Association (ASTA) color values, respectively. The total carotenoid content and ASTA values of the 226 pepper genetic resources were found to be in the range of 7.04–2430.85 mg/100 g dry weight (DW) and 0–221.32, respectively. Capsanthin, capsorubin, lutein, zeaxanthin, antheraxanthin, violaxanthin, α-carotene, β-carotene, and β-cryptoxanthin were the individual carotenoids studied. The average content of each carotenoid (n = 226) in mg/100 g DW was as follows: capsanthin (325.77), antheraxanthin (136.34), capsorubin (82.36), β-carotene (59.11), violaxanthin (46.54), zeaxanthin (43.21), α-carotene (13.91), β-cryptoxanthin (9.67), and lutein (2.72). A strong positive correlation was observed between total carotenoid content and ASTA value (r = 0.965). Likewise, the individual carotenoid content and ASTA value revealed a strong correlation, such as antheraxanthin (r = 0.964), capsanthin (r = 0.946), and capsorubin (r = 0.858). Three genetic resources with a total carotenoid content above 2000 mg/100 g DW were obtained, such as IT261426 (2430.85 mg/100 g DW), IT183657 (2077.55 mg/100 g DW), and IT261213 (2062.54 mg/100 g DW). The findings of this study will assist in the selection of genetic resources with high carotenoid content and ASTA value that can be used to develop and breed new pepper varieties. Also, detailed results of ASTA value correlation with carotenoids in C. chinense genetic resources are provided.

Transcriptomics Integrated with Metabolomics Unveil Carotenoids Accumulation and Correlated Gene Regulation in White and Yellow-Fleshed Turnip (Brassica rapa ssp. rapa)

Turnip (Brassica rapa ssp. rapa) is considered to be a highly nutritious and health-promoting vegetable crop, whose flesh color can be divided into yellow and white. It is widely accepted that yellow-fleshed turnips have higher nutritional value. However, reports about flesh color formation is lacking. Here, the white-fleshed inbred line, W21, and yellow-fleshed inbred line, W25, were profiled from the swollen root of the turnip at three developmental periods to elucidate the yellow color formation. Transcriptomics integrated with metabolomics analysis showed that the PSY gene was the key gene affecting the carotenoids formation in W25. The coding sequence of BrrPSY-W25 was 1278 bp and that of BrrPSY-W21 was 1275 bp, and BrrPSY was more highly expressed in swollen roots in W25 than in W21. Transient transgenic tobacco leaf over-expressing BrrPSY-W and BrrPSY-Y showed higher transcript levels and carotenoids contents. Results revealed that yellow turnip formation is due to high expression of the PSY gene rather than mutations in the PSY gene, indicating that a post-transcriptional regulatory mechanism may affect carotenoids formation. Results obtained in this study will be helpful for explaining the carotenoids accumulation of turnips.

Identification of QTLs for root color and carotenoid contents in Japanese orange carrot F2 populations

Carrot is a major source of provitamin A in a human diet. Two of the most important traits for carrot breeding are carotenoid contents and root color. To examine genomic regions related to these traits and develop DNA markers for carrot breeding, we performed an association analysis based on a general liner model using genome-wide single nucleotide polymorphism (SNPs) in two F2 populations, both derived from crosses of orange root carrots bred in Japan. The analysis revealed 21 significant quantitative trait loci (QTLs). To validate the detection of the QTLs, we also performed a QTL analysis based on a composite interval mapping of these populations and detected 32 QTLs. Eleven of the QTLs were detected by both the association and QTL analyses. The physical position of some QTLs suggested two possible candidate genes, an Orange (Or) gene for visual color evaluation, and the α- and β-carotene contents and a chromoplast-specific lycopene β-cyclase (CYC-B) gene for the β/α carotene ratio. A KASP marker developed on the Or distinguished a quantitative color difference in a different, related breeding line. The detected QTLs and the DNA marker will contribute to carrot breeding and the understanding of carotenoid biosynthesis and accumulation in orange carrots.

SlWRKY35 positively regulates carotenoid biosynthesis by activating the MEP pathway in tomato fruit

Carotenoids are vital phytonutrients widely recognised for their health benefits. Therefore, it is vital to thoroughly investigate the metabolic regulatory network underlying carotenoid biosynthesis and accumulation to open new leads towards improving their contents in vegetables and crops. The outcome of our study defines SlWRKY35 as a positive regulator of carotenoid biosynthesis in tomato. SlWRKY35 can directly activate the expression of the 1-deoxy-d-xylulose 5-phosphate synthase (SlDXS1) gene to reprogramme metabolism towards the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, leading to enhanced carotenoid accumulation. We also show that the master regulator SlRIN directly regulates the expression of SlWRKY35 during tomato fruit ripening. Compared with the SlLCYE overexpression lines, coexpression of SlWRKY35 and SlLCYE can further enhance lutein production in transgenic tomato fruit, indicating that SlWRKY35 represents a potential target towards designing innovative metabolic engineering strategies for carotenoid derivatives. In addition to providing new insights into the metabolic regulatory network associated with tomato fruit ripening, our data define a new tool for improving fruit content in specific carotenoid compounds.

Plant carotenoids: recent advances and future perspectives

Carotenoids are isoprenoid metabolites synthesized de novo in all photosynthetic organisms. Carotenoids are essential for plants with diverse functions in photosynthesis, photoprotection, pigmentation, phytohormone synthesis, and signaling. They are also critically important for humans as precursors of vitamin A synthesis and as dietary antioxidants. The vital roles of carotenoids to plants and humans have prompted significant progress toward our understanding of carotenoid metabolism and regulation. New regulators and novel roles of carotenoid metabolites are continuously revealed. This review focuses on current status of carotenoid metabolism and highlights recent advances in comprehension of the intrinsic and multi-dimensional regulation of carotenoid accumulation. We also discuss the functional evolution of carotenoids, the agricultural and horticultural application, and some key areas for future research.

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.

The Genetic Components of a Natural Color Palette: A Comprehensive List of Carotenoid Pathway Mutations in Plants

Carotenoids comprise the most widely distributed natural pigments. In plants, they play indispensable roles in photosynthesis, furnish colors to flowers and fruit and serve as precursor molecules for the synthesis of apocarotenoids, including aroma and scent, phytohormones and other signaling molecules. Dietary carotenoids are vital to human health as a source of provitamin A and antioxidants. Hence, the enormous interest in carotenoids of crop plants. Over the past three decades, the carotenoid biosynthesis pathway has been mainly deciphered due to the characterization of natural and induced mutations that impair this process. Over the year, numerous mutations have been studied in dozens of plant species. Their phenotypes have significantly expanded our understanding of the biochemical and molecular processes underlying carotenoid accumulation in crops. Several of them were employed in the breeding of crops with higher nutritional value. This compendium of all known random and targeted mutants available in the carotenoid metabolic pathway in plants provides a valuable resource for future research on carotenoid biosynthesis in plant species.

Alternative transcription and feedback regulation suggest that SlIDI1 is involved in tomato carotenoid synthesis in a complex way

Carotenoid pigments confer photoprotection and visual attraction and serve as precursors for many important signaling molecules. Herein, the orange-fruited phenotype of a tomato elite inbred line resulting from sharply reduced carotenoid levels and an increased β-carotene-to-lycopene ratio in fruit was shown to be controlled by a single recessive gene, oft3. BSA-Seq combined with fine mapping delimited the oft3 gene to a 71.23 kb interval on chromosome 4, including eight genes. Finally, the oft3 candidate gene SlIDI1, harboring a 116 bp deletion mutation, was identified by genome sequence analysis. Further functional complementation and CRISPR-Cas9 knockout experiments confirmed that SlIDI1 was the gene underlying the oft3 locus. qRT-PCR analysis revealed that the expression of SlIDI1 was highest in flowers and fruit and increased with fruit ripening or flower maturation. SlIDI1 simultaneously produced long and short transcripts by alternative transcription initiation and alternative splicing. Green fluorescent protein fusion expression revealed that the long isoform was mainly localized in plastids and that an N-terminal 59-amino acid extension sequence was responsible for plastid targeting. Short transcripts were identified in leaves and fruit by 5' RACE and in fruit by 3' RACE, which produced corresponding proteins lacking transit peptides and/or putative peroxisome targeting sequences, respectively. In SlIDI1 mutant fruit, SlBCH1 transcription involved in β-carotenoid catabolism was obviously suppressed, which may be responsible for the higher β-carotene-to-lycopene ratio and suggested potential feedback regulatory mechanisms involved in carotenoid pathway flux.

Carotenoids and Apocarotenoids in Planta: Their Role in Plant Development, Contribution to the Flavour and Aroma of Fruits and Flowers, and Their Nutraceutical Benefits

Carotenoids and apocarotenoids are diverse classes of compounds found in nature and are important natural pigments, nutraceuticals and flavour/aroma molecules. Improving the quality of crops is important for providing micronutrients to remote communities where dietary variation is often limited. Carotenoids have also been shown to have a significant impact on a number of human diseases, improving the survival rates of some cancers and slowing the progression of neurological illnesses. Furthermore, carotenoid-derived compounds can impact the flavour and aroma of crops and vegetables and are the origin of important developmental, as well as plant resistance compounds required for defence. In this review, we discuss the current research being undertaken to increase carotenoid content in plants and research the benefits to human health and the role of carotenoid derived volatiles on flavour and aroma of fruits and vegetables.

Development of fruit color in Rubus chingii Hu (Chinese raspberry): A story about novel offshoots of anthocyanin and carotenoid biosynthesis

Rubus chingii, is widely distributed in many Asian countries and well known for its medicinal and dietary properties. Diversity of fruit color in raspberry has been attributed to the presence of either anthocyanins or carotenoids. In this study, we investigated anthocyanins and carotenoids, and their biosynthesis by LC-MS/MS. Six anthocyanins mainly consisted of flavanol-anthocyanins while five carotenoids mainly consisted of β-citraurin esters. Flavanol-anthocyanins were produced from an offshoot of the anthocyanin biosynthesis, which started with biosynthesis of flavanols and anthocyanidin by leucoanthocyanidin reductase (LAR)/anthocyanidin reductase (ANR) and anthocyanidin synthase (ANS/LDOX) respectively. β-citraurin esters were produced from cleavage of zeaxanthin and esterification by organic acid, which was an offshoot of the carotenoid biosynthesis. The offshoot started with biosynthesis of zeaxanthin and β-citraurin by carotene β-hydroxylase (CHYB/LUT5) and carotenoid cleavage dioxygenase (CCD) respectively. During fruit ripening, biosynthesis of flavanols and anthocyanins was down-regulated by genes/proteins involved in phenylpropanoid and flavonoid biosynthesis, while biosynthesis of β-citraurin esters was up-regulated by imbalanced expression of genes/proteins involved in β,β-ring and β, ε-ring hydroxylation. Thus, β-citraurin esters, instead of anthocyanins imparted reddish color to the ripe fruit. These pigments and their biosynthesis in R. chingii are totally different from what occurs in other raspberry species.

HPLC-DAD-APCI-MS as a Tool for Carotenoid Assessment of Wild and Cultivated Cherry Tomatoes

Carotenoids are naturally occurring fat-soluble pigments found in many organisms. Because of their extensively conjugated carbon–carbon double bond system, carotenoids are potent antioxidants. Although the most abundant carotenoid and best singlet oxygen quencher found in red tomatoes is lycopene, carotenoid profiles may vary between genotypes. The objective of this work was to perform carotenoid profile indentification using HPLC-DAD-APCI-MS in ten wild cherry tomato accessions and one cultivated tomato. A mixture of hexane/acetone/ethanol (50:25:25) and 0.1% BHT was used for carotenoid extraction. For separation, a C30 column at 30 °C with a gradient consisting of methanol, methyl-tert-butyl ether, and water was used for their analysis. Ten major carotenoids were quantified within cherry tomato samples. All accessions present different profiles and quantities of carotenoids. Wild red tomatoes had more lycopene content that commercial tomato, whereas yellow tomatoes present no lycopene. From a functional viewpoint, higher concentrations of carotenoids that could play an antioxidant activity were measured from accessions IAC401, IAC426, LA1480, IAC391, and LA2692. This trait means that these germplasms may be targets for commercial activities. To the best of our knowledge, this is the first time that HPLC-DAD-APCI-MS has been used to analyze these accessions of wild cherry tomatoes that are both functionally promising and suitable for projects with social implementation at a local scale.

Daucus carota DcPSY2 and DcLCYB1 as Tools for Carotenoid Metabolic Engineering to Improve the Nutritional Value of Fruits

Carotenoids are pigments with important nutritional value in the human diet. As antioxidant molecules, they act as scavengers of free radicals enhancing immunity and preventing cancer and cardiovascular diseases. Moreover, α-carotene and β-carotene, the main carotenoids of carrots (Daucus carota) are precursors of vitamin A, whose deficiency in the diet can trigger night blindness and macular degeneration. With the aim of increasing the carotenoid content in fruit flesh, three key genes of the carotenoid pathway, phytoene synthase (DcPSY2) and lycopene cyclase (DcLCYB1) from carrots, and carotene desaturase (XdCrtI) from the yeast Xanthophyllomyces dendrorhous, were optimized for expression in apple and cloned under the Solanum chilense (tomatillo) polygalacturonase (PG) fruit specific promoter. A biotechnological platform was generated and functionally tested by subcellular localization, and single, double and triple combinations were both stably transformed in tomatoes (Solanum lycopersicum var. Microtom) and transiently transformed in Fuji apple fruit flesh (Malus domestica). We demonstrated the functionality of the S. chilense PG promoter by directing the expression of the transgenes specifically to fruits. Transgenic tomato fruits expressing DcPSY2, DcLCYB1, and DcPSY2-XdCRTI, produced 1.34, 2.0, and 1.99-fold more total carotenoids than wild-type fruits, respectively. Furthermore, transgenic tomatoes expressing DcLCYB1, DcPSY2-XdCRTI, and DcPSY2-XdCRTI-DcLCYB1 exhibited an increment in β-carotene levels of 2.5, 3.0, and 2.57-fold in comparison with wild-type fruits, respectively. Additionally, Fuji apple flesh agroinfiltrated with DcPSY2 and DcLCYB1 constructs showed a significant increase of 2.75 and 3.11-fold in total carotenoids and 5.11 and 5.84-fold in β-carotene, respectively whereas the expression of DcPSY2-XdCRTI and DcPSY2-XdCRTI-DcLCYB1 generated lower, but significant changes in the carotenoid profile of infiltrated apple flesh. The results in apple demonstrate that DcPSY2 and DcLCYB1 are suitable biotechnological genes to increase the carotenoid content in fruits of species with reduced amounts of these pigments.

Overexpression of Ginkgo biloba Hydroxy-2-methyl-2-(E)-butenyl 4-diphosphate reductase 2 gene (GbHDR2) in Nicotiana tabacum cv. Xanthi

2-C-Methyl-d-erythrol-4-phosphate (MEP) pathway in plant supplies isoprene building blocks for carotenoids and chlorophylls essential in photosynthesis as well as plant hormones such as gibberellin and abscisic acid. To assess the effect of overexpression of the terminal enzyme of the MEP pathway, 1-hydroxy-2-methyl-2-(E)-butenyl-4-diphosphate reductase (HDR), transgenic Nicotiana tabacum overexpressing class 2 HDR from Ginkgo biloba (GbHDR2) under the control of 35S promoter was constructed. Contents of chlorophylls a and b in transgenic tobacco were enhanced by 19 and 7%, respectively, compared to those of the wild type. The carotenoid level was also 18% higher than that in the control plant. As a result, photosynthetic rate of the transgenic tobacco was increased by up to 51%. Diterepenoid duvatrienediol content of transgenic tobacco was also elevated by at least sixfold. To explore the molecular basis of the enhanced isoprenoid accumulation, transcript levels of the key genes involved in the isoprenoid biosynthesis were measured. Transcript levels of geranylgeranyl diphosphate synthase (GGPP), kaurene synthase (KS), gibberellic acid 20 oxidase (GA20ox), and phytoene desaturase (PD) genes in the transgenic tobacco leaves were about twofold higher compared to the wild type. Therefore, upregulation of down-stream genes involved in biosynthesis of di- and tetraterpenoids due to GbHDR2 overexpression was responsible for elevated production of isoprenoids and enhanced photosynthetic rate.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02887-5.

Exogenous Application of 5-Aminolevulinic Acid Promotes Coloration and Improves the Quality of Tomato Fruit by Regulating Carotenoid Metabolism

5-Aminolevulinic acid (ALA) plays an important role in plant growth and development. It can also be used to enhance crop resistance to environmental stresses and improve the color and internal quality of fruits. However, there are limited reports regarding the effects of ALA on tomato fruit color and its regulatory mechanisms. Therefore, in this study, the effects of exogenous ALA on the quality and coloration of tomato fruits were examined. Tomato (Solanum lycopersicum "Yuanwei No. 1") fruit surfaces were treated with different concentrations of ALA (0, 100, and 200 mg⋅L-1) on the 24th day after fruit setting (mature green fruit stage), and the content of soluble sugar, titratable acid, soluble protein, vitamin C, and total free amino acids, as well as amino acid components, intermediates of lycopene synthetic and metabolic pathways, and ALA metabolic pathway derivatives were determined during fruit ripening. The relative expression levels of genes involved in lycopene synthesis and metabolism and those involved in ALA metabolism were also analyzed. The results indicated that exogenous ALA (200 mg⋅L-1) increased the contents of soluble sugars, soluble proteins, total free amino acids, and vitamin C as well as 11 kinds of amino acid components in tomato fruits and reduced the content of titratable acids, thus improving the quality of tomato fruits harvested 4 days earlier than those of the control plants. In addition, exogenous ALA markedly improved carotenoid biosynthesis by upregulating the gene expression levels of geranylgeranyl diphosphate synthase, phytoene synthase 1, phytoene desaturase, and lycopene β-cyclase. Furthermore, exogenous ALA inhibited chlorophyll synthesis by downregulating the genes expression levels of Mg-chelatase and protochlorophyllide oxidoreductase. These findings suggest that supplementation with 200 mg⋅L-1 ALA not only enhances the nutritional quality and color of the fruit but also promotes early fruit maturation in tomato.

Natural Genetic Diversity in Tomato Flavor Genes

Fruit flavor is defined as the perception of the food by the olfactory and gustatory systems, and is one of the main determinants of fruit quality. Tomato flavor is largely determined by the balance of sugars, acids and volatile compounds. Several genes controlling the levels of these metabolites in tomato fruit have been cloned, including LIN5, ALMT9, AAT1, CXE1, and LoxC. The aim of this study was to identify any association of these genes with trait variation and to describe the genetic diversity at these loci in the red-fruited tomato clade comprised of the wild ancestor Solanum pimpinellifolium, the semi-domesticated species Solanum lycopersicum cerasiforme and early domesticated Solanum lycopersicum. High genetic diversity was observed at these five loci, including novel haplotypes that could be incorporated into breeding programs to improve fruit quality of modern tomatoes. Using newly available high-quality genome assemblies, we assayed each gene for potential functional causative polymorphisms and resolved a duplication at the LoxC locus found in several wild and semi-domesticated accessions which caused lower accumulation of lipid derived volatiles. In addition, we explored gene expression of the five genes in nine phylogenetically diverse tomato accessions. In general, the expression patterns of these genes increased during fruit ripening but diverged between accessions without clear relationship between expression and metabolite levels.

Metabolite profile and genes/proteins expression in β-citraturin biosynthesis during fruit ripening in Chinese raspberry (Rubus chingii Hu)

Carotenoids are one of the most abundant pigments in raspberries. Rubus chingii Hu, indigenous to China, is traditionally consumed for health benefits. However, the carotenoid composition and pathways of R. chingii have not yet been studied. In this study, the components of carotenoids and genes/proteins involved in their biosynthesis were investigated during four fruit ripening phases via LC-MS/MS. Zeaxanthin, β-citraurin and its esters, first identified in Rubus, gradually accumulated during fruit maturation. These compounds, rather than anthocyanins, were responsible for the ripe fruit coloration. In carotenoid metabolism, upstream synthesis genes of RcPSY2 (CL1406.Contig2), RcPDS1 (CL7625.Contig2), RcZDS1 (CL590.Contig6) and RcCRTISO1 (CL6919.Contig2) were up-regulated in gene/protein expression to accelerate carotene biosynthesis. Downstream genes of RcLUT5CHYB/CYP97A (CL8884.Contig3) and RcCHYB/BCH (CL7966.Contig1) were up-regulated in gene/protein expression, while RcCHYE/CYP97C (CL9380.Contig1/2) were maintained at low levels. RcLCYE (Unigene19570) was down-regulated while RcLCYB (CL7586.Contig1) was up-regulated and then down-regulated. These differential gene/protein expressions between LCYB and LCYE, and between CHYE and CHYB led to zeaxanthin accumulation by elevating its biosynthetic enzymes and lowering enzymes for lutein biosynthesis. In apocarotenoid biosynthesis, RcCCD (CL1310.Contig3) was up-regulated in gene/protein expression, which raised the content of β-citraurin and its esters. Additionally, these genes/proteins diverged into different subgroups with distinct pattens of expression, suggesting their difference in function. For example, RcPSY1/3, RcZDS2, and RcCRTISO2/3 genes were expressed at very low levels, suggesting that they may be active in other tissues rather than in fruit. The mechanism of zeaxanthin and β-citraurin biosynthesis is responsible for fruit coloration, which is completely novel to Rubus.

Skin colour, carotenogenesis and chlorophyll degradation mutant alleles: genetic orchestration behind the fruit colour variation in tomato

The genetics underlying the fruit colour variation in tomato is an interesting area of both basic and applied research in plant biology. There are several factors, like phytohormones, environmental signals and epistatic interactions between genes, which modulate the ripe fruit colour in tomato. However, three aspects: genetic regulation of skin pigmentation, carotenoid biosynthesis and ripening-associated chlorophyll degradation in tomato fruits are of pivotal importance. Different genes along with their mutant alleles governing the aforementioned characters have been characterized in detail. Moreover, the interaction of these mutant alleles has been explored, which has paved the way for developing novel tomato genotypes with unique fruit colour and beneficial phytonutrient composition. In this article, we review the genes and the corresponding mutant alleles underlying the variation in tomato skin pigmentation, carotenoid biosynthesis and ripening-associated chlorophyll degradation. The possibility of generating novel fruit colour-variants using different combinations of these mutant alleles is documented. Furthermore, the involvement of some other mutant alleles (like those governing purple fruit colour and high fruit pigmentation), not belonging to the aforementioned three categories, are discussed in brief. The simplified representation of the assembled information in this article should not only help a broad range of readers in their basic understanding of this complex phenomenon but also trigger them for further exploration of the same. The article would be useful for genetic characterization of fruit colour-variants and molecular breeding for fruit colour improvement in tomato using the well-characterized mutant alleles.

European Database of Carotenoid Levels in Foods. Factors Affecting Carotenoid Content

Many studies indicate that diets including carotenoid-rich foods have positive effects on human health. Some of these compounds are precursors of the essential nutrient vitamin A. The present work is aimed at implementing a database of carotenoid contents of foods available in the European market. Factors affecting carotenoid content were also discussed. Analytical data available in peer-reviewed scientific literature from 1990 to 2018 and obtained by HPLC/UHPLC were considered. The database includes foods classified according to the FoodEx2 system and will benefit compilers, nutritionists and other professionals in areas related to food and human health. The results show the importance of food characterization to ensure its intercomparability, as large variations in carotenoid levels are observed between species and among varieties/cultivars/landraces. This highlights the significance of integrating nutritional criteria into agricultural choices and of promoting biodiversity. The uncertainty quantification associated with the measurements of the carotenoid content was very rarely evaluated in the literature consulted. According to the EuroFIR data quality evaluation system for food composition tables, the total data quality index mean was 24 in 35, reflecting efforts by researchers in the analytical methods, and less resources in the sampling plan documentation.

Increase of Yield, Lycopene, and Lutein Content in Tomatoes Grown Under Continuous PAR Spectrum LED Lighting

Light emitting diodes (LEDs) are an energy efficient alternative to high-pressure sodium (HPS) lighting in tomato cultivation. In the past years, we have learned a lot about the effect of red and blue LEDs on plant growth and yield of tomatoes. From previous studies, we know that plants absorb and utilize most of the visible spectrum for photosynthesis. This part of the spectrum is referred to as the photosynthetically active radiation (PAR). We designed a LED fixture with an emission spectrum that partially matches the range of 400 to 700 nm and thus partially covers the absorption spectrum of photosynthetic pigments in tomato leaves. Tomato plants grown under this fixture were significantly taller and produced a higher fruit yield (14%) than plants grown under HPS lighting. There was no difference in the number of leaves and trusses, leaf area, stem diameter, the electron transport rate, and the normalized difference vegetation index. Lycopene and lutein contents in tomatoes were 18% and 142% higher when they were exposed to the LED fixture. However, the ß-carotene content was not different between the light treatments. Transpiration rate under LED was significantly lower (40%), while the light use efficiency (LUE) was significantly higher (19%) compared to HPS lighting. These data show that an LED fixture with an emission spectrum covering the entire PAR range can improve LUE, yields, and content of secondary metabolites in tomatoes compared to HPS lighting.