Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin

Cloned genes and genetic regulation of anthocyanin biosynthesis in maize, a comparative review

Anthocyanins are plant-based pigments that are primarily present in berries, grapes, purple yam, purple corn and black rice. The research on fruit corn with a high anthocyanin content is not sufficiently extensive. Considering its crucial role in nutrition and health it is vital to conduct further studies on how anthocyanin accumulates in fruit corn and to explore its potential for edible and medicinal purposes. Anthocyanin biosynthesis plays an important role in maize stems (corn). Several beneficial compounds, particularly cyanidin-3-O-glucoside, perlagonidin-3-O-glucoside, peonidin 3-O-glucoside, and their malonylated derivatives have been identified. C1, C2, Pl1, Pl2, Sh2, ZmCOP1 and ZmHY5 harbored functional alleles that played a role in the biosynthesis of anthocyanins in maize. The Sh2 gene in maize regulates sugar-to-starch conversion, thereby influencing kernel quality and nutritional content. ZmCOP1 and ZmHY5 are key regulatory genes in maize that control light responses and photomorphogenesis. This review concludes the molecular identification of all the genes encoding structural enzymes of the anthocyanin pathway in maize by describing the cloning and characterization of these genes. Our study presents important new understandings of the molecular processes behind the manufacture of anthocyanins in maize, which will contribute to the development of genetically modified variants of the crop with increased color and possible health advantages.

Model-assisted analysis for tuning anthocyanin composition in grape berries

Anthocyanin composition is responsible for the red colour of grape berries and wines, and contributes to their organoleptic quality. However, anthocyanin biosynthesis is under genetic, developmental and environmental regulation, making its targeted fine-tuning challenging. We constructed a mechanistic model to simulate the dynamics of anthocyanin composition throughout grape ripening in Vitis vinifera, employing a consensus anthocyanin biosynthesis pathway. The model was calibrated and validated using six datasets from eight cultivars and 37 growth conditions. Tuning the transformation and degradation parameters allowed us to accurately simulate the accumulation process of each individual anthocyanin under different environmental conditions. The model parameters were robust across environments for each genotype. The coefficients of determination (R2) for the simulated versus observed values for the six datasets ranged from 0.92 to 0.99, while the relative root mean square errors (RRMSEs) were between 16.8 and 42.1 %. The leave-one-out cross-validation for three datasets showed R2 values of 0.99, 0.96 and 0.91, and RRMSE values of 28.8, 32.9 and 26.4 %, respectively, suggesting a high prediction quality of the model. Model analysis showed that the anthocyanin profiles of diverse genotypes are relatively stable in response to parameter perturbations. Virtual experiments further suggested that targeted anthocyanin profiles may be reached by manipulating a minimum of three parameters, in a genotype-dependent manner. This model presents a promising methodology for characterizing the temporal progression of anthocyanin composition, while also offering a logical foundation for bioengineering endeavours focused on precisely adjusting the anthocyanin composition of grapes.

The flavour of grape colour: anthocyanin content tunes aroma precursor composition by altering the berry microenvironment

Anthocyaninless (white) instead of black/red (coloured) fruits develop in grapevine cultivars without functional VviMYBA1 and VviMYBA2 genes, and this conditions the colour of wines that can be produced. To evaluate whether this genetic variation has additional consequences on fruit ripening and composition, we performed comparisons of microenvironment, transcriptomics, and metabolomics of developing grapes between near-isogenic white- and black-berried somatic variants of Garnacha and Tempranillo cultivars. Berry temperature was as much as 3.5 ºC lower in white- compared to black-berried Tempranillo. An RNA-seq study combined with targeted and untargeted metabolomics revealed that ripening fruits of white-berried variants were characterized by the up-regulation of photosynthesis-related and other light-responsive genes and by their higher accumulation of specific terpene aroma precursors, fatty acid-derived aldehyde volatiles, and phenylpropanoid precursor amino acids. MYBA1-MYBA2 function proved essential for flavonol trihydroxylation in black-berried somatic variants, which were also characterized by enhanced expression of pathogen defence genes in the berry skin and increased accumulation of C6-derived alcohol and ester volatiles and γ-aminobutyric acid. Collectively, our results indicate that anthocyanin depletion has side-effects on grape composition by altering the internal microenvironment of the berry and the partitioning of the phenylpropanoid pathway. Our findings show how fruit colour can condition other fruit features, such as flavour potential and stress homeostasis.

Genome-wide identification, comparative analysis and functional roles in flavonoid biosynthesis of cytochrome P450 superfamily in pear (Pyrus spp.)

BACKGROUND

The cytochrome P450 (CYP) superfamily is the largest enzyme metabolism family in plants identified to date, and it is involved in many biological processes, including secondary metabolite biosynthesis, hormone metabolism and stress resistance. However, the P450 gene superfamily has not been well studied in pear (Pyrus spp.).

RESULTS

Here, the comprehensive identification and a comparative analysis of P450 superfamily members were conducted in cultivated and wild pear genomes. In total, 338, 299 and 419 P450 genes were identified in Chinese white pear, European pear and the wild pear, respectively. Based on the phylogenetic analyses, pear P450 genes were divided into ten clans, comprising 48 families. The motif and gene structure analyses further supported this classification. The expansion of the pear P450 gene family was attributed to whole-genome and single-gene duplication events. Several P450 gene clusters were detected, which have resulted from tandem and proximal duplications. Purifying selection was the major force imposed on the long-term evolution of P450 genes. Gene dosage balance, subfunctionalization and neofunctionalization jointly drove the retention and functional diversification of P450 gene pairs. Based on the association analysis between transcriptome expression profiles and flavonoid content during fruit development, three candidate genes were identified as being closely associated with the flavonoid biosynthesis, and the expression of one gene was further verified using qRT-PCR and its function was validated through transient transformation in pear fruit.

CONCLUSIONS

The study results provide insights into the evolution and biological functions of P450 genes in pear.

Uncovering nutritional metabolites and candidate genes involved in flavonoid metabolism in Houttuynia cordata through combined metabolomic and transcriptomic analyses

The perennial herb Houttuynia cordata has long been cultivated and used as medicinal and edible plant in Asia. Nowadays, increasing attention is attracted due to its numerous health benefits. Flavonoids are the main chemical constituents exerting pharmacological activities. In the present study, we investigated both metabolome and transcriptome of two H. cordata accessions (6# and 7#) with distinct flavonoids contents. In total 397 metabolites, i.e., 220 flavonoids, 92 amino acids and derivatives, 20 vitamins, and 65 saccharides were abundant in aboveground part. Cyanidin-3-O-rutinoside and quercetin-3-O-galactoside were the most abundant flavonoids, which can be categorized into seven classes, namely anthocyanidins, chalcones, flavanols, flavanones, flavanonols, flavones, and flavonols. Flavonols was the most abundant group. Contents of 112 flavonoids differed significantly between the two accessions, with catechin-(7,8-bc)-4α-(3,4-dihydroxyphenyl)-dihydro-2-(3H)-one, cinchonain Id, and cinchonain Ic being the dominant flavonoid metabolites among them. Pinocembrin-7-O-neohesperidoside, pinocembrin-7-O-rutinoside, and kaempferol-3-O-galactoside-4'-O-glucoside were uniquely abundant in accession 7. Transcriptome data revealed a total of 110 different expressed genes related to flavonoid metabolism, with more highly expressed genes observed in 7#. We annotated a total of 19 differential flavonoid metabolites and 34 differentially expressed genes that are associated with the flavonoid metabolic network. Based on the transcriptome and qPCR data a total of 8 key candidate genes involved in flavonoid metabolism were identified. The ANS gene were found to play an important role in the synthesis of cyanidin-3-O-glucoside, while the CHI, F3'H and FLS genes were mainly responsible for controlling the levels of flavanones, flavones, and flavonols, respectively. Collectively, the present study provides important insights into the molecular mechanism underlying flavonoid metabolism in H. cordata.

Metabolomic and transcriptomic analyses reveal the effects of grafting on blood orange quality

Introduction

Blood orange (Citrus sinensis L.) is a valuable source of nutrition because it is enriched in anthocyanins and has high organoleptic properties. Grafting is commonly used in citriculture and has crucial effects on various phenotypes of the blood orange, including its coloration, phenology, and biotic and abiotic resistance. Still, the underlying genetics and regulatory mechanisms are largely unexplored.

Methods

In this study, we investigated the phenotypic, metabolomic, and transcriptomic profiles at eight developmental stages of the lido blood orange cultivar (Citrus sinensis L. Osbeck cv. Lido) grafted onto two rootstocks.

Results and discussion

The Trifoliate orange rootstock provided the best fruit quality and flesh color for Lido blood orange. Comparative metabolomics suggested significant differences in accumulation patterns of metabolites and we identified 295 differentially accumulated metabolites. The major contributors were flavonoids, phenolic acids, lignans and coumarins, and terpenoids. Moreover, transcriptome profiling resulted in the identification of 4179 differentially expressed genes (DEGs), and 54 DEGs were associated with flavonoids and anthocyanins. Weighted gene co-expression network analysis identified major genes associated to 16 anthocyanins. Furthermore, seven transcription factors (C2H2, GANT, MYB-related, AP2/ERF, NAC, bZIP, and MYB) and five genes associated with anthocyanin synthesis pathway (CHS, F3H, UFGT, and ANS) were identified as key modulators of the anthocyanin content in lido blood orange. Overall, our results revealed the impact of rootstock on the global transcriptome and metabolome in relation to fruit quality in lido blood orange. The identified key genes and metabolites can be further utilized for the quality improvement of blood orange varieties.

Integrative analysis of grapevine (Vitis vinifera L) transcriptome reveals regulatory network for Chardonnay quality formation

Anthocyanins, total phenols, soluble sugar and fruit shape plays a significant role in determining the distinct fruit quality and customer preference. However, for the majority of fruit species, little is known about the transcriptomics and underlying regulatory networks that control the generation of overall quality during fruit growth and ripening. This study incorporated the quality-related transcriptome data from 6 ecological zones across 3 fruit development and maturity phases of Chardonnay cultivars. With the help of this dataset, we were able to build a complex regulatory network that may be used to identify important structural genes and transcription factors that control the anthocyanins, total phenols, soluble sugars and fruit shape in grapes. Overall, our findings set the groundwork to improve grape quality in addition to offering novel views on quality control during grape development and ripening.

Functional characterization of 5'-regulatory region of flavonoid 3',5'-hydroxylase-1 gene of banana plants

Generation of crops with broad-spectrum tolerance to biotic and abiotic stress conditions depends upon availability of genetic elements suitable for varied situations and diverse genotypes. Here, we characterize the 5'-upstream regulatory region of flavonoid 3'5'-hydroxylase-1 (F3'5'H-1) gene from banana and analyzed its tissue-specific and stress-mediated activation in genetic background of tobacco plants. MusaF3'5'H-1 is a stress-responsive gene as its expression is induced in banana after application of salicylic acid and methyl jasmonate while its transcript levels were drastically reduced in response to drought, high salinity and abscisic acid. P_MusaF3'5'H-1 harbours cis-elements associated with stress conditions and those responsible for tissue-specific expression. Transgenic lines harbouring P_MusaF3'5'H-1-GUS displays strong GUS expression in guard cells of stomata indicating guard cell preferred activity of P_MusaF3'5'H-1 while its activity was undetectable in roots. Drought and high salinity induce strong expression of GUS in transgenic tobacco lines and exposure to abscisic acid, salicylic acid and methyl jasmonate revealed distinct profiles of GUS expression in transgenic lines confirming involvement of F3'5'H-1 in plant stress responses. Fluorescent β-galactosidase assay revealed induction profiles of P_MusaF3'5'H-1 at different time points in transgenic lines exposed to salicylic acid and abscisic acid while strong suppression in GUS expression was observed after application of methyl jasmonate. The guard cell preferred activity of P_MusaF3'5'H-1 and stress-mediated expression profiles of MusaF3'5'H-1 indicated the suitability of P_MusaF3'5'H-1 for generating stress-enduring crops and analyzing guard cell functions.

Transcriptomic-based analysis to identify candidate genes for blue color rose breeding

Analysis of the flower color formation mechanism of 'Rhapsody in Blue' by BF and WF transcriptomes reveals that RhF3'H and RhGT74F2 play a key role in flower color formation. Rosa hybrida has colorful flowers and a high ornamental value. Although rose flowers have a wide range of colors, no blue roses exist in nature, and the reason for this is unclear. In this study, the blue-purple petals (BF) of the rose variety 'Rhapsody in Blue' and the white petals (WF) of its natural mutant were subjected to transcriptome analysis to find genes related to the formation of the blue-purple color. The results showed that the anthocyanin content was significantly higher in BF than in WF. A total of 1077 differentially expressed genes (DEGs) were detected by RNA-Seq analysis, of which 555 were up-regulated and 522 were down-regulated in the WF vs. BF petals. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of the DEGs revealed that a single gene up-regulated in BF was related to multiple metabolic pathways including metabolic process, cellular process, protein-containing complex, etc. Additionally, the transcript levels of most of the structural genes related to anthocyanin synthesis were significantly higher in BF than in WF. Selected genes were analyzed by qRT-PCR and the results were highly consistent with the RNA-Seq results. The functions of RhF3'H and RhGT74F2 were verified by transient overexpression analyses, and the results confirmed that both affect the accumulation of anthocyanins in 'Rhapsody in Blue'. We have obtained comprehensive transcriptome data for the rose variety 'Rhapsody in Blue'. Our results provide new insights into the mechanisms underlying rose color formation and even blue rose formation.

Multi-omics analyses reveal new insights into nutritional quality changes of alfalfa leaves during the flowering period

High-quality alfalfa is an indispensable resource for animal husbandry and sustainable development. Its nutritional quality changes dramatically during its life cycle and, at present, no molecular mechanisms for nutrient metabolic variation in alfalfa leaves at different growth stages have been clearly reported. We have used correlation and network analyses of the alfalfa leaf metabolome, proteome, and transcriptome to explore chlorophyll, flavonoid, and amino acid content at two development stages: budding stage (BS) and full-bloom stage (FBS). A high correlation between the expression of biosynthetic genes and their metabolites revealed significant reductions in metabolite content as the plant matured from BS to FBS. l-Glutamate, the first molecule of chlorophyll biosynthesis, decreased, and the expression of HemA, which controls the transformation of glutamyl-tRNA to glutamate 1-semialdehyde, was down-regulated, leading to a reduction in leaf chlorophyll content. Flavonoids also decreased, driven at least in part by increased expression of the gene encoding CYP75B1: flavonoid 3'-monooxygenase, which catalyzes the hydroxylation of dihydroflavonols and flavonols, resulting in degradation of flavonoids. Expression of NITRILASE 2 (NIT2) and Methyltransferase B (metB), which regulate amino acid metabolism and influence the expression of genes of the glycolysis-TCA pathway, were down-regulated, causing amino acid content in alfalfa leaves to decrease at FBS. This study provides new insights into the complex regulatory network governing the content and decrease of chlorophyll, amino acids, flavonoids, and other nutrients in alfalfa leaves during maturation. These results further provide a theoretical basis for the generation of alfalfa varieties exhibiting higher nutritional quality, high-yield cultivation, and a timely harvest.

Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits

Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.

Demethylation of the 3' LTR region of retrotransposon in VvMYBA1BEN allele enhances anthocyanin biosynthesis in berry skin and flesh in 'Brazil' grape

Black-skinned and red-fleshed grape 'Brazil' is a bud sport of rosy-skinned 'Benitaka'. 'Brazil' has a much higher anthocyanin content in the skin than that of 'Benitaka' and is characterized by the accumulation of anthocyanins in the flesh. Our genomic analysis of the VvMYBA loci, which regulate anthocyanin biosynthesis, suggested that the difference in skin and flesh color between 'Brazil' and 'Benitaka' cannot be explained by genomic alteration at the loci. Expression levels of VvMYBA1 and anthocyanin biosynthesis-related genes in skin and flesh were significantly higher in 'Brazil' than in 'Benitaka' throughout berry development. DNA methylation levels in the 3' long terminal repeat (LTR) of a retrotransposon in the upstream region of VvMYBA1^BEN allele were clearly higher in the skin and flesh of 'Benitaka' than in those of 'Brazil' throughout berry development. These findings suggest that a dramatic decrease in DNA methylation level in the 3' LTR of the retrotransposon in the VvMYBA1^BEN allele in 'Brazil' increases the expression levels of VvMYBA1 and anthocyanin accumulation in skin and flesh. Our findings also suggest that skin and flesh colors are inherited together and vary depending on the presence or absence of the VvMYBA1^BEN allele.

Cold stress regulates accumulation of flavonoids and terpenoids in plants by phytohormone, transcription process, functional enzyme, and epigenetics

Plants make different defense mechanisms in response to different environmental stresses. One common way is to produce secondary metabolites. Temperature is the main environmental factor that regulates plant secondary metabolites, especially flavonoids and terpenoids. Stress caused by temperature decreasing to 4-10 °C is conducive to the accumulation of flavonoids and terpenoids. However, the accumulation mechanism under cold stress still lacks a systematic explanation. In this review, we summarize three aspects of cold stress promoting the accumulation of flavonoids and terpenoids in plants, that is, by affecting (1) the content of endogenous plant hormones, especially jasmonic acid and abscisic acid; (2) the expression level and activity of important transcription factors, such as bHLH and MYB families. This aspect also includes post-translational modification of transcription factors caused by cold stress; (3) key enzyme genes expression and activity in the biosynthesis pathway, in addition, the rate-limiting enzyme and glycosyltransferases genes are responsive to cold stress. The systematic understanding of cold stress regulates flavonoids, and terpenoids will contribute to the future research of genetic engineering breeding, metabolism regulation, glycosyltransferases mining, and plant synthetic biology.

Physiological and Transcriptional Responses to Saline Irrigation of Young 'Tempranillo' Vines Grafted Onto Different Rootstocks

The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young 'Tempranillo' (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m-1 and a Saline treatment with 3.5 dS m-1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl- and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards.

Genome-wide transcriptome analysis and characterization of the cytochrome P450 flavonoid biosynthesis genes in pigeon pea (Cajanus cajan)

226 CcCYP450 genes were identified at the genomic level and were classified into 45 clades based on phylogenetic analysis. CcCYP75B165 gene was found that might play important roles in the biosynthesis of flavonoids in pigeon pea, and was significantly induced by methyl jasmonate (MeJA). The cytochrome P450 mono-oxygenase (CYP450) superfamily plays a key role in the flavonoid biosynthesis pathway and resists different kinds of stresses. Several CYP450 genes have been identified to be involved in the biosynthesis of crop protection agents. However, the CcCYP450 genes from pigeon pea have not been identified. Here, 226 CcCYP450 genes were identified at the genomic level by analysing the gene structure, distribution on chromosomes, gene duplication, and conserved motifs and were classified into 45 clades based on phylogenetic analysis. RNA-seq analysis revealed clear details of CcCYP450 genes that varied with time of MeJA (methyl jasmonate) induction. Among them, six CcCYP450 subfamily genes were found that might play important roles in the biosynthesis of flavonoids in pigeon pea. The overexpression of CcCYP75B165 in pigeon pea significantly induced the accumulation of genistin and downregulated the contents of cajaninstilbene acid, apigenin, isovitexin, and genistein and the expression of flavonoid synthase genes. This study provides theoretical guidance and plant genetic resources for cultivating new pigeon pea varieties with high flavonoid contents and exploring the molecular mechanisms of the biosynthesis of flavonoids under MeJA treatment.

SmMYB113 Is a Key Transcription Factor Responsible for Compositional Variation of Anthocyanin and Color Diversity Among Eggplant Peels

To understand the color formation mechanism in eggplant (Solanum melongena L.) peel, a metabolomic analysis was performed in six cultivars with different peel colors. A total of 167 flavonoids, including 16 anthocyanins, were identified based on a UPLC-MS/MS approach. Further analysis revealed that the delphinidins/flavonoids ratio was consistent with the purple coloration of eggplant peels, and SmF3'5'H expression level was consistent with the delphinidin 3-O-glucoside and delphinidin 3-O-rutinoside contents, the main anthocyanins in the purple-peels eggplant cultivars identified in this study. SmMYB113 overexpression promoted anthocyanins accumulation in eggplant peels and pulps. Metabolomic analysis revealed that delphinidins were still the main anthocyanins class in the peels and pulps of SmMYB113-OE4, but most anthocyanins were glycosylated at the 5-position of the B-ring. Our results provide new insights into the anthocyanin composition of eggplant peels and demonstrate the importance of SmMYB113 in stimulating anthocyanin biosynthesis in eggplant fruits.

Transcriptomic and metabolomic analysis reveals the difference between large and small flower taxa of Herba Epimedii during flavonoid accumulation

Herba Epimedii, as a traditional Chinese herb, is divided into large and small flower taxa, and can invigorate sexuality and strengthen muscles and bones. Herba Epimedii is rich in flavonoids, which largely contribute to its medicinal benefits. In our previous studies, we have found that the flavonoids content was much more in small than large flower taxa. To further identify molecular mechanisms of flavonoids metabolism in Herba Epimedii, combined metabolome and transcriptomic analyses were performed to profile leaves and flowers. Association analysis revealed that the expression of genes involved in flavonoid biosynthesis showed significant differences between small and large flower taxa. Eleven flavonols significantly increased in small compared to large flower taxa. Moreover, genes encoding O-methyltransferase played crucial roles in flavonoids metabolism by an integrated analysis. Taken together, these data highlight the breeding tendency of small flower taxa to improve the quality of Herba Epimedii.

Flavonoid biosynthesis in four Dendrobium species based on transcriptome sequencing and metabolite analysis

BACKGROUND

Dendrobium is a genus of plants used as traditional Chinese herbal medicines, with high economic and medicinal value.

METHODS AND RESULTS

To reveal the mechanism of flavonoid biosynthesis in Dendrobium, the metabolites and transcriptomes of four Dendrobium species (D. chrysotoxum, D. nobile, D. fimbriatum, and D. denneanum) were analyzed comprehensively. Ultra-high-performance liquid chromatography-tandem mass spectrometry analysis revealed ten flavonoid compounds in Dendrobium. In total, 100,096 unigenes were obtained from the transcript database of the four Dendrobium species. Among the identified differentially expressed genes, 51 were associated with flavonoid biosynthesis, and 670 differentially expressed transcription factors were predicted, including 194 MYB, 87 bHLH, and 100 WRKY family transcription factors, respectively. Transcriptome analysis showed that the expression levels of structural genes such as chalcone synthase (CHS), cinnamate-4-hydroxylase (C4H), and flavonoid 3'-hydroxylase (F3'H) were lower in D. chrysotoxum, D. nobile, and D. fimbriatum than those in D. denneanum, which may be the main reason for the low flavonoid contents in D. chrysotoxum, D. nobile, and D. fimbriatum.

CONCLUSIONS

The expression level of structural genes corresponded to the accumulation level of flavonols in the different Dendrobium species. The results deepen the understanding of the molecular mechanism of flavonoid biosynthesis in Dendrobium and provide novel insights into the synthesis and accumulation of flavonoids in Dendrobium.

Integrative Analyses of Metabolomes and Transcriptomes Provide Insights into Flavonoid Variation in Grape Berries

Flavonoids in grapes contribute the quality of the berry, but the flavonoid diversity and the regulatory networks underlying the variation require a further investigation. In this study, we integrated multi-omics data to systematically explore the global metabolic and transcriptional profiles in the skins and pulps of three grape cultivars. The results revealed large-scale differences involved in the flavonoid metabolic pathway. A total of 133 flavonoids, including flavone and flavone C-glycosides, were identified. Beyond the visible differences of anthocyanins, there was large variation in other sub-branched flavonoids, most of which were positively correlated with anthocyanins in grapes. The expressions of most flavonoid biosynthetic genes and the major regulators MYBA1 were strongly consistent with the changes in flavonoids. Integrative analysis identified two novel transcription factors (MYB24 and MADS5) and two ubiquitin proteins (RHA2) as promising regulatory candidates for flavonoid biosynthesis in grapes. Further verification in various grape accessions indicated that five major genes including flavonol 3'5'-hydroxylase (F3'5'H), UDP-glucose:flavonoid 3-O-glycosyl-transferase, anthocyanin O-methyltransferase, acyltransferase (3AT), and glutathione S-transferase (GST4) controlled flavonoid variation in grape berries. These findings provide valuable information for understanding the mechanism of flavonoid biosynthesis in grape berries and the further development of grape health products.

The expansion and diversity of the CYP75 gene family in Vitaceae

The CYP75 gene family plays an important role in flavonoid biosynthesis in plants. Little is known about the evolution of the gene family within the grape family. Here, we extracted the CYP75 genes from transcriptome data of 15 grape species and 36 representative genomes from other plants to explore the evolutionary history of the CYP75 gene family in Vitaceae. The structure of the CYP75 protein sequences is highly conserved with the variation mainly occurring in the N terminal and the middle region. The evolutionary analyses suggested classifying the CYP75 gene family into three groups in Vitaceae, namely Vitaceae A1, Vitaceae A2 and Vitaceae B. The Vitaceae A1 and A2 belong to the CYP75A subfamily and the Vitaceae B belongs to the CYP75B subfamily. Within the Vitaceae A1, most Vitaceae taxa present only one copy of the CYP75A protein sequence except for Vitis vinifera with a high number of sequences, which might have originated through recent gene duplications after its split from the other species. Vitaceae A2 contain only CYP75A sequences from Vitaceae sister to one from Camellia sinensis, probably representing a relict lineage. The CYP75B proteins were found to be dominated in Vitaceae and other angiosperms. Our results provide important insights into understanding the evolutionary history of the CYP75 gene family in Vitaceae and other angiosperms.

Effects of leaf removal on the accumulation of anthocyanins and the expression of anthocyanin biosynthetic genes in Cabernet Sauvignon (Vitis vinifera L.) grapes

BACKGROUND

Anthocyanins, a major flavonoid class, determine the color and quality of wine. Recent research revealed that basal leaf removal can increase the content of these compounds. This study determined the effects of basal leaf removal on the anthocyanin profiles of Cabernet Sauvignon grapes.

RESULTS

The effects of basal leaf removal on anthocyanin composition in Cabernet Sauvignon grapes were investigated over two growing seasons. Leaf removal at 5% veraison (VB6) and at 100% veraison (VC6) was compared with a control. Reducing sugar and total anthocyanin contents in the leaf removal group were significantly higher than in the control group at harvest for both vintages. Leaf removal increased the content of individual anthocyanins and significantly improved the malvidin-3-O-glucoside (Mv-3-glc), peonidin-3-O-glucoside (Pn-3-glc), and malvidin-3-O-(6-acetyl)-glucoside (Mv-3-acglc) content of the VB6 group. At harvest, VB6 treatment increased the transcript abundance of structural and regulator genes in the anthocyanin pathway, especially VvF3'5'H, VvLDOX, and VvDFR.

CONCLUSIONS

Our results suggest that leaf removal at 5% veraison may be useful for improving the anthocyanin content in grapes. © 2020 Society of Chemical Industry.

Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii)

As one of the largest transcription factor family, basic helix-loop-helix (bHLH) transcription factor family plays an important role in plant metabolism, physiology and growth. Berry color is one of the important factors that determine grape quality. However, the bHLH transcription factor family's function in anthocyanin synthesis of grape berry has not been studied systematically. We identified 115 bHLH transcription factors in grape genome and phylogenetic analysis indicated that bHLH family could be classified into 25 subfamilies. First, we screened six candidate genes by bioinformatics analysis and expression analysis. We found one of the candidate genes VdbHLH037 belonged to III (f) subfamily and interacted with genes related to anthocyanin synthesis through phylogenetic analysis and interaction network prediction. Therefore, we speculated that VdbHLH037 participated in the anthocyanin synthesis process. To confirm this, we transiently expressed VdbHLH037 in grape and Arabidopsis transformation. Compared with the control, transgenic materials can accumulate more anthocyanins. These results provide a good base to study the function of the VdbHLH family in anthocyanin synthesis of grape berry.

Melatonin alters the secondary metabolite profile of grape berry skin by promoting VvMYB14-mediated ethylene biosynthesis

The interplay between melatonin and ethylene in the regulation of fruit metabolism and the underlying molecular mechanism of this interplay remain largely unclear. Here, widely targeted metabolomics analysis revealed a total of 464 metabolites present in berry skin. Among them, 27 significantly differentially accumulated metabolites (DAMs) were produced in response to melatonin treatment in the presence or absence of 1-MCP. Most of the DAMs were secondary metabolites, including flavonoids, phenolic acids, stilbenes, and flavonols. Additionally, the accumulation of 25 DAMs was regulated by melatonin via ethylene. RNA-seq analysis indicated that melatonin primarily regulated the pathways of plant hormone signal transduction and secondary metabolite biosynthesis via ethylene. Gene-metabolite association analysis showed that melatonin regulated the expression of the VvSTS1, VvF3H, VvLAR2, and VvDFR genes, suggesting that these genes may play key roles in regulating secondary metabolites in the skin; additionally, VvMYB14 and VvACS1 were suggested to be involved in the regulation of secondary metabolites. Further experiments revealed that melatonin induced the expression of VvMYB14 and that VvMYB14 increased ethylene production by transcriptionally activating VvACS1, thereby affecting the accumulation of secondary metabolites. Collectively, melatonin promotes ethylene biosynthesis and alters secondary metabolite accumulation through the regulation of VvACS1 by VvMYB14.

High temperature at veraison inhibits anthocyanin biosynthesis in berry skins during ripening in 'Kyoho' grapevines

We examined the effects of high temperature (HT) at veraison (the onset of ripening) on coloration and anthocyanin biosynthesis in berry skins of 'Kyoho' grapevines (Vitis labruscana L.). The vines were subjected to control, HT (6 °C higher than the control for 10 days), and intermittent HT (IHT; 6 °C higher than the control for 4 days followed by control temperature for 3 days and then 6 °C higher than the control for another 3 days) conditions from 50 to 60 days after full bloom (DAFB) in temperature-controlled rooms. Under control conditions, berry skins were tinted purple from 55 DAFB and turned to reddish-purple thereafter until 80 DAFB, concurrently with the anthocyanin accumulation. The HT and IHT treatments greatly inhibited the coloration and anthocyanin accumulation, with greater inhibition by the HT treatment. The HT and IHT treatments significantly inhibited the expressions of early (EBGs) and late anthocyanin biosynthetic genes (LBGs), and the transcription factor gene VlMYBA2. Abscisic acid (ABA) contents in the control berry skins increased from 50 DAFB, peaked at 55 DAFB, and decreased thereafter. The HT and IHT treatments reduced the increase in ABA contents, with no significant difference between HT- and IHT-treated vines. Gibberellin (GA) contents decreased during veraison in the berry skins of control and IHT-treated vines, but remained unchanged in those of HT-treated vines. These results suggest that the coloration and anthocyanin biosynthesis in berry skins are associated with changes in the ABA/GA ratio.

Mitigating Heat Wave and Exposure Damage to "Cabernet Sauvignon" Wine Grape With Partial Shading Under Two Irrigation Amounts

Rising temperatures in most agricultural regions of the world are associated with a higher incidence of extreme weather events such as heat waves. We performed an experiment to mitigate the impact of heat waves and exposure of berries in grapevine (Vitis vinifera cv. "Cabernet Sauvignon") with untreated vines (Exposed) or with fruit-zone partial shading (Shaded) under 40 and 80% replacement of crop evapotranspiration (ET _c ) with sustained deficit irrigation in a factorially arranged experiment. The trial was performed in a vineyard with vertically shoot positioned trellis with a row orientation that concentrated solar radiation exposure on the southwest aspect of the fruit zone. Leaf stomatal conductance (g _s ) and net carbon assimilation (A _N ) were significantly lower in shaded leaves under partial fruit-zone shading that resulted in lower pruning mass for Shaded treatments. Stem water potential (Ψ _stem ) responded to a large extent to increased irrigation. However, grapevines with partial fruit-zone shading had transiently better water status under 40% ET _c . Cluster maximum temperatures were 3.9°C greater in Exposed grapevines. Exposed clusters had transiently lower acidity and higher pH. However, Exposed clusters on 40% ET _c had higher total soluble solids (TSS). The experimental vineyard suffered a 4-day heat wave 21 days before harvest, resulting in 25% of the clusters being damaged in Exposed treatment, regardless of irrigation amount. Furthermore, berries in Exposed treatments suffered a great loss of anthocyanins and flavonols even if they were not damaged by direct solar exposure. The pre-planting decision of using a vertically shoot positioned trellis that concentrated solar radiation on the Southwest aspect offered mild protection in a hot climate region with a sunny growing season with extreme heat events during the execution of study. The extreme conditions under which this study was conducted are not unusual, and have become more expected. Our work provided evidence of the vulnerability of grape berry to heat waves and exposure during heat wave events and possible protection methods to mitigate these effects in situ in context of climate change.

Targeted Metabolomic and Transcript Level Analysis Reveals Quality Characteristic of Chinese Wild Grapes (Vitis davidii Foex)

Native to China, spine grapes (Vitis davidii Foex) are an important wild grape species. Here, the quality characteristics of one white and three red spine grape clones were evaluated via targeted metabolomic and transcription level analysis. Xiangzhenzhu (XZZ) had the highest soluble sugar and organic acid content. Malvidin-3-acetyl-glucoside and cyanidin-3-glucoside were the characteristic anthocyanins in spine grapes, and significant differences in anthocyanin composition between different clones were detected. Anthocyanins were not detected in Baiyu (BY) grapes. The transcript levels of VdGST, VdF3′H, VdOMT, VdLDOX, and VdUFGT were significantly related to the anthocyanin biosynthesis and proportions. A total of 27 kinds of glycosidically bound volatiles (including alcohols, monoterpenes, esters, aldehydes, ketones, and phenolic acid) were identified in spine grapes, with Gaoshan #4 (G4) and BY grapes having the highest concentrations. The VdGT expression levels were closely related to glycosidically bound volatile concentrations. These results increase our understanding of the quality of wild spine grapes and further promote the development and use of wild grape resources.

Sugar Signaling During Fruit Ripening

Sugars play a key role in fruit quality, as they directly influence taste, and thus consumer acceptance. Carbohydrates are the main resources needed by the plant for carbon and energy supply and have been suggested to be involved in all the important developmental processes, including embryogenesis, seed germination, stress responses, and vegetative and reproductive growth. Recently, considerable progresses have been made in understanding regulation of fruit ripening mechanisms, based on the role of ethylene, auxins, abscisic acid, gibberellins, or jasmonic acid, in both climacteric and non-climacteric fruits. However, the role of sugar and its associated molecular network with hormones in the control of fruit development and ripening is still poorly understood. In this review, we focus on sugar signaling mechanisms described up to date in fruits, describing their involvement in ripening-associated processes, such as pigments accumulation, and their association with hormone transduction pathways, as well as their role in stress-related responses.

Transcriptomic differences between male and female Trachycarpus fortunei

Trachycarpus fortunei (Hook.) is a typical dioecious plant, which has important economic value. There is currently no sex identification method for the early stages of T. fortunei growth. The aim of this study was to obtain expression and site differences between male and female T. fortunei transcriptomes. Using the Illumina sequencing platform, the transcriptomes of T. fortunei male and female plants were sequenced. By analyzing transcriptomic differences, the chromosomal helical binding protein (CHD1), serine/threonine protein kinase (STPK), cytochrome P450 716B1, and UPF0136 were found to be specifically expressed in T. fortunei males. After single nucleotide polymorphism (SNP) detection, a total of 12 male specific sites were found and the THUMP domain protein homologs were found to be male-biased expressed. Cytokinin dehydrogenase 6 (CKX6) was upregulated in male flowers and the lower concentrations of cytokinin (CTK) may be more conducive to male flower development. During new leaf growth, flavonoid and flavonol biosynthesis were initiated. Additionally, the flavonoids, 3',5'-hydroxylase (F3'5'H), flavonoids 3'-hydroxylase, were upregulated, which may cause the pale yellow phenotype. Based on these data, it can be concluded that inter-sex differentially expressed genes (DEGs) and specific SNP loci may be associated with sex determination in T. fortunei.

New quantitative trait locus (QTLs) and candidate genes associated with the grape berry color trait identified based on a high-density genetic map

BACKGROUND

Berry color is an important trait in grapes and is mainly determined by the anthocyanin content and composition. To further explore the coloring mechanism of grape berries, the F1 population of Vitis vinifera 'Red Globe' × 'Muscat Hamburg' was used to map the color locus, and transcriptome analysis was performed to assist in screening candidate genes.

RESULTS

A total of 438,407 high-quality single-nucleotide polymorphisms (SNPs) were obtained from whole-genome resequencing (WGS) of the population, and 27,454 SNPs were selected to construct a high-density genetic map. The selected SNPs were clustered into 19 linkage groups (LGs) spanning a genetic distance of 1442.638 cM. Berry color was evaluated by color grade, chromatic aberration, total anthocyanin content and anthocyanin composition. The Pearson correlation coefficients of these phenotypes in 2017 and 2018 were significant at the 0.01 level. The major color locus of MYBA1 and MYBA2 on LG2 was identified, explaining between 26 and 63.6% of all phenotypic variance. Furthermore, 9 additional QTLs with smaller effects were detected on Chr2, Chr4, Chr6, Chr11 and Chr17. Combined with the gene annotation and RNA-seq data, multiple new candidate genes were selected from the above QTLs.

CONCLUSION

These results indicated that grape berry color is a quantitative trait controlled by a major color locus and multiple minor loci. Though the major color locus was consistent with previous studies, several minor QTLs and candidate genes associated with grape berry color and anthocyanin accumulation were identified in this study. And the specific regulatory mechanism still needs to be further explored.

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

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

Variation of Growth-to-Ripening Time Interval Induced by Abscisic Acid and Synthetic Auxin Affecting Transcriptome and Flavor Compounds in Cabernet Sauvignon Grape Berry

Abscisic acid (ABA) and auxin are important hormones controlling the ripening progression of grape berry, and both the initiation and duration of ripening can dramatically affect the berry quality. However, the responses of flavor compounds to the hormones are inadequately understood. In this study, ABA and synthetic auxin α-naphthaleneacetic acid (NAA) were sprayed on Cabernet Sauvignon berries before véraison, and comparative transcriptomic and metabolic analysis were conducted to investigate the influence on berry quality-related metabolites. The 1000 mg/L ABA (ABA1000) and 200 mg/L NAA (NAA200) treated grapes exhibited shorter and longer phenological intervals compared to the control, respectively. The transcriptomic comparison between pre-véraison and véraison revealed that the varied ripening initiation and duration significantly affected the expression of genes related to specific metabolism, particularly in the biosynthetic metabolism of anthocyanin and volatile compounds. The up-regulated VviF3’H in both ABA1000-treated and NAA200-treated berries increased the proportion of 3′-substituted anthocyanins, and the 3′5′-substituted anthocyanins were largely reduced in the NAA200-treated berries. Concurrently, VviCCD4a and VviCCD4b were up-regulated, and the norisoprenoids were correspondingly elevated in the NAA200-treated berries. These data suggest that ABA and NAA applications may be useful in controlling the ripening and improving the flavor of the grape berry.

Comparative transcriptome analysis of two contrasting wolfberry genotypes during fruit development and ripening and characterization of the LrMYB1 transcription factor that regulates flavonoid biosynthesis

Background

Lycium barbarum and L. ruthenicum have been used as traditional medicinal plants in China and other Asian counties for centuries. However, the molecular mechanisms underlying fruit development and ripening, as well as the associated production of medicinal and nutritional components, have been little explored in these two species.

Results

A competitive transcriptome analysis was performed to identify the regulators and pathways involved in the fruit ripening of red wolfberry (L. barbarum) and black wolfberry (L. ruthenicum) using an Illumina sequencing platform. In total, 155,606 genes and 194,385 genes were detected in red wolfberry (RF) and black wolfberry (BF), respectively. Of them, 20,335, 24,469, and 21,056 genes were differentially expressed at three different developmental stages in BF and RF. Functional categorization of the differentially expressed genes revealed that phenylpropanoid biosynthesis, flavonoid biosynthesis, anthocyanin biosynthesis, and sugar metabolism were the most differentially regulated processes during fruit development and ripening in the RF and BF. Furthermore, we also identified 38 MYB transcription factor-encoding genes that were differentially expressed during black wolfberry fruit development. Overexpression of LrMYB1 resulted in the activation of structural genes for flavonoid biosynthesis and led to an increase in flavonoid content, suggesting that the candidate genes identified in this RNA-seq analysis are credible and might offer important utility.

Conclusion

This study provides novel insights into the molecular mechanism of Lycium fruit development and ripening and will be of value to novel gene discovery and functional genomic studies.

Uncovering the evolutionary origin of blue anthocyanins in cereal grains

Functional divergence after gene duplication plays a central role in plant evolution. Among cereals, only Hordeum vulgare (barley), Triticum aestivum (wheat) and Secale cereale (rye) accumulate delphinidin-derived (blue) anthocyanins in the aleurone layer of grains, whereas Oryza sativa (rice), Zea mays (maize) and Sorghum bicolor (sorghum) do not. The underlying genetic basis for this natural occurrence remains elusive. Here, we mapped the barley Blx1 locus involved in blue aleurone to an approximately 1.13 Mb genetic interval on chromosome 4HL, thus identifying a trigenic cluster named MbHF35 (containing HvMYB4H, HvMYC4H and HvF35H). Sequence and expression data supported the role of these genes in conferring blue-coloured (blue aleurone) grains. Synteny analyses across monocot species showed that MbHF35 has only evolved within distinct Triticeae lineages, as a result of dispersed gene duplication. Phylogeny analyses revealed a shared evolution pattern for MbHF35 in Triticeae, suggesting that these genes have co-evolved together. We also identified a Pooideae-specific flavonoid 3',5'-hydroxylase (F3'5'H) lineage, termed here Mo_F35H2, which has a higher amino acid similarity with eudicot F3'5'Hs, demonstrating a scenario of convergent evolution. Indeed, selection tests identified 13 amino acid residues in Mo_F35H2 that underwent positive selection, possibly driven by protein thermostablility selection. Furthermore, through the interrogation of barley germplasm there is evidence that HvMYB4H and HvMYC4H have undergone human selection. Collectively, our study favours blue aleurone as a recently evolved trait resulting from environmental adaptation. Our findings provide an evolutionary explanation for the absence of blue anthocyanins in other cereals and highlight the importance of gene functional divergence for plant diversity and environmental adaptation.

Overexpression of the GbF3'H1 Gene Enhanced the Epigallocatechin, Gallocatechin, and Catechin Contents in Transgenic Populus

Ginkgo biloba L. leaves are a flavonoid resource for the pharmaceutical industry. The flavonoid 3'-hydroxylase (F3'H) is a key enzyme in the flavonoid biosynthesis pathway. However, the role of F3'H in flavonoid biosynthesis and metabolism is unclear. In this study, we characterized and functionally analyzed the ginkgo F3'H gene GbF3'H1 that encodes a protein of 520 amino acids. Expression profiling showed that GbF3'H1 was highly expressed in the leaves of ginkgo in September. Subcellular localization showed that GbF3'H1 occurred predominately in the cytoplasm. Transgenic poplars overexpressing GbF3'H1 had more red pigmentation in leaves than did wild-type (WT) plants. Furthermore, the concentrations of epigallocatechin, gallocatechin, and catechin in the downstream products synthesized by flavonoids were significantly higher in the transgenic plants than in the WT plants. These results indicate that the overexpression of GbF3'H1 enhances flavonoid production in transgenic plants and provides new insights into flavonoid biosynthesis and metabolism.

Chitosan Application in Vineyards (Vitis vinifera L. cv. Tinto Cão) Induces Accumulation of Anthocyanins and Other Phenolics in Berries, Mediated by Modifications in the Transcription of Secondary Metabolism Genes

Despite the numerous beneficial properties and uses of chitosan in agriculture, the molecular mechanisms behind its elicitation potential are still unclear. This study aimed at understanding the effect of chitosan application in the levels of phenolic compounds of Vitis vinifera L. red grapes berry skin (cv. Tinto Cão) during veraison. Grapevines were treated with chitosan (0.01% in 0.01% acetic acid) while control grapevines were sprayed with 0.01% acetic acid. Results showed that several monomeric anthocyanins increased significantly in berry skins after treatment with chitosan. Additionally, Catechin, Rutin and Querecetin-3-O-galactoside were also recorded in higher amount upon chitosan treatment. Besides modulating the phenolic content, chitosan treatment also induced modifications in several target genes encoding key enzymes and transporters involved in secondary metabolic pathways. For instance, the genes PAL, CHS, F3H, ANR, UFGT, ABCC1, GST, MATE1 were upregulated in leaves and berry skins at veraison cessation in response to chitosan treatment. Overall, the results demonstrated that chitosan has a stimulatory effect on the accumulation of phenolic compounds, including anthocyanins, mediated by modifications in the transcription of key genes involved in their biosynthesis and transport in grape berries.

Genetic analysis of a white-to-red berry skin color reversion and its transcriptomic and metabolic consequences in grapevine (Vitis vinifera cv. 'Moscatel Galego')

BACKGROUND

Somatic mutations occurring within meristems of vegetative propagation material have had a major role in increasing the genetic diversity of the domesticated grapevine (Vitis vinifera subsp. vinifera). The most well studied somatic variation in this species is the one affecting fruit pigmentation, leading to a plethora of different berry skin colors. Color depletion and reversion are often observed in the field. In this study we analyzed the origin of a novel white-to-red skin color reversion and studied its possible metabolic and transcriptomic consequences on cv. 'Muscat à Petits Grains Blancs' (synonym cv. 'Moscatel Galego Branco'), a member of the large family of Muscats.

RESULTS

The mild red-skinned variant (cv. 'Muscat à Petits Grains Rouge', synonym cv. 'Moscatel Galego Roxo'), characterized by a preferential accumulation of di-hydroxylated anthocyanins, showed in heterozygosis a partially-excised Gret1 retrotransposon in the promoter region of the MYBA1 anthocyanin regulator, while MYBA2 was still in homozygosis for its non-functional allele. Through metabolic (anthocyanin, resveratrol and piceid quantifications) and transcriptomic (RNA-Seq) analyses, we show that within a near-isogenic background, the transcriptomic consequences of color reversion are largely associated to diminished light/UV-B responses probably as a consequence of the augment of metabolic sunscreens (i.e. anthocyanins).

CONCLUSIONS

We propose that the reduced activity of the flavonoid tri-hydroxylated sub-branch and decreased anthocyanin synthesis and modification (e.g. methylation and acylation) are the potential causes for the mild red-skinned coloration in the pigmented revertant. The observed positive relation between anthocyanins and stilbenes could be attributable to an increased influx of phenylpropanoid intermediaries due to the replenished activity of MYBA1, an effect yet to be demonstrated in other somatic variants.

Mapping and Identifying a Candidate Gene Plr4, a Recessive Gene Regulating Purple Leaf in Rice, by Using Bulked Segregant and Transcriptome Analysis with Next-Generation Sequencing

The anthocyanin biosynthesis of rice is a major concern due to the potential nutritional value. Purple appears in various organs and tissues of rice such as pericarp, flower organs, leaves, leaf sheaths, internodes, ligules, apex, and stigma. At present, there are many studies on the color of rice pericarp, but the gene and mechanism of other organs such as leaves are still unclear, and the gene regulatory network of specific organ coloring has not been systematically understood. In this study, genetic analysis demonstrated that the purple leaf traits of rice were regulated by a recessive gene. The green leaf cultivar Y58S and purple leaf cultivar XianHongB were used to construct the mapping population. A set of near isogenicline (NIL) (BC₃F₁) was bred via crossing and back-crossing. The generations of BC₃F₂ appeared to separate four phenotypes, pl1, pl2, pl3, and pl4, due to the occurrence of a purple color in different organs. We constructed three bulked segregant analysis (BSA) pools (pl1-pl2, pl1-pl3, and pl1-pl4) by using the separated generations of BC₃F₅ and mapped the purple leaf gene plr4 to the vicinity of 27.9-31.1 Mb on chromosome 4. Subsequently, transcriptome sequencing (RNA-Seq) for pl3 and pl2 was used to analyze the differentially expressed genes in the localization interval, where 12 unigenes exhibited differential expression in which two genes (Os04g0577800, Os04g0616400) were downregulated. The two downregulated genes (Os04g0577800 and Os04g0616400) are possible candidate genes because of the recessive genetic characteristics of the purple leaf genes. These results will facilitate the cloning of plr4 and illustrate the molecular mechanisms of the anthocyanin synthesis pathway.

Molecular cloning and functional characterization of AcGST1, an anthocyanin-related glutathione S-transferase gene in kiwifruit (Actinidia chinensis)

AcGST1, an anthocyanin-related GST, may functions as a carrier to transport anthocyanins from ER to tonoplast in kiwifruit. It was positively regulated by AcMYBF110 through directly binding to its promoter. Anthocyanins are synthesized in the cytoplasmic surface of the endoplasmic reticulum but accumulate predominantly in the vacuole. Previous studies in model and ornamental plants have suggested that a member of the glutathione S-transferase (GST) gene family is involved in sequestration of anthocyanins into the vacuole. However, little is known about anthocyanin-related GST protein in kiwifruit. Here, four putative AcGSTs were identified from the genome of the red-fleshed Actinidia chinensis cv 'Hongyang'. Expression analyses reveal only the expression of AcGST1 was highly consistent with anthocyanin accumulation. Molecular complementation of Arabidopsis tt19 demonstrates AcGST1 can complement the anthocyanin-less phenotype of tt19. Transient expression in Actinidia arguta fruits further confirms that AcGST1 is functional in anthocyanin accumulation in kiwifruit. In vitro assays show the recombinant AcGST1 increases the water solubility of cyanidin-3-O-galactoside (C3Gal) and cyanidin-3-O-xylo-galactoside (C3XG). We further show that AcGST1 protein is localized not only in the ER but also on the tonoplast, indicating AcGST1 (like AtTT19) may functions as a carrier protein to transport anthocyanins to the tonoplast in kiwifruit. Moreover, the promoter of AcGST1 can be activated by AcMYBF110, based on results from transient dual-luciferase assays and yeast one-hybrid assays. EMSAs show that AcMYBF110 binds directly to CAGTTG and CCGTTG motifs in the AcGST1 promoter. These results indicate that AcMYBF110 plays an important role in transcriptional regulation of AcGST1 and, therefore, in controlling accumulation of anthocyanins in kiwifruit.

Variation of Anthocyanin Content and Profile Throughout Fruit Development and Ripening of Highbush Blueberry Cultivars Grown at Two Different Altitudes

Blueberry (Vaccinium corymbosum L.) is a widely consumed fruit and a rich source of bioactive compounds, namely, the polyphenol class of anthocyanins. Little information is available about the influence of internal (genetic and developmental) and external (environmental) factors on the levels of phenolic metabolites in blueberry fruit. In light of this consideration, total polyphenolic and flavonoid content, anthocyanin accumulation and composition were evaluated in cv. "Duke" and "Brigitta" grown at two different altitudes in Valtellina, a valley of the Alps in Northern Italy. During berry ripening, there is a developmentally coordinated shift from cyanidin-type, di-substituted anthocyanins toward delphinidin-based, tri-substituted pigments. At the lower altitude location, higher temperatures, not exceeding optimum, resulted in a more quickly berry developmental pattern and in higher anthocyanin concentrations in the early phases of ripening. At later stages of ripening, berries of both cultivars at higher altitude compensate for these initial temperature effects, and no differences were recorded in ripe fruit grown in the two locations. We conclude that anthocyanin accumulation is strongly regulated by development and genotype, and the environmental factors, associated to the altitude gradient, exert in the trial conditions only a fine-tuning influence. Fruits reach the full-ripening stage simultaneously at both sites because the initial gap in pigment levels is counterbalanced at the higher altitude by a faster rate of accumulation at later phases of the ripening process.

Differential regulation of the anthocyanin profile in purple kiwifruit (Actinidia species)

Anthocyanins are a group of secondary metabolites that colour fruit and flowers orange, red, purple or blue depending on a number of factors, such as the basic structure, co-pigmentation, metal ion complexation and vacuolar pH. The biosynthesis of anthocyanin is regulated at the transcriptional level by a group of transcription factors, the MYB-bHLH-WD40 (MBW) complex. In this study, the purple colouration in several kiwifruit (Actinidia) species was identified and characterised as red cyanidin-based and blue delphinidin-based anthocyanins. The differential pigmentation in the skin and flesh can be attributed to the differential ratio of cyanidin and delphinidin derivatives accumulated in the total anthocyanin profile. The expression of anthocyanin biosynthetic genes chalcone synthase (CHS), flavonoid 3-O-glucosyltransferase (F3GT), flavonoid 3'-hydroxylase (F3'H) and flavonoid 3'5'-hydroxylase (F3'5'H) is crucial for anthocyanin accumulation. However, the balance of expression of the F3'H and F3'5'H genes appears responsible for the ratio of cyanidin and delphinidin derivatives, while a lack of CHS, F3GT and MYB110 expression is responsible for a lack of total anthocyanins. The transcriptional regulation of the F3'H and F3'5'H promoters by the R2R3 MYB transcription factor MYB110 is markedly different in tobacco transient assays. When kiwifruit MYB10 or MYB110 are over-expressed in Actinidia chinensis both cyanidin-based and delphinidin-based anthocyanins are elevated, but F3'H and F3'5'H genes are not strongly correlated with MYB expression. These results suggest that the core kiwifruit anthocyanin pathway genes are dependent on characterised MYB transcription factors, while other regulatory proteins are more directly responsible for the expression of the F3'H and F3'5'H genes.

Berry color variation in grapevine as a source of diversity

Even though it is one of the oldest perennial domesticated fruit crops in the world, grapevine (Vitis vinifera L.) cultivation today is the result of both conventional breeding practices (i.e. hybridizations adopted during the last century) and vegetative propagation. Human-assisted asexual propagation has allowed the maintenance of desired traits but has largely impacted the frequency of spontaneous somatic mutations observed in the field. Consequently, many grapevine fruit attributes to date have been artificially selected, including: fruit yield, compactness, size and composition, the latter being greatly diversified in the pursuit of altering berry skin coloration. The present review provides an overview of various aspects related to grapevine diversity, with a special emphasis on grape berry skin color variation and will discuss the current knowledge of how grape skin color variation is affected by the synthesis of phenolic compounds, particularly anthocyanins and their underlying genetic factors. We hope this knowledge will be useful in supporting the importance of the berry color trait diversity in cultivated grapevines, which is used as basis for selection during breeding programs because of its application for vine growers, winemakers and consumers.

Transcriptome Sequencing and Metabolism Analysis Reveals the role of Cyanidin Metabolism in Dark-red Onion (Allium cepa L.) Bulbs

Onion (Allium cepa L.) is an important bulbous vegetable crop that possesses important properties related to health as well as extraordinary colors. Naturally white onion bulbs were used in this study to reveal the complex metabolic mechanisms that underlie phenotypic traits, especially bulb pigmentation. Six libraries (three dark-red and three white) were constructed and analyzed to elucidate differences in cyanidin (Cy) metabolism between dark-red and white onion bulbs. Libraries were screened using RNA-sequencing (RNA-seq) to reveal the differentially expressed genes (DEGs) involved in anthocyanin biosynthesis at the transcriptional level. Comparison with the Kyoto Encyclopedia of Genes and Genomes (KEGG) database shows that a total of 27 unigenes participate in onion anthocyanin biosynthesis and 16 DEGs perform critical roles in flavonoid biosynthesis. Expression patterns of color-related flavonoid compounds associated with the onion anthocyanin biosynthesis pathway (ABP) show that flavonoid 3′,5′-hydroxylase (F3′5′H) and dihydroflavonol 4-reductase (DFR) genes play crucial roles in the biosynthesis of dark-red bulbs, the expression levels of flavonol synthase (FLS) and DFR genes may act to block blue pigmentation, and the loss of Cy from white onion bulbs might explain multibranching in the synthesis of this compound. Positive variation in the F3′5′H/F3′H ratio also affects onion bulb color diversity. The transcriptome presented here provides a basis for future onion molecular breeding based on variations in the diversity of ornamental plant pigmentation.

Low night temperature at veraison enhances the accumulation of anthocyanins in Corvina grapes (Vitis Vinifera L.)

Climate change is a major concern in grape production worldwide. Nights have been warming much faster than the days, raising attention on the effect of night temperatures on grape and wine composition. In this study we evaluated the effect of night temperatures on grape coloration in the cv. Corvina (Vitis vinifera L.). In 2015 and 2016 potted plants were cooled overnight (10-11 °C) during two berry ripening phases, veraison (TV) or post-veraison (TPV), and compared to control vines (C) grown at ambient night temperature (15-20 °C on average). Cooling treatment around veraison (TV) hastened berry anthocyanin accumulation, while the same treatment applied after veraison (TPV) was ineffective. Molecular analysis revealed an increased transcription of four key genes in anthocyanin biosynthesis (CHS3, F3H1, MYBA1 and UFGT) in TV treatment. These results suggest that the anthocyanin biosynthesis capacity was enhanced by cool nights during veraison. However, since the gene expression was not always temporally correlated to the increase in anthocyanin concentration, we speculate on the presence of mechanisms, such as enzymatic regulation or anthocyanin transport, which may contribute in determining the anthocyanin accumulation under low night temperatures.

Grapevine fanleaf virus affects grape (Vitis vinifera) berry anthocyanin content via the transcriptional regulation of anthocyanin biosynthetic genes

Grapevine fanleaf virus (GFLV) causes grapevine fanleaf degeneration, one of the oldest known viral diseases of grapevines. The virus has been found in all winegrowing regions around the world. In the seasons 2011-12 a comparison between field grown GFLV-infected and healthy grapevines was conducted for the cultivars Schioppettino in North-Eastern Italy and Refošk in South-Western Slovenia. Our research showed that GFLV infection caused a drop of the yield due to reduction of both cluster weight and berry weight. Besides the yield, the berry composition was also affected; in detail, anthocyanin concentration increased in both varieties but significantly only in the case of Schioppettino. Upregulation of the F3'5'H gene and downregulation of F3'H gene in the berries of GFLV infected vines compared with the ones of healthy control vines resulted in modified proportions between di- and tri- hydroxylated or methylated derivatives of anthocyanins. The F3H1 gene was identified to be the most strongly regulated gene of the flavonoid biosynthetic pathway by GFLV infection, indicating its important role in increasing anthocyanin concentration in grapes of GFLV infected vines as compared with healthy controls.

Grape Berry Acclimation to Excessive Solar Irradiance Leads to Repartitioning between Major Flavonoid Groups

Warm viticulture regions are associated with inferior wines, resulting from the interaction between microclimate and fruit biochemistry. Solar irradiance triggers biosynthetic processes in the fruit and dominates its thermal balance. Therefore, deciphering its impact on fruit metabolism is pivotal to develop strategies for fruit protection and ameliorate its quality traits. Here, we modified light quality and intensity in the fruit-zone and integrated micrometeorology with grape and wine metabolomics, allowing a complete assessment, from field to bottle. We analyzed the dynamics of fruit's adaptation to altered conditions during ripening and constructed temporal-based metabolic networks. Micrometeorological modifications shifted the balance between the major flavonoids, associating increased solar exposure with lower levels of anthocyanins and flavan-3-ols, and higher flavonols. Differences were fixed from 2 weeks postveraison until harvest, suggesting a controlled acclimation response rather than external modulation. Differences in grape composition manifested in the wine and resulted in higher color intensity and improved wine hue under partial shading.

Exogenous Applications of Brassinosteroids Improve Color of Red Table Grape (Vitis vinifera L. Cv. "Redglobe") Berries

Color and other quality parameters of "Redglobe" grape (Vitis vinifera L.) berries were evaluated after treatment with brassinosteroid (BR) analogs. Three BRs analogs (24-epibrassinolide, Triol, or Lactone) were applied at three concentrations (0.0, 0.4, or 0.8 mg⋅L^-1), at the onset of veraison. A commercial formulation (B-2000^®) was also applied, at a recommended rate of 0.06 mg⋅L^-1. The tested BR analogs were effective improving berry color (evaluated as color index for red grapes, CIRG), increasing the levels of soluble solids and anthocyanins, and changing the types of anthocyanins present without altering other quality and yield parameters. The effects of BR analogs on color enhancement could be explained by an increase in soluble solids content and/or anthocyanin content. Treatment with 24-epibrassinolide (at 0.4 mg⋅L^-1) or the commercial formulation tended to favor the production of dihydroxylated anthocyanins, which are responsible for the red and pink colors of grape berries. Results indicate that the use of BRs constitutes a potential tool in the production of table grapes. This is the first report of this enhancement effect in a productive context.

Gallocatechin biosynthesis via a flavonoid 3',5'-hydroxylase is a defense response in Norway spruce against infection by the bark beetle-associated sap-staining fungus Endoconidiophora polonica

One of the best-studied defense responses to fungal infection in Norway spruce (Picea abies) is the biosynthesis of flavan-3-ols, which accumulate as monomers or polymers known as proanthocyanidins. The individual flavan-3-ol units consist of compounds with a 3',4'-dihydroxylated B ring [2,3-(trans)-(+)-catechin or 2,3-(cis)-(-)-epicatechin] and compounds with a 3',4',5'-trihydroxylated B ring [2,3 (trans)-(+)-gallocatechin or 2,3-(cis)-(-)-epigallocatechin]. While much is known about the biosynthesis and biological activity of catechin in Norway spruce, there is little comparable information about gallocatechin or epigallocatechin. We found that there was a significant increase in the gallocatechin content of Norway spruce bark and wood after inoculation with the bark beetle-associated sap-staining fungus Endoconidiophora polonica. Gallocatechins increased proportionally more than catechins as both monomers and units of polymers. A flavonoid 3',5'-hydroxylase gene identified in Norway spruce was shown by heterologous expression in Nicotiana benthamiana to be involved in the conversion of 2,3 (trans)-(+)-catechin to 2,3 (trans)-(+)-gallocatechin. The formation of the trihydroxylated B ring in Norway spruce occurs at the level of flavan-3-ols, rather than at the level of dihydroflavonols as in many angiosperms. The transcript abundance of the flavonoid 3',5'-hydroxylase gene also increased significantly during fungal infection underlining its importance in gallocatechin biosynthesis. Comparisons of the effect of 2,3 (trans)-(+)-catechin and 2,3 (trans)-(+)-gallocatechin on fungal growth revealed that 2,3 (trans)-(+)-catechin is a stronger inhibitor of fungal growth, while 2,3 (trans)-(+)-gallocatechin is a stronger inhibitor of melanin biosynthesis.