The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L

GhLCYε-3 characterized as a lycopene cyclase gene responding to drought stress in cotton

Drought stress significantly affects crop productivity. Carotenoids are essential photosynthetic pigment for plants, bacteria, and algae, with signaling and antioxidant functions. Lutein is a crucial branch product in the carotenoid synthesis pathway, which effectively improves the stress tolerance of higher plants. lycopene cyclase, a central enzyme for lutein synthesis, holds great significance in regulating lutein production. This research establishes a correlation between lutein content and stress resistance by measuring the drought resistance and lutein content of various cotton materials. To identify which crucial genes are associated with lutein, the lycopene cyclase family (LCYs) was analyzed. The research found that LCYs form a highly conserved family divided into two subfamilies, LCY-ε (lycopene ε-cyclase) and LCY-β (lycopene β-cyclase). Most members of the LCY family contain photoresponsive elements and abscisic acid elements. qRT-PCR demonstrates showed that most genes responded positively to drought stress, and GhLCYε-3 was expressed significantly differently under drought stress. Virus-induced gene silencing (VIGS) assay showed that the content of GhLCYε-3 was significantly increased with MDA and PRO, and the contents of chlorophyll and lutein were significantly decreased in pYL156 plants. The decrease in GhLCYε-3 expression is speculated to lead to reduced lutein content in vivo, resulting in the accumulation of reactive oxygen species (ROS) and decreased drought tolerance. This research enriched the understanding of LCY gene family and lutein function, and provided a new reference for cotton planting in arid areas.

Synopsis

Lycopene cyclase plays an important role in enhancing the ability of scavenging ROS and drought resistance of plants.

Vineyard microclimate alterations induced by black inter-row mulch through transcriptome reshaped the flavoromics of cabernet sauvignon grapes

BACKGROUND

Weed control is essential for agricultural floor management in vineyards and the inter-row mulching is an eco-friendly practice to inhibit weed growth via filtering out photosynthetically active radiation. Besides weed suppression, inter-row mulching can influence grapevine growth and the accumulation of metabolites in grape berries. However, the complex interaction of multiple factors in the field challenges the understanding of molecular mechanisms on the regulated metabolites. In the current study, black geotextile inter-row mulch (M) was applied for two vintages (2016-2017) from anthesis to harvest. Metabolomics and transcriptomics analysis were conducted in two vintages, aiming to provide insights into metabolic and molecular responses of Cabernet Sauvignon grapes to M in a semi-arid climate.

RESULTS

Upregulation of genes related to photosynthesis and heat shock proteins confirmed that M weakened the total light exposure and grapes suffered heat stress, resulting in lower sugar-acid ratio at harvest. Key genes responsible for enhancements in phenylalanine, glutamine, ornithine, arginine, and C6 alcohol concentrations, and the downward trend in ε-viniferin, anthocyanins, flavonols, terpenes, and norisoprenoids in M grapes were identified. In addition, several modules significantly correlated with the metabolic biomarkers through weighted correlation network analysis, and the potential key transcription factors regulating the above metabolites including VviGATA11, VviHSFA6B, and VviWRKY03 were also identified.

CONCLUSION

This study provides a valuable overview of metabolic and transcriptomic responses of M grapes in semi-arid climates, which could facilitate understanding the complex regulatory network of metabolites in response to microclimate changes.

Effects of full shading of clusters from véraison to ripeness on fruit quality and volatile compounds in Cabernet Sauvignon grapes

Sunlight exposure of grape clusters is frequently reported to influence grape aromas greatly. Among them, the effects of full shading (FS) of clusters on fruit quality and volatile compounds in grape berries has scarcely been investigated. In the present study, the effects of FS from véraison to ripeness on fruit quality and volatile compounds in Cabernet Sauvignon grapes were studied. The results showed that FS treatment reduced fruit size and berry weight, delayed fruit maturity, and decreased the contents of anthocyanins, phenols, and tannins in grape berries. In addition, volatile compounds in grape berries were analyzed, and 55 and 53 volatile compounds were detected in the control (CK) and FS groups, respectively. The results indicated that the concentrations of straight-chain fatty aldehydes, straight-chain fatty alcohols, straight-chain fatty acids, and branched-chain fatty acids, norisoprenoids, and total concentration of volatile compounds were all higher in FS group than in CK group. Specifically, FS treatment had significant promoting effects on the concentrations of β-damascenone, terpineol, 2-ethyl-1-hexanol, and 2-hexenal, and remarkably decreased the concentrations of geranial, benzeneacetaldehyde, neral, and ethyl acetate. Partial least squares-discriminant analysis (PLS-DA) revealed a clear separation between the control (CK) and FS groups, and showed that 2-hexenal and hexanal were the main characteristic aroma compounds in the FS group. Moreover, an increase in the intensity of fruity, herbaceous, floral, and mushroom aromas was recorded in FS grapes. This study provides new insights into the effects of the exclusion of sunlight exposure on volatile compound accumulation in grape berries.

Application of benzothiadiazole to Cabernet Gernischt grapes (Vitis vinifera L.) for quality improvement: Effects on aroma metabolism precursors and related genes expression

Pre-harvest spraying of benzothiadiazole (BTH) can improve the winemaking properties of grapes, especially their aroma compounds and phenolics. Limited research has explored the molecular mechanisms by which BTH influences the accumulation of grape aroma precursors during early grape development. This study investigated the effects and putative molecular mechanisms of applying 0.37 mM BTH through whole-plant spraying on the accumulation of aroma metabolism precursors and gene expression in Cabernet Gernischt grapes during ripening. The results showed that BTH treatment increased the levels of fructose, alanine, aspartate, threonine, myristic acid, myristoleic acid, palmitic acid, β-cryptoxanthin, norisoprenoids and methoxypyrazines. Contrarily, it decreased the levels of glucose, sucrose, phenylalanine, tyrosine, leucine, valine, glycine, arginine, histidine, total unsaturated fatty acids (particularly linoleic acid), zeaxanthin, lutein, and organic acids. Additionally, BTH upregulated the expression of genes associated with the production and degradation of amino acids, fatty acids, and carotenoids while decreasing the expression of genes involved in the synthesis and degradation of soluble sugars and organic acids. Ten different metabolites, including fumaric acid, were identified as potential biological markers for distinguishing BTH-treated grapes from control grapes. The study demonstrates that BTH treatment had a substantial impact on the concentration and developmental patterns of aroma metabolism precursors. Furthermore, it altered the winemaking characteristics of Cabernet Gernischt grapes by modulating genes associated with the production and breakdown of metabolites.

MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries

Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency. Light-responsive flavonol and monoterpene levels increased in anthocyanin-depleted areas in correlation with increasing MYB24 expression. Cistrome analysis suggested that MYB24 binds to the promoters of 22 terpene synthase (TPS) genes, as well as 32 photosynthesis/light-related genes, including carotenoid pathway members, the flavonol regulator HY5 HOMOLOGUE (HYH), and other radiation response genes. Indeed, TPS35, TPS09, the carotenoid isomerase gene CRTISO2, and HYH were activated in the presence of MYB24 and MYC2. We suggest that MYB24 modulates ultraviolet and high-intensity visible light stress responses that include terpene and flavonol synthesis and potentially affects carotenoids. The MYB24 regulatory network is developmentally triggered after the onset of berry ripening, while the absence of anthocyanin sunscreens accelerates its activation, likely in a dose-dependent manner due to increased radiation exposure. Anthocyanins and flavonols in variegated berry skins act as effective sunscreens but for different wavelength ranges. The expression patterns of stress marker genes in red and white sections of 'Béquignol' berries strongly suggest that MYB24 promotes light stress amelioration but only partly succeeds during late ripening.

Non-climacteric fruit development and ripening regulation: 'the phytohormones show'

Fruit ripening involves numerous physiological, structural, and metabolic changes that result in the formation of edible fruits. This process is controlled at different molecular levels, with essential roles for phytohormones, transcription factors, and epigenetic modifications. Fleshy fruits are classified as either climacteric or non-climacteric species. Climacteric fruits are characterized by a burst in respiration and ethylene production at the onset of ripening, while regulation of non-climacteric fruit ripening has been commonly attributed to abscisic acid (ABA). However, there is controversy as to whether mechanisms regulating fruit ripening are shared between non-climacteric species, and to what extent other hormones contribute alongside ABA. In this review, we summarize classic and recent studies on the accumulation profile and role of ABA and other important hormones in the regulation of non-climacteric fruit development and ripening, as well as their crosstalk, paying special attention to the two main non-climacteric plant models, strawberry and grape. We highlight both the common and different roles of these regulators in these two crops, and discuss the importance of the transcriptional and environmental regulation of fruit ripening, as well as the need to optimize genetic transformation methodologies to facilitate gene functional analyses.

Unveiling the molecular mechanism involving anthocyanins in pineapple peel discoloration during fruit maturation

Peel color is a key factor that affects the fruit's aesthetic and economic values. Limited knowledge is available on the regulation of pineapple peel discoloration. Here, we report that a decrease in anthocyanin biosynthesis, particularly cyanidin, is predominantly associated with the pineapple peel color change during maturation. The findings suggest that the changes in the expression of key structural genes (early and late biosynthetic genes) of the anthocyanin (cyanidin) biosynthesis pathway are responsible for peel discoloration. Based on a gene co-expression analysis and a transient expression, two transcription factors i.e., AcHOX21 and AcMYB12, were identified, whose' downregulation leads to reduced anthocyanin accumulation with fruit maturation. The endogenous levels of jasmonic acid, gibberellic acid, and auxins are also involved in anthocyanin-content-led peel discoloration. Overall, the discovery of genes regulating anthocyanin biosynthesis in pineapple peel provides a theoretical basis for improving the fruit's aesthetic value through genetic engineering.

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

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

Grape phytochrome-interacting factor VvPIF1 negatively regulates carotenoid biosynthesis by repressing VvPSY expression

Phytochrome-interacting factors (PIFs) play important roles in light-mediated secondary metabolism; however, the roles of PIFs in grape fruit carotenogenesis remain unclear. Here, by identifying the PIF family genes in grapes, we focused on the role of VvPIF1 in carotenoid metabolism. During grape berry development, VvPIF1 expression was negatively correlated with carotenoid accumulation and the transcription of phytoene synthase 1/2 (VvPSY1/2), which encodes the major flux-controlling enzymes for carotenoid biosynthesis. Light significantly repressed VvPIF1 expression, but induced the expression of carotenogenic genes including VvPSY1/2. VvPIF1 functioned as a nucleus-localized protein and interacted with the light photoreceptor VvphyB. Overexpression of VvPIF1 resulted in the downregulation of the endogenous PIF1 gene, which may unexpectedly induce carotenoid accumulation and PSY expression in tobacco leaves. The transgenic grape leaves and tomato fruits with high VvPIF1 expression produced a significant decrease in carotenoid concentrations, with suppressed transcription of PSY and other carotenogenic genes. Further biochemical assays demonstrated that VvPIF1 bound directly to the promoters of VvPSY1/2 to inhibit their transcription. Collectively, we conclude that VvPIF1 negatively regulates carotenoid biosynthesis by repressing VvPSY expression in grapes. These findings shed light on the role and mode of action of PIFs in the carotenoid regulatory network of grapes.

Integrative analysis of metabolome and transcriptome profiles to highlight aroma determinants in Aglianico and Falanghina grape berries

BACKGROUND

The biochemical makeup of grape berries at harvest is essential for wine quality and depends on a fine transcriptional regulation occurring during berry development. In this study, we conducted a comprehensive survey of transcriptomic and metabolomic changes occurring in different berry tissues and developmental stages of the ancient grapes Aglianico and Falanghina to establish the patterns of the secondary metabolites contributing to their wine aroma and investigate the underlying transcriptional regulation.

RESULTS

Over two hundred genes related to aroma were found, of which 107 were differentially expressed in Aglianico and 99 in Falanghina. Similarly, 68 volatiles and 34 precursors were profiled in the same samples. Our results showed a large extent of transcriptomic and metabolomic changes at the level of isoprenoids (terpenes, norisoprenoids), green leaf volatiles (GLVs), and amino acid pathways, although the terpenoid metabolism was the most distinctive for Aglianico, and GLVs for Falanghina. Co-expression analysis that integrated metabolome and transcriptome data pinpointed 25 hub genes as points of biological interest in defining the metabolic patterns observed. Among them, three hub genes encoding for terpenes synthases (VvTPS26, VvTPS54, VvTPS68) in Aglianico and one for a GDP-L-galactose phosphorylase (VvGFP) in Falanghina were selected as potential active player underlying the aroma typicity of the two grapes.

CONCLUSION

Our data improve the understanding of the regulation of aroma-related biosynthetic pathways of Aglianico and Falanghina and provide valuable metabolomic and transcriptomic resources for future studies in these varieties.

Biosynthesis of Chlorophyll and Other Isoprenoids in the Plastid of Red Grape Berry Skins

Despite current knowledge showing that fruits like tomato and grape berries accumulate different components of the light reactions and Calvin cycle, the role of green tissues in fruits is not yet fully understood. In mature tomato fruits, chlorophylls are degraded and replaced by carotenoids through the conversion of chloroplasts in chromoplasts, while in red grape berries, chloroplasts persist at maturity and chlorophylls are masked by anthocyanins. To study isoprenoid and lipid metabolism in grape skin chloroplasts, metabolites of enriched organelle fractions were analyzed by high-performance liquid chromatography-high-resolution mass spectrometry (HPLC-HRMS) and the expression of key genes was evaluated by real-time polymerase chain reaction (PCR) in berry skins and leaves. Overall, the results indicated that chloroplasts of the grape berry skins, as with leaf chloroplasts, share conserved mechanisms of synthesis (and degradation) of important components of the photosynthetic machinery. Some of these components, such as chlorophylls and their precursors, and catabolites, carotenoids, quinones, and lipids have important roles in grape and wine sensory characteristics.

Transcriptome analysis reveals the fruit color variation in Ailanthus altissima

Anthocyanins are responsible for the intensity of color in plants; however, the systematic mechanisms underlying the color differences in the fruit of Ailanthus altissima remain unknown. Therefore, this study aims to analyze the transcriptomes of the white and red fruit of A. altissima by screening and validating the key genes involved in flavonoid and anthocyanin biosynthesis. Samples of A. altissima fruit were collected 30, 45, and 60 days after flowering, and their pigment and sugar content were determined. The anthocyanin content was significantly higher in red than in white fruits. Transcriptome analysis was also performed on the fruit samples, 73,807 unigenes were assembled and annotated to seven databases. Twenty-one co-expressed modules were identified via weighted gene co-expression network analysis, of which two were associated with flavonoids and anthocyanins. Furthermore, in three growth stages, 126, 30, and 124 differentially expressed genes were screened between white and red fruit. Genes involved in flavonoid and anthocyanin metabolism were identified. AaDFR (A. altissima bifunctional dihydroflavonol 4-reductase/flavanone 4-reductase) and AaANS (A. altissima anthocyanidin synthase) were associated with flavonoid and anthocyanin metabolism. Members of the AaDFR and AaANS families were also identified, and their basic physicochemical characteristics, conserved domains, motif compositions, phylogenetics, and expression levels were analyzed. The overexpression of AaDFR and AaANS in transgenic Arabidopsis significantly increased the content of seed and foliar flavonoids and anthocyanins. The study elucidated the different mechanisms underlying fruit color development and provided insight into A. altissima plants breeding with commercially desirable properties.

Genetic architecture of berry aroma compounds in a QTL (quantitative trait loci) mapping population of interspecific hybrid grapes (Vitis labruscana × Vitis vinifera)

BACKGROUND

Although grapes accumulate diverse groups of volatile compounds, their genetic regulation in different cultivars remains unelucidated. Therefore, this study investigated the volatile composition in the berries of an interspecific hybrid population from a Vitis labruscana 'Campbell Early' (CE) × Vitis vinifera 'Muscat of Alexandria' (MA) cross to understand the relationship among volatile compounds and their genetic regulation. Then, a quantitative trait locus (QTL) analysis of its volatile compounds was conducted.

RESULTS

While MA contained higher concentrations of monoterpenes and norisoprenoids, CE contained higher concentrations of C6 compounds, lactones and shikimic acid derivatives, including volatiles characteristic to American hybrids, i.e., methyl anthranilate, o-aminoacetophenone and mesifurane. Furthermore, a cluster analysis of volatile profiles in the hybrid population discovered ten coordinately modulated free and bound volatile clusters. QTL analysis identified a major QTL on linkage group (LG) 5 in the MA map for 14 monoterpene concentrations, consistent with a previously reported locus. Additionally, several QTLs detected in the CE map affected the concentrations of specific monoterpenes, such as linalool, citronellol and 1,8-cineol, modifying the monoterpene composition in the berries. As for the concentrations of five norisoprenoids, a major common QTL on LG2 was discovered first in this study. Several QTLs with minor effects were also discovered in various volatile groups, such as lactones, alcohols and shikimic acid derivatives.

CONCLUSIONS

An overview of the profiles of aroma compounds and their underlying QTLs in a population of interspecific hybrid grapes in which muscat flavor compounds and many other aroma compounds were mixed variously were elucidated. Coordinate modulation of the volatile clusters in the hybrid population suggested an independent mechanism for controlling the volatiles of each group. Accordingly, specific QTLs with significant effects were observed for terpenoids, norisoprenoids and some volatiles highly contained in CE berries.

Comparative Evaluation of Secreted Plant Carotenoid Cleavage Dioxygenase 1 (CCD1) Enzymes in Saccharomyces cerevisiae

Enabling technologies in synthetic biology now present the opportunity to engineer wine yeast for enhanced novel aromas. In doing so, improved wine products will increase the desirability of wine for the consumer and add value to the winemaker. The action of the enzyme carotenoid cleavage dioxygenase 1 (CCD1) on β-carotene to produce β-ionone is of interest to improve the aroma and flavour of the wine. Engineering the yeast, Saccharomyces cerevisiae, to produce higher concentrations of CCD1 in grape-must presents an opportunity to increase the levels of this volatile organic compound, thus enhancing the organoleptic properties of wine. To this end, four phylogenetically diverse plant CCD1 genes were synthesised with a secretion signal peptide and transformed into S. cerevisiae. The relative ability of each enzyme secreted into the yeast supernatant to cleave the deep orange C40 β-carotene was determined by spectrophotometry; furthermore, the by-product of such cleavage, the highly aromatic C13 β-ionone, was assessed by head-space solid-phase micro-extraction, with analysis and detection by GCMS. Reduction in β-carotene levels and release of β-ionone from the supernatant were validated by LCMS detection of CCD1. These experiments demonstrated that expression in yeast of the CCD1s derived from Petunia hybrida and Vitis vinifera and their subsequent secretion into the medium provided superior efficacy in both β-carotene reduction and β-ionone liberation. We anticipate this knowledge being of benefit to future winemakers in producing a vinous product with enhanced organoleptic properties.

Oxalic Acid Preharvest Treatment Improves Colour and Quality of Seedless Table Grape 'Magenta' Upregulating on-Vine Abscisic Acid Metabolism, Relative VvNCED1 Gene Expression, and the Antioxidant System in Berries

The effect of oxalic acid (OA) in determining poorly coloured table grape quality remains relatively unknown. Some red cultivars, such as seedless table grape 'Magenta' are characterised by a poor berry colour, an attribute highly demanded by the consumer. The aim of this research was to elucidate the effect of a preharvest OA treatment (5 mM) on berry colour and quality of table grape by investigating its role in berry development, on-vine ripening, and postharvest senescence. We found that OA significantly increased abscisic acid (ABA) and ABA glucose ester (ABA-GE) content in treated berries. This increase was mediated by changes in the ABA biosynthetic pathway, specifically by the upregulation of the 9-cis-epoxycarotenoid dioxygenase (VvNCED1) gene. The accumulation of ABA in treated berries resulted in colour improvement and a higher individual and total anthocyanins content at harvest compared with control; whereas at harvest, OA-treated table grapes showed a significantly lower glucose and fructose content and a higher content of tartaric, ascorbic, and succinic acids. Furthermore, antioxidant enzyme activity was increased during berry development in OA-treated berries. On the other hand, those berries treated with OA showed a delay in loss of firmness and colour during cold storage, as well as less susceptibility to postharvest decay incidence. This effect of OA delaying the senescence process was also related to enzymatic antioxidant system stimulation. For the first time, the role of OA on increasing quality, mainly colour, in table grapes was elucidated, highlighting that this treatment upregulated ABA metabolism, relative VvNCED1 gene expression and antioxidant system, delaying postharvest berry senescence.

Transcriptomic Analysis Provides Insights into Foliar Zinc Application Induced Upregulation in 2-Acetyl-1-pyrroline and Related Transcriptional Regulatory Mechanism in Fragrant Rice

The involvement of zinc (Zn) in terms of aroma formation has been rarely investigated. This study shows that the regulation of 2-acetyl-1-pyrroline (2AP) biosynthesis was evaluated in two different rice cultivars under foliar Zn application. The results showed that the 2AP and Zn contents in leaves and grains were improved substantially under foliar Zn application. The 2AP content was positively related to the expression P5CS2 gene, contents of proline, 1-pyrroline, and Δ1-pyrroline-5-carboxylate (P5C), and the activity of pyrroline-5-carboxylate synthase (P5CS) under Zn application in fragrant rice. Multiple transcription factors (TFs) were differently expressed, such as bZIPs, NACs, and MYBs, to play a role under Zn treatments in fragrant rice, suggesting the crucial role of 46 differently expressed TFs in 2AP improvements in fragrant rice. Furthermore, this study showed that the optimal foliar Zn application at a concentration of 30 mg L^-1 could increase the 2AP content of aromatic rice and keep the yield stable or increase the yield. TFs were involved in regulating to promote the 2AP formation in aromatic rice under the foliar Zn application. However, the relationship between 2AP biosynthesis pathway genes and TFs in fragrant rice remains to be further studied.

The Effect of Water Deficit on Two Greek Vitis vinifera L. Cultivars: Physiology, Grape Composition and Gene Expression during Berry Development

Plants are exposed to numerous abiotic stresses. Drought is probably the most important of them and determines crop distribution around the world. Grapevine is considered to be a drought-resilient species, traditionally covering semiarid areas. Moreover, in the case of grapevine, moderate water deficit is known to improve the quality traits of grape berries and subsequently wine composition. However, against the backdrop of climate change, vines are expected to experience sustained water deficits which could be detrimental to both grape quality and yield. The influence of water deficit on two Greek Vitis vinifera L. cultivars, 'Agiorgitiko' and 'Assyrtiko', was investigated during the 2019 and 2020 vintages. Vine physiology measurements in irrigated and non-irrigated plants were performed at three time-points throughout berry development (green berry, veraison and harvest). Berry growth and composition were examined during ripening. According to the results, water deficit resulted in reduced berry size and increased levels of soluble sugars, total phenols and anthocyanins. The expression profile of specific genes, known to control grape color, aroma and flavor was altered by water availability during maturation in a cultivar-specific manner. In agreement with the increased concentration of phenolic compounds due to water deficit, genes of the phenylpropanoid pathway in the red-skinned Agiorgitiko exhibited higher expression levels and earlier up-regulation than in the white Assyrtiko. The expression profile of the other genes during maturation or in response to water deficit was depended on the vintage.

Light Microclimate-Driven Changes at Transcriptional Level in Photosynthetic Grape Berry Tissues

Viticulture practices that change the light distribution in the grapevine canopy can interfere with several physiological mechanisms, such as grape berry photosynthesis and other metabolic pathways, and consequently impact the berry biochemical composition, which is key to the final wine quality. We previously showed that the photosynthetic activity of exocarp and seed tissues from a white cultivar (Alvarinho) was in fact responsive to the light microclimate in the canopy (low and high light, LL and HL, respectively), and that these different light microclimates also led to distinct metabolite profiles, suggesting a berry tissue-specific interlink between photosynthesis and metabolism. In the present work, we analyzed the transcript levels of key genes in exocarps and seed integuments of berries from the same cultivar collected from HL and LL microclimates at three developmental stages, using real-time qPCR. In exocarp, the expression levels of genes involved in carbohydrate metabolism (VvSuSy1), phenylpropanoid (VvPAL1), stilbenoid (VvSTS1), and flavan-3-ol synthesis (VvDFR, VvLAR2, and VvANR) were highest at the green stage. In seeds, the expression of several genes associated with both phenylpropanoid (VvCHS1 and VvCHS3) and flavan-3-ol synthesis (VvDFR and VvLAR2) showed a peak at the véraison stage, whereas that of RuBisCO was maintained up to the mature stage. Overall, the HL microclimate, compared to that of LL, resulted in a higher expression of genes encoding elements associated with both photosynthesis (VvChlSyn and VvRuBisCO), carbohydrate metabolism (VvSPS1), and photoprotection (carotenoid pathways genes) in both tissues. HL also induced the expression of the VvFLS1 gene, which was translated into a higher activity of the FLS enzyme producing flavonol-type flavonoids, whereas the expression of several other flavonoid pathway genes (e.g., VvCHS3, VvSTS1, VvDFR, and VvLDOX) was reduced, suggesting a specific role of flavonols in photoprotection of berries growing in the HL microclimate. This work suggests a possible link at the transcriptional level between berry photosynthesis and pathways of primary and secondary metabolism, and provides relevant information for improving the management of the light microenvironment at canopy level of the grapes.

Profiling Analysis of Volatile and Non-volatile Compounds in Vitis Vinifera Berries (cv. Chardonnay) and Spontaneous Bud Mutation

A novel clonal variety of Vitis vinifera was identified from “Chardonnay” using inter-simple sequence repeat (ISSR) markers and called “bud mutation. ” The metabolomic profiles in Chardonnay and bud mutation berries indicated essential differences in the expression of key genes in the pathways of 2-C-methyl-D-erythritol-4-phosphate (MEP) and lipoxygenase-hydroperoxide lyase (LOX-HPL). Bud mutation fruits also matured 10 days earlier than Chardonnay and have higher carotenoid, sugar, and acidic compound contents. Furthermore, the gene expression was examined in the biosynthetic pathways of two ripening-associated hormones, abscisic acid (ABA) and jasmonic acid (JA), which significantly increased in bud mutation compared with the Chardonnay fruit. The synthesis and metabolism of amino acids, terpenes, fatty acids, volatile components, and specialized metabolites significantly increased in bud mutation. Therefore, in comparison with Chardonnay, bud mutation is considered a highly aroma-producing grape variety for an improvement in the beverage industry.

Carotenoid Accumulation and the Expression of Carotenoid Metabolic Genes in Mango during Fruit Development and Ripening

Carotenoids are considered to be important components in mango fruits. However, there is a lack of understanding about the regulation of carotenoids in mango. To gain an insight into the carotenoid metabolism pathway, carotenoid content and the expression of carotenoid metabolic genes were investigated in the peel and pulp of mango during fruit development and ripening in three cultivars, ‘Kaituk’, ‘Nam Dok Mai No.4′, and ‘Nam Dok Mai Sithong’, which are different in color. The highest carotenoid content was observed in ‘Kaituk’, followed by ‘Nam Dok Mai No.4′ and ‘Nam Dok Mai Sithong’, with the major carotenoid being β-carotene. The gene expression analysis found that carotenoid metabolism in mango fruit was primarily regulated at the transcriptional level. The changing patterns of carotenoid biosynthetic gene expression (MiPSY, MiPDS, MiZDS, MiCRTISO, MiLCYb, MiLCYe, MiHYb, and MiZEP) were similar to carotenoid accumulation, and ‘Kaituk’ exhibited a higher expression level than the other two cultivars. In addition, the differential regulation of carotenoid catabolic genes was found to be a mechanism responsible for variability in carotenoid content among the three mango cultivars. The expression of carotenoid catabolic genes (MiCCD1, MiNCED2, and MiNCED3) more rapidly decreased in ‘Kaituk’, resulting in a larger amount of carotenoids in ‘Kaituk’ than the other two cultivars.

Carotenoid cleavage dioxygenases (HD-CCD1A and B) contribute as strong negative regulators of β-carotene in Indian bread wheat (cv. HD2967)

Wheat (Triticum aestivum L.) is the most common cereal crop that is considered to be deficient in provitamin A carotenoids. Carotenoids are prone to degrade into apocarotenoids by the activity of carotenoid cleavage dioxygenases (CCDs). Hence, in this study, multiple CCDs were cloned from commercial Indian wheat cultivar HD2967 to understand their role in provitamin A carotenoids degradation. The homoeolog specific expression of HD-CCD1 and HD-CCD4 at different grain filling stages revealed the higher expression of transcripts arising from the A and B subgenomes of HD-CCD1. Furthermore, the grain development stages showed a strong negative correlation of HD-CCD1A (r = - 0.969) and B (r = - 0.970) homoeologs expression to that of β-carotene accumulation. It suggested that they could be potentially involved in deciding the turn-over of β-carotene in wheat grain. Three-dimensional (3D) structures for all six homoeologs of HD-CCD1 and HD-CCD4 were predicted using maize VP14 template to gain better insight into their molecular mechanism. Ramachandran plot assessment revealed that ~ 90% of residues are in the most favoured region. Docking studies with various carotenoid substrates revealed the higher affinity of HD-CCD1A and B for β-carotene and β-cryptoxanthin. Bacterial complementation analysis validated the functional role of all six homoeologs with HD-CCD1B showing the highest activity followed by HD-CCD1A for β-carotene degradation. Results of this study provide valuable insights into the characteristics of HD-CCDs in wheat and thereby justifying them (HD-CCD1A and B) as the candidate genes for employing genome editing tools for developing β-carotene enriched wheat grains.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02775-y.

Tailoring Alginate/Chitosan Microparticles Loaded with Chemical and Biological Agents for Agricultural Application and Production of Value-Added Foods

This work reviews the recent development of biopolymer-based delivery systems for agricultural application. Encapsulation into biopolymer microparticles ensures the protection and targeted delivery of active agents while offering controlled release with higher efficiency and environmental safety for ecological and sustainable plant production. Encapsulation of biological agents provides protection and increases its survivability while providing an environment safe for growth. The application of microparticles loaded with chemical and biological agents presents an innovative way to stimulate plant metabolites synthesis. This enhances plants’ defense against pests and pathogens and results in the production of higher quality food (i.e., higher plant metabolites share). Ionic gelation was presented as a sustainable method in developing biopolymeric microparticles based on the next-generation biopolymers alginate and chitosan. Furthermore, this review highlights the advantages and disadvantages of advanced formulations against conventional ones. The significance of plant metabolites stimulation and their importance in functional food production is also pointed out. This review offers guidelines in developing biopolymeric microparticles loaded with chemical and biological agents and guidelines for the application in plant production, underlining its effect on the plant metabolites synthesis.

Grape Berry Secondary Metabolites and Their Modulation by Abiotic Factors in a Climate Change Scenario-A Review

Temperature, water, solar radiation, and atmospheric CO₂ concentration are the main abiotic factors that are changing in the course of global warming. These abiotic factors govern the synthesis and degradation of primary (sugars, amino acids, organic acids, etc.) and secondary (phenolic and volatile flavor compounds and their precursors) metabolites directly, via the regulation of their biosynthetic pathways, or indirectly, via their effects on vine physiology and phenology. Several hundred secondary metabolites have been identified in the grape berry. Their biosynthesis and degradation have been characterized and have been shown to occur during different developmental stages of the berry. The understanding of how the different abiotic factors modulate secondary metabolism and thus berry quality is of crucial importance for breeders and growers to develop plant material and viticultural practices to maintain high-quality fruit and wine production in the context of global warming. Here, we review the main secondary metabolites of the grape berry, their biosynthesis, and how their accumulation and degradation is influenced by abiotic factors. The first part of the review provides an update on structure, biosynthesis, and degradation of phenolic compounds (flavonoids and non-flavonoids) and major aroma compounds (terpenes, thiols, methoxypyrazines, and C13 norisoprenoids). The second part gives an update on the influence of abiotic factors, such as water availability, temperature, radiation, and CO₂ concentration, on berry secondary metabolism. At the end of the paper, we raise some critical questions regarding intracluster berry heterogeneity and dilution effects and how the sampling strategy can impact the outcome of studies on the grapevine berry response to abiotic factors.

Changes in abscisic acid metabolism in relation to the maturation of grapevine (Vitis vinifera L., cv. Mencía) somatic embryos

BACKGROUND

Somatic embryogenesis in grapevines is a complex process that depends on many physiological and genetic factors. One of its main limitations is the process of precocious germination of the somatic embryos in differentiation medium. This process lowers plant conversion rates from the somatic embryos, and it is probably caused by a low endogenous abscisic acid (ABA) content.

RESULTS

Precocious germination of the somatic embryos was successfully avoided by culturing grapevine cv. Mencía embryogenic aggregates over a semipermeable membrane extended on top of the differentiation medium. The weekly analysis of the endogenous ABA and ABA-glucosyl ester (ABA-GE) contents in the aggregates showed their rapid accumulation. The expression profiles of 9-cis-epoxycarotenoid dioxygenase (VvNCED1), 8'-hydroxylase (VvHyd2), UDP-glucosyltransferase (VvUGT) and β-glucosidase (VvBG2) genes in grapevine revealed that the occurrence of a first accumulation peak of endogenous ABA in the second week of culture over the semipermeable membrane was mainly dependent on the expression of the VvNCED1 gene. A second increase in the endogenous ABA content was observed in the fourth week of culture. At this point in the culture, our results suggest that of those genes involved in ABA accumulation, one (VvNCED1) was repressed, while another (VvBG2) was activated. Similarly, of those genes related to a reduction in ABA levels, one (VvUGT) was repressed while another (VvHyd2) was activated. The relative expression level of the VvNCED1 gene in embryogenic aggregates cultured under the same conditions and treated with exogenous ABA revealed the significant downregulation of this gene.

CONCLUSIONS

Our results demonstrated the involvement of ABA metabolism in the control of the maturation of grapevine somatic embryos cultured over a semipermeable membrane and two important control points for their endogenous ABA levels. Thus, subtle differences in the expression of the antagonistic genes that control ABA synthesis and degradation could be responsible for the final level of ABA during the maturation of grapevine somatic embryos in vitro. In addition, the treatment of somatic embryos with exogenous ABA suggested the feedback-based control of the expression of the VvNCED1 gene by ABA during the maturation of grapevine somatic embryos.

Long-Term Impact of Chemical and Alternative Fungicides Applied to Grapevine cv Nebbiolo on Berry Transcriptome

Viticulture is one of the horticultural systems in which antifungal treatments can be extremely frequent, with substantial economic and environmental costs. New products, such as biofungicides, resistance inducers and biostimulants, may represent alternative crop protection strategies respectful of the environmental sustainability and food safety. Here, the main purpose was to evaluate the systemic molecular modifications induced by biocontrol products as laminarin, resistance inducers (i.e., fosetyl-Al and potassium phosphonate), electrolyzed water and a standard chemical fungicide (i.e., metiram), on the transcriptomic profile of ‘Nebbiolo’ grape berries at harvest. In addition to a validation of the sequencing data through real-time polymerase chain reaction (PCR), for the first-time the expression of some candidate genes in different cell-types of berry skin (i.e., epidermal and hypodermal layers) was evaluated using the laser microdissection approach. Results showed that several considered antifungal treatments do not strongly affect the berry transcriptome profile at the end of season. Although some treatments do not activate long lasting molecular defense priming features in berry, some compounds appear to be more active in long-term responses. In addition, genes differentially expressed in the two-cell type populations forming the berry skin were found, suggesting a different function for the two-cell type populations.

Bunch Microclimate Affects Carotenoids Evolution in cv. Nebbiolo (V. vinifera L.)

This study investigates the impact of bunch microclimate on the evolution of some relevant carotenoids in Nebbiolo grapes. Four bunch-zone microclimates, defined by different vineyard aspect and vine vigor, were characterized by radiation and temperature indices. Berry samples were collected from green phase up to harvest, during two consecutive seasons and carotenoid determination was assessed by High-Performance Liquid Chromatography (HPLC). High carotenoid concentrations were highlighted in Nebbiolo. Lutein and neoxanthin contents (μg berry−1) varied similarly in both seasons achieving a concentration peak after veraison especially in the cooler plots while a variety effect on the lutein seasonal trend was presumed. Conversely, β-carotene content remained generally constant during ripening, with the exception of the south plots showing dissimilar evolution between the seasons. Furthermore, higher temperature in the less vigorous and south facing vineyards led to lower amounts of carotenoids, both during ripening and at harvest. Bunch zone temperature and light condition may affect both synthesis and degradation of grape carotenoids determining their amount and profile at harvest. These findings add further knowledge about the influence of climate changes on grape aroma precursors, and are useful to adapt cultural strategies and preserve grape quality consequently.

VviWRKY40, a WRKY Transcription Factor, Regulates Glycosylated Monoterpenoid Production by VviGT14 in Grape Berry

Glycosylated volatile precursors are important, particularly in wine grape berries, as they contribute to the final aroma in wines by releasing volatile aglycones during yeast fermentation and wine storage. Previous study demonstrated that VviGT14 was functioned as a critical monoterpene glucosyltransferase in grape berry, while the transcriptional regulation mechanism of VviGT14 was still unknown. Here we identified VviWRKY40 as a binding factor of VviGT14 promoter by both DNA pull-down and yeast one-hybrid screening, followed by a series of in vitro verification. VviWRKY40 expression pattern negatively correlated with that of VviGT14 in grape berries. And the suppressor role of VviWRKY40 was further confirmed by using the dual luciferase assay with Arabidopsis protoplast and grape cell suspension system. Furthermore, the grape suspension cell ABA treatment study showed that ABA downregulated VviWRKY40 transcript level but promoted that of VviGT14, indicating that VviWRKY40 was at the downstream of ABA signal transduction network to regulate monoterpenoid glycosylation. These data extend our knowledge of transcriptional regulation of VviGT14, and provide new targets for grape breeding to alter monoterpenoid composition.

Modulation of volatile compound metabolome and transcriptome in grape berries exposed to sunlight under dry-hot climate

BACKGROUND

Basal leaf removal is widely practiced to increase grape cluster sunlight exposure that controls berry rot and improves quality. Studies on its influence on volatile compounds in grape berries have been performed mostly in Mediterranean or marine climate regions. It is uncertain whether similar efficiency can be achieved when grape berries are grown under continental climate. This study aimed to dissect the variation in volatile compound production and transcriptome in sunlight-exposed grape berries in a dry-hot climate region and to propose the key genes related to the variation.

RESULTS

Four cluster sunlight exposure strategies, including basal leaf removal at pepper-corn size stage, leaf removal at véraison (LR-V), leaf moving at véraison (LM-V), and half-leaf removal at véraison, were implemented at the north foot of the Mt. Tianshan region of northwestern China. Various cluster exposure treatments resulted in a decline in the concentrations of norisoprenoids and monoterpenes in ripening grape berries. Both β-carotene and lutein, the substrates of norisoprenoid biosynthesis, were reduced by cluster sunlight exposure. K-means cluster analysis showed that some genes involved in biosynthesis such as VviTPS55, VviTPS60, VviTPS66, VviCCD4a and VviCCD4b exhibited lower expression levels in exposed berries at least at one of the tested stages. Two C6-derived esters with fruity attributes, ethyl hexanoate and hexyl acetate, were reduced markedly. In contrast, main C6 alcohol compound levels were elevated in the LR-V- and LM-V-treated grape berries, which corresponded to the up-regulated expression of VviLOXA, VviLOXO and VviADH1 in the oxylipin pathway. Most of the differentially expressed genes in the exposed and control berries were enriched to the "stress response" processes, and this transcriptome difference was accumulated as the berries matured. Besides, LR-V treatment stimulated a significant up-regulation in photosynthesis-related genes in the grape berries, which did not happen with LM-V treatment.

CONCLUSIONS

Cluster sunlight exposure in dry-hot climate viticulture resulted in different volatile-targeted transcriptomic and metabolic responses from those obtained in the temperate Mediterranean or marine climate region. Therefore, a modified canopy management should be adopted to improve the aroma of grape berries.

A sense of place: transcriptomics identifies environmental signatures in Cabernet Sauvignon berry skins in the late stages of ripening

BACKGROUND

Grape berry ripening is influenced by climate, the main component of the "terroir" of a place. Light and temperature are major factors in the vineyard that affect berry development and fruit metabolite composition.

RESULTS

To better understand the effect of "place" on transcript abundance during the late stages of berry ripening, Cabernet Sauvignon berries grown in Bordeaux and Reno were compared at similar sugar levels (19 to 26 °Brix (total soluble solids)). Day temperatures were warmer and night temperatures were cooler in Reno. °Brix was lower in Bordeaux berries compared to Reno at maturity levels considered optimum for harvest. RNA-Seq analysis identified 5528 differentially expressed genes between Bordeaux and Reno grape skins at 22°Brix. Weighted Gene Coexpression Network Analysis for all expressed transcripts for all four °Brix levels measured indicated that the majority (75%) of transcript expression differed significantly between the two locations. Top gene ontology categories for the common transcript sets were translation, photosynthesis, DNA metabolism and catabolism. Top gene ontology categories for the differentially expressed genes at 22°Brix involved response to stimulus, biosynthesis and response to stress. Some differentially expressed genes encoded terpene synthases, cell wall enzymes, kinases, transporters, transcription factors and photoreceptors. Most circadian clock genes had higher transcript abundance in Bordeaux. Bordeaux berries had higher transcript abundance with differentially expressed genes associated with seed dormancy, light, auxin, ethylene signaling, powdery mildew infection, phenylpropanoid, carotenoid and terpenoid metabolism, whereas Reno berries were enriched with differentially expressed genes involved in water deprivation, cold response, ABA signaling and iron homeostasis.

CONCLUSIONS

Transcript abundance profiles in the berry skins at maturity were highly dynamic. RNA-Seq analysis identified a smaller (25% of total) common core set of ripening genes that appear not to depend on rootstock, vineyard management, plant age, soil and climatic conditions. Much of the gene expression differed between the two locations and could be associated with multiple differences in environmental conditions that may have affected the berries in the two locations; some of these genes may be potentially controlled in different ways by the vinegrower to adjust final berry composition and reach a desired result.

Characterization of two Vitis vinifera carotenoid cleavage dioxygenases by heterologous expression in Saccharomyces cerevisiae

Norisoprenoids are produced from carotenoids under oxidative degradation mediated by carotenoid cleavage dioxygenases (CCDs) and contribute to floral and fruity notes in grape berries and wine. The diversity of CCD substrates and products has been demonstrated by in vitro recombinant proteins extracted from Escherichia coli expressing CCD genes and of in vivo proteins in an E. coli system co-expressing genes for carotenoid synthesis and cleavage. In the current study, VvCCD1 and VvCCD4b were isolated from the cDNA library of Vitis vinifera L. cv. Cabernet Sauvignon and then transformed into carotenoid-accumulating recombinant Saccharomyces cerevisiae strains. The expression of the target genes was monitored during the yeast growth period, and the accumulation of carotenoids and norisoprenoids in the recombinant strains was measured. The results indicated that both of the VvCCDs cleaved β-carotene at the 7, 8 (7', 8') position into β-cyclocitral for the first time. Additionally, the two enzymes also degraded β-carotene at the 9, 10 (9', 10') position to generate β-ionone and cleaved lycopene at the 5, 6 (5', 6') position into 6-methyl-5-hepten-2-one. These findings suggested that the VvCCDs may possess more cleavage characteristics under the eukaryotic expression system in S. cerevisiae than the prokaryotic system in E. coli, which could better explain the biochemical functions of VvCCDs in grape berries.

Transcriptional regulation of abscisic acid biosynthesis and signal transduction, and anthocyanin biosynthesis in 'Bluecrop' highbush blueberry fruit during ripening

Highbush blueberry (Vaccinium corymbosum) fruit accumulate high levels of anthocyanins during ripening, which might be controlled by abscisic acid (ABA), a signal molecule in non-climacteric fruits. For an integrated view of the ripening process from ABA to anthocyanin biosynthesis, we analyzed the transcriptomes of ‘Bluecrop’ highbush blueberry fruit using RNA-Seq at three ripening stages, categorized based on fruit skin coloration: pale green at ca. 30 days after full bloom (DAFB), reddish purple at ca. 40 DAFB, and dark purple at ca. 50 DAFB. Mapping the trimmed reads against the reference sequences yielded 25,766 transcripts. Of these, 143 transcripts were annotated to encode five ABA biosynthesis enzymes, four ABA signal transduction regulators, four ABA-responsive transcription factors, and 12 anthocyanin biosynthesis enzymes. The analysis of differentially expressed genes between the ripening stages revealed that 11 transcripts, including those encoding nine-cis-epoxycarotenoid dioxygenase, SQUAMOSA-class MADS box transcription factor, and flavonoid 3′,5′-hydroxylase, were significantly up-regulated throughout the entire ripening stages. In fruit treated with 1 g L⁻¹ ABA, at least nine transcripts of these 11 transcripts as well as one transcript encoding flavonoid 3′-hydroxylase were up-regulated, presumably promoting anthocyanin accumulation and fruit skin coloration. These results will provide fundamental information demonstrating that ABA biosynthesis and signal transduction, and anthocyanin biosynthesis are closely associated with anthocyanin accumulation and skin coloration in highbush blueberry fruit during ripening.

The genetic basis of grape and wine aroma

The grape is one of the oldest and most important horticultural crops. Grape and wine aroma has long been of cultural and scientific interest. The diverse compound classes comprising aroma result from multiple biosynthetic pathways. Only fairly recently have researchers begun to elucidate the genetic mechanisms behind the biosynthesis and metabolism of grape volatile compounds. This review summarizes current findings regarding the genetic bases of grape and wine aroma with an aim towards highlighting areas in need of further study. From the literature, we compiled a list of functionally characterized genes involved in berry aroma biosynthesis and present them with their corresponding annotation in the grape reference genome.

ABA promotes starch synthesis and storage metabolism in dormant grapevine buds

In grapevine (Vitis vinifera L.) buds, the short day (SD)-photoperiod induces endodormancy and increases the level of ABA and the expression of ABA key biosynthesis genes, which suggests that ABA could be the mediator of the photoperiodic induction of endodormancy. In the present study, it was established that during the development of the endodormancy, the content of ABA and the accumulation of starch increased in parallel in the buds; however, these increases occurred after the buds were already in the state of endodormancy. Despite this finding the exogenous applications of ABA to single-bud cuttings increased the starch content and up-regulated the expression of starch synthesis genes (VvSS1 and VvSS3) and down-regulated the expression of sucrose metabolism genes, invertase (VvINV) and sucrose phosphate synthase (VvSUPS). In addition, the manipulation of the endogenous content of ABA in the grapevine buds by applications of hydrogen cyanamide and uniconazole-P, revealed that the depth of the endodormancy depends on the ABA levels. Taken together, the results indicate that the development of the endodormancy in grapevine buds is associated with the accumulation of starch and a shift in metabolism towards a storage metabolism; as ABA stimulates both processes, it must play an important role in the maintenance and release but not the induction of endodormancy in grapevine buds.

Comparison of transcriptional expression patterns of phenols and carotenoids in 'Kyoho' grapes under a two-crop-a-year cultivation system

To fully utilize the characteristic climatic conditions in the southern region of China, a two-crop-a-year cultivation system technique for ‘Kyoho’ grape was developed during the past decade. After summer harvest in June, appropriate pruning and chemical treatments promote flowering and fruiting, which enables a second harvest in late December. Due to climatic differences between the two crop growing seasons, grape phenol and carotenoid metabolism differ greatly. The reported study analyzed the transcriptome of the carotenoid and phenylpropanoid/flavonoid pathways in grapes at four different stages during the two growing seasons. Compared with those in summer grapes, expression levels of the majority of genes involved in the carotenoid metabolic pathway in winter grapes were generally upregulated. This result was associated with lower rainfall and much more abundant sunlight during the second growing season. On the other hand, summer cropping strongly triggered the expression of upstream genes in the phenylpropanoid/flavonoid pathway at E-L 33 and E-L 35. Transcript levels of flavonoid 3’,5’-hydroxylase (F3’5’H), flavonoid 3’-hydroxylase (F3’H), flavonoid 3-hydroxylase (F3H) and glutathione S-transferase (GST) were upregulated in winter grapes at the mature stage. Together, these results might indicate that more flavonoids would be synthesized in ripe winter grapes during the mature stage of the second crop under much drier conditions, longer sunlight hours and lower temperature. These data provide a theoretical foundation for the secondary metabolism of berries grown under two-crop-a-year cultivation systems.

Full-Length Transcriptome Survey and Expression Analysis of Cassia obtusifolia to Discover Putative Genes Related to Aurantio-Obtusin Biosynthesis, Seed Formation and Development, and Stress Response

The seed is the pharmaceutical and breeding organ of Cassia obtusifolia, a well-known medical herb containing aurantio-obtusin (a kind of anthraquinone), food, and landscape. In order to understand the molecular mechanism of the biosynthesis of aurantio-obtusin, seed formation and development, and stress response of C. obtusifolia, it is necessary to understand the genomics information. Although previous seed transcriptome of C. obtusifolia has been carried out by short-read next-generation sequencing (NGS) technology, the vast majority of the resulting unigenes did not represent full-length cDNA sequences and supply enough gene expression profile information of the various organs or tissues. In this study, fifteen cDNA libraries, which were constructed from the seed, root, stem, leaf, and flower (three repetitions with each organ) of C. obtusifolia, were sequenced using hybrid approach combining single-molecule real-time (SMRT) and NGS platform. More than 4,315,774 long reads with 9.66 Gb sequencing data and 361,427,021 short reads with 108.13 Gb sequencing data were generated by SMRT and NGS platform, respectively. 67,222 consensus isoforms were clustered from the reads and 81.73% (61,016) of which were longer than 1000 bp. Furthermore, the 67,222 consensus isoforms represented 58,106 nonredundant transcripts, 98.25% (57,092) of which were annotated and 25,573 of which were assigned to specific metabolic pathways by KEGG. CoDXS and CoDXR genes were directly used for functional characterization to validate the accuracy of sequences obtained from transcriptome. A total of 658 seed-specific transcripts indicated their special roles in physiological processes in seed. Analysis of transcripts which were involved in the early stage of anthraquinone biosynthesis suggested that the aurantio-obtusin in C. obtusifolia was mainly generated from isochorismate and Mevalonate/methylerythritol phosphate (MVA/MEP) pathway, and three reactions catalyzed by Menaquinone-specific isochorismate synthase (ICS), 1-deoxy-d-xylulose-5-phosphate synthase (DXS) and isopentenyl diphosphate (IPPS) might be the limited steps. Several seed-specific CYPs, SAM-dependent methyltransferase, and UDP-glycosyltransferase (UDPG) supplied promising candidate genes in the late stage of anthraquinone biosynthesis. In addition, four seed-specific transcriptional factors including three MYB Transcription Factor (MYB) and one MADS-box Transcription Factor (MADS) transcriptional factors) and alternative splicing might be involved with seed formation and development. Meanwhile, most members of Hsp20 genes showed high expression level in seed and flower; seven of which might have chaperon activities under various abiotic stresses. Finally, the expressional patterns of genes with particular interests showed similar trends in both transcriptome assay and qRT-PCR. In conclusion, this is the first full-length transcriptome sequencing reported in Caesalpiniaceae family, and thus providing a more complete insight into aurantio-obtusin biosynthesis, seed formation and development, and stress response as well in C. obtusifolia.

Exogenous strigolactone interacts with abscisic acid-mediated accumulation of anthocyanins in grapevine berries

Besides signalling to soil organisms, strigolactones (SLs) control above- and below-ground morphology, in particular shoot branching. Furthermore, SLs interact with stress responses, possibly thanks to a crosstalk with the abscisic acid (ABA) signal. In grapevine (Vitis vinifera L.), ABA drives the accumulation of anthocyanins over the ripening season. In this study, we investigated the effects of treatment with a synthetic strigolactone analogue, GR24, on anthocyanin accumulation in grape berries, in the presence or absence of exogenous ABA treatment. Experiments were performed both on severed, incubated berries, and on berries attached to the vine. Furthermore, we analysed the corresponding transcript concentrations of genes involved in anthocyanin biosynthesis, and in ABA biosynthesis, metabolism, and membrane transport. During the experiment time courses, berries showed the expected increase in soluble sugars and anthocyanins. GR24 treatment had no or little effect on anthocyanin accumulation, or on gene expression levels. Exogenous ABA treatment activated soluble sugar and anthocyanin accumulation, and enhanced expression of anthocyanin and ABA biosynthetic genes, and that of genes involved in ABA hydroxylation and membrane transport. Co-treatment of GR24 with ABA delayed anthocyanin accumulation, decreased expression of anthocyanin biosynthetic genes, and negatively affected ABA concentration. GR24 also enhanced the ABA-induced activation of ABA hydroxylase genes, while it down-regulated the ABA-induced activation of ABA transport genes. Our results show that GR24 affects the ABA-induced activation of anthocyanin biosynthesis in this non-climacteric fruit. We discuss possible mechanisms underlying this effect, and the potential role of SLs in ripening of non-ABA-treated berries.

Chlorophyll, carotenoid and vitamin C metabolism regulation in Actinidia chinensis 'Hongyang' outer pericarp during fruit development

Ascorbic acid (AsA), chlorophyll and carotenoid contents and their associated gene expression patterns were analysed in Actinidia chinensis 'Hongyang' outer pericarp. The results showed chlorophyll degradation during fruit development and softening, exposed the yellow carotenoid pigments. LHCB1 and CLS1 gene expressions were decreased, while PPH2 and PPH3 gene expressions were increased, indicating that downregulation of chlorophyll biosynthesis and upregulation of its degradation, caused chlorophyll degradation. A decrease in the expression of the late carotenoid biosynthesis and maintenance genes (LCYB1, LCYE1, CYP1, CYP2, ZEP1, VDE1, VDE2, and NCED2) and degradation gene (CCD1), showed biosynthesis and degradation of carotenoid could be regulatory factors involved in fruit development. Most genes expression data of L-galactose and recycling pathway were agreement with the AsA concentrations in the fruit, suggesting these are the predominant pathways of AsA biosynthesis. GMP1, GME1 and GGP1 were identified as the key genes controlling AsA biosynthesis in 'Hongyang' outer pericarp.

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components.

Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

Changes in the performance of genotypes in different environments are defined as genotype × environment (G×E) interactions. In grapevine (Vitis vinifera), complex interactions between different genotypes and climate, soil and farming practices yield unique berry qualities. However, the molecular basis of this phenomenon remains unclear. To dissect the basis of grapevine G×E interactions we characterized berry transcriptome plasticity, the genome methylation landscape and within-genotype allelic diversity in two genotypes cultivated in three different environments over two vintages. We identified, through a novel data-mining pipeline, genes with expression profiles that were: unaffected by genotype or environment, genotype-dependent but unaffected by the environment, environmentally-dependent regardless of genotype, and G×E-related. The G×E-related genes showed different degrees of within-cultivar allelic diversity in the two genotypes and were enriched for stress responses, signal transduction and secondary metabolism categories. Our study unraveled the mutual relationships between genotypic and environmental variables during G×E interaction in a woody perennial species, providing a reference model to explore how cultivated fruit crops respond to diverse environments. Also, the pivotal role of vineyard location in determining the performance of different varieties, by enhancing berry quality traits, was unraveled.

Genome-wide identification and characterization of genes involved in carotenoid metabolic in three stages of grapevine fruit development

Carotenoids not only play indispensable roles in plant growth and development but also enhance nutritional value and health benefits for humans. In this study, total carotenoids progressively decreased during fruit ripening. Fifty-four genes involving in mevalonate (MVA), 2-C-methyl-D-erythritol 4-phosphate (MEP), carotenoid biosynthesis and catabolism pathway were identified. The expression levels of most of the carotenoid metabolism related genes kept changing during fruit ripening generating a metabolic flux toward carotenoid synthesis. Down regulation of VvDXS, VvDXR, VvGGPPS and VvPSY and a dramatic increase in the transcription levels of VvCCD might be responsible for the reduction of carotenoids content. The visible correlation between carotenoid content and gene expression profiles suggested that transcriptional regulation of carotenoid biosynthesis pathway genes is a key mechanism of carotenoid accumulation. In addition, the decline of carotenoids was also accompanied with the reduction of chlorophyll content. The reduction of chlorophyll content might be due to the obstruction in chlorophyll synthesis and acceleration of chlorophyll degradation. These results will be helpful for better understanding of carotenoid biosynthesis in grapevine fruit and contribute to the development of conventional and transgenic grapevine cultivars for further enrichment of carotenoid content.

Comparison of transcriptional expression patterns of carotenoid metabolism in 'Cabernet Sauvignon' grapes from two regions with distinct climate

The downstream flux of carotenoid metabolism in grape berries includes the biosynthesis of norisoprenoids, a group of important aroma compounds, and the production of ABA, a well-known plant hormone. This study focused on the transcriptional profiling comparison of genes participating in the biosynthesis of carotenoids, norisoprenoids, and ABA in Vitis vinifera 'Cabernet Sauvignon' grapes at pea size, veraison, and ripening stages. The grapes were obtained from Changli (CL, eastern China) and Gaotai (GT, western China) regions and analyzed using RNA-sequencing technology. The transcripts required for the carotenoid biosynthesis pathway showed a coordinated expression pattern, mainly expressing at green stage for CL and at veraison for GT, respectively. However, the carotenoid content evolution was not coincident with the timing and pattern of related gene expressions, since more carotenoids were accumulated at veraison in CL relative to two weeks before veraison in GT. Interestingly, norisoprenoid content was higher in GT than in CL, particularly at veraison and ripening, while the key gene encoding carotenoid cleavage dioxygenases, VvCCD1, showed an inverse relationship within the two regions. Higher flux was expected through the carotenoid pathway into ABA production in GT, based on the higher expression level of 9-cis-epoxycarotenoid dioxygenase and drought growing conditions. Most components involved in ABA and ethylene signaling showed distinct expression profiles in the two regions. These results revealed that downstream flux of carotenoid metabolism in grape berries showed regional differences. This study lays a foundation for future research to explore the molecular basis of climatic influences on carotenoid, norisoprenoid, and ABA biosynthesis.

The common transcriptional subnetworks of the grape berry skin in the late stages of ripening

BACKGROUND

Wine grapes are important economically in many countries around the world. Defining the optimum time for grape harvest is a major challenge to the grower and winemaker. Berry skins are an important source of flavor, color and other quality traits in the ripening stage. Senescent-like processes such as chloroplast disorganization and cell death characterize the late ripening stage.

RESULTS

To better understand the molecular and physiological processes involved in the late stages of berry ripening, RNA-seq analysis of the skins of seven wine grape cultivars (Cabernet Franc, Cabernet Sauvignon, Merlot, Pinot Noir, Chardonnay, Sauvignon Blanc and Semillon) was performed. RNA-seq analysis identified approximately 2000 common differentially expressed genes for all seven cultivars across four different berry sugar levels (20 to 26 °Brix). Network analyses, both a posteriori (standard) and a priori (gene co-expression network analysis), were used to elucidate transcriptional subnetworks and hub genes associated with traits in the berry skins of the late stages of berry ripening. These independent approaches revealed genes involved in photosynthesis, catabolism, and nucleotide metabolism. The transcript abundance of most photosynthetic genes declined with increasing sugar levels in the berries. The transcript abundance of other processes increased such as nucleic acid metabolism, chromosome organization and lipid catabolism. Weighted gene co-expression network analysis (WGCNA) identified 64 gene modules that were organized into 12 subnetworks of three modules or more and six higher order gene subnetworks. Some gene subnetworks were highly correlated with sugar levels and some subnetworks were highly enriched in the chloroplast and nucleus. The petal R package was utilized independently to construct a true small-world and scale-free complex gene co-expression network model. A subnetwork of 216 genes with the highest connectivity was elucidated, consistent with the module results from WGCNA. Hub genes in these subnetworks were identified including numerous members of the core circadian clock, RNA splicing, proteolysis and chromosome organization. An integrated model was constructed linking light sensing with alternative splicing, chromosome remodeling and the circadian clock.

CONCLUSIONS

A common set of differentially expressed genes and gene subnetworks from seven different cultivars were examined in the skin of the late stages of grapevine berry ripening. A densely connected gene subnetwork was elucidated involving a complex interaction of berry senescent processes (autophagy), catabolism, the circadian clock, RNA splicing, proteolysis and epigenetic regulation. Hypotheses were induced from these data sets involving sugar accumulation, light, autophagy, epigenetic regulation, and fruit development. This work provides a better understanding of berry development and the transcriptional processes involved in the late stages of ripening.

Bioinformatic and expression analyses on carotenoid dioxygenase genes in fruit development and abiotic stress responses in Fragaria vesca

Carotenoid dioxygenases, including 9-cis-epoxycarotenoid dioxygenases (NCEDs) and carotenoid cleavage dioxygenases (CCDs), can selectively cleave carotenoids into various apocarotenoid products that play important roles in fleshy fruit development and abiotic stress response. In this study, we identified 12 carotenoid dioxygenase genes in diploid strawberry Fragaria vesca, and explored their evolution with orthologous genes from nine other species. Phylogenetic analyses suggested that the NCED and CCDL groups moderately expanded during their evolution, whereas gene numbers of the CCD1, CCD4, CCD7, and CCD8 groups maintained conserved. We characterized the expression profiles of FveNCED and FveCCD genes during flower and fruit development, and in response to several abiotic stresses. FveNCED1 expression positively responded to osmotic, cold, and heat stresses, whereas FveNCED2 was only induced under cold stress. In contrast, FveNCED2 was the unique gene highly and continuously increasing in receptacle during fruit ripening, which co-occurred with the increase in endogenous abscisic acid (ABA) content previously reported in octoploid strawberry. The differential expression patterns suggested that FveNCED1 and FveNCED2 were key genes for ABA biosynthesis in abiotic stress responses and fruit ripening, respectively. FveCCD1 exhibited the highest expression in most stages of flower and fruit development, while the other FveCCDs were expressed in a subset of stages and tissues. Our study suggests distinct functions of FveNCED and FveCCD genes in fruit development and stress responses and lays a foundation for future study to understand the roles of these genes and their metabolites, including ABA and other apocarotenoid products, in the growth and development of strawberry.

Regulation of Banana Phytoene Synthase (MaPSY) Expression, Characterization and Their Modulation under Various Abiotic Stress Conditions

Phytoene synthase (PSY) is a key regulatory enzyme of carotenoid biosynthesis pathway in plants. The present study examines the role of PSY in carotenogenesis and stress management in banana. Germplasm screening of 10 Indian cultivars showed that Nendran (3011.94 μg/100 g dry weight) and Rasthali (105.35 μg/100 g dry weight) contained the highest and lowest amounts of β-carotene, respectively in ripe fruit-pulp. Nendran ripe pulp also showed significantly higher antioxidant activity as compared to Rasthali. Meta-analysis of three banana PSY genes (MaPSY1, MaPSY2, and MaPSY3) was performed to identify their structural features, subcellular, and chromosomal localization in banana genome. The distinct expression patterns of MaPSY1, MaPSY2, and MaPSY3 genes were observed in various tissues, and fruit developmental stages of these two contrasting cultivars, suggesting differential regulation of the banana PSY genes. A positive correlation was observed between the expression of MaPSY1 and β-carotene accumulation in the ripe fruit-peel and pulp of Nendran. The presence of stress responsive cis-regulatory motifs in promoter region of MaPSY genes were correlated with the expression pattern during various stress (abscisic acid, methyl jasmonate, salicylic acid and dark) treatments. The positive modulation of MaPSY1 noticed under abiotic stresses suggested its role in plant physiological functions and defense response. The amino acid sequence analysis of the PSY proteins in contrasting cultivars revealed that all PSY comprises conserved domains related to enzyme activity. Bacterial complementation assay has validated the functional activity of six PSY proteins and among them PSY1 of Nendran (Nen-PSY1) gave the highest activity. These data provide new insights into the regulation of PSY expression in banana by developmental and stress related signals that can be explored in the banana improvement programs.

Transcriptomic Analyses of Ascorbic Acid and Carotenoid Metabolites Influenced by Root Restriction during Grape Berry Development and Ripening

Ascorbic acid (AsA) and carotenoids are recognized as crucial metabolites for various biological processes in plants. The contents of AsA and carotenoids in fruits are influenced by external environmental stimuli, such as water, temperature, light, and hormones. However, it is still not clear whether it can be affected by root restriction (RR) treatment. In this study, "Summer Black" grape berries (Vitis vinifera × V. labrusca) under RR and control treatments during development and ripening were used as materials. The results showed that RR significantly increased the contents of AsA, and the transcript VIT_08s0040g03150 related to AsA recycling pathways may be the main regulator for AsA. Similarly, the contents of most of the carotenoids at the earlier stages significantly increased by RR; the enzyme crtB encoded by VIT_12s0028g00960 and the enzyme crtZ encoded by VIT_02s0025g00240 and VIT_16s0050g01090 were inferred to play major roles in the carotenoid metabolic pathways.