Using the combined analysis of transcripts and metabolites to propose key genes for differential terpene accumulation across two regions

Integrated Transcriptomic and Metabolomic Analysis Revealed Abscisic Acid-Induced Regulation of Monoterpene Biosynthesis in Grape Berries

Monoterpenes are a class of volatile organic compounds that play crucial roles in imparting floral and fruity aromas to Muscat-type grapes. However, our understanding of the regulatory mechanisms underpinning monoterpene biosynthesis in grapes, particularly following abscisic acid (ABA) treatment, remains elusive. This study aimed to explore the impact of exogenous ABA on monoterpene biosynthesis in Ruiduhongyu grape berries by employing Headspace Solid-Phase Micro-Extraction Gas Chromatography-Mass Spectrometry (HS-SPME/GC-MS) analysis and transcriptome sequencing. The results suggested significant differences in total soluble solids (TSS), pH, and total acid content. ABA treatment resulted in a remarkable increase in endogenous ABA levels, with concentrations declining from veraison to ripening stages. ABA treatment notably enhanced monoterpene concentrations, particularly at the E_L37 and E_L38 stages, elevating the overall floral aroma of grape berries. According to the variable gene expression patterns across four developmental stages in response to ABA treatment, the E_L37 stage had the largest number of differential expressed genes (DEGs), which was correlated with a considerable change in free monoterpenes. Furthermore, functional annotation indicated that the DEGs were significantly enriched in primary and secondary metabolic pathways, underlining the relationship between ABA, sugar accumulation, and monoterpene biosynthesis. ABA treatment upregulated key genes involved in the methylerythritol phosphate (MEP) pathway, enhancing carbon allocation and subsequently impacting terpene synthesis. This study also identified transcription factors, including MYB and AP2/ERF families, potentially modulating monoterpene and aroma-related genes. Weighted gene co-expression network analysis (WGCNA) linked ABA-induced gene expression to monoterpene accumulation, highlighting specific modules enriched with genes associated with monoterpene biosynthesis; one of these modules (darkgreen) contained genes highly correlated with most monoterpenes, emphasizing the role of ABA in enhancing grape quality during berry maturation. Together, these findings provide valuable insights into the multifaceted effects of exogenous ABA on monoterpene compounds and grape berry flavor development, offering potential applications in viticulture and enology.

A conjoint analysis of renal structure and omics characteristics reveal new insight to yak high-altitude hypoxia adaptation

BACKGROUND

Yaks have unique adaptive mechanisms to the hypoxic environment, in which the kidney plays an important role. The aim of this study was to explore the histological changes of yak kidney at different altitudes and the metabolites and genes associated with adaptation to the hypoxic environment.

METHODS

We analyzed the tissue structure and transcriptomic metabolomic data of yak kidney tissue at two altitudes, 2600 and 4400 m. We compared and identified the morphological adaptations of the kidney and the metabolites and genes associated with hypoxia adaptation in yaks. Changes in renal morphological adaptations, differential metabolites and genes were compared and identified, combining the two in a joint analysis.

RESULTS

High-altitude yak kidneys showed significant adaptive changes: increased mitochondria, increased glomerular thylakoid area, and decreased localized ribosomes. Transcriptomics and metabolomics identified 69 DAMs (Differential metabolites) and 594 DEGs (differential genes). Functional enrichment analysis showed that the DAMs were associated with protein digestion and absorption, ABC transporter, and MTOR signaling pathway; the DEGs were significantly enriched in Cholesterol metabolism and P53 signaling pathway. The joint analysis indicated that metabolites such as lysine and arginine, as well as key genes such as ABCB5 and COL1A2, were particularly affected under hypoxic conditions, whereas changes in mitochondria in the tissue structure may be related to the expression of MFN1 and OPA1, and changes in glomerular thylakoid membranes are related to VEGFA and TGFB3.

CONCLUSION

The kidney regulates metabolites and gene expression related to hormone synthesis, protein metabolism, and angiogenesis by adjusting the mitochondrial and glomerular thylakoid membrane structure to support the survival of yaks in high-altitude environments.

Transcriptomic and free monoterpene analyses of aroma reveal that isopentenyl diphosphate isomerase inhibits monoterpene biosynthesis in grape (Vitis vinifera L.)

BACKGROUND

Monoterpenes are among the most important volatile aromatic compounds contributing to the flavor and aroma of grapes and wine. However, the molecular basis of monoterpene biosynthesis has not yet been fully elucidated.

RESULTS

In our study, transcriptomics and gas chromatography-mass spectrometry (GC-MS) were used to mine candidate genes and transcription factors involved in monoterpene biosynthesis between high-monoterpene and zero-monoterpene table grape cultivars. We found that monoterpene biosynthesis was positively correlated by the expression of five genes encoding 1-deoxy-D-xylulose-5-phosphate synthase (VvDXSs), one encoding 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (VvHDR), three hydroxy-3-methylglutaryl-CoA synthases (VvHMGSs) and one mevalonate kinase (VvMVK), whereas the expression of one isopentenyl diphosphate isomerase (VvIDI) and one 3-hydroxy-3-methylglutaryl-CoA reductase (VvHMGR) negatively correlated monoterpene biosynthesis. Of these genes, VvIDI was selected to validate its function in monoterpene accumulation through a transient overexpression experiment, and was shown to inhibit the biosynthesis of grape linalool and α-terpineol. Meanwhile, we found that a 64-amino acid extension sequence at the N-terminus can guide the VvIDI protein to target the chloroplast.

CONCLUSIONS

The findings of this study should help to guide future functional analysis of key genes as well as mining the potential regulatory mechanism of monoterpene biosynthesis in grapes and grape products.

Targeted metabolomics analysis based on HS-SPME-GC-MS to discriminate geographical origin of 'Muscat Hamburg' grape and wine

Monoterpenes are typical aroma components in muscat grapes and wines, closely related to its geographical origins. However, the mechanism underlying the geographical differences of monoterpenes remains to be elucidated, especially in the Chinese viticulture regions. This study investigated the diversity of six Chinese viticultural vineyards (YT, XF, SS, XX, WW and CL) in the monoterpene composition of Vitis vinifera L. cv.'Muscat Hamburg' grapes and the resulted wines. Monoterpenes were analyzed by HS-SPME- GC-MS. The total amount of free and bound monoterpenes varied dramatically between grapes of different vineyards, and their contents were obviously higher in YT region grapes. The OAVs for 18 monoterpenes of grapes from the YT vineyard were relative higher than those of other regions, and the floral odor could distinguish grapes from different regions. The total free monoterpenes were highest in the YT region wine. Concentrations of total bound monoterpenes ranged from 711.13 μg/L (XF region) to 1078.30 μg/L (CL region). A correlation analysis showed that all monoterpenes showeda positive correlation with mean relative humidity, sum rainfall, and a negative correlation with sum duration of sunshine and mean temperature. This study would provide some new insights to understand the geographical differences of monoterpenes, and the results would facilitate the effective viticultural treatment of grapes to improve the quality of the aroma.

Ethylene-responsive VviERF003 modulates glycosylated monoterpenoid synthesis by upregulating VviGT14 in grapes

Terpenoids are important contributors to the aroma of grapes and wines. Grapes contain terpenoids in both volatile free form and non-volatile glycosidic form, with the latter being more abundant. Glycosylated terpenoids are deemed as latent aromatic potentials for their essential role in adding to the flowery and fruity bouquet of wines. However, the transcriptional regulatory mechanism underlying glycosylated terpenoid biosynthesis remains poorly understood. Our prior study identified an AP2/ERF transcription factor, VviERF003, through DNA pull-down screening using the promoter of terpenoid glycosyltransferase VviGT14 gene. This study demonstrated that both genes were co-expressed and synchronized with the accumulation of glycosylated monoterpenoids during grape maturation. VviERF003 can bind to the VviGT14 promoter and promote its activity according to yeast one-hybrid and dual-luciferase assays. VviERF003 upregulated VviGT14 expression in vivo, leading to increased production of glycosylated monoterpenoids based on the evidence from overexpression or RNA interference in leaves, berry skins, and calli of grapes, as well as tomato fruits. Additionally, VviERF003 and VviGT14 expressions and glycosylated monoterpenoid levels were induced by ethylene in grapes. The findings suggest that VviERF003 is ethylene-responsive and stimulates glycosylated monoterpenoid biosynthesis through upregulating VviGT14 expression.

Metabolomic and transcriptomic integrated analysis revealed the decrease of monoterpenes accumulation in table grapes during long time low temperature storage

Low temperature is the commonly used technique for maintaining the quality of table grapes during postharvest storage. However, this technique could strongly affect the aromatic flavor of fruit. Monoterpenes are the key compounds contributing to the Muscat aromas of grapes. The detailed information and molecular mechanisms underlying the changes in monoterpenes during postharvest low temperature storage have not been thoroughly characterized. In this study, the effects of low temperature storage on the free and bound monoterpene profiles in four cultivars of table grape were determined at both the transcriptomic and metabolomic levels. A total of 27 compounds in both free and bound forms were identified in the four cultivars and showed quantitative differences between the cultivars. Hierarchical cluster and principal component analysis indicated that the free and bound monoterpene profiles were remarkably affected by the low temperature storage. The monoterpenes in the same biosynthesis pathway were clustered together and showed similar evolution trends during low temperature storage. And the content of most of free monoterpenes underwent a rapid decline during low-temperature storage at a certain stage, but the time was different in 4 grape cultivars. Transcriptomic analysis revealed that the expression of DXS, HDR, GPPS and TPS genes involved in the monoterpene synthesis pathway were consistent with the changes in the accumulation of monoterpene compounds. While the expression of HMGS, HMGR genes in MVA pathway and branch genes GGPPS and FPPS were negatively correlated with the accumulation of monoterpenes. The findings provide new insights into the underlying mechanisms of the berry aroma flavor change during low temperature storage.

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.

Basic leucine zipper gene VvbZIP61 is expressed at a quantitative trait locus for high monoterpene content in grape berries

The widely appreciated muscat flavor of grapes and wine is mainly attributable to the monoterpenes that accumulate in ripe grape berries. To identify quantitative trait loci (QTL) for grape berry monoterpene content, an F1 mapping population was constructed by a cross between two grapevine genotypes, one with neutral aroma berries (cv. 'Beifeng') and the other with a pronounced muscat aroma (elite Vitis vinifera line '3-34'). A high-density genetic linkage map spanning 1563.7 cM was constructed using 3332 SNP markers that were assigned to 19 linkage groups. Monoterpenes were extracted from the berry of the F1 progeny, then identified and quantified by gas chromatography-mass spectrometry. Twelve stable QTLs associated with the amounts of 11 monoterpenes in berries were thus identified. In parallel, the levels of RNA in berries from 34 diverse cultivars were estimated by RNA sequencing and compared to the monoterpene content of the berries. The expression of five genes mapping to stable QTLs correlated well with the monoterpene content of berries. These genes, including the basic leucine zipper VvbZIP61 gene on chromosome 12, are therefore considered as potentially being involved in monoterpene metabolism. Overexpression of VvbZIP61 in Vitis amurensis callus through Agrobacterium-mediated transformation significantly increased the accumulation of several monoterpenes in the callus, including nerol, linalool, geranial, geraniol, β-myrcene, and D-limonene. It is hypothesized that VvbZIP61 expression acts to increase muscat flavor in grapes. These results advance our understanding of the genetic control of monoterpene biosynthesis in grapes and provide important information for the marker-assisted selection of aroma compounds in grape breeding.

The beneficial effect of leaf removal during fruit set on physiological, biochemical, and qualitative indices and volatile organic compound profile of the Cypriot reference cultivar 'Xynisteri'

BACKGROUND

'Xynisteri' is the reference Cypriot white cultivar that, despite its significant societal and economic impact, is poorly characterized regarding its qualitative properties, while scarce information exists regarding its aroma profile. In the current study, the effect of leaf removal during fruit set (BBCH 71) on 6-year cordon-trained, spur-pruned grapevines was assessed and an array of physiological, biochemical, and qualitative indices were monitored during successive developmental stages (BBCH 75, BBCH 85, BBCH 87, and BBCH 89). Grapes were additionally monitored for the volatile organic compounds (VOCs) profile during the advanced on-vine developmental stages (BBCH 85-BBCH 89) with the employment of gas chromatography-mass spectrometry (GC-MS), Fourier-transform near infrared (FT-NIR) spectra and electronic nose (E-nose) techniques.

RESULTS

Grape berries from the vines subjected to leaf removal were characterized by higher solid soluble sugars (SSC), titratable acidity (TA), tartaric acid, and ammonium nitrogen contents, while this was not the case for assimilable amino nitrogen (primary amino nitrogen). A total of 75 compounds were identified and quantified, including aliphatic alcohols, benzenic compounds, phenols, vanillins, monoterpenes, and C₁₃ -norisoprenoids. Leaf removal led to enhanced amounts of glycosylated aroma compounds, mainly monoterpenes, and C₁₃ -norisoprenoids. Chemometric analysis, used through FT-NIR and E-nose, showed that the aromatic patterns detected were well associated to the grape ripening trend and differences between leaf removal-treated and control grapes were detectable during fully ripe stage.

CONCLUSION

Leaf removal at fruit set resulted in an overall induction of secondary metabolism, with special reference to glycosylated aroma compounds, namely monoterpenes and C₁₃ -norisoprenoids. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Obtaining new grapevine varieties with unique aromas has been a long-standing goal of breeders. Norisoprenoids are of particular interest to wine producers and researchers, as these compounds are responsible for the important varietal aromas in wine, characterized by a complex floral and fruity smell, and are likely present in all grape varieties. However, the single-nucleotide polymorphism (SNP) loci and candidate genes genetically controlling the norisoprenoid content in grape berry remain unknown. To this end, in this study, we investigated 13 norisoprenoid traits across two years in an F₁ population consisting of 149 individuals from a hybrid of Vitis vinifera L. cv. Muscat Alexandria and V. vinifera L. cv. Christmas Rose. Based on 568,953 SNP markers, genome-wide association analysis revealed that 27 candidate SNP loci belonging to 18 genes were significantly associated with the concentrations of norisoprenoid components in grape berry. Among them, 13 SNPs were confirmed in a grapevine germplasm population comprising 97 varieties, including two non-synonymous mutations SNPs within the VvDXS1 and VvGGPPS genes, respectively in the isoprenoid metabolic pathway. Genotype analysis showed that the grapevine individuals with the heterozygous genotype C/T at chr5:2987350 of VvGGPPS accumulated higher average levels of 6-methyl-5-hepten-2-one and β-cyclocitral than those with the homozygous genotype C/C. Furthermore, VvGGPPS was highly expressed in individuals with high norisoprenoids concentrations. Transient overexpression of VvGGPPS in the leaves of Vitis quinquangularis and tobacco resulted in an increase in norisoprenoid concentrations. These findings indicate the importance of VvGGPPS in the genetic control of norisoprenoids in grape berries, serving as a potential molecular breeding target for aroma.

Water deficit before veraison is crucial in regulating berry VOCs concentration in Sangiovese grapevines

The impact of water deficit on volatile organic compounds (VOCs) responsible for grape aroma remains quite unclear. The aim of this study was to evaluate the effect of different timing and intensity of water deficit on berry VOCs and on their biosynthetic pathways. Fully irrigated control vines were compared with the following treatments: i) two different levels of water deficit from berry pea-size through veraison, ii) one level of water deficit during the lag-phase, and iii) two different levels of water deficit from veraison through harvest. At harvest, total VOC concentrations were higher in berries of water stressed vines from berry pea size through veraison or during the lag phase, whereas post-veraison water deficit determined similar concentrations as control. This pattern was even more pronounced for the glycosylated fraction and was also observed for single compounds, mainly monoterpenes and C13-norisoprenoids. On the other hand, free VOCs were higher in berries from lag phase or post-veraison stressed vines. The significant glycosylated and free VOCs increment measured after the short water stress limited to the lag phase highlight the pivotal role played by this stage in berry aroma compound biosynthesis modulation. The severity of water stress before veraison was also important, since glycosylated VOCs showed a positive correlation with the pre-veraison daily water stress integral. The RNA-seq analysis showed a wide regulation induced by irrigation regimes on terpenes and carotenoids biosynthetic pathways. The terpene synthases and glycosyltransferases as well as genes of the network of transcription factors were upregulated, especially in berries from pre-veraison stressed vines. Since the timing and intensity of water deficit contribute to regulate berry VOCs, irrigation management can be used to achieve high-quality grapes while saving water.

Characterization of key odor-active compounds in Chinese Dornfelder wine and its regional variations by application of molecular sensory science approaches

In this study, aroma characteristics and odor-active compounds in Dornfelder wines from three main production regions of China were comprehensively investigated for the first time. The leading features of Chinese Dornfelder wines were black fruit, violet, acacia/lilac, red fruit, spice, dried plum, honey, and hay based on check-all-that-apply. Wines from the Northern Foothills of Tianshan Mountains and Eastern Foothills of Helan Mountains were dominated by floral and fruity aromas, while wines from the Jiaodong Peninsula were characterized by mushroom/earth, hay, and medicinal material notes. Aroma profiles of Dornfelder wines in three regions were successfully reconstructed with 61 volatiles determined by AEDA-GC-O/MS and OAV. Through aroma reconstitution, omission tests, and descriptive analysis, terpenoids could be regarded as varietal characteristic compounds directly contributing to floral perception in Dornfelder wines. Guaiacol, eugenol, and isoeugenol were further revealed to have a synergistic effect with linalool and geraniol on violet, acacia/lilac, spice, and black fruit.

Grapevine mono- and sesquiterpenes: Genetics, metabolism, and ecophysiology

Mono- and sesquiterpenes are volatile organic compounds which play crucial roles in human perception of table grape and wine flavour and aroma, and as such their biosynthesis has received significant attention. Here, the biosynthesis of mono- and sesquiterpenes in grapevine is reviewed, with a specific focus on the metabolic pathways which lead to formation of these compounds, and the characterised genetic variation underlying modulation of this metabolism. The bottlenecks for terpene precursor formation in the cytosol and plastid are understood to be the HMG-CoA reductase (HMGR) and 1-deoxy-D-xylylose-5-phosphate synthase (DXS) enzymes, respectively, and lead to the formation of prenyldiphosphate precursors. The functional plasticity of the terpene synthase enzymes which act on the prenyldiphosphate precursors allows for the massive variation in observed terpene product accumulation. This diversity is further enhanced in grapevine by significant duplication of genes coding for structurally diverse terpene synthases. Relatively minor nucleotide variations are sufficient to influence both product and substrate specificity of terpene synthase genes, with these variations impacting cultivar-specific aroma profiles. While the importance of these compounds in terms of grape quality is well documented, they also play several interesting roles in the grapevine's ecophysiological interaction with its environment. Mono- and sesquiterpenes are involved in attraction of pollinators, agents of seed dispersal and herbivores, defence against fungal infection, promotion of mutualistic rhizobacteria interaction, and are elevated in conditions of high light radiation. The ever-increasing grapevine genome sequence data will potentially allow for future breeders and biotechnologists to tailor the aroma profiles of novel grapevine cultivars through exploitation of the significant genetic variation observed in terpene synthase genes.

Transcriptomic and metabolomic insights into the role of the flgK gene in the pathogenicity of Pseudomonas plecoglossicida to orange-spotted grouper (Epinephelus coioides)

Pseudomonas plecoglossicida is the pathogen responsible for visceral white spot disease in large yellow croaker (Larimichthys crocea) and orange-spotted grouper (Epinephelus coioides). Previously, RNA sequencing showed that P. plecoglossicida flgK gene expression was significantly up-regulated in orange-spotted grouper spleens during infection. To explore the role of flgK in P. plecoglossicida pathogenicity, RNA interference (RNAi) was performed to silence the P. plecoglossicida flgK gene, and the mutant (flgK-RNAi strain) with the best silencing efficiency (89.40%) was chosen for further study. Results showed that flgK gene silencing significantly attenuated P. plecoglossicida motility, adhesion, and biofilm formation. Compared to those fish infected with the wild-type strain of P. plecoglossicida, orange-spotted grouper infected with the flgK-RNAi strain showed a 55% increase in the survival rate and a one-day delay in time of first death, with fewer pathogens in the spleen and fewer white spots on the spleen surface. RNAi of flgK significantly affected the transcriptome and metabolome of the spleen in infected orange-spotted grouper. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that the C-type lectin receptor signaling pathway was the most significantly changed immune-related pathway and the mitogen-activated protein kinase (MAPK) signaling pathway was related to multiple immune-related pathways. Furthermore, arginine biosynthesis and glycerophospholipid metabolism were the most significantly changed metabolism-related pathways. These findings suggest that flgK is a virulence gene of P. plecoglossicida. Furthermore, flgK appears to be involved in the regulation of motility, adhesion, and biofilm formation in P. plecoglossicida, as well as in the regulation of inflammatory and immune responses of orange-spotted grouper to P. plecoglossicida infection.

Reducing the source/sink ratio of grapevine to face global warming in a semi-arid climate: Effects on volatile composition of Cabernet Sauvignon grapes and wines

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Distal leaf removal increased the solar radiation of the cluster zone in the first few days after applying LR treatments.

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Distal leaf removal was beneficial for accumulating C6 alcohols, terpenes, and the free form of (Z)-β-damascenone in grapes.

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Distal leaf removal significantly increased the fruity and floral intensity of wines because of the increased esters and β-damascenone.

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Whether leaf removal in the same vines over consecutive years or not (1-LRs vs 2-LRs) had limited effects on wines aroma profiles.

The heterogeneity of the vineyard environment caused high variability in grape metabolites and flavor profiles, and the phenomenon was more prominent in recent years of climate change. Herein, distal leaf removal was applied in semi-arid Xinjiang to adjust the source to sink ratio of grapevines for three consecutive years (2018–2020). The grape-derived volatiles showed high correlations with specific climate factors such as temperature changes in the growth period. Results showed that distal leaf removal increased the solar radiation reaching the clusters in the first few days after applying LR treatments while not affecting the temperature. The improvement in fruity and floral aroma intensity by distal leaf removal was founded not only in grape metabolites but also in wines. Moderate cluster exposure brought by distal leaf removal was beneficial for the accumulation of isoprenoids, which therefore increased the fruity and floral intensity of wines. The carry-over effect did not show in consecutively defoliated vines among vintages regarding the wine aroma profile.

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.

Monoterpenoids Evolution and MEP Pathway Gene Expression Profiles in Seven Table Grape Varieties

This research investigated the evolution of both monoterpenoids and expression profiles of related biosynthesis genes in the MEP pathway in seven different table grape varieties from veraison to maturity stage in two seasons, and the correlation was further evaluated between monoterpenoid accumulation and expression of these genes studied in these varieties. Results showed that linalool, trans-furan linalool oxide, geraniol, and cis-furan linalool oxide were the main compounds in the five Muscat varieties two seasons. ‘Zaomeiguixiang’ had the highest contents of geraniol and β-Citronellol. ‘Xiangfei’ had the most abundant of linalool and cis-furan linalool oxide, whereas the neutral varieties of ‘Moldova’ and ‘Christmas Rose’ had the least amount. Monoterpenoid volatiles have been grouped in three evolutionary patterns in the berry development of these varieties. ‘Zaomeiguixiang’ and ‘Xiangfei’ had distinct different pattern of terpenoids evolution profiles. Pearson’s correlation analysis showed that in the MEP pathway, the first biosynthesis gene VvDXS3 was significantly correlated to the accumulation of monoterpenoids, and appeared to be an important candidate gene for synthesis of the monoterpenoids.

Identification of Pseudo-R genes in Vitis vinifera and characterization of their role as immunomodulators in host-pathogen interactions

INTRODUCTION

Duplication events are fundamental to co-evolution in host-pathogen interactions. Pseudogenes (Ψs) are dysfunctional paralogs of functional genes and resistance genes (Rs) in plants are the key to disarming pathogenic invasions. Thus, deciphering the roles of pseudo-R genes in plant defense is momentous.

OBJECTIVES

This study aimed to functionally characterize diverse roles of the resistance Ψs as novel gene footprints and as significant gene regulators in the grapevine genome.

METHODS

PlantPseudo pipeline and HMM-profiling identified whole-genome duplication-derived (WGD) Ψs associated with resistance genes (Ψ-Rs). Further, novel antifungal and antimicrobial peptides were characterized for fungal associations using protein-protein docking with Erysiphe necator proteins. miRNA and tasiRNA target sites and transcription factor (TF) binding sites were predicted in Ψ-Rs. Finally, differential co-expression patterns in Ψ-Rs-lncRNAs-coding genes were identified using the UPGMA method.

RESULTS

2,746 Ψ-Rs were identified from 31,032 WGD Ψs in the genome of grapevine. 69-antimicrobial and 81-antifungal novel peptides were generated from Ψ-Rs. The putative genic potential was predicted for five novel antifungal peptides which were further characterized by docking against E. necator proteins. 395 out of 527 resistance loci-specific Ψ-Rs were acting as parental gene mimics. Further, to explore the diverse roles of Ψ-Rs in plant-defense, we identified 37,026 TF-binding sites, 208 miRNA, and 99 tasiRNA targeting sites on these Ψ-Rs. 194 Ψ-Rs were exhibiting tissue-specific expression patterns. The co-expression network analysis between Ψs-lncRNA-genes revealed six out of 79 pathogen-responsive Ψ-Rs as significant during pathogen invasion.

CONCLUSIONS

Our study provides pathogen responsive Ψ-Rs integral for pathogen invasion, which will offer a useful resource for future experimental validations. In addition, our findings on novel peptide generations from Ψ-Rs offer valuable insights which can serve as a useful resource for predicting novel genes with the futuristic potential of being investigated for their bioactivities in the plant system.

Different Temperature and UV Patterns Modulate Berry Maturation and Volatile Compounds Accumulation in Vitis sp

Volatile compounds (VCs) in grapevine berries play an important role in wine quality; however, such compounds and vine development can be sensitive to environmental conditions. Due to this sensitivity, changes in temperature patterns due to global warming are likely to further impact grape production and berry composition. The aim of this study was to determine the possible effects of different growing-degree day accumulation patterns on berry ripening and composition at harvest. An experimental field was conducted using Vitis sp. L'Acadie blanc, in Nova Scotia, Canada. Using on-the-row mini-greenhouses, moderate temperature increase and reduced ultraviolet (UV) exposure were triggered in grapevines during pre-veraison (inflorescence to the beginning of berry softening), post-veraison (berry softening to full maturity), and whole season (inflorescence to full maturity), while controls were left without treatment. Free and bound VCs were extracted from berries sampled at three different phenological stages between veraison and maturity before analysis by gas chromatography-mass spectrometry (GC-MS). Berries from grapevines exposed to higher temperatures during early berry development (pre-veraison and whole) accumulated significantly higher concentrations of benzene derivatives 2-phenylethanol and benzyl alcohol at harvest, but lower concentrations of hydroxy-methoxy-substituted volatile phenols, terpenes, and C13-norisoprenoids than the control berries. These results illustrate the importance of different environmental interactions in berry composition and suggest that temperature could potentially modulate phenylpropanoid and mevalonate metabolism in developing berries. This study provides insights into the relationships between abiotic conditions and secondary metabolism in grapevine and highlights the significance of early developmental stages on berry quality at harvest.

Effects of Fruit Bagging Treatment with Different Types of Bags on the Contents of Phenolics and Monoterpenes in Muscat-Flavored Table Grapes

The effects of fruit bagging treatments with seven different types of bags on the physicochemical characteristics of three table grape cultivars: RuiduZaohong (RDZH), RuiduHongyu (RDHY), and RuiduHongmei (RDHM) were investigated. Headspace-solid-phase micro-extraction combined with gas chromatography mass spectrometry (HS-SPME-GC-MS) was used to determine the compositions of monoterpenes in the fruit. The results showed that the total soluble solids in RDZH and RDHY fruits treated with the transparent, mesh, yellow, white, and blue bags were significantly higher than the control. The sugar–acid ratio of RDZH was optimized under the transparent bag and yellow bag treatments, and both significantly increased the sugar-acid ratio of RDHY and RDHM. Additionally, mesh bag, transparent bag, and white bag improved the contents of phenolics to a certain extent. The most abundant volatiles were linalool, geraniol, β-myrcene, β-cis-ocimene, and β-trans-ocimene, of which linalool was the main aroma component. The least squares discriminant analysis results showed that linalool, 4-terpineol, and terpinolen could be used to distinguish the main contribution of different bagging treatments for RDZH. Trans-isogeraniol, α-terpineol, and terpinolen could be used for RDHY. Trans-isogeraniol, β-myrcene, and terpinolen could be used for RDHM. In conclusion, transparent and white bags promoted the accumulation of phenolics and monoterpenes while pink and blue bags showed inhibitory effects.

Regional Variation of Chemical Characteristics in Young Marselan (Vitis vinifera L.) Red Wines from Five Regions of China

The environmental conditions of wine regions determine the flavor characteristics of wine. The characterization of the chemical composition and sensory profiles of young Marselan wines from five wine-producing regions in China was investigated by gas chromatography-mass spectrometry (MS), high-performance liquid chromatography–triple-quadrupole MS/MS and descriptive analysis. Young Marselan wines can be successful discriminated based on concentrations of volatile compounds, but not phenolic compounds, by orthogonal partial least squares discriminant analysis according to regions. Compared to Jiaodong Peninsula (JDP) and Bohai Bay (BHB) regions, there were relatively lower average concentrations of varietal volatiles (mainly including β-citronellol, geraniol, and (E)-β-damasenone) and several fermentation aroma compounds (including isoamyl acetate, octanoic acid, decanoic acid, ethyl decanoate, etc.) but higher levels of acetic acid in Xinjiang (XJ), Loess Plateau (LP), and Huaizhuo Basin (HZB) regions, which were related to their characteristic environmental conditions. Marselan wines from HZB, LP, and XJ regions were characterized by lower L values and higher a and C_ab values. Marselan wines from XJ were discriminated from the wines from other regions due to their higher concentrations of several flavonols. Sensory analysis indicated that Marselan wines from HZB region were characterized by relatively low intensities of floral and fruity aromas compared to other regions.

Transcriptomics Integrated with Metabolomics Reveals the Effect of Cluster Thinning on Monoterpene Biosynthesis in 'Muscat Hamburg' Grape

Monoterpenes are crucial to floral and fruit aromas in grapes and wines. Cluster thinning is a common practice for improving grape quality. Using Vitis vinifera cv. Muscat Hamburg, the effects of three cluster-thinning regimes on the biosynthesis and accumulation of monoterpenes from véraison to harvest were investigated at the transcriptomics and targeted metabolomics levels. It was observed that more intense thinning produced higher concentrations of total monoterpenes, particularly in their bound forms. The numbers of differentially expressed genes among the three treatments were 193, 200, and 238 at the three developmental stages. In total, 10 modules were identified from a weighted gene correlation network analysis, and one module including 492 unigenes was associated with monoterpene metabolism. These findings provide new insights into the molecular basis of the relationship between cluster thinning and monoterpene biosynthesis in Muscat Hamburg grape. Cluster thinning could be carefully considered for its application in production.

Characterization of terpene biosynthesis in Melaleuca quinquenervia and ecological consequences of terpene accumulation during myrtle rust infection

Plants use a wide array of secondary metabolites including terpenes as defense against herbivore and pathogen attack, which can be constitutively expressed or induced. Here, we investigated aspects of the chemical and molecular basis of resistance against the exotic rust fungus Austropuccinia psidii in Melaleuca quinquenervia, with a focus on terpenes. Foliar terpenes of resistant and susceptible plants were quantified, and we assessed whether chemotypic variation contributed to resistance to infection by A. psidii. We found that chemotypes did not contribute to the resistance and susceptibility of M. quinquenervia. However, in one of the chemotypes (Chemotype 2), susceptible plants showed higher concentrations of several terpenes including α-pinene, limonene, 1,8-cineole, and viridiflorol compared with resistant plants. Transcriptome profiling of these plants showed that several TPS genes were strongly induced in response to infection by A. psidii. Functional characterization of these TPS showed them to be mono- and sesquiterpene synthases producing compounds including 1,8-cineole, β-caryophyllene, viridiflorol and nerolidol. The expression of these TPS genes correlated with metabolite data in a susceptible plant. These results suggest the complexity of resistance mechanism regulated by M. quinquenervia and that modulation of terpenes may be one of the components that contribute to resistance against A. psidii.

Effects of methyl jasmonate on the monoterpenes of Muscat Hamburg grapes and wine

BACKGROUND

The importance of monoterpenes in grape and wine aroma has compelled researchers to focus on developing methods to increase their abundance. Recent research has revealed that exogenous elicitors can increase the contents of these compounds. This study determined the effects of methyl jasmonate (MeJA) preharvest treatments on the monoterpene profiles of Muscat Hamburg grapes and wine.

RESULTS

A total of 27 monoterpenes were identified for Muscat Hamburg grapes and wine. The contents of most of the monoterpenes (free and glycosylated forms) in the grapes and wine increased in response to MeJA. An analysis of the expression of the genes in the terpenoid biosynthesis pathway indicated that the related biosynthetic pathways were activated by MeJA. The transcript levels of some genes were consistent with monoterpene production, including VviCSLinNer, VviGwbOciF, VviPNRLin, VviGT14 and VviUGT85A1L1. The developmental expression patterns of the VviPP2B1 and VviMYB24 transcription factor genes were positively correlated with monoterpene accumulation in ripening grapes.

CONCLUSIONS

Our results suggest that MeJA may be useful for improving the aroma quality of grapes and wines.

Evolution of volatile profile and aroma potential of table grape Hutai-8 during berry ripening

Hutai-8 (Vitis vinifera × Vitis labrusca) is a table grape widely cultivated in China. In order to determine the changes in volatile profile and aroma potential during berry ripening, a total of 84 free and 73 bound aroma compounds were identified and quantified using headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME-GC-MS). Aldehydes and esters were found to be the main volatile compounds in Hutai-8. They accumulated up to 70 days after flowering (DAF) and then decreased. Bound esters and alcohols were prominent. The concentration of bound esters in Hutai-8 at DAF80 was 714.90 µg/L. β-Damascenone, hexanal, (E)-2-hexenal, (E,Z)-2,6-nonadienal, (E)-2-nonenal, and ethyl octanoate significantly contributed to the volatile profile of Hutai-8. The odor activity value (OAV) of hexanal was the highest at DAF80, reaching 351.51. β-Damascenone mainly appeared midway through the maturation process, reaching a concentration of 12.79 µg/L. The majority of free components reached a maximum in DAF70, while the bound components continuously accumulated throughout the mature period. These results suggest that in addition to being a table grape, Hutai-8 has potential for brewing and other processing.

Transcriptomic and Metabolic Analyses Provide New Insights into the Effects of Exogenous Sucrose on Monoterpene Synthesis in "Muscat Hamburg" Grapes

Monoterpenes provide strong floral and fruit aromas to grapes and wines. In the present study, the effects of exogenous sucrose on the monoterpenes metabolites were studied at the metabolomic and transcriptomic levels in "Muscat Hamburg" grape berries. 6% sucrose aqueous solution was used as treatment, applied at the berry color change stage and 8 days after the first application. Transcriptomics analysis was carried out on berries collected at three phenological stages (berries with intermediate Brix values, E-L 36; berries not quite ripe, E-L 37; and berries harvest-ripe, E-L 38). Our results showed that the sucrose application induced the accumulation of monoterpenes at harvest, especially geraniol and geranic acid. The summary of the number of differentially expressed genes between the control and treatment was 3465, 977, and 2843 at E-L 36, E-L 37, and E-L 38, respectively. Weighted gene correlation network analysis was constructed based on the RNA-seq data, and the MElightyellow module was probably correlated with monoterpene metabolism, comprising 131 unigenes. Quantitative real-time polymerase chain expression analysis of five key differentially expressed genes in terpenoid pathways validated the RNA-seq-derived expression profiles (R² = 0.8143). Our findings provided new insights into the regulation of monoterpene biosynthesis in grape berries under exogenous sucrose.

Two Sides to One Story-Aroma Chemical and Sensory Signature of Lugana and Verdicchio Wines

Lugana and Verdicchio are two Italian white wines with a Protected Designation of Origin (PDO) label. These two wine types are produced in different regions using the same grape variety. The aim of this work is to investigate the existence of volatile chemical markers that could help to elucidate differences between Lugana and Verdicchio wines both at chemical and sensory levels. Thirteen commercial wine samples were analyzed by Gas Chromatography-Mass Spectrometry (GC-MS), and 76 volatile compounds were identified and quantified. Verdicchio and Lugana had been differentiated on the basis of 19 free and glycosidically bound compounds belonging to the chemical classes of terpenes, benzenoids, higher alcohols, C₆ alcohols and norisoprenoids. Samples were assessed by means of a sorting task sensory analysis, resulting in two clusters formed. These results suggested the existence of 2 product types with specific sensory spaces that can be related, to a good extend, to Verdicchio and Lugana wines. Cluster 1 was composed of six wines, 4 of which were Lugana, while Cluster 2 was formed of 7 wines, 5 of which were Verdicchio. The first cluster was described as “fruity”, and “fresh/minty”, while the second as “fermentative” and “spicy”. An attempt was made to relate analytical and sensory data, the results showed that damascenone and the sum of 3 of esters the ethyl hexanoate, ethyl octanoate and isoamyl acetate, was characterizing Cluster 1. These results highlighted the primary importance of geographical origin to the volatile composition and perceived aroma of Lugana and Verdicchio wines.

Effect of the Seasonal Climatic Variations on the Accumulation of Fruit Volatiles in Four Grape Varieties Under the Double Cropping System

The double cropping system has been widely applied in many subtropical viticultural regions. In the 2-year study of 2014-2015, four grape varieties were selected to analyze their fruit volatile compounds in four consecutive seasons in the Guangxi region of South China, which had a typical subtropical humid monsoon climate. Results showed that berries of winter seasons had higher concentrations of terpenes, norisoprenoids, and C6/C9 compounds in "Riesling," "Victoria," and "Muscat Hamburg" grapes in both of the two vintages. However, in the "Cabernet Sauvignon" grapes, only the berries of the 2014 winter season had higher terpene concentrations, but lower norisoprenoid concentrations than those of the corresponding summer season. The Pearson correlation analysis showed the high temperature was the main climate factor that affected volatile compounds between the summer and winter seasons. Hexanal, γ-terpinene, terpinen-4-ol, cis-furan linalool oxide, and trans-pyran linalool oxide were all negatively correlated with the high-temperature hours in all of the four varieties. Transcriptome analysis showed that the upregulated VviDXSs, VviPSYs, and VviCCDs expressions might contribute to the accumulations of terpenes or norisoprenoids in the winter berries of these varieties. Our results provided insights into how climate parameters affected grape volatiles under the double cropping system, which might improve the understanding of the grape berries in response to the climate changes accompanied by extreme weather conditions in the future.

Dynamic changes in monoterpene accumulation and biosynthesis during grape ripening in three Vitis vinifera L. cultivars

Monoterpenes are important aroma components in grapes and wines. We analyzed the free and bound monoterpene profiles and the transcript levels of terpenoid biosynthesis genes in Vitis Vinifera cvs. Muscat Hamburg, Riesling, and Sauvignon Blanc grapes at five ripening stages. Principal component analyses revealed that the three cultivars had different free monoterpene profiles at harvest and the early stage of ripening. In all cultivars, the total bound monoterpene contents were higher than the free monoterpene contents during grape ripening. The changes in monoterpene profiles in different grape varieties were correlated with the transcript levels of some VviTPS and VviGT genes. In Riesling, the VviGT14 and VviUGT88A1L1 transcript levels were related to geraniol glucoside accumulation. In Muscat Hamburg, the VviPNLGl1, VviPNLGl2, and VviPNLGl4 transcript levels were related to linalool accumulation. Understanding the dynamic changes in monoterpene accumulation and biosynthesis will allow winemakers to devise strategies to improve grape and wine aromas.

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.

Characterization of Transcriptional Expression and Regulation of Carotenoid Cleavage Dioxygenase 4b in Grapes

Norisoprenoids are important aromatic volatiles contributing to the pleasant floral/fruity odor in grapes and wine. They are produced from carotenoids through the cleavage of carotenoid cleavage dioxygenases (CCDs). However, the underlying mechanisms regulating VvCCD expression remain poorly understood. In this study, we showed that VvCCD4b expression was positively correlated with the accumulation of β-damascenone, β-ionone, 6-methyl-5-hepten-2-one, geranylacetone, dihydroedulan I, and total norisoprenoids in developing grapes in two vintages from two regions. VvCCD4b was found to be principally expressed in flowers, mature leaves, and berries. Abscisic acid strongly induced the expression of this gene. Additionally, the present study preliminarily indicated that the activity of the VvCCD4b promoter was dropped under 37°C treatment and also responded to the illumination change. VvCCD4b was expressed in parallel with VvMADS4 in developing grape berries. The latter is a MADS family transcription factor and nucleus-localized protein that was captured by yeast one-hybrid. A dual-luciferase reporter assay in tobacco leaves revealed that VvMADS4 downregulated the activity of the VvCCD4b promoter. VvMADS4 overexpression in grape calli and Vitis quinquangularis Rehd. leaves repressed the VvCCD4b expression. In summary, this work demonstrates that VvCCD4b expression is positively correlated with the accumulation of norisoprenoids, and VvMADS4 is a potential negative regulator of VvCCD4b. Our results provide a new perspective for understanding the regulation of VvCCD4b expression and norisoprenoid accumulation in grapes.

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.

Influence of cluster thinning and girdling on aroma composition in 'Jumeigui' table grape

Cluster thinning and girdling are common and simple practices applied to improve berry quality in table grape cultivation. However, there is limited information about the accumulation and biosynthesis of the entire aromatic profile under cluster thinning and girdling, notably in table grapes. This research investigated the influences of cluster thinning and girdling (alone or in combination) on aroma profiles, particularly the changes in biosynthesis and accumulation of Muscat-flavored related compounds from véraison to harvest in 'Jumeigui' grape. Cluster thinning and girdling (alone or in combination) significantly increased the concentrations of total soluble solids (TSS) and key aromatic compounds at harvest, with higher concentrations of both under cluster thinning than girdling. Berry weight and titratable acidity (TA) were unaffected by cluster thinning, girdling, or in combination at harvest. Linalool, the most abundant and active odorant related to Muscat flavor, accumulated in 28.6% and 20.2% higher concentrations from cluster thinning than control and girdling at maturity, respectively. Furthermore, higher DXS3 transcript abundance in cluster thinning groups might contribute to the increased accumulation of terpenes and linalool in 'Jumeigui' grape. The results will contribute to further understand the mechanism of source/sink ratio modulation on aroma accumulation and better apply cluster thinning and girdling for grape production.

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.

Effect of cluster zone leaf removal on monoterpene profiles of Sauvignon Blanc grapes and wines

Monoterpenes contribute to the varietal aromas of grapes and wines. We determined the effects of cluster zone leaf removal on the monoterpene profiles of Sauvignon Blanc grape berries and wines, and on the expression of key genes in the terpenoid pathway. Leaf removal at two intensities (half basic, 50%; full basic, 100%) was conducted at two weeks before veraison, veraison, and two weeks after veraison. Half basic leaf removal increased the pH and decreased the tartaric acid content in grapes and wines. The concentrations of most free- and bound-form monoterpenes in grapes were increased by early leaf removal. The total monoterpene contents were increased in wines in the defoliation treatments, but were significantly lower in wines from the full basic leaf removal treatments than in wines from the half basic leaf removal treatments. The defoliation treatments resulted in increased transcript levels of some key genes in terpene biosynthesis (VvPNLinNer1, VvPNLinNer2, VvPNLNGl1, VvPNLNGl2, and VvUGT88A1L1).

Transcriptome profiles of three Muscat table grape cultivars to dissect the mechanism of terpene biosynthesis

Vitis vinifera is widely grown worldwide for making wine and for use as table grapes. Of the existing cultivars, some have a floral and fruity flavour, referred to as a Muscat flavour. It is well-documented that this flavour originates from a series of terpene compounds, but the mechanism of terpene content differences among the Muscat-type cultivars remains unclear. Transcript and terpene metabolite profiles were integrated to elucidate the molecular mechanism of this phenomenon. In this research, three genotypes with different aromatic strengths were investigated by RNA sequencing. A total of 27 fruit samples from three biological replicates were sequenced on Illumina HiSeq2000 at three stages, corresponding to the veraison; berries had intermediate Brix value and were harvest-ripe. After quality assessment and data clearance, a total of 254.18 Gb of data with more than 97% Q20 bases were obtained, approximately 9.41 Gb data were generated per sample. These results will provide a valuable dataset for the discovery of the mechanism of terpene biosynthesis.

Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine

Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes–i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like ‘photosynthesis’ and ‘oxidative phosphorylation’. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.

Comparative metabolic profiling of Vitis amurensis and Vitis vinifera during cold acclimation

Vitis amurensis is a wild Vitis plant that can withstand extreme cold temperatures. However, the accumulation of metabolites during cold acclimation (CA) in V. amurensis remains largely unknown. In this study, plantlets of V. amurensis and V. vinifera cv. Muscat of Hamburg were treated at 4 °C for 24 and 72 h, and changes of metabolites in leaves were detected by gas chromatography coupled with time-of-flight mass spectrometry. Most of the identified metabolites, including carbohydrates, amino acids, and organic acids, accumulated in the two types of grape after CA. Galactinol, raffinose, fructose, mannose, glycine, and ascorbate were continuously induced by cold in V. amurensis, but not in Muscat of Hamburg. Twelve metabolites, including isoleucine, valine, proline, 2-oxoglutarate, and putrescine, increased in V. amurensis during CA. More galactinol, ascorbate, 2-oxoglutarate, and putrescine, accumulated in V. amurensis, but not in Muscat of Hamburg, during CA, which may be responsible for the excellent cold tolerance in V. amurensis. The expression levels of the genes encoding β-amylase (BAMY), galactinol synthase (GolS), and raffinose synthase (RafS) were evaluated by quantitative reverse transcription-PCR. The expression BAMY (VIT_02s0012 g00170) and RafS (VIT_05s0077 g00840) were primarily responsible for the accumulation of maltose and raffinose, respectively. The accumulation of galactinol was attributed to different members of GolS in the two grapes. In conclusion, these results show the inherent differences in metabolites between V. amurensis and V. vinifera under CA.

Concealed ester formation and amino acid metabolism to volatile compounds in table grape (Vitis vinifera L.) berries

Volatile esters contribute to the aroma and flavor of many fruits but are normally absent in grape berries (Vitis vinifera L.). To examine the biosynthetic potential of grape berries to form volatile esters, berry sections were incubated with exogenous L-Phe, L-Leu or L-Met. In general, amino-acid incubation caused the accumulation of the respective aldehydes and alcohols. Moreover, L-Leu incubation resulted in the accumulation of 3-methylbutyl acetate and L-Phe incubation resulted in the accumulation 2-phenylethyl acetate in 'Muscat Hamburg' but not in the other grape accessions. Exogenous L-Met administration did not result in volatile esters accumulation but the accumulation of sulfur volatile compounds such as methional and dimethyl disulfide was prominent. Berry-derived cell-free extracts displayed differential alcohol acetyltransferase activities and supported the formation of 3-methylbutyl acetate and benzyl acetate. 2-Phenylethyl acetate was produced only in 'Muscat Hamburg' cell-free extracts. VvAAT2, a newly characterized gene, was preferentially expressed in 'Muscat Hamburg' berries and functionally expressed in E. coli. VvAAT2 possesses alcohol acetyltransferase activity utilizing benzyl alcohol, 2-phenylethanol, hexanol or 3-methylbutanol as substrates. Our study demonstrates that grape berries have a concealed potential to accumulate volatile esters and this process is limited by substrate availability.

Induction of Terpene Biosynthesis in Berries of Microvine Transformed with VvDXS1 Alleles

Terpenoids, especially monoterpenes, are major aroma-impact compounds in grape and wine. Previous studies highlighted a key regulatory role for grapevine 1-deoxy-D-xylulose 5-phosphate synthase 1 (VvDXS1), the first enzyme of the methylerythritol phosphate pathway for isoprenoid precursor biosynthesis. Here, the parallel analysis of VvDXS1 genotype and terpene concentration in a germplasm collection demonstrated that VvDXS1 sequence has a very high predictive value for the accumulation of monoterpenes and also has an influence on sesquiterpene levels. A metabolic engineering approach was applied by expressing distinct VvDXS1 alleles in the grapevine model system "microvine" and assessing the effects on downstream pathways at transcriptional and metabolic level in different organs and fruit developmental stages. The underlying goal was to investigate two potential perturbation mechanisms, the former based on a significant over-expression of the wild-type (neutral) VvDXS1 allele and the latter on the ex-novo expression of an enzyme with increased catalytic efficiency from the mutated (muscat) VvDXS1 allele. The integration of the two VvDXS1 alleles in distinct microvine lines was found to alter the expression of several terpenoid biosynthetic genes, as assayed through an ad hoc developed TaqMan array based on cDNA libraries of four aromatic cultivars. In particular, enhanced transcription of monoterpene, sesquiterpene and carotenoid pathway genes was observed. The accumulation of monoterpenes in ripe berries was higher in the transformed microvines compared to control plants. This effect is predominantly attributed to the improved activity of the VvDXS1 enzyme coded by the muscat allele, whereas the up-regulation of VvDXS1 plays a secondary role in the increase of monoterpenes.

Effects of sunlight exclusion on the profiles of monoterpene biosynthesis and accumulation in grape exocarp and mesocarp

Terpenes are important aroma compounds in table Muscat grape and wine, and their content in the berry can be affected by sunlight. The effects of sunlight exclusion on monoterpene profiles and relevant gene expression profiles in the exocarp and mesocarp of table Muscat grape 'Jingxiangyu' at different development stages were thoroughly surveyed by bagging pre-veraison clusters in special opaque boxes. The responses of monoterpenes to sunlight treatments varied in three types, representatively linalool, ocimene and geraniol. Linalool was the most sensitive compound to sunlight, whose biosynthesis was severely inhibited by sunlight exclusion and then was elevated by re-exposure. Ocimene and glycosylated geraniol showed a certain suppressive and stimulative responses to sunlight exclusion respectively. Further transcription analysis revealed that VvPNLinNer1, VvCSbOci, VvGT7 and VvGT14 genes were mainly responsible for monoterpene accumulation and sensitivity to sunlight. VvDXS2 and VvDXR genes were partially related to the differential accumulation of total terpenes under different sunlight treatments.

Drawing Links from Transcriptome to Metabolites: The Evolution of Aroma in the Ripening Berry of Moscato Bianco (Vitis vinifera L.)

Monoterpenes confer typical floral notes to "Muscat" grapevine varieties and, to a lesser extent, to other aromatic non-Muscat varieties. Previous studies have led to the identification and functional characterization of some enzymes and genes in this pathway. However, the underlying genetic map is still far from being complete. For example, the specific steps of monoterpene metabolism and its regulation are largely unknown. With the aim of identifying new candidates for the missing links, we applied an integrative functional genomics approach based on the targeted metabolic and genome-wide transcript profiling of Moscato Bianco ripening berries. In particular, gas chromatography-mass spectrometry analysis of free and bound terpenoid compounds was combined with microarray analysis in the skins of berries collected at five developmental stages from pre-veraison to over-ripening. Differentially expressed metabolites and probes were identified in the pairwise comparison between time points by using the early stage as a reference. Metabolic and transcriptomic data were integrated through pairwise correlation and clustering approaches to discover genes linked with particular metabolites or groups of metabolites. These candidate transcripts were further checked for co-localization with quantitative trait loci (QTLs) affecting aromatic compounds. Our findings provide insights into the biological networks of grapevine secondary metabolism, both at the catalytic and regulatory levels. Examples include a nudix hydrolase as component of a terpene synthase-independent pathway for monoterpene biosynthesis, genes potentially involved in monoterpene metabolism (cytochrome P450 hydroxylases, epoxide hydrolases, glucosyltransferases), transport (vesicle-associated proteins, ABCG transporters, glutathione S-transferases, amino acid permeases), and transcriptional control (transcription factors of the ERF, MYB and NAC families, intermediates in light- and circadian cycle-mediated regulation with supporting evidence from the literature and additional regulatory genes with a previously unreported association to monoterpene accumulation).

Constructing Integrated Networks for Identifying New Secondary Metabolic Pathway Regulators in Grapevine: Recent Applications and Future Opportunities

Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening. Lately, proteomic-related networks and those integrating genome-wide analyses of promoter regulatory elements have also been generated. The integration of all these data in multilayered networks allows building complex maps of molecular regulation and interaction. This perspective article describes the currently available network data and related resources for grapevine. With the aim of illustrating data integration approaches into network construction and analysis in grapevine, we searched for berry-specific regulators of the phenylpropanoid pathway. We generated a composite network consisting of overlaying maps of co-expression between structural and transcription factor genes, integrated with the presence of promoter cis-binding elements, microRNAs, and long non-coding RNAs (lncRNA). This approach revealed new uncharacterized transcription factors together with several microRNAs potentially regulating different steps of the phenylpropanoid pathway, and one particular lncRNA compromising the expression of nine stilbene synthase (STS) genes located in chromosome 10. Application of network-based approaches into multi-omics data will continue providing supplementary resources to address important questions regarding grapevine fruit quality and composition.

Monoterpenyl Glycosyltransferases Differentially Contribute to Production of Monoterpenyl Glycosides in Two Aromatic Vitis vinifera Varieties

HIGHLIGHTS A similar trend on accumulation of glycosidically bound monoterpenes was observed in both varietiesTwo VvGT7 alleles mutations occurred at key sites in Muscat blanc à PetitVvGT14 exerted a major role in production of monoterpenyl glycosides in both varieties Terpenoids are the major aroma components and generally exist as both free and glycosidically-bound forms, of which nonvolatile glycosides account for a large fraction in grape berries. Our previous study has indicated that differential accumulation of monoterpenyl glycosides in Vitis vinifera "Muscat blanc à Petit" between two regions is closely correlated to monoterpenyl glucosyltransferase (VvGT14, XM_002285734.2) transcript abundance. However, it has not been determined yet whether this correlation also exists in other Vitis vinifera varieties. This study investigated the evolution of free and glycosidically bound monoterpenes in two Vitis vinifera variety "Muscat blanc à Petit" and "Gewurztraminer" under two vintages, and further assessed the relation between the accumulation of bound monoterpenes and two monoterpenyl glycosyltransferase transcript levels. Results showed that free monoterpenes exhibited three evolution patterns in both varieties during berry development of two vintages, whereas glycosidically bound monoterpenes showed a concentration elevation with berry maturation. The Cis-rose oxide and geraniol were major components contributing to the aroma odors of "Gewürztraminer" grapes while linalool was major aroma contributor to the "Muscat blanc à Petit grain" grapes. The accumulation of glycosidically bound monoterpenes in both varieties was accompanied with the high expression of VvGT7 (XM_002276510.2) and VvGT14. Only one allele of VvGT7 was found in the variety "Gewürztraminer" and no mutation was observed in its enzyme active sites. XB-VvGT7-4 and XB-VvGT7-5 were two alleles of VvGT7 detected in "Muscat blanc à Petit grain." The mutation on its enzyme active site inhibited the activity of XB-VvGT7-4, whereas VvGT7-5 exhibited an alteration on enzyme activity due to the insertion mutation at the position 443. Only one VvGT14 allele was found in both varieties, and the VvGT14 allele in both varieties showed the similarity on amino acid sequence. No mutation occurred in active sites of VvGT14 allele. These indicated that VvGT7 and VvGT14 differentially contributed to the production of monoterpenyl glycosides in these Vitis Vinifera varieties.

Transcriptomic and Metabolomic Networks in the Grape Berry Illustrate That it Takes More Than Flavonoids to Fight Against Ultraviolet Radiation

Plants are constantly challenged by environmental fluctuations. In response, they have developed a wide range of morphological and biochemical adaptations committed to ameliorate the effects of abiotic stress. When exposed to higher solar radiation levels, plants activate the synthesis of a large set of enzymes and secondary metabolites as part of a complex sunscreen and antioxidant defense mechanism. Grapevine (Vitis vinifera L.) has become a widely used system for studying adaptive responses to this type of stress since changes in berry composition, positively influenced by increased ultraviolet (UV) radiation levels, improve the quality of wines subsequently produced. Despite the fact that most of the attention has been directed toward the synthesis of flavonoids, recent transcriptomic and metabolomic studies have shown that stilbenoids and isoprenoids (e.g., terpenes and carotenoids) are also an important part of the grape UV-response machinery. This minireview focuses on the latest findings referring to the metabolic responses of grapes to UV radiation and proposes a model for its transcriptional control. Depending on the berry developmental stage and the type of radiation (i.e., irradiance level, exposure length), increased UV levels activate different metabolic pathways through the activity of master regulators belonging to the basic Leucine Zipper Domain (bZIP) and R2R3-MYB transcription factor families. This transcriptional control is influenced by the interaction of other environmental factors such as light, temperature or soil water availability. In grapevine, phenylpropanoids are part of, but are not the whole story, in the fight against radiation damage.

Use of response surface methodology for the assessment of changes in the volatile composition of Moscato bianco (Vitis vinifera L.) grape berries during ripening

The changes in the volatile composition of Moscato bianco grapes were evaluated during ripening. Grape berries were sampled for five weeks (16-20 °Brix) and sorted for each date in ten density classes (1.05-1.12g/cm(3)). The highest total concentration of free terpenes was found at 19.3 °Brix; however, total concentration of the bound fraction increased significantly throughout ripening. Response surface methodology was used to assess the simultaneous effect of sampling time and berry density on the volatile composition, which was satisfactorily fitted to regression models for some key terpene compounds. Total free and bound terpenes were more affected by grape density than by sampling date. The same behaviour was observed for free and bound linalool and bound nerol, whereas the stronger effect of sampling date was exhibited for bound t-rose oxide, c-rose oxide and geraniol. The results showed that the sampling strategy impacted strongly on the aroma quality of berries.