Search

Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (10(3) CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (a(w)), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with a(w). Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of a(w) and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.

Aim. We aimed to study the impact of water deficit on the concentration of key flavour and phenolic secondary metabolites of wines.Methods and results. A drought-stress field trial was conducted on Vitis vinifera cv. Merlot and Tocai Friulano for two seasons. Fully irrigated (C) and deficit irrigated (D) grapes were microvinified and the resulting wines were analysed to determine the concentrations of anthocyanins, tannins, and free and glycosidically-bound Volatile Organic Compounds (VOCs). A descriptive sensory test was undertaken on the same wines. Water stressed grapes produced wines with higher concentrations of anthocyanins in Merlot and of free and glycosidically-bound monoterpenes in Tocai Friulano. Both cultivars displayed higher amounts of glycosidically-bound C13-norisoprenoids.Conclusions. Previously observed drought-induced compositional changes to the grapes were transfered to the wines, with an increase in polyphenols and VOCs. However, the timing and the duration of the water stress in the field only heavily impacted the final wine composition with major metabolic modification when the severe water deficit started early (at approximately 40 days after anthesis) and lasted over the entire season until harvest.Significance and impact of the study. This study highlights the positive role of a controlled water deficit on the composition of the wines in terms of secondary metabolites.

Bound volatiles are odorless aroma reservoirs that modify flavor when released during food processing, and their determination is important to understand the aroma of fruit beverages. However, the generation of oxidation/degradation artifacts during analyses of glycosidically-bound volatiles has not been compared across fruit species and their dependence on diverse acidic and enzymatic hydrolytic conditions remains unclear. This work aimed to optimize and compare different hydrolytic conditions for the analysis of glycosidically-bound volatiles in blueberries, raspberries, and grapes with a solid-phase microextraction - gas chromatography/mass spectrometry (SPME-GC/MS) methodology. Enzymatic hydrolyses using AR2000® at 100 mg

Lignin, the second most abundant biopolymer, is a promising renewable energy source and chemical feedstock. A key element of lignin biosynthesis is unknown: how do lignin precursors (monolignols) get from inside the cell out to the cell wall where they are polymerized? Modeling indicates that monolignols can passively diffuse through lipid bilayers, but this has not been tested experimentally. We demonstrate significant monolignol diffusion occurs when laccases, which consume monolignols, are present on one side of the membrane. We hypothesize that lignin polymerization could deplete monomers in the wall, creating a concentration gradient driving monolignol diffusion. We developed a two-photon microscopy approach to visualize lignifying Arabidopsis thaliana root cells. Laccase mutants with reduced ability to form lignin polymer in the wall accumulated monolignols inside cells. In contrast, active transport inhibitors did not decrease lignin in the wall and scant intracellular phenolics were observed. Synthetic liposomes were engineered to encapsulate laccases, and monolignols crossed these pure lipid bilayers to form polymer within. A sink-driven diffusion mechanism explains why it has been difficult to identify genes encoding monolignol transporters and why the export of varied phenylpropanoids occurs without specificity. It also highlights an important role for cell wall oxidative enzymes in monolignol export.

In grapevines, as in other plants, sucrose and its constituents glucose and fructose are fundamentally important and carry out a multitude of roles. The aims of this review are three-fold. First, to provide a summary of the metabolism and transport of sucrose in grapevines, together with new insights and interpretations. Second, to stress the importance of considering the compartmentation of metabolism. Third, to outline the key role of acid invertase in osmoregulation associated with sucrose metabolism and transport in plants.

Background Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest. Results The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca2+ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened. Conclusions The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program. Electronic supplementary material The online version of this article (10.1186/s12870-019-1652-y) contains supplementary material, which is available to authorized users.

International audience; Tartaric acid (TA) is an obscure end point to the catabolism of ascorbic acid (Asc). Here, it is proposed as a « specialized primary metabolite », originating from carbohydrate metabolism but with restricted distribution within the plant kingdom and lack of known function in primary metabolic pathways. Grapes fall into the list of high TA-accumulators, with biosynthesis occurring in both leaf and berry. Very little is known of the TA biosynthetic pathway enzymes in any plant species, although recently some progress has been made in this space. New technologies in grapevine research such as the development of global co-expression network analysis tools and genome-wide association studies, should enable more rapid progress. There is also a lack of information regarding roles for this organic acid in plant metabolism. Therefore this review aims to briefly summarize current knowledge about the key intermediates and enzymes of TA biosynthesis in grapes and the regulation of its precursor, ascorbate, followed by speculative discussion around the potential roles of TA based on current knowledge of Asc metabolism, TA biosynthetic enzymes and other aspects of fruit metabolism.

The abscisic acid (ABA) increase and auxin decline are both indicators of ripening initiation in grape berry, and norisoprenoid accumulation also starts at around the onset of ripening. However, the relationship between ABA, auxin, and norisoprenoids remains largely unknown, especially at the transcriptome level. To investigate the transcriptional and posttranscriptional regulation of the ABA and synthetic auxin 1-naphthaleneacetic acid (NAA) on norisoprenoid production, we performed time-series GC-MS and RNA-seq analyses on Vitis vinifera L. cv. Cabernet Sauvignon grape berries from pre-veraison to ripening. Higher levels of free norisoprenoids were found in ABA-treated mature berries in two consecutive seasons, and both free and total norisoprenoids were significantly increased by NAA in one season. The expression pattern of known norisoprenoid-associated genes in all samples and the up-regulation of specific alternative splicing isoforms of VviDXS and VviCRTISO in NAA-treated berries were predicted to contribute to the norisoprenoid accumulation in ABA and NAA-treated berries. Combined weighted gene co-expression network analysis (WGCNA) and DNA affinity purification sequencing (DAP-seq) analysis suggested that VviGATA26, and the previously identified switch genes of myb RADIALIS (VIT_207s0005g02730) and MAD-box (VIT_213s0158g00100) could be potential regulators of norisoprenoid accumulation. The positive effects of ABA on free norisoprenoids and NAA on total norisoprenoid accumulation were revealed in the commercially ripening berries. Since the endogenous ABA and auxin are sensitive to environmental factors, this finding provides new insights to develop viticultural practices for managing norisoprenoids in vineyards in response to changing climates.

Wine fermentation processes are driven by complex microbial systems, which comprise eukaryotic and prokaryotic microorganisms that participate in several biochemical interactions with the must and wine chemicals and modulate the organoleptic properties of wine. Among these, yeasts play a fundamental role, since they carry out the alcoholic fermentation (AF), converting sugars to ethanol and CO2 together with a wide range of volatile organic compounds. The contribution of Saccharomyces cerevisiae, the reference organism associated with AF, has been extensively studied. However, in the last decade, selected non-Saccharomyces strains received considerable commercial and oenological interest due to their specific pro-technological aptitudes and the positive influence on sensory quality. This review aims to highlight the inter-specific variability within the heterogeneous class of non-Saccharomyces in terms of synthesis and release of volatile organic compounds during controlled AF in wine. In particular, we reported findings on the presence of model non-Saccharomyces organisms, including Torulaspora delbrueckii, Hanseniaspora spp, Lachancea thermotolerans, Metschnikowia pulcherrima, Pichia spp. and Candida zemplinina, in combination with S. cerevisiae. The evidence is discussed from both basic and applicative scientific perspective. In particular, the oenological significance in different kind of wines has been underlined.

International audience; Lignin is a key secondary cell wall chemical constituent, and is both a barrier to biomass utilization and a potential source of bioproducts. The Arabidopsis transcription factors MYB58 and MYB63 have been shown to upregulate gene expression of the general phenylpropanoid and monolignol biosynthetic pathways. The overexpression of these genes also results in dwarfism. The vascular integrity, soluble phenolic profiles, cell wall lignin, and transcriptomes associated with these MYB-overexpressing lines were characterized. Plants with high expression of MYB58 and MYB63 had increased ectopic lignin and the xylem vessels were regular and open, suggesting that the stunted growth is not associated with loss of vascular conductivity. MYB58 and MYB63 overexpression lines had characteristic soluble phenolic profiles with large amounts of monolignol glucosides and sinapoyl esters, but decreased flavonoids. Because loss of function lac4 lac17 mutants also accumulate monolignol glucosides, we hypothesized that LACCASE overexpression might decrease monolignol glucoside levels in the MYB-overexpressing plant lines. When laccases related to lignification (LAC4 or LAC17) were co-overexpressed with MYB63 or MYB58, the dwarf phenotype was rescued. Moreover, the overexpression of either LAC4 or LAC17 led to wild-type monolignol glucoside levels, as well as wild-type lignin levels in the rescued plants. Transcriptomes of the rescued double MYB63- OX/LAC17-OX overexpression lines showed elevated, but attenuated, expression of the MYB63 gene itself and the direct transcriptional targets of MYB63. Contrasting the dwarfism from overabundant monolignol production with dwarfism from lignin mutants provides insight into some of the proposed mechanisms of lignin modification-induced dwarfism.

Review of grapevine drought responses and the search for drought-tolerant varieties that can increase the sustainability of viticulture in the context of climate change., Water availability is arguably the most important environmental factor limiting crop growth and productivity. Erratic precipitation patterns and increased temperatures resulting from climate change will likely make drought events more frequent in many regions, increasing the demand on freshwater resources and creating major challenges for agriculture. Addressing these challenges through increased irrigation is not always a sustainable solution so there is a growing need to identify and/or breed drought-tolerant crop varieties in order to maintain sustainability in the context of climate change. Grapevine (Vitis vinifera), a major fruit crop of economic importance, has emerged as a model perennial fruit crop for the study of drought tolerance. This review synthesizes the most recent results on grapevine drought responses, the impact of water deficit on fruit yield and composition, and the identification of drought-tolerant varieties. Given the existing gaps in our knowledge of the mechanisms underlying grapevine drought responses, we aim to answer the following question: how can we move towards a more integrative definition of grapevine drought tolerance?

Flavonoids impart color and mouthfeel to grapes and wine and are very sensitive to environmental conditions. Growth chamber experiments were performed to investigate the effect of temperature regimes and the differences between day/night temperatures on anthocyanins and flavonols in Merlot grapes. Among the regimes tested, the ones with diurnal 20°C determined the highest levels of anthocyanins and flavonols. Higher diurnal temperatures decreased those levels but increased the proportion of methoxylated and acylated species. When regimes with the same day temperature but different night temperatures were compared, differences between day/night temperatures did not affect anthocyanins, unless a difference of 25°C between day and night temperatures was imposed. When regimes with the same night temperature but different day temperatures were compared, the regime with higher day temperature had a lower anthocyanin level. No relationships were observed between the effects of temperature regimes on anthocyanin level and the expression of key anthocyanin genes. However, the effects on anthocyanin acylation level were consistent with the effects on the acyltransferase expression, and the effects on flavonol level were consistent with the effects on the expression of key flavonol genes. This study indicates that, in Merlot grapes, anthocyanins and flavonols are mostly sensitive to day temperatures.

The phosphorylation status of MYB75 at T-131 affects protein stability, flavonoid profiles, and patterns of gene expression. The Arabidopsis transcription factor Myeloblastosis protein 75 (MYB75, AT1G56650) is known to act as a positive transcriptional regulator of genes required for flavonoid and anthocyanin biosynthesis. MYB75 was also shown to negatively regulate lignin and other secondary cell wall biosynthetic genes (Bhargava et al. in Plant Physiol 154(3):1428–1438, 2010). While transcriptional regulation of MYB75 has been described in numerous publications, little is known about post-translational control of MYB75 protein function. In a recent publication, light-induced activation of a MAP kinase (MPK4, AT4G01370) in Arabidopsis was reported to lead to MYB75 phosphorylation at two canonical MPK target sites, threonines, T-126 and T-131. This double phosphorylation event positively influenced MYB75 protein stability (Li et al. in Plant Cell 28(11):2866–2883, 2016). We have examined this phenomenon through use of phosphomutant forms of MYB75 and found that MYB75 is phosphorylated primarily at T-131, and that the phosphorylation of MYB75 recombinant protein in vitro can be catalyzed by multiple MAP kinases, including MPK3 (AT3G45640), MPK6 (AT2G43790), MPK4 and MPK11 (AT1G01560). We also demonstrate that MYB75 can bind to a large number of Arabidopsis MPK’s in vitro, suggesting it could be a target of multiple signalling pathways. The impact of MYB75 phosphorylation at T-131 on the function of this transcription factor, in terms of localization, stability, and protein–protein interactions with known binding partners was examined in transgenic lines expressing phosphomimic and phosphonull versions of MYB75, to capture the behaviour of permanently phosphorylated and unphosphorylated MYB75 protein, respectively. In addition, we describe how ectopic over-expression of different phosphovariant forms of MYB75 (MYB75WT, MYB75T131A, and MYB75T131E) affects flavonoid biochemical profiles and global changes of gene expression in the corresponding transgenic Arabidopsis plants.

Early leaf removal (ELR) applied in the grapevine cluster zone at bloom or pre-bloom (PB) is a vineyard practice commonly utilized to reduce fruit disease and yield. In addition, the literature reports that ELR enhances fruit quality, however, little research has deciphered the potential factors regulating this response. In this work, the objective was to understand whether the increase in fruit quality in response to manual or mechanical leaf removal is due to changes in fruit-zone microclimate, vine physiology, or ripening/stress related hormone biosynthesis. In ‘Merlot’ (Vitis vinifera L.) vines, 60% of leaf area was removed from shoots in three ways: 1) manual removal of 5 leaves (PB-MA), 2) mechanical removal (PB-ME), and 3) simulated mechanical removal (PB-SIM), which was implemented by removing the distal portion of leaves on the first eight nodes to understand whether PB-ME improves fruit quality via enhanced microclimate conditions or plant stress. Yield was reduced in PB-ME and PB-SIM, while total soluble solids was not different at harvest; meaning that ELR decreased the partitioning of carbohydrates to fruit. Anthocyanins and flavonols were enhanced by PB-ME, however neither ABA nor ethylene were similarly altered. Instead, the leaf area at nodes above the fruit-zone was lower in PB-ME compared to non-defoliated ones, which increased post-veraison fruit temperature (+2.8 °C). These parameters correlated with anthocyanins at harvest. In conclusion, skin phenylpropanoid concentrations were influenced by canopy density above the fruit-zone. Additionally, ripening-related phytohormones were not involved in the response of phenylpropanoid biosynthesis in vine subjected to ELR.

This work focused on the development of starch-based (potato, corn, sweet potato, green bean and tapioca) edible packaging film incorporated with blueberry pomace powder (BPP). The optical, mechanical, thermal, and physicochemical properties were subsequently tested. The film color was not affected by the addition of BPP. BPP incorporated into corn and green bean starch films showed increased light barrier properties, indicating a beneficial effect to prevent UV radiation-induced food deterioration. Film thickness and transparency were not primarily affected by changing the starch type or the BPP concentration, although the corn starch films were the most transparent. Furthermore, all films maintained structural integrity and had a high tensile strength. The water vapor transmission rate of all the films was found to be greater than conventional polyethylene films. The average solubility of all the films made from different starch types was between 24 and 37%, which indicates the usability of these films for packaging, specifically for low to intermediate moisture foods. There were no statistical differences in Differential Scanning Calorimetry parameters with changes in the starch type and pomace levels. Migration assays showed a greater release of the active compounds from BPP into acetic acid medium (aqueous food simulant) than ethanol medium (fatty food simulant). The incorporation of BPP into starch-chitosan films resulted in the improvement of film performance, thereby suggesting the potential for applying BPP into starch-based films for active packaging.

Blueberry aroma is one of the most important quality traits that influences consumer purchasing decisions. This study aimed to optimize and validate a solid-phase microextraction-gas chromatography/mass spectrometry (SPME-GC/MS) method for the quantification of 73 volatile compounds in northern highbush blueberries. A SPME extraction of blueberries with water and specific proportions of sodium chloride, citric acid, and ascorbic acid, for 60 min at 50 °C using a divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS) fiber was optimal. The method was validated for sensitivity, reproducibility, linearity, and accuracy, and used to quantify volatile compounds through matrix-matched calibration curves in six blueberry cultivars (‘Duke’, ‘Draper’, ‘Bluecrop’, ‘Calypso’, ‘Elliott’, and ‘Last Call’). Terpenes represented the most abundant volatile fraction, followed by aldehydes and alcohols. Linalool and 2-(E)-hexenal were key compounds that differentiated blueberry cultivars via Principal Component Analysis (PCA). Enantiomeric analyses revealed an excess of (−)-limonene, (−)-α-pinene, and (+)-linalool for all cultivars with potential impacts on the blueberry aroma.

Drought events are a major challenge for many horticultural crops, including grapes, which are often cultivated in dry and warm climates. It is not understood how the cuticle contributes to the grape berry response to water deficit (WD); furthermore, the cuticular waxes and the related biosynthetic pathways are poorly characterized in this fruit. In this study, we identified candidate wax-related genes from the grapevine genome by phylogenetic and transcriptomic analyses. Developmental and stress response expression patterns of these candidates were characterized across pre-existing RNA sequencing data sets and confirmed a high responsiveness of the pathway to environmental stresses. We then characterized the developmental and WD-induced changes in berry cuticular wax composition, and quantified differences in berry transpiration. Cuticular aliphatic wax content was modulated during development and an increase was observed under WD, with wax esters being strongly up-regulated. These compositional changes were related to up-regulated candidate genes of the aliphatic wax biosynthetic pathway, including CER10, CER2, CER3, CER1, CER4, and WSD1. The effect of WD on berry transpiration was not significant. This study indicates that changes in cuticular wax amount and composition are part of the metabolic response of the grape berry to WD, but these changes do not reduce berry transpiration., Water deficit caused an increase in grape berry aliphatic cuticular wax load and changes in wax composition, yet these modifications did not reduce the berry cuticle transpiration rate.

BackgroundGene expression analyses are conducted using multiple approaches and increasingly research has been focused on assessing gene expression at the level of a tissue or even single-cells. To date, methods to assess gene expression at the single-cell in plant tissues have been semi-quantitative, require tissue disruption, and/or involve laborious, possibly artifact-inducing manipulation. In this work, we used grape berries (Vitis vinifera L. Zinfandel) as a model in order to examine the validity and reproducibility of an in-situ gene expression analysis method combining a cell pressure probe (CPP) with quantitative PCR (qPCR).ResultsWe developed a method to directly assess gene expression levels via qPCR from cellular fluids sampled in-situ with a CPP. Cellular fluids, with volumes in the picoliter range, were collected from intact berries with a CPP at various depths across skin and mesocarp tissues. The expression of a key anthocyanin biosynthetic gene, UDP-glucose: flavonoid 3-O-glucosyltransferase (VviUFGT), was analyzed as a test case since its expression is restricted to cells producing anthocyanins in grape berry skins during ripening. The method identifies samples contaminated with significant levels of genomic DNA by amplifying a region of VviUFGT that spans an intron. Therefore false positives were discarded which occurred in 28% of the samples tested. Shallow probing of skin cells showed high VviUFGT expression as expected while deeper probing of mesocarp cells resulted in no VviUFGT expression.ConclusionsThe clear correspondence of VviUFGT expression to the targeted cell samples suggests that the in-situ gene expression analysis using a CPP is reliable and does not result in contamination as the probe moves through tissues. This method can be paired to single-cell transcriptomic analyses in the future. We conclude that this technique represents a minimally invasive method of sampling plant cells in-situ which creates an opportunity for the analysis of cellular level, spatiotemporal responses in heterogeneous plant tissues.

The cannabis leaf is iconic, but it is the flowers of cannabis that are consumed for the psychoactive and medicinal effects of their specialized metabolites. Cannabinoid metabolites, together with terpenes, are produced in glandular trichomes. Superficially, stalked and sessile trichomes in cannabis only differ in size and whether they have a stalk. The objectives of this study were: to define each trichome type using patterns of autofluorescence and secretory cell numbers, to test the hypothesis that stalked trichomes develop from sessile-like precursors, and to test whether metabolic specialization occurs in cannabis glandular trichomes. A two-photon microscopy technique using glandular trichome intrinsic autofluorescence was developed which demonstrated that stalked glandular trichomes possessed blue autofluorescence correlated with high cannabinoid levels. These stalked trichomes had 12-16 secretory disc cells and strongly monoterpene-dominant terpene profiles. In contrast, sessile trichomes on mature flowers and vegetative leaves possessed red-shifted autofluorescence, eight secretory disc cells and less monoterpene-dominant terpene profiles. Moreover, intrinsic autofluorescence patterns and disc cell numbers supported a developmental model where stalked trichomes develop from apparently sessile trichomes. Transcriptomes of isolated floral trichomes revealed strong expression of cannabinoid and terpene biosynthetic genes, as well as uncharacterized genes highly co-expressed with CBDA synthase. Identification and characterization of two previously unknown and highly expressed monoterpene synthases highlighted the metabolic specialization of stalked trichomes for monoterpene production. These unique properties and highly expressed genes of cannabis trichomes determine the medicinal, psychoactive and sensory properties of cannabis products.

A major goal of viticulture is to exert control over ripening and produce fruit of reproducible yield and quality. This implies developing effective viticultural practices, breeding cultivars with improved characteristics, and requires considering the numerous variables that can influence development and ripening, like cultivar-specific traits, regional climate, and stresses. Molecular tools aid these efforts. Among them, transcriptome measurements that capture expression across the genome allow monitoring which genomic features are transcribed given the aforementioned variables. The technologies used to study the transcriptome have rapidly improved and become less expensive since the early 2000s, increasing the feasibility of developing molecular marker-driven practices. This chapter briefly reviews the history and state of transcriptomic technologies since they have been applied to grapevine, reviews the seminal publications that have used these tools, and proposes a direction for this field in the future.

Because of their economic and cultural importance, grapes are arguably the most studied fruit crop and are considered a model system for research on non-climacteric fruits. The sequencing of the grapevine genome has led to major discoveries that have increased our understanding of the molecular regulation of fruit ripening and berry metabolism, and how the environment and viticultural practices affect berry physiology. This chapter reviews the most recent studies on the molecular and metabolic pathways associated with grape berry ripening including the pathways involved in berry growth and softening, and sugar, organic acid, phenolic, and aroma accumulation. The role of hormones and hormone crosstalk, as well as a compendium of the most recent research on transcription factors (TFs) and non-coding RNAs are presented.

Regulated deficit irrigation (RDI) is a viticultural practice known to improve grape phenolics and color in red grapes; however, the impact of this practice on grape aromas remains largely unknown. The effects of RDI treatments applied at various berry developmental stages on canopy, yield, and free and glycoside-bound terpenes of the berry were investigated for three consecutive seasons. All RDI treatments reduced leaf photosynthesis and yield, but not when applied after veraison. Berry total soluble solids at harvest were reduced by RDI applied after veraison or throughout the season. Despite reducing berry sugars, RDI applied after veraison increased the concentration at harvest of key free terpenes for Gewürztraminer grapes such as geraniol and citronellol. RDI treatments down-regulated some terpene genes, which indicates that the observed changes in terpene concentration were not transcriptionally regulated. This study suggests that RDI applied after version can potentially improve wine aroma in Gewürztraminer.

A common irrigation strategy is to replenish the soil water reservoir according to evapotranspiration (ET). However, the ET from plants under deficit irrigation is not well explored and is normally assumed to be a constant fraction of their respective well-watered condition. In the current experiment, we hypothesized that the ratio between the ET of well-watered (WW) and water deficit (WD) grapevines is not constant but depends on the reference ET (ETO). The hypothesis was tested using lysimeters over two consecutive seasons to measure the ET of WD grapevines (Vitis vinifera L.) that were irrigated at 35 % of a second set of lysimeters with WW vines. The WD treatment started at veraison and resulted in a quick depletion of the soil water reservoir; thereafter a relatively stable soil water content (θ) and crop coefficient (KC) were measured. The ET of the WD vines was 20–75 % lower than that of the WW vines, depending on the reference evapotranspiration (ETO). Under high ETO, the difference between the treatments was much larger than under low ETO. The dynamic ratio between the ET of the treatments demonstrates the difficulty in predicting the ET of WD plants and suggests that irrigation according to a constant fraction from a WW plant might result in either excessive or insufficient irrigation amounts. The high correlation between instantaneous stomatal conductance (g s) measurements and KC emphasizes the advantage of utilizing g s to improve current irrigation models.

The development and accumulation of secondary metabolites in grapes determine wine color, taste, and aroma. This study aimed to investigate the effect of leaf removal before flowering, a practice recently introduced to reduce cluster compactness and Botrytis rot, on anthocyanin, tannin, and methoxypyrazine concentrations in 'Merlot' grapes and wines. Leaf removal before flowering was compared with leaf removal after flowering and an untreated control. No effects on tannin and anthocyanin concentrations in grapes were observed. Both treatments reduced levels of 3-isobutyl-2-methoxypyrazine (IBMP) in the grapes and the derived wines, although the after-flowering treatment did so to a greater degree in the fruit specifically. Leaf removal before flowering can be used to reduce cluster compactness, Botrytis rot, and grape and wine IBMP concentration and to improve wine color intensity but at the expense of cluster weight and vine yield. Leaf removal after flowering accomplishes essentially the same results without loss of yield.

Drought stress affects anthocyanin accumulation and modification in vegetative and reproductive plant tissues. Anthocyanins are the most abundant flavonoids in grape (Vitis vinifera L.) coloured berry genotypes and are essential markers of grape winemaking quality. They are mostly mono- and di-methylated, such modifications increase their stability and improve berry quality for winemaking. Anthocyanin methylation in grape berries is induced by drought stress. A few caffeoyl-CoA O-methyltransferases (CCoAOMTs) active on anthocyanins have been described in grape. However, no drought-activated O-methyltransferases have been described in grape berries yet.In this study, we characterized VvCCoAOMT, a grapevine gene known to induce methylation of CoA esters in cultured grape cells. Transcript accumulation of VvCCoAOMT was detected in berry skins, and increased during berry ripening on the plant, and in cultured berries treated with ABA, concomitantly with accumulation of methylated anthocyanins, suggesting that anthocyanins may be substrates of this enzyme. Contrary as previously observed in cell cultures, biotic stress (Botrytis cinerea inoculation) did not affect VvCCoAOMT gene expression in leaves or berries, while drought stress increased VvCCoAOMT transcript in berries. The recombinant VvCCoAOMT protein showed in vitro methylating activity on cyanidin 3-O-glucoside. We conclude that VvCCoAOMT is a multifunctional O-methyltransferase that may contribute to anthocyanin methylation activity in grape berries, in particular under drought stress conditions.

This is a correction to: Journal of Experimental Botany, Volume 71, Issue 16, 6 August 2020, Pages 4658–4676, https://doi.org/10.1093/jxb/eraa245

Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation

Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset. This revealed strong correlations between ATL proteins and diverse signal transduction components and transcriptional regulators, in particular those involved in immunity. An enrichment analysis of cis-regulatory elements in ATL gene promoters and related co-expressed genes highlighted the importance of hormones in the regulation of ATL gene expression. Our work identified several ATL proteins as candidates for further studies aiming to decipher specific grapevine resistance mechanisms activated in response to pathogens.

Background and Aims In recent years, increasing summer temperature, coupled with reduced and erratic rainfall during the growing season, has induced accelerated fruit ripening in several regions, resulting in an undesirable increase in wine alcohol concentration. This study was designed to evaluate the impact of canopy and water management on grape sugar and flavonoid accumulation, with the goal of reducing wine alcohol concentration while conserving or enhancing the concentration of phenolic substances. Methods and Results In 2011 and 2012, two irrigation treatments (I – irrigated and DI – deficit irrigated) and two canopy heights (HC – high canopy and SC – short canopy) were applied in a Merlot vineyard. No interactions between treatments were observed, and thus independent results were obtained; DI berries had significantly higher sugar concentration (+5%) than that of I in both years and higher wine alcohol concentration only in 2012. Short canopy berries had lower sugar concentration (−4%) and lower wine alcohol (−8%) (only in 2011) than that of HC. Anthocyanins and tannins in berry and wine were increased by water deficit and not affected by severe trimming. Conclusions Deficit irrigation did not reduce berry sugar concentration and wine alcohol concentration but did enhance desirable wine attributes. Berry sugar concentration and alcohol concentration in wine were reduced by SC in one of the two seasons. Water deficit and severe trimming showed independent effects on berry composition. Significance of the Study Severe canopy reduction at early stages of ripening can reduce sugars without affecting the accumulation of anthocyanins in Merlot. Conversely, DI applied before veraison, despite promoting anthocyanins accumulation, may also increase berry sugar concentration at harvest.

Postveraison water deficit is a common strategy implemented to improve fruit composition in many wine-growing regions. However, contrasting results are often reported on fruit size and composition, a challenge for generalizing the positive impact of this technique. Our research investigated the effect of water deficit (WD) imposed at veraison on Merlot grapevines, during two experimental seasons (2014-2015). In both years WD resulted in reduced carbon assimilation rates and leaf shedding. However, the treatment effect on the analyzed berry parameters varied between seasons. Modification of skin metabolites was more evident in 2015 than in 2014, despite the similar soil water content and water stress physiological parameters (gas exchange, water potential) recorded in the two experimental years. Higher solar radiation and air temperature in 2015 than in 2014 hint for the involvement of atmospheric parameters in fulfilling the potential effect of WD. Our results suggest that the interaction between water availability and weather conditions plays a crucial role in modulating the grape berry composition.

Grapevine fanleaf virus (GFLV) causes grapevine fanleaf degeneration, one of the oldest known viral diseases of grapevines. The virus has been found in all winegrowing regions around the world. In the seasons 2011–12 a comparison between field grown GFLV-infected and healthy grapevines was conducted for the cultivars Schioppettino in North-Eastern Italy and Refošk in South-Western Slovenia. Our research showed that GFLV infection caused a drop of the yield due to reduction of both cluster weight and berry weight. Besides the yield, the berry composition was also affected; in detail, anthocyanin concentration increased in both varieties but significantly only in the case of Schioppettino. Upregulation of the F3ʹ5ʹH gene and downregulation of F3ʹH gene in the berries of GFLV infected vines compared with the ones of healthy control vines resulted in modified proportions between di- and tri- hydroxylated or methylated derivatives of anthocyanins. The F3H1 gene was identified to be the most strongly regulated gene of the flavonoid biosynthetic pathway by GFLV infection, indicating its important role in increasing anthocyanin concentration in grapes of GFLV infected vines as compared with healthy controls.

Coordinated transcriptional and metabolic reprogramming ensures a plant’s continued growth and survival under adverse environmental conditions. Transcription factors (TFs) act to modulate gene expression through complex cis-regulatory element (CRE) interactions. Genome-wide analysis of known plant CREs was performed for all currently predicted protein-coding gene promoters in grapevine (Vitis vinifera L.). Many CREs such as abscisic acid (ABA)-responsive, drought-responsive, auxin-responsive, and evening elements, exhibit bona fide CRE properties such as strong position bias towards the transcription start site (TSS) and over-representation when compared with random promoters. Genes containing these CREs are enriched in a large repertoire of plant biological pathways. Large-scale transcriptome analyses also show that these CREs are highly implicated in grapevine development and stress response. Numerous CRE-driven modules in condition-specific gene co-expression networks (GCNs) were identified and many of these modules were highly enriched for plant biological functions. Several modules corroborate known roles of CREs in drought response, pathogen defense, cell wall metabolism, and fruit ripening, whereas others reveal novel functions in plants. Comparisons with Arabidopsis suggest a general conservation in promoter architecture, gene expression dynamics, and GCN structure across species. Systems analyses of CREs provide insights into the grapevine cis-regulatory code and establish a foundation for future genomic studies in grapevine.

Plant phenolics have been for many years a theme of major scientific and applied interest. Grape berry phenolics contribute to organoleptic properties, color and protection against environmental challenges. Climate change has already caused significant warming in most grape-growing areas of the world, and the climatic conditions determine, to a large degree, the grape varieties that can be cultivated as well as wine quality. In particular, heat, drought and light/UV intensity severely affect phenolic metabolism and, thus, grape composition and development. In the variety Chardonnay, water stress increases the content of flavonols and decreases the expression of genes involved in biosynthesis of stilbene precursors. Also, polyphenolic profile is greatly dependent on genotype and environmental interactions. This review deals with the diversity and biosynthesis of phenolic compounds in the grape berry, from a general overview to a more detailed level, where the influence of environmental challenges on key phenolic metabolism pathways is approached. The full understanding of how and when specific phenolic compounds accumulate in the berry, and how the varietal grape berry metabolism responds to the environment is of utmost importance to adjust agricultural practices and thus, modify wine profile., This work was supported by European Union Funds (FEDER/COMPETE-Operational Competitiveness Programme) and by national funds (FCT-Portuguese Foundation for Science and Technology) under the project FCOMP-01-0124-FEDER-022692 and the research project PTDC/AGR-ALI/100636/2008. This work was also supported by the European project INNOVINE (ref. 311775), and from the networking activities within the European funded COST ACTION FA1106 “QualityFruit” and COST Action FA1003 “East-West Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding”., info:eu-repo/semantics/publishedVersion