Increasing the source/sink ratio in Vitis vinifera (cv Sangiovese) induces extensive transcriptome reprogramming and modifies berry ripening

Influence of mixed and single infection of grapevine leafroll-associated viruses and viral load on berry quality

Grapevine leafroll disease is a viral disease that affects grapevines (Vitis vinifera L.) and has a severe economic impact on viticulture. In this study, the effect of grapevine leafroll-associated viruses (GLRaV) on berry quality was investigated in clones of cultivar cv. Crimson Seedless table grapes infected with GLRaV. RT-PCR confirmed the identity of the clones: clone 3236, infected only with GLRaV-3 (termed single); clone 3215, infected with GLRaV-3, GLRaV-4 strain 9 and grapevine virus A (termed mixed); and a viral free clone of the same genetic background of the infected clones (termed control). The berry quality indices of size, sugar, acidity and anthocyanin content were measured at harvest maturity. RT-qPCR was used to determine the viral load. The study was repeated over 2 year. A two-way, multivariate analysis of variance was applied with clone and year as independent variables and the measured berry quality parameters as a dependent variable. All dependent variables were significantly affected by viral infection (Wilks, λ, (2,33) = 0.033895, P-value <0.001), while only titratable acidity was affected by year. The average berry dry mass decreased (P-value <0.001). The water content of both infected clones was greater than that of the control (P-value <0.001). Both infected clones displayed reduced sugar content as a fraction of the berry dry mass (P-value <0.001). The anthocyanin and the phenol content of the infected clones were significantly reduced compared with the control clone (P < 0.001, P < 0.05, clone 3236 and clone 3215, respectively). Finally, the viral load was highly variable, and no quantitative relationship between viral load and berry composition was found.

Phloem anatomy predicts berry sugar accumulation across 13 wine-grape cultivars

Introduction

Climate change is impacting the wine industry by accelerating ripening processes due to warming temperatures, especially in areas of significant grape production like California. Increasing temperatures accelerate the rate of sugar accumulation (measured in ⁰Brix) in grapes, however this presents a problem to wine makers as flavor profiles may need more time to develop properly. To alleviate the mismatch between sugar accumulation and flavor compounds, growers may sync vine cultivars with climates that are most amenable to their distinct growing conditions. However, the traits which control such cultivar specific climate adaptation, especially for ⁰Brix accumulation rate, are poorly understood. Recent studies have shown that higher rates of fruit development and sugar accumulation are predicted by larger phloem areas in different organs of the plant.

Methods

Here we test this phloem area hypothesis using a common garden experiment in the Central Valley of Northern California using 18 cultivars of the common grapevine (Vitis vinifera) and assess the grape berry sugar accumulation rates as a function of phloem area in leaf and grape organs.

Results

We find that phloem area in the leaf petiole organ as well as the berry pedicel is a significant predictor of ⁰Brix accumulation rate across 13 cultivars and that grapes from warm climates overall have larger phloem areas than those from hot climates. In contrast, other physiological traits such as photosynthetic assimilation and leaf water potential did not predict berry accumulation rates.

Discussion

As hot climate cultivars have lower phloem areas which would slow down brix accumulation, growers may have inadvertently been selecting this trait to align flavor development with sugar accumulation across the common cultivars tested. This work highlights a new trait that can be easily phenotyped (i.e., petiole phloem area) and be used for growers to match cultivar more accurately with the temperature specific climate conditions of a growing region to obtain satisfactory sugar accumulation and flavor profiles.

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

BACKGROUND

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

RESULTS

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

CONCLUSION

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

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

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

Juxtaposition of the Source-to-Sink Ratio and Fruit Exposure to Solar Radiation on cv. Merlot (Vitis vinifera L.) Berry Phenolics in a Cool versus Warm Growing Region

The grapevine source-to-sink ratio and berry exposure to solar radiation both influence grape flavonoid biosynthesis and accumulation. Here, we compared these concepts on cv. Merlot in two different growing locations (Michigan (MI) and Friuli-Venezia Giulia (FVG), IT) to understand whether the environment influences flavonoid sensitivity to these parameters. Three levels of leaf removal (LR0, LR5, LR8) were implemented at the pea-size phenological stage to compare conditions of increased cluster light exposure with a decreasing vine source-to-sink ratio on berry flavonoid accumulation. Treatments did not affect total soluble solids (TSSs) or pH, but titratable acidity (TA) was lower in LR8 at harvest in both locations. LR5 increased anthocyanins and flavonols in MI but decreased most phenolics in FVG. The decreased expression of VviLAR1 and VviF3'5'Hh during ripening supported the lower concentrations of flavan-3-ol monomers and anthocyanins in FVG. In summary, flavonoid biosynthesis and accumulation were more sensitive to solar radiation than the source-to-sink ratio, and the vineyard environment dictated whether solar radiation was beneficial or detrimental to flavonoid biosynthesis.

Flavonoid biosynthesis is differentially altered in detached and attached ripening bilberries in response to spectral light quality

Light spectral quality is known to affect flavonoid biosynthesis during fruit ripening. However, the response of fruits to different light conditions, when ripening autonomously from the parent plant (detached), has been less explored. In this study, we analyzed the effect of light quality on detached and naturally ripening (attached) non-climacteric wild bilberry (Vaccinium myrtillus L.) fruits accumulating high amounts of anthocyanins and flavonols. Our results indicated contrasting responses for the accumulation of phenolic compounds in the berries in response to red and blue light treatments. For detached berries, supplemental blue light resulted in the highest accumulation of anthocyanins, while naturally ripening berries had elevated accumulation under supplemental red light treatment. Both red and blue supplemental light increased the expression levels of all the major structural genes of the flavonoid pathway during ripening. Notably, the key regulatory gene of anthocyanin biosynthesis, VmMYBA1, was found to express fivefold higher under blue light treatment in the detached berries compared to the control. The red light treatment of naturally ripening berries selectively increased the delphinidin branch of anthocyanins, whereas in detached berries, blue light increased other anthocyanin classes along with delphinidins. In addition, red and far-red light had a positive influence on the accumulation of flavonols, especially quercetin and myricetin glycoside derivatives, in both ripening conditions. Our results of differential light effects on attached and detached berries, which lacks signaling from the mother plant, provide new insights in understanding the light-mediated regulatory mechanisms in non-climacteric fruit ripening.

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

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

Biosynthesis and Cellular Functions of Tartaric Acid in Grapevines

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.

Decreased sink/source ratio enhances hexose transport in the fruits of greenhouse tomatoes: integration of gene expression and biochemical analyses

To examine the physiological role of hexose transporters in determining the sink strength of individual fruits, the regulation of hexose transporters gene expression was studied when the sink/source ratio was artificially altered under the greenhouse condition; this was done in two cultivars of tomato, i.e. Grandella and Isabella. The sink/source ratio treatments included: saving one fruit per truss (1F), two fruits per truss (2F), three fruits per truss (3F) and no fruit pruning (control). The results showed that fruit thinning could increase starch, sucrose, and hexose contents in the fruits; it could also modulate the activity of the key enzymes and the expression of tomato hexose transporter genes (LeHTs). Based on the relative transcript levels, all examined LeHTs were unregulated at the end of cell division and the cell expansion stage of fruit development, but the strongest expression level observed at the onset of ripening was related to LeHT1 and LeHT2. Given the concomitancy of cell wall invertase (EC 3.2.1.26) activity and the LeHTs relative expression cell wall, invertase activity seemed to be involved in the expression level of LeHTs. The increased trends of the LeHTs expression with the decrease of the sink/source ratio confirmed the role of hexose transporters in determining the sink strength of the tomato fruits.

Foliar application of specific yeast derivative enhances anthocyanins accumulation and gene expression in Sangiovese cv (Vitis vinifera L.)

The effect of elicitors on secondary metabolism in vines is receiving much interest, since it has been shown that they are able to increase the accumulation of phenolics, especially anthocyanins. This research aims to investigate the biochemical and molecular effects of the application of a commercial yeast derivative (Saccharomyces cerevisiae) on the accumulation of anthocyanins in potted Sangiovese vines. Experiments were performed on three consecutive years and the yeast derivative was applied at the beginning and at the end of veraison. Technological ripening, accumulation of anthocyanins and expression of the main genes involved in their biosynthesis were assessed. Technological ripening proceeded in a similar way in both treated and untreated berries in the three years. A significant increase in the concentration of anthocyanins was instead detected, following the induction by the yeast derivative of the expression of the genes involved in their biosynthesis. The research highlights the possibility of applying a specific inactivated yeast to increase the anthocyanin concentration even under the current climate change conditions, in Sangiovese, a cultivar extremely sensitive to high temperatures.

Potassium and Magnesium Mediate the Light and CO2 Photosynthetic Responses of Grapevines

Potassium (K) and magnesium (Mg) deficiency are common stresses that can impact on grape yield and quality, but their effects on photosynthesis have received little attention. Understanding the diffusional and biochemical limitations to photosynthetic constraints will help to guide improvements in cultural practices. Accordingly, the photosynthetic response of Vitis vinifera cvs. Shiraz and Chardonnay to K or Mg deficiency was assessed under hydroponic conditions using miniature low-nutrient-reserve vines. Photosynthesis was at least partly reduced by a decline in stomatal conductance. Light and CO₂-saturated photosynthesis, maximum rate of ribulose 1.5 bisphospate (RuBP) carboxylation (V_cmax) and maximum rate of electron transport (J_max) all decreased under K and Mg deficiency. Likewise, chlorophyll fluorescence and electron transport were lower under both nutrient deficiencies while dark respiration increased. K deficiency drastically reduced shoot biomass in both cultivars, while root biomass was greatly reduced under both Mg and K deficiency. Taken together, these results indicate that the decrease in biomass was likely due to both stomatal and biochemical limitations in photosynthesis. Optimising photosynthesis through adequate nutrition will thus support increases in biomass with carry-on positive effects on crop yields.

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.

Impacts of Pre-bloom Leaf Removal on Wine Grape Production and Quality Parameters: A Systematic Review and Meta-Analysis

Wine grape (Vitis vinifera L.) is the most widely cultivated fruit crop in the world. However, the climactic characteristics in some growing regions are suboptimal for grape production, including short season length and excess precipitation. Grape growers can utilize an array of methods to mitigate these issues, including "early leaf removal," a management practice involving the removal of leaves from selected basal nodes along shoots around bloom. This meta-analysis reviews the extensive literature on this practice, with specific regards to application at "pre-bloom" (PB). One hundred seventy-five publications on the topic of "early leaf removal" were identified using key terms and subsequently narrowed via eight data curation steps. The comparison between treated (PB) and control plants in these studies revealed two important results. First, PB lowered bunch rot disease (-61%), partially through reducing the compactness of clusters. Second, PB promoted a significant increase in fruit total soluble solids (°Brix, +5.2%), which was related to the increase in the leaf-to-fruit ratio. Furthermore, cultivar and rootstock were found to have a large influence on the success of PB, while the contribution of climate was smaller. In conclusion, PB significantly lowers yield and bunch rot disease and increases °Brix, both of which improve grape and wine quality.

Changes in global aroma profiles of Cabernet Sauvignon in response to cluster thinning

Cluster thinning (CT) is a common practice to prevent overcropping in viticulture. CT affects vine balance between vegetative and productive growth and further modifies grape composition. This study investigated the effects of cluster thinning treatments applied at pea-size stage (CT-AF) and the onset of veraison (CT-V), respectively, on volatile compounds of Cabernet Sauvignon in two seasons (2013-2014). The experimental vineyard was located in the north-west of China with semi-arid and monsoon climate. CT exhibited limited effects on the evolutions of volatile compounds. CT-AF exhibited an inhibition on 6-methyl-5-heptene-2-one accumulation. There were no differences in terpene concentrations between CT-treated and control grapes regardless of CT time. Regarding C₆/C₉ compounds and their derivatives, CT-AF decreased nonanal concentration whilst CT-V increased (Z)-3-hexen-1-ol concentration. Additionally, there were increases in nonanal, (E)-2-hexen-1-ol, (Z)-2-hexen-1-ol and (Z)-3-hexen-1-ol concentrations in grapes with delayed CT. Among benzene derivatives, earlier CT resulted in lower phenol concentrations.

Effects of delayed winter pruning on vine performance and grape composition in cv. Merlot

Delaying winter pruning until after budburst is a technique that can retard vine phenological phases and reduce grape sugar concentration at harvest. Given these characteristics, many studies have recently been conducted to verify the ability of pruning after budburst to contrast the negative effects of climate change. In our trial, vines of the cv. Merlot, trained to a VSP spur pruned cordon, were pre-pruned leaving 8 nodes per shoot and hand finished when the shoots sprouted by the apical nodes were at BBCH13 (treatment LP) and BBCH18 stage (treatment VLP). Vines refinished during winter were used as control (WP). Anthocyanins and tannins of skin and seeds were analysed after both exhaustive extraction (total content) and extraction conducted with a hydroalcoholic solution (extractable portion). Vines refinished after budburst showed reduced leaf area, yield, cluster and berry weights; technological maturity of these vines was delayed as lower sugar concentration and pH were observed at harvest. Treatment VLP had a stronger effect than LP on these parameters. Considering phenolic compounds, the skin and seed tannin concentration increased only in VLP, while no effect was found on anthocyanins. In conclusion, delaying pruning until after budburst revealed interesting prospects for contrasting the negative effects of climate change.

Biochemical and molecular effects of yeast extract applications on anthocyanin accumulation in cv. Sangiovese

The effect of biotic and abiotic elicitors on the secondary metabolism in grapevine is gaining a lot of interest, as it has been shown that they can increase the accumulation of phenolic compounds and anthocyanins in particular. The aim of this research was to verify the biochemical and molecular effects of the application of LalVigne™ MATURE (Lallemand, St. Simon, France), 100% inactivated natural yeast (Saccharomyces cerevisiae) on the anthocyanin accumulation in potted plants of Sangiovese. In both years, LVM plants did not differ from C in technological ripening at harvest. A significant increase in anthocyanin concentration and the expression of genes involved in their biosynthesis was found in 2016 in LVM grapes compared to C, while in 2017, a year with extremely warm temperatures, the anthocyanins of C and LVM were comparable, despite a slight increase in LVM after the second treatment.

Enhancement of Fruit Technological Maturity and Alteration of the Flavonoid Metabolomic Profile in Merlot ( Vitis vinifera L.) by Early Mechanical Leaf Removal

Removal of basal leaves near blooms inevitably affects grapevine balance and cluster microclimate conditions, improving fruit quality. Mechanization of this practice allows growers to save time and resources, but to our knowledge, it has not yet been compared with the manual application of this practice in a cool-climate region where seasonal temperatures frequently limit fruit technological maturity and phenolic ripening in red Vitis vinifera cultivars. In our research, berry sugar concentration was highest with prebloom mechanical treatment (PB-ME). Furthermore, metabolomics analysis revealed that PB-ME favored the accumulation of significantly more disubstituted anthocyanins and flavonols and OH-substituted anthocyanins compared with manual application. Given that vine balance was similar between treatments, increased ripening with PB-ME is likely due to enhanced microclimate conditions and higher carbon partitioning through a younger canopy containing basal leaf fragments proximal to fruit. This information provides an important strategy for consistently ripening red Vitis vinifera cultivars in cool climates.

Effects of cluster thinning on vine photosynthesis, berry ripeness and flavonoid composition of Cabernet Sauvignon

Cluster thinning is a common practice for regulating vine yield and grape quality. The effects of cluster thinning on vine photosynthesis, berry ripeness and flavonoid composition of V. vinifera L. Cabernet Sauvignon were evaluated during two seasons. Half of the clusters were removed at pea-size and veraison relative to two controls, respectively. Both cluster thinning treatments significantly increased pruning weight and decreased yield. No effects of cluster thinning on berry growth, ripeness and flavonol composition were observed. Early cluster thinning decreased the photosynthetic rate at pea-size, but the effect diminished at post-veraison. Early cluster thinning significantly promoted the biosynthesis of anthocyanins but decreased the proportion of 3'5'-hydroxylated and acylated anthocyanins at veraison. Late cluster thinning decreased the proportions of 3'5'-hydroxylated and acylated anthocyanins. Additionally, Cluster thinning showed inconsistent effects on flavan-3-ol composition over the two seasons.

Low source-sink ratio reduces reserve starch in grapevine woody canes and modulates sugar transport and metabolism at transcriptional and enzyme activity levels

Severe leaf removal decreases storage starch and sucrose in grapevine cv. Cabernet Sauvignon fruiting cuttings and modulates the activity of key enzymes and the expression of sugar transporter genes. Leaf removal is an agricultural practice that has been shown to modify vineyard efficiency and grape and wine composition. In this study, we took advantage of the ability to precisely control the number of leaves to fruits in Cabernet Sauvignon fruiting cuttings to study the effect of source-sink ratios (2 (2L), 6 (6L) and 12 (12) leaves per cluster) on starch metabolism and accumulation. Starch concentration was significantly higher in canes from 6L (42.13 ± 1.44 mg g DW^-1) and 12L (43.50 ± 2.85 mg g DW^-1) than in 2L (22.72 ± 3.10 mg g DW^-1) plants. Moreover, carbon limitation promoted a transcriptional adjustment of genes involved in starch metabolism in grapevine woody tissues, including a decrease in the expression of the plastidic glucose-6-phosphate translocator, VvGPT1. Contrarily, the transcript levels of the gene coding the catalytic subunit VvAGPB1 of the VvAGPase complex were higher in canes from 2L plants than in 6L and 12L, which positively correlated with the biochemical activity of this enzyme. Sucrose concentration increased in canes from 2L to 6L and 12L plants, and the amount of total phenolics followed the same trend. Expression studies showed that VvSusy transcripts decreased in canes from 2L to 6L and 12L plants, which correlated with the biochemical activity of insoluble invertase, while the expression of the sugar transporters VvSUC11 and VvSUC12, together with VvSPS1, which codes an enzyme involved in sucrose synthesis, increased. Thus, sucrose seems to control starch accumulation through the adjustment of the cane sink strength.

Ripening Transcriptomic Program in Red and White Grapevine Varieties Correlates with Berry Skin Anthocyanin Accumulation

Grapevine (Vitis vinifera) berry development involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptome during berry development, most have focused on a single grapevine variety, so there is a lack of comparative data representing different cultivars. Here, we report, to our knowledge, the first genome-wide transcriptional analysis of 120 RNA samples corresponding to 10 Italian grapevine varieties collected at four growth stages. The 10 varieties, representing five red-skinned and five white-skinned berries, were all cultivated in the same experimental vineyard to reduce environmental variability. The comparison of transcriptional changes during berry formation and ripening allowed us to determine the transcriptomic traits common to all varieties, thus defining the core transcriptome of berry development, as well as the transcriptional dynamics underlying differences between red and white berry varieties. A greater variation among the red cultivars than between red and white cultivars at the transcriptome level was revealed, suggesting that anthocyanin accumulation during berry maturation has a direct impact on the transcriptomic regulation of multiple biological processes. The expression of genes related to phenylpropanoid/flavonoid biosynthesis clearly distinguished the behavior of red and white berry genotypes during ripening but also reflected the differential accumulation of anthocyanins in the red berries, indicating some form of cross talk between the activation of stilbene biosynthesis and the accumulation of anthocyanins in ripening berries.

Whole Plant Temperature Manipulation Affects Flavonoid Metabolism and the Transcriptome of Grapevine Berries

Among environmental factors, temperature is the one that poses serious threats to viticulture in the present and future scenarios of global climate change. In this work, we evaluated the effects on berry ripening of two thermal regimes, imposed from veraison to harvest. Potted vines were grown in two air-conditioned greenhouses with High Temperature (HT) and Low Temperature (LT) regimes characterized by 26 and 21°C as average and 42 and 35°C as maximum air daily temperature, respectively. We conducted analyses of the main berry compositional parameters, berry skin flavonoids and berry skin transcriptome on HT and LT berries sampled during ripening. The two thermal conditions strongly differentiated the berries. HT regime increased sugar accumulation at the beginning of ripening, but not at harvest, when HT treatment contributed to a slight total acidity reduction and pH increase. Conversely, growing temperatures greatly impacted on anthocyanin and flavonol concentrations, which resulted as strongly reduced, while no effects were found on skin tannins accumulation. Berry transcriptome was analyzed with several approaches in order to identify genes with different expression profile in berries ripened under HT or LT conditions. The analysis of whole transcriptome showed that the main differences emerging from this approach appeared to be more due to a shift in the ripening process, rather than to a strong rearrangement at transcriptional level, revealing that the LT temperature regime could delay berry ripening, at least in the early stages. Moreover, the results of the in-depth screening of genes differentially expressed in HT and LT did not highlight differences in the expression of transcripts involved in the biosynthesis of flavonoids (with the exception of PAL and STS) despite the enzymatic activities of PALs and UFGT being significantly higher in LT than HT. This suggests only a partial correlation between molecular and biochemical data in our conditions and the putative existence of post-transcriptional and post-translational mechanisms playing significant roles in the regulation of flavonoid metabolic pathways and in particular of anthocyanins.

Transcriptome analysis of genes involved in anthocyanins biosynthesis and transport in berries of black and white spine grapes (Vitis davidii)

Background

The color of berry skin is an important economic trait for grape and is essentially determined by the components and content of anthocyanins. The fruit color of Chinese wild grapes is generally black, and the profile of anthocyanins in Chinese wild grapes is significantly different from that of Vitis vinifera. However, V. davidii is the only species that possesses white berry varieties among Chinese wild grape species. Thus, we performed a transcriptomic analysis to compare the difference of transcriptional level in black and white V. davidii, in order to find some key genes that are related to anthocyanins accumulation in V. davidii.

Results

The results of anthocyanins detection revealed that 3,5-O-diglucoside anthocyanins is the predominant anthocyanins in V. davidii. It showed obvious differences from V. vinifera in the profile of the composition of anthocyanins. The transcriptome sequencing by Illumina mRNA-Seq technology generated an average of 57 million 100-base pair clean reads from each sample. Differential gene expression analysis revealed thousands of differential expression genes (DEGs) in the pairwise comparison of different fruit developmental stages between and within black and white V. davidii. After the analysis of functional category enrichment and differential expression patterns of DEGs, 46 genes were selected as the candidate genes. Some genes have been reported as being related to anthocyanins accumulation, and some genes were newly found in our study as probably being related to anthocyanins accumulation. We inferred that 3AT (VIT_03s0017g00870) played an important role in anthocyanin acylation, GST4 (VIT_04s0079g00690) and AM2 (VIT_16s0050g00910) played important roles in anthocyanins transport in V. davidii. The expression of some selected DEGs was further confirmed by quantitative real-time PCR (qRT-PCR).

Conclusions

The present study investigated the transcriptomic profiles of berry skin from black and white spine grapes at three fruit developmental stages by Illumina mRNA-Seq technology. It revealed the variety specificity of anthocyanins accumulation in V. davidi at the transcriptional level. The data reported here will provide a valuable resource for understanding anthocyanins accumulation in grapes, especially in V. davidii.

Electronic supplementary material

The online version of this article (doi:10.1186/s41065-016-0021-1) contains supplementary material, which is available to authorized users.

The Terroir Concept Interpreted through Grape Berry Metabolomics and Transcriptomics

Terroir refers to the combination of environmental factors that affect the characteristics of crops such as grapevine (Vitis vinifera) according to particular habitats and management practices. This article shows how certain terroir signatures can be detected in the berry metabolome and transcriptome of the grapevine cultivar Corvina using multivariate statistical analysis. The method first requires an appropriate sampling plan. In this case study, a specific clone of the Corvina cultivar was selected to minimize genetic differences, and samples were collected from seven vineyards representing three different macro-zones during three different growing seasons. An untargeted LC-MS metabolomics approach is recommended due to its high sensitivity, accompanied by efficient data processing using MZmine software and a metabolite identification strategy based on fragmentation tree analysis. Comprehensive transcriptome analysis can be achieved using microarrays containing probes covering ~99% of all predicted grapevine genes, allowing the simultaneous analysis of all differentially expressed genes in the context of different terroirs. Finally, multivariate data analysis based on projection methods can be used to overcome the strong vintage-specific effect, allowing the metabolomics and transcriptomics data to be integrated and analyzed in detail to identify informative correlations.

Impact of cluster thinning on transcriptional regulation of anthocyanin biosynthesis-related genes in 'Summer Black' grapes

Cluster thinning is an agronomic practice that strongly affects anthocyanin biosynthesis in the skin of grape berries. However, the impact of cluster thinning on anthocyanin biosynthesis has not been fully elucidated at the molecular level. Here, we investigated its effects on the berry quality, the biosynthesis of anthocyanins, and the expression levels of related genes from the onset of véraison to harvest in 'Summer Black' grapes. It was observed that the total soluble solid and anthocyanin content in berry skin significantly increased under cluster thinning, whereas the berry weight and titratable acidity showed no differences from the beginning of véraison to harvest. The expression level of most anthocyanin biosynthesis-related genes was significantly up-regulated by cluster thinning from the beginning of véraison and was higher at its end compared to the control. Up-regulation of flavonoid 3',5'-hydroxylase (F3'5'H) and O-methyltransferase (OMT) expression, and down-regulation of flavonoid 3'-hydroxylase (F3'H) expression were observed, which might be the cause of shift in the anthocyanin profile. These findings provide insights into the molecular basis of the relationship between cluster thinning and anthocyanin biosynthesis in the grape berry skin.

The grapevine VviPrx31 peroxidase as a candidate gene involved in anthocyanin degradation in ripening berries under high temperature

Anthocyanin levels decline in some red grape berry varieties ripened under high-temperature conditions, but the underlying mechanism is not yet clear. Here we studied the effects of two different temperature regimes, representing actual Sangiovese (Vitis vinifera L.) viticulture regions, on the accumulation of mRNAs and enzymes controlling berry skin anthocyanins. Potted uniform plants of Sangiovese were kept from veraison to harvest, in two plastic greenhouses with different temperature conditions. The low temperature (LT) conditions featured average and maximum daily air temperatures of 20 and 29 °C, respectively, whereas the corresponding high temperature (HT) conditions were 22 and 36 °C, respectively. The anthocyanin concentration at harvest was much lower in HT berries than LT berries although their profile was similar under both conditions. Under HT conditions, the biosynthesis of anthocyanins was suppressed at both the transcriptional and enzymatic levels, but peroxidase activity was higher. This suggests that the low anthocyanin content of HT berries reflects the combined impact of reduced biosynthesis and increased degradation, particularly the direct role of peroxidases in anthocyanin catabolism. Overexpression of VviPrx31 decreased anthocyanin contents in Petunia hybrida petals under heat stress condition. These data suggest that high temperature can stimulate peroxidase activity thus anthocyanin degradation in ripening grape berries.

New candidate genes for the fine regulation of the colour of grapes

In the last decade, great progress has been made in clarifying the main determinants of anthocyanin accumulation in grape berry skin. However, the molecular details of the fine variation among cultivars, which ultimately contributes to wine typicity, are still not completely understood. To shed light on this issue, the grapes of 170 F1 progeny from the cross 'Syrah'×'Pinot Noir' were characterized at the mature stage for the content of 15 anthocyanins during four growing seasons. This huge data set was used in combination with a dense genetic map to detect genomic regions controlling the anthocyanin pathway both at key enzymatic points and at particular branches. Genes putatively involved in fine tuning the global regulation of anthocyanin biosynthesis were identified by exploring the gene predictions in the QTL (quantitative trait locus) confidence intervals and their expression profile during berry development in offspring with contrasting anthocyanin accumulation. New information on some aspects which had scarcely been investigated so far, such as anthocyanin transport into the vacuole, or completely neglected, such as acylation, is provided. These genes represent a valuable resource in grapevine molecular-based breeding programmes to improve both fruit and wine quality and to tailor wine sensory properties according to consumer demand.

Metabolomic profiling in tomato reveals diel compositional changes in fruit affected by source-sink relationships

A detailed study of the diurnal compositional changes was performed in tomato (Solanum lycopersicum cv. Moneymaker) leaves and fruits. Plants were cultivated in a commercial greenhouse under two growth conditions: control and shaded. Expanding fruits and the closest mature leaves were harvested during two different day/night cycles (cloudy or sunny day). High-throughput robotized biochemical phenotyping of major compounds, as well as proton nuclear magnetic resonance and mass spectrometry metabolomic profiling, were used to measure the contents of about 70 metabolites in the leaves and 60 metabolites in the fruits, in parallel with ecophysiological measurements. Metabolite data were processed using multivariate, univariate, or clustering analyses and correlation networks. The shaded carbon-limited plants adjusted their leaf area, decreased their sink carbon demand and showed subtle compositional modifications. For source leaves, several metabolites varied along a diel cycle, including those directly linked to photosynthesis and photorespiration. These metabolites peaked at midday in both conditions and diel cycles as expected. However, transitory carbon storage was limited in tomato leaves. In fruits, fewer metabolites showed diel fluctuations, which were also of lower amplitude. Several organic acids were among the fluctuating metabolites. Diel patterns observed in leaves and especially in fruits differed between the cloudy and sunny days, and between the two conditions. Relationships between compositional changes in leaves and fruits are in agreement with the fact that several metabolic processes of the fruit appeared linked to its momentary supply of sucrose.

Differential responses of sugar, organic acids and anthocyanins to source-sink modulation in Cabernet Sauvignon and Sangiovese grapevines

Grape berry composition mainly consists of primary and secondary metabolites. Both are sensitive to environment and viticultural management. As a consequence, climate change can affect berry composition and modify wine quality and typicity. Leaf removal techniques can impact berry composition by modulating the source-to-sink balance and, in turn, may mitigate some undesired effects due to climate change. The present study investigated the balance between technological maturity parameters such as sugars and organic acids, and phenolic maturity parameters such as anthocyanins in response to source-sink modulation. Sugar, organic acid, and anthocyanin profiles were compared under two contrasting carbon supply levels in berries of cv. Cabernet Sauvignon and Sangiovese collected at 9 and 14 developmental stages respectively. In addition, whole-canopy net carbon exchange rate was monitored for Sangiovese vines and a mathematic model was used to calculate the balance between carbon fixation and berry sugar accumulation. Carbon limitation affected neither berry size nor the concentration of organic acids at harvest. However, it significantly reduced the accumulation of sugars and total anthocyanins in both cultivars. Most interestingly, carbon limitation decreased total anthocyanin concentration by 84.3% as compared to the non source-limited control, whereas it decreased sugar concentration only by 27.1%. This suggests that carbon limitation led to a strong imbalance between sugars and anthocyanins. Moreover, carbon limitation affected anthocyanin profiles in a cultivar dependent manner. Mathematical analysis of carbon-balance indicated that berries used a higher proportion of fixed carbon for sugar accumulation under carbon limitation (76.9%) than under carbon sufficiency (48%). Thus, under carbon limitation, the grape berry can manage the metabolic fate of carbon in such a way that sugar accumulation is maintained at the expense of secondary metabolites.

Multiomics in grape berry skin revealed specific induction of the stilbene synthetic pathway by ultraviolet-C irradiation

Grape (Vitis vinifera) accumulates various polyphenolic compounds, which protect against environmental stresses, including ultraviolet-C (UV-C) light and pathogens. In this study, we looked at the transcriptome and metabolome in grape berry skin after UV-C irradiation, which demonstrated the effectiveness of omics approaches to clarify important traits of grape. We performed transcriptome analysis using a genome-wide microarray, which revealed 238 genes up-regulated more than 5-fold by UV-C light. Enrichment analysis of Gene Ontology terms showed that genes encoding stilbene synthase, a key enzyme for resveratrol synthesis, were enriched in the up-regulated genes. We performed metabolome analysis using liquid chromatography-quadrupole time-of-flight mass spectrometry, and 2,012 metabolite peaks, including unidentified peaks, were detected. Principal component analysis using the peaks showed that only one metabolite peak, identified as resveratrol, was highly induced by UV-C light. We updated the metabolic pathway map of grape in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and in the KaPPA-View 4 KEGG system, then projected the transcriptome and metabolome data on a metabolic pathway map. The map showed specific induction of the resveratrol synthetic pathway by UV-C light. Our results showed that multiomics is a powerful tool to elucidate the accumulation mechanisms of secondary metabolites, and updated systems, such as KEGG and KaPPA-View 4 KEGG for grape, can support such studies.

Transcriptomic analysis of the late stages of grapevine (Vitis vinifera cv. Cabernet Sauvignon) berry ripening reveals significant induction of ethylene signaling and flavor pathways in the skin

BACKGROUND

Grapevine berry, a nonclimacteric fruit, has three developmental stages; the last one is when berry color and sugar increase. Flavors derived from terpenoid and fatty acid metabolism develop at the very end of this ripening stage. The transcriptomic response of pulp and skin of Cabernet Sauvignon berries in the late stages of ripening between 22 and 37 °Brix was assessed using whole-genome micorarrays.

RESULTS

The transcript abundance of approximately 18,000 genes changed with °Brix and tissue type. There were a large number of changes in many gene ontology (GO) categories involving metabolism, signaling and abiotic stress. GO categories reflecting tissue differences were overrepresented in photosynthesis, isoprenoid metabolism and pigment biosynthesis. Detailed analysis of the interaction of the skin and pulp with °Brix revealed that there were statistically significantly higher abundances of transcripts changing with °Brix in the skin that were involved in ethylene signaling, isoprenoid and fatty acid metabolism. Many transcripts were peaking around known optimal fruit stages for flavor production. The transcript abundance of approximately two-thirds of the AP2/ERF superfamily of transcription factors changed during these developmental stages. The transcript abundance of a unique clade of ERF6-type transcription factors had the largest changes in the skin and clustered with genes involved in ethylene, senescence, and fruit flavor production including ACC oxidase, terpene synthases, and lipoxygenases. The transcript abundance of important transcription factors involved in fruit ripening was also higher in the skin.

CONCLUSIONS

A detailed analysis of the transcriptome dynamics during late stages of ripening of grapevine berries revealed that these berries went through massive transcriptional changes in gene ontology categories involving chemical signaling and metabolism in both the pulp and skin, particularly in the skin. Changes in the transcript abundance of genes involved in the ethylene signaling pathway of this nonclimacteric fruit were statistically significant in the late stages of ripening when the production of transcripts for important flavor and aroma compounds were at their highest. Ethylene transcription factors known to play a role in leaf senescence also appear to play a role in fruit senescence. Ethylene may play a bigger role than previously thought in this non-climacteric fruit.

Transcriptome analysis of ripe and unripe fruit tissue of banana identifies major metabolic networks involved in fruit ripening process

BACKGROUND

Banana is one of the most important crop plants grown in the tropics and sub-tropics. It is a climacteric fruit and undergoes ethylene dependent ripening. Once ripening is initiated, it proceeds at a fast rate making postharvest life short, which can result in heavy economic losses. During the fruit ripening process a number of physiological and biochemical changes take place and thousands of genes from various metabolic pathways are recruited to produce a ripe and edible fruit. To better understand the underlying mechanism of ripening, we undertook a study to evaluate global changes in the transcriptome of the fruit during the ripening process.

RESULTS

We sequenced the transcriptomes of the unripe and ripe stages of banana (Musa accuminata; Dwarf Cavendish) fruit. The transcriptomes were sequenced using a 454 GSFLX-Titanium platform that resulted in more than 7,00,000 high quality (HQ) reads. The assembly of the reads resulted in 19,410 contigs and 92,823 singletons. A large number of the differentially expressed genes identified were linked to ripening dependent processes including ethylene biosynthesis, perception and signalling, cell wall degradation and production of aromatic volatiles. In the banana fruit transcriptomes, we found transcripts included in 120 pathways described in the KEGG database for rice. The members of the expansin and xyloglucan transglycosylase/hydrolase (XTH) gene families were highly up-regulated during ripening, which suggests that they might play important roles in the softening of the fruit. Several genes involved in the synthesis of aromatic volatiles and members of transcription factor families previously reported to be involved in ripening were also identified.

CONCLUSIONS

A large number of differentially regulated genes were identified during banana fruit ripening. Many of these are associated with cell wall degradation and synthesis of aromatic volatiles. A large number of differentially expressed genes did not align with any of the databases and might be novel genes in banana. These genes can be good candidates for future studies to establish their role in banana fruit ripening. The datasets developed in this study will help in developing strategies to manipulate banana fruit ripening and reduce post harvest losses.

A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries

Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated with physiological ripening stages and the transcriptional changes between stages within the ripening programme. In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified, mainly due to the lack of mutants for comparative transcriptomic studies. A feature in grape cluster ripening (Vitis vinifera cv. Pinot noir), where all berries do not initiate the ripening at the same time, was exploited to study their shifted ripening programmes in parallel. Berries that showed marked ripening state differences in a véraison-stage cluster (ripening onset) ultimately reached similar ripeness states toward maturity, indicating the flexibility of the ripening programme. The expression variance between these véraison-stage berry classes, where 11% of the genes were found to be differentially expressed, was reduced significantly toward maturity, resulting in the synchronization of their transcriptional states. Defined quantitative expression changes (transcriptional distances) not only existed between the véraison transitional stages, but also between the véraison to maturity stages, regardless of the berry class. It was observed that lagging berries complete their transcriptional programme in a shorter time through altered gene expressions and ripening-related hormone dynamics, and enhance the rate of physiological ripening progression. Finally, the reduction in expression variance of genes can identify new genes directly associated with ripening and also assess the relevance of gene activity to the phase of the ripening programme.

Crop management impacts the efficiency of quantitative trait loci (QTL) detection and use: case study of fruit load×QTL interactions

Mapping studies using populations with introgressed marker-defined genomic regions are continuously increasing knowledge about quantitative trait loci (QTL) that correlate with variation in important crop traits. This knowledge is useful for plant breeding, although combining desired traits in one genotype might be complicated by the mode of inheritance and co-localization of QTL with antagonistic effects, and by physiological trade-offs, and feed-back or feed-forward mechanisms. Therefore, integrating advances at the genetic level with insight into influences of environment and crop management on crop performance remains difficult. Whereas mapping studies can pinpoint correlations between QTL and phenotypic traits for specific conditions, ignoring or overlooking the importance of environment or crop management can jeopardize the relevance of such assessments. Here, we focus on fruit load (a measure determining competition among fruits on one plant) and its strong modulation of QTL effects on fruit size and composition. Following an integral approach, we show which fruit traits are affected by fruit load, to which underlying processes these traits can be linked, and which processes at lower and higher integration levels are affected by fruit load (and subsequently influence fruit traits). This opinion paper (i) argues that a mechanistic framework to interpret interactions between fruit load and QTL effects is needed, (ii) pleads for consideration of the context of agronomic management when detecting QTL, (iii) makes a case for incorporating interacting factors in the experimental set-up of QTL mapping studies, and (iv) provides recommendations to improve efficiency in QTL detection and use, with particular focus on model-based marker-assisted breeding.

VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine)

Background

Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera.

Description

The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis) whereby the recovered sub-networks reconfirm established plant gene functions and also identify novel associations.

Conclusions

Together, we present valuable insights into grapevine transcriptional regulation by developing network models applicable to researchers in their prioritisation of gene candidates, for on-going study of biological processes related to grapevine development, metabolism and stress responses.

iTRAQ-based quantitative proteomics of developing and ripening muscadine grape berry

Grapes are among the widely cultivated fruit crops in the world. Grape berries like other nonclimacteric fruits undergo a complex set of dynamic, physical, physiological, and biochemical changes during ripening. Muscadine grapes are widely cultivated in the southern United States for fresh fruit and wine. To date, changes in the metabolites composition of muscadine grapes have been well documented; however, the molecular changes during berry development and ripening are not fully known. The aim of this study was to investigate changes in the berry proteome during ripening in muscadine grape cv. Noble. Isobaric tags for relative and absolute quantification (iTRAQ) MS/MS was used to detect statistically significant changes in the berry proteome. A total of 674 proteins were detected, and 76 were differentially expressed across four time points in muscadine berry. Proteins obtained were further analyzed to provide information about its potential functions during ripening. Several proteins involved in abiotic and biotic stimuli and sucrose and hexose metabolism were upregulated during berry ripening. Quantitative real-time PCR analysis validated the protein expression results for nine proteins. Identification of vicilin-like antimicrobial peptides indicates additional disease tolerance proteins are present in muscadines for berry protection during ripening. The results provide new information for characterization and understanding muscadine berry proteome and grape ripening.

Hormonal and metabolic regulation of source-sink relations under salinity and drought: from plant survival to crop yield stability

Securing food production for the growing population will require closing the gap between potential crop productivity under optimal conditions and the yield captured by farmers under a changing environment, which is termed agronomical stability. Drought and salinity are major environmental factors contributing to the yield gap ultimately by inducing premature senescence in the photosynthetic source tissues of the plant and by reducing the number and growth of the harvestable sink organs by affecting the transport and use of assimilates between and within them. However, the changes in source-sink relations induced by stress also include adaptive changes in the reallocation of photoassimilates that influence crop productivity, ranging from plant survival to yield stability. While the massive utilization of -omic technologies in model plants is discovering hundreds of genes with potential impacts in alleviating short-term applied drought and salinity stress (usually measured as plant survival), only in relatively few cases has an effect on crop yield stability been proven. However, achieving the former does not necessarily imply the latter. Plant survival only requires water status conservation and delayed leaf senescence (thus maintaining source activity) that is usually accompanied by growth inhibition. However, yield stability will additionally require the maintenance or increase in sink activity in the reproductive structures, thus contributing to the transport of assimilates from the source leaves and to delayed stress-induced leaf senescence. This review emphasizes the role of several metabolic and hormonal factors influencing not only the source strength, but especially the sink activity and their inter-relations, and their potential to improve yield stability under drought and salinity stresses.

Selective defoliation affects plant growth, fruit transcriptional ripening program and flavonoid metabolism in grapevine

BACKGROUND

The selective removal of grapevine leaves around berry clusters can improve the quality of ripening fruits by influencing parameters such as the berry sugar and anthocyanin content at harvest. The outcome depends strongly on the timing of defoliation, which influences the source-sink balance and the modified microclimate surrounding the berries. We removed the basal leaves from Vitis vinifera L. cv Sangiovese shoots at the pre-bloom and veraison stages, and investigated responses such as shoot growth, fruit morphology and composition compared to untreated controls. Moreover, we performed a genome-wide expression analysis to explore the impact of these defoliation treatments on berry transcriptome.

RESULTS

We found that pre-bloom defoliation improved berry quality traits such as sugar and anthocyanin content, whereas defoliation at veraison had a detrimental effect, e.g. less anthocyanin and higher incidence of sunburn damage. Genome-wide expression analysis during berry ripening revealed that defoliation at either stage resulted in major transcriptome reprogramming, which slightly delayed the onset of ripening. However, a closer investigation of individual gene expression profiles identified genes that were specifically modulated by defoliation at each stage, reflecting the uncoupling of metabolic processes such as flavonoid biosynthesis, cell wall and stress metabolism, from the general ripening program.

CONCLUSIONS

The specific transcriptional modifications we observed following defoliation at different time points allow the identification of the developmental or metabolic processes affected in berries thus deepening the knowledge of the mechanisms by which these agronomical practices impact the final berry ripening traits.

Transcriptome analysis at four developmental stages of grape berry (Vitis vinifera cv. Shiraz) provides insights into regulated and coordinated gene expression

Background

Vitis vinifera berry development is characterised by an initial phase where the fruit is small, hard and acidic, followed by a lag phase known as veraison. In the final phase, berries become larger, softer and sweeter and accumulate an array of organoleptic compounds. Since the physiological and biochemical makeup of grape berries at harvest has a profound impact on the characteristics of wine, there is great interest in characterising the molecular and biophysical changes that occur from flowering through veraison and ripening, including the coordination and temporal regulation of metabolic gene pathways. Advances in deep-sequencing technologies, combined with the availability of increasingly accurate V. vinifera genomic and transcriptomic data, have enabled us to carry out RNA-transcript expression analysis on a global scale at key points during berry development.

Results

A total of 162 million 100-base pair reads were generated from pooled Vitis vinifera (cv. Shiraz) berries sampled at 3-weeks post-anthesis, 10- and 11-weeks post-anthesis (corresponding to early and late veraison) and at 17-weeks post-anthesis (harvest). Mapping reads from each developmental stage (36-45 million) onto the NCBI RefSeq transcriptome of 23,720 V. vinifera mRNAs revealed that at least 75% of these transcripts were detected in each sample. RNA-Seq analysis uncovered 4,185 transcripts that were significantly upregulated at a single developmental stage, including 161 transcription factors. Clustering transcripts according to distinct patterns of transcription revealed coordination in metabolic pathways such as organic acid, stilbene and terpenoid metabolism. From the phenylpropanoid/stilbene biosynthetic pathway at least 46 transcripts were upregulated in ripe berries when compared to veraison and immature berries, and 12 terpene synthases were predominantly detected only in a single sample. Quantitative real-time PCR was used to validate the expression pattern of 12 differentially expressed genes from primary and secondary metabolic pathways.

Conclusions

In this study we report the global transcriptional profile of Shiraz grapes at key stages of development. We have undertaken a comprehensive analysis of gene families contributing to commercially important berry characteristics and present examples of co-regulation and differential gene expression. The data reported here will provide an invaluable resource for the on-going molecular investigation of wine grapes.

Berry flesh and skin ripening features in Vitis vinifera as assessed by transcriptional profiling

Background

Ripening of fleshy fruit is a complex developmental process involving the differentiation of tissues with separate functions. During grapevine berry ripening important processes contributing to table and wine grape quality take place, some of them flesh- or skin-specific. In this study, transcriptional profiles throughout flesh and skin ripening were followed during two different seasons in a table grape cultivar ‘Muscat Hamburg’ to determine tissue-specific as well as common developmental programs.

Methodology/Principal Findings

Using an updated GrapeGen Affymetrix GeneChip® annotation based on grapevine 12×v1 gene predictions, 2188 differentially accumulated transcripts between flesh and skin and 2839 transcripts differentially accumulated throughout ripening in the same manner in both tissues were identified. Transcriptional profiles were dominated by changes at the beginning of veraison which affect both pericarp tissues, although frequently delayed or with lower intensity in the skin than in the flesh. Functional enrichment analysis identified the decay on biosynthetic processes, photosynthesis and transport as a major part of the program delayed in the skin. In addition, a higher number of functional categories, including several related to macromolecule transport and phenylpropanoid and lipid biosynthesis, were over-represented in transcripts accumulated to higher levels in the skin. Functional enrichment also indicated auxin, gibberellins and bHLH transcription factors to take part in the regulation of pre-veraison processes in the pericarp, whereas WRKY and C2H2 family transcription factors seems to more specifically participate in the regulation of skin and flesh ripening, respectively.

Conclusions/Significance

A transcriptomic analysis indicates that a large part of the ripening program is shared by both pericarp tissues despite some components are delayed in the skin. In addition, important tissue differences are present from early stages prior to the ripening onset including tissue-specific regulators. Altogether, these findings provide key elements to understand berry ripening and its differential regulation in flesh and skin.