Transcriptomic and metabolite analyses of Cabernet Sauvignon grape berry development

Volatilomics of Cabernet Sauvignon grapes and sensory perception of wines are affected by canopy side in vineyards with different row orientations

This study aimed to clarify how microclimate diversity altered volatilomics in Cabernet Sauvignon grapes and wines. Four row-oriented vineyards were selected, and metabolites of grapes and wines were determined from separate canopy sides. Results showed that shaded sides received 59% of the solar radiation and experienced 55% of the high-temperature days compared to the exposed sides on average. Grape primary metabolites were slightly affected by the canopy side. Herbaceous aromas were consistently more abundant in grapes and wines from shaded clusters. Heat-stressed canopy sides accelerated terpenoid loss and increased norisoprenoid levels in grapes, while β-damascenone in north-side wines was 13%-32% higher than that in south-side wines of the east-west vineyard. The northeast-southwest vineyard showed the most notable variation in taste and aroma sensory scores, with four parameters significantly different. There were 32 aroma series identified in wines, and banana, pineapple, and strawberry odors were highly correlated with aroma sensory score.

Abscisic acid and ethylene coordinating fruit ripening under abiotic stress

Fleshy fruit metabolism is intricately influenced by environmental changes, yet the hormonal regulations underlying these responses remain poorly elucidated. ABA and ethylene, pivotal in stress responses across plant vegetative tissues, play crucial roles in triggering fleshy fruit ripening. Their actions are intricately governed by complex mechanisms, influencing key aspects such as nutraceutical compound accumulation, sugar content, and softening parameters. Both hormones are essential orchestrators of significant alterations in fruit development in response to stressors like drought, salt, and temperature fluctuations. These alterations encompass colour development, sugar accumulation, injury mitigation, and changes in cell-wall degradation and ripening progression. This review provides a comprehensive overview of recent research progress on the roles of ABA and ethylene in responding to drought, salt, and temperature stress, as well as the molecular mechanisms controlling ripening in environmental cues. Additionally, we propose further studies aimed at genetic manipulation of ABA and ethylene signalling, offering potential strategies to enhance fleshy fruit resilience in the face of future climate change scenarios.

Regulatory mechanism of GA3 application on grape (Vitis vinifera L.) berry size

Gibberellin A3 (GA3) is often used as a principal growth regulator to increase plant size. Here, we applied Tween-20 (2%)-formulated GA3 (T1:40 mg/L; T2:70 mg/L) by dipping the clusters at the initial expansion phase of 'Red Globe' grape (Vitis vinifera L.) in 2018 and 2019. Tween-20 (2%) was used as a control. The results showed that GA3 significantly increased fruit cell length, cell size, diameter, and volume. The hormone levels of auxin (IAA) and zeatin (ZT) were significantly increased at 2 h (0 d) -1 d after application (DAA0-1) and remained significantly higher at DAA1 until maturity. Conversely, ABA exhibited an opposite trend. The mRNA and non-coding sequencing results yielded 436 differentially expressed mRNA (DE_mRNAs), 79 DE_lncRNAs and 17 DE_miRNAs. These genes are linked to hormone pathways like cysteine and methionine metabolism (ko00270), glutathione metabolism (ko00480) and plant hormone signal transduction (ko04075). GA3 application reduced expression of insensitive dwarf 2 (GID2, VIT_07s0129g01000), small auxin-upregulated RNA (SAUR, VIT_08s0007g03120) and 1-aminocyclopropane-1-carboxylate synthase (ACS, VIT_18s0001g08520), but increased SAUR (VIT_04s0023g00560) expression. These four genes were predicted to be negatively regulated by vvi-miR156, vvi-miR172, vvi-miR396, and vvi-miR159, corresponding to specific lncRNAs. Therefore, miRNAs could affect grape size by regulating key genes GID2, ACS and SAUR. The R2R3 MYB family member VvRAX2 (VIT_08s0007g05030) was upregulated in response to GA3 application. Overexpression of VvRAX2 in tomato transgenic lines increased fruit size in contrast to the wild type. This study provides a basis and genetic resources for elucidating the novel role of ncRNAs in fruit development.

Ethylene biosynthesis and signal transduction during ripening and softening in non-climacteric fruits: an overview

In recent years, the ethylene-mediated ripening and softening of non-climacteric fruits have been widely mentioned. In this paper, recent research into the ethylene-mediated ripening and softening of non-climacteric fruits is summarized, including the involvement of ethylene biosynthesis and signal transduction. In addition, detailed studies on how ethylene interacts with other hormones to regulate the ripening and softening of non-climacteric fruits are also reviewed. These findings reveal that many regulators of ethylene biosynthesis and signal transduction are linked with the ripening and softening of non-climacteric fruits. Meanwhile, the perspectives of future research on the regulation of ethylene in non-climacteric fruit are also proposed. The overview of the progress of ethylene on the ripening and softening of non-climacteric fruit will aid in the identification and characterization of key genes associated with ethylene perception and signal transduction during non-climacteric fruit ripening and softening.

Berry shrivel in grapevine: a review considering multiple approaches

Grapevine berry shrivel, a ripening disorder, causes significant economic losses in the worldwide wine and table grape industries. An early interruption in ripening leads to this disorder, resulting in shriveling and reduced sugar accumulation affecting yield and fruit quality. Loss of sink strength associated with berry mesocarp cell death is an early symptom of this disorder; however, potential internal or external triggers are yet to be explored. No pathogens have been identified that might cause the ripening syndrome. Understanding the underlying causes and mechanisms contributing to berry shrivel is crucial for developing effective mitigation strategies and finding solutions for other ripening disorders associated with climacteric and non-climacteric fruits. This review discusses alterations in the fruit ripening mechanism induced by berry shrivel disorder, focusing primarily on sugar transport and metabolism, cell wall modification and cell death, and changes in the phytohormone profile. The essential open questions are highlighted and analyzed, thus identifying the critical knowledge gaps and key challenges for future research.

Proteomic and Low-Polar Metabolite Profiling Reveal Unique Dynamics in Fatty Acid Metabolism during Flower and Berry Development of Table Grapes

Grapevine development and ripening are complex processes that involve several biochemical pathways, including fatty acid and lipid metabolism. Fatty acids are essential components of lipids, which play crucial roles in fruit maturation and flavor development. However, the dynamics of fatty acid metabolism in grape flowers and berries are poorly understood. In this study, we present those dynamics and investigate the mechanisms of fatty acid homeostasis on 'Thompson Seedless' berries using metabolomic and proteomic analyses. Low-polar metabolite profiling indicated a higher abundance of fatty acids at the pre-flowering and pre-veraison stages. Proteomic analyses revealed that grape flowers and berries display unique profiles of proteins involved in fatty acid biosynthesis, triacylglycerol assembly, fatty acid β-oxidation, and lipid signaling. These findings show, for the first time, that fatty acid metabolism also plays an important role in the development of non-oil-rich tissues, opening new perspectives about lipid function and its relation to berry quality.

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

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

Proteomic and metabolomic integration reveals the effects of pre-flowering cytokinin applications on central carbon metabolism in table grape berries

Consumers around the world prefer high quality table grapes. To achieve higher quality traits at ripening, grapevine producers apply different plant growth regulators. The synthetic cytokinin forchlorfenuron N-(2-chloro-4-pyridinyl)-N'-phenylurea (CPPU) is widely used, its effect on grape quality is poorly understood. We hypothesized that the use of CPPU in pre-flowering can lead to changes in the metabolism that affects grape quality at harvest. Therefore, we investigated the role of CPPU applications on the quality of grapes by integrating proteomics and metabolomics. CPPU-treated grapevines showed a significant increase in berry size and firmness. Proteomic analyses indicated that CPPU-treated berries accumulated enzymes associated with carbohydrate metabolism, glycolysis, and tricarboxylic acid (TCA) cycle at harvest. Metabolomic analyses showed shifts in the abundance of compounds associated with carbohydrate metabolism and TCA cycle in CPPU-treated grapes. These findings suggest that CPPU applications modulate central carbon metabolism, improving grape berry quality.

Bunch microclimate influence amino acids and phenolic profiles of Pinot noir grape berries

Introduction

The increase of temperature due to climate change at different phenological stages of grapevine has already been demonstrated to affect accumulation of primary and secondary metabolites in grape berries. This has a significant implication for Pinot noir especially in New Zealand context as these compounds can have direct and indirect effects on wine quality.

Methods

This study investigates how varying bunch microclimate through changes in temperature applied at veraison stage can affect: fresh weight, total soluble solids, the accumulation of anthocyanins, total phenolics and amino acids of the grape berries. This was studied over two growing seasons (2018/19 and 2019/20) with Pinot noir vines being grown at two different temperatures in controlled environment (CE) chambers. The vines were exposed to 800 µmol/m2/s irradiance with diurnal changes in day (22°C or 30°C) and night (15°C) temperatures. This experimental set up enabled us to determine the accumulation of these metabolite at harvest (both seasons) and throughout berry development (second season).

Results and discussion

The results showed that berry weight was not influenced by temperature increase. The total soluble solids (TSS) were significantly increased at 30°C, however, this was not at the expense of berry weight (i.e., water loss). Anthocyanin content was reduced at higher temperature in the first season but there was no change in phenolic content in response to temperature treatments in either season. The concentrations of total amino acids at harvest increased in response to the higher temperature in the second season only. In addition, in the time course analysis of the second season, the accumulation of amino acids was increased at mid-ripening and ripening stage with the increased temperature. Significant qualitative changes in amino acid composition specifically the α-ketoglutarate family (i.e., glutamine, arginine, and proline) were found between the two temperatures.

Significance

This study is the first to provide detailed analysis and quantification of individual amino acids and phenolics in Pinot noir in response to changes in temperature applied at veraison which could aid to develop adaptation strategies for viticulture in the future.

Modulation of the Berry Skin Transcriptome of cv. Tempranillo Induced by Water Stress Levels

Climate change in the Mediterranean area is making summers warmer and dryer. Grapevine (Vitis vinifera L.) is mostly important for wine production in Mediterranean countries, and the variety Tempranillo is one of the most cultivated in Spain and Portugal. Drought decreases yield and quality and causes important economic losses. As full irrigation has negative effects on quality and water is scarce in this region, deficit irrigation is often applied. In this research, we studied the effects of two deficit irrigation treatments, Sustained Deficit Irrigation (SDI) and Regulated Deficit Irrigation (RDI), on the transcriptome of grape berries at full maturation, through RNAseq. The expression of differentially regulated genes (DEGs) was also monitored through RT-qPCR along berry development. Most transcripts were regulated by water stress, with a similar distribution of up- and down-regulated transcripts within functional categories (FC). Primary metabolism was the more severely affected FC under water stress, followed by signaling and transport. Almost all DEGs monitored were significantly up-regulated by severe water stress at veraison. The modulation of an auxin response repression factor, AUX22D, by water stress indicates a role of this gene in the response to drought. Further, the expression of WRKY40, a TF that regulates anthocyanin biosynthesis, may be responsible for changes in grape quality under severe water stress.

Comparative transcriptomic profiling of peach and nectarine cultivars reveals cultivar-specific responses to chilled postharvest storage

INTRODUCTION

Peach (Prunus persica (L.) Batsch,) and nectarine fruits (Prunus persica (L.) Batsch, var nectarine), are characterized by a rapid deterioration at room temperature. Therefore, cold storage is widely used to delay fruit post-harvest ripening and extend fruit commercial life. Physiological disorders, collectively known as chilling injury, can develop typically after 3 weeks of low-temperature storage and affect fruit quality.

METHODS

A comparative transcriptomic analysis was performed to identify regulatory pathways that develop before chilling injury symptoms are detectable using next generation sequencing on the fruits of two contrasting cultivars, one peach (Sagittaria) and one nectarine, (Big Top), over 14 days of postharvest cold storage.

RESULTS

There was a progressive increase in the number of differentially expressed genes between time points (DEGs) in both cultivars. More (1264) time point DEGs were identified in 'Big Top' compared to 'Sagittaria' (746 DEGs). Both cultivars showed a downregulation of pathways related to photosynthesis, and an upregulation of pathways related to amino sugars, nucleotide sugar metabolism and plant hormone signal transduction with ethylene pathways being most affected. Expression patterns of ethylene related genes (including biosynthesis, signaling and ERF transcription factors) correlated with genes involved in cell wall modification, membrane composition, pathogen and stress response, which are all involved later during storage in development of chilling injury.

DISCUSSION

Overall, the results show that common pathways are activated in the fruit of 'Big Top' nectarine and 'Sagittaria' peach in response to cold storage but include also differences that are cultivar-specific responses.

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.

Molecular and physiologic mechanisms of advanced ripening by trunk girdling at early veraison of 'Summer Black' grape

Although the effects of girdling on grape berry development have been widely studied, the underlying mechanisms are poorly understood, especially at the molecular level. This study investigated the effect of trunk girdling on grape (Vitis L.) berry maturation. Girdling was performed on 5-year-old 'Summer Black' grapevines at early veraison, and transcriptional and physiologic analyses were performed. Trunk girdling promoted sugar accumulation and color development in berries and accelerated berry ripening by 25 days. Genes related to sucrose cleavage and polysaccharide degradation were upregulated at the transcriptional level, which was associated with increased monosaccharide accumulation and berry softening. Anthocyanin biosynthesis and accumulation were also enhanced by trunk girdling through the upregulation of anthocyanin biosynthesis genes including phenylalanine ammonia-lyase and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT). The increased expression of two VvUFGT genes was accompanied by the upregulation of VvMYBA2 under girdling. The upregulation of genes involved in ethylene biosynthesis and hormone (abscisic acid and brassinosteroid) responses and downregulation of genes involved in indoleacetic acid biosynthesis and response may have also promoted berry ripening in the girdling group. A total of 120 differentially expressed transcription factor genes from 29 gene families including MYB, ERF, and MYB-related were identified in the girdling group, which may participate in the regulation of berry development and ripening. These results provide molecular-level insight into the positive effects of trunk girdling on berry development in grapes.

Regulated deficit irrigation: an effective way to solve the shortage of agricultural water for horticulture

The deficient agricultural water caused by water shortage is a crucial limiting factor of horticultural production. Among many agricultural water-saving technologies, regulated deficit irrigation (RDI) has been proven to be one of the effective technologies to improve water use efficiency and reduce water waste on the premise of maintaining the quality of agricultural products. RDI was first reported more than 40 years ago, although it has been applied in some areas, little is known about understanding of the implementation method, scope of application and detailed mechanism of RDI, resulting in the failure to achieve the effect that RDI should have. This review refers to the research on RDI in different crops published in recent years, summarizes the definition, equipment condition, function, theory illumination, plant response and application in different crops of RDI, and looks forward to its prospect. We expect that this review will provide valuable guidance for researchers and producers concerned, and support the promotion of RDI in more horticultural crops.

Impact of hormone applications on ripening-related metabolites in Gewürztraminer grapes (Vitis vinifera L.): The key role of jasmonates in terpene modulation

Terpenes play a formative role in grape and wine flavor, particularly for high-terpenic cultivars. Differences in terpene profiles influence grape varietal character and vintage quality. Little is known about the endogenous factors controlling terpene biosynthesis in grape. Through multiple experiments, six hormones (abscisic acid, ABA; ethylene, ETH; jasmonic acid, JA; methyl jasmonate, MeJA; indole-3-acetic acid, IAA; 1-naphthaleneacetic acid, NAA) that either promote or repress ripening were applied to Gewürztraminer clusters near veraison to gauge their effect on ripening and terpene biosynthesis. Jasmonates (JA, MeJA) increased terpene concentrations and the expression of terpene genes in grapes. Such increases were not associated to increases of other ripening-related metabolites such as sugars or anthocyanins. MeJA also affected the expression of several hormone related genes, increased IAA levels, and reduced sugar and anthocyanin concentration in grapes. This research provides novel insights into terpene regulation by ripening-related hormones and jasmonates in grapes.

Grafting with rootstocks promotes phenolic compound accumulation in grape berry skin during development based on integrative multi-omics analysis

In viticulture, grafting has been practiced widely and influences grape development as well as berry and wine quality. However, there is limited understanding of the effects of rootstocks on grape phenolic compounds, which are located primarily in the berry skin and contribute to certain sensory attributes of wine. In this study, scion-rootstock interactions were investigated at the green-berry stage and the veraison stage when grapevines were hetero-grafted with three commonly used rootstock genotypes (5BB, 101-14MG, and SO4). Physiological investigations showed that hetero-grafts, especially CS/5BB, contained higher concentrations of total proanthocyanidins (PAs) and various PA components in berry skins compared with the auto-grafted grapevines. Further metabolomics analysis identified 105 differentially accumulated flavonoid compounds, the majority of which, including anthocyanins, PAs, and flavonols, were significantly increased in the berry skins of hetero-grafted grapevines compared with auto-grafted controls. In addition, transcriptomic analysis of the same samples identified several thousand differentially expressed genes between hetero-grafted and auto-grafted vines. The three rootstocks not only increased the transcript levels of stilbene, anthocyanin, PA, and flavonol synthesis genes but also affected the expression of numerous transcription factor genes. Taken together, our results suggest that hetero-grafting can promote phenolic compound accumulation in grape berry skin during development. These findings provide new insights for improving the application value of grafting by enhancing the accumulation of nutritious phenolic components in grape.

The Effect of Irrigation-Initiation Timing on the Phenolic Composition and Overall Quality of Cabernet Sauvignon Wines Grown in a Semi-Arid Climate

In semi-arid areas, vineyards grown for winemaking are usually mildly irrigated by drip irrigation systems in a manner maintaining drought stress. This practice ensures the proper development of vegetative and reproductive organs on the one hand, and on the other, the development of high-quality grapes which can be hampered by overly abundant water application. In previous work, we have developed and demonstrated an irrigation model suitable for high-quality grape production in semi-arid areas. Here, we tackle the question of proper irrigation initiation dates—should one wait for vines to develop drought stress before the initiation of irrigation, or rather commence irrigation earlier? Our results show that vines which undergo initial irrigation late in the growing season tend to develop a lower midday stem water potential even after irrigation initiation. In addition, these vines tend to produce a lower number of bunches per vine and smaller berry size, leading to lower yields. The wine produced from the late-irrigated treatments had a higher phenolic content, primarily due to higher levels of catechin and epicatechin. Their levels increased as irrigation initiation dates were delayed, while caffeic acid levels showed an opposite trend. Late irrigation also led to higher color intensities compared to those of irrigation at earlier stages, due to higher levels of most anthocyanins. Finally, we show that the overall wine sensory score, representing its overall quality, was approximately five points higher for wines made from delayed irrigation treatments compared to wines made from early season irrigation treatments.

Stable QTL for malate levels in ripe fruit and their transferability across Vitis species

Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%), and based on two and five years of data, respectively, their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.

Transcriptomic Analysis of Root Restriction Effects on the Primary Metabolites during Grape Berry Development and Ripening

Root restriction (RR) has been reported to enhance grape berry quality in diverse aspects of grape life. In this study, RR-induced increases in the main primary metabolites in the grape berry and the expression of their related genes were studied at different developmental stages. Mainly the transcriptomic and metabolomic level were analyzed using ‘Summer Black’ grape berry as a material. The main results were as follows: A total of 11 transcripts involved in the primary metabolic pathways were significantly changed by the RR treatment. Metabolites such as sugars, organic acids, amino acids, starch, pectin, and cellulose were qualitatively and quantitatively analyzed along with their metabolic pathways. Sucrose synthase (VIT_07s0005g00750, VIT_11s0016g00470) and sucrose phosphate synthase (VIT_18s0089g00410) were inferred to play critical roles in the accumulation of starch, sucrose, glucose, and fructose, which was induced by the RR treatment. RR treatment also promoted the malic acid and tartaric acid accumulation in the young berry. In addition, the grape berries after the RR treatment tended to have lower pectin and cellulose content.

Effects of Different Treatments on Physicochemical Characteristics of ‘Kyoho’ Grapes during Storage at Low Temperature

Low temperature storage is widely used to maintain the postharvest quality of table grape. However, grape clusters easily undergo deterioration without treatment during the storage time. The main goal of this study was to evaluate the effect of postharvest 1-methylcyclopropene (1-MCP), calcium chloride (1%) and ethanol (16%), and the combination of 1-MCP with calcium chloride and ethanol treatments on maintenance of quality of table grapes ‘Kyoho’ (Vitis vinifera × Vitis labrusca) under 5 °C and 0 °C storage. Changes in decay incidence, weight loss, rachis browning and quality indexes of grape clusters were investigated. The results were as follows: all treatments significantly reduced the decay incidence, weight loss, rachis browning at both low temperatures storage; 1-MCP had positive effect for reducing the decay incidence in early stage, but no effect in late stage; there are no significant variations of taste and color quality indexes under two low temperatures storage, regardless of the treatments. Overall findings suggested that the combination of 1-MCP with calcium chloride and ethanol treatment is suitable for short-term 0 °C storage, while for long-term 0 °C storage, calcium chloride (1%) and ethanol (16%) treatment should be selected.

A proteomic analysis shows the stimulation of light reactions and inhibition of the Calvin cycle in the skin chloroplasts of ripe red grape berries

The role of photosynthesis in fruits still challenges scientists. This is especially true in the case of mature grape berries of red varieties lined by an anthocyanin-enriched exocarp (skin) almost impermeable to gases. Although chlorophylls are degraded and replaced by carotenoids in several fruits, available evidence suggests that they may persist in red grapes at maturity. In the present study, chloroplasts were isolated from the skin of red grape berries (cv. Vinhão) to measure chlorophyll levels and the organelle proteome. The results showed that chloroplasts (and chlorophylls) are maintained in ripe berries masked by anthocyanin accumulation and that the proteome of chloroplasts from green and mature berries is distinct. Several proteins of the light reactions significantly accumulated in chloroplasts at the mature stage including those of light-harvesting complexes of photosystems I (PSI) and II (PSII), redox chain, and ATP synthase, while chloroplasts at the green stage accumulated more proteins involved in the Calvin cycle and the biosynthesis of amino acids, including precursors of secondary metabolism. Taken together, results suggest that although chloroplasts are more involved in biosynthetic reactions in green berries, at the mature stage, they may provide ATP for cell maintenance and metabolism or even O2 to feed the respiratory demand of inner tissues.

Secondary Metabolites Coordinately Protect Grapes from Excessive Light and Sunburn Damage during Development

Sunburn is a physiological disorder that reduces grape quality and vineyard yield. It is the result of excessive sunlight and high temperatures. As climate change continues to increase air temperatures, reports of sunburn damage in vineyards worldwide are becoming more frequent. Grapes produce secondary metabolites (carotenoids, polyphenols and aroma compounds) to counter photooxidative stress and acclimate to higher radiation environments. This study evaluated changes in these compounds in during ripening when grapes were exposed post-flowering (ED) and at véraison (LD), and compared them to a nondefoliated control (ND). ND contained more α-terpineol and violaxanthin, and the defoliated treatments contained more zeaxanthin, β-carotene, C₆ compounds and flavonoids. ED berries adapted better to higher-light environments, displayed larger changes in secondary metabolite concentrations and lower levels of sunburn damage than LD berries did. The composition of berries with increasing sunburn damage was evaluated for the first time. Berries with no damage had the lowest concentrations of flavonoids and oxidized glutathione, and the highest concentrations of chlorophyll and α-terpineol. As damage increased, destruction of photosynthetic pigments, increase in polyphenols and loss of aroma compounds were evidenced. A significant effect of temperature and developmental stage on grape composition was also observed. This study provides a holistic overview of changes in secondary metabolites experienced by grape berries when exposed to excessive light, how these vary along development and how they affect sunburn incidence.

Mitigating Grapevine Red Blotch Virus Impact on Final Wine Composition

Grapevine red blotch virus (GRBV), the causative agent of red blotch disease, causes significant decreases in sugar and anthocyanin accumulation in grapes, suggesting a delay in ripening events. Two mitigation strategies were investigated to alleviate the impact of GRBV on wine composition. Wines were made from Cabernet Sauvignon (CS) (Vitis vinifera) grapevines, grafted onto 110R and 420A rootstocks, in 2016 and 2017. A delayed harvest and chaptalization of diseased grapes were employed to decrease chemical and sensory impacts on wines caused by GRBV. Extending the ripening of the diseased fruit produced wines that were overall higher in aroma compounds such as esters and terpenes and alcohol-related (hot and alcohol) sensory attributes compared to wines made from diseased fruit harvested at the same time as healthy fruit. In 2016 only, a longer hangtime of GRBV infected fruit resulted in wines with increased anthocyanin concentrations compared to wines made from GRBV diseased fruit that was harvested at the same time as healthy fruit. Chaptalization of the diseased grapes in 2017 produced wines chemically more similar to wines made from healthy fruit. However, this was not supported by sensory analysis, potentially due to high alcohol content masking aroma characteristics.

Alternative splicing regulation appears to play a crucial role in grape berry development and is also potentially involved in adaptation responses to the environment

BACKGROUND

Alternative splicing (AS) produces transcript variants playing potential roles in proteome diversification and gene expression regulation. AS modulation is thus essential to respond to developmental and environmental stimuli. In grapevine, a better understanding of berry development is crucial for implementing breeding and viticultural strategies allowing adaptation to climate changes. Although profound changes in gene transcription have been shown to occur in the course of berry ripening, no detailed study on splicing modifications during this period has been published so far. We report here on the regulation of gene AS in developing berries of two grapevine (Vitis vinifera L.) varieties, Gewurztraminer (Gw) and Riesling (Ri), showing distinctive phenotypic characteristics. Using the software rMATS, the transcriptomes of berries at four developmental steps, from the green stage to mid-ripening, were analysed in pairwise comparisons between stages and varieties.

RESULTS

A total of 305 differential AS (DAS) events, affecting 258 genes, were identified. Interestingly, 22% of these AS events had not been reported before. Among the 80 genes that underwent the most significant variations during ripening, 22 showed a similar splicing profile in Gw and Ri, which suggests their involvement in berry development. Conversely, 23 genes were subjected to splicing regulation in only one variety. In addition, the ratios of alternative isoforms were different in Gw and Ri for 35 other genes, without any change during ripening. This last result indicates substantial AS differences between the two varieties. Remarkably, 8 AS events were specific to one variety, due to the lack of a splice site in the other variety. Furthermore, the transcription rates of the genes affected by stage-dependent splicing regulation were mostly unchanged, identifying AS modulation as an independent way of shaping the transcriptome.

CONCLUSIONS

The analysis of AS profiles in grapevine varieties with contrasting phenotypes revealed some similarity in the regulation of several genes with developmental functions, suggesting their involvement in berry ripening. Additionally, many splicing differences were discovered between the two varieties, that could be linked to phenotypic specificities and distinct adaptive capacities. Together, these findings open perspectives for a better understanding of berry development and for the selection of grapevine genotypes adapted to climate change.

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

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

Impact of Rootstock and Season on Red Blotch Disease Expression in Cabernet Sauvignon (V. vinifera)

Grapevine red blotch virus (GRBV), the causative agent of grapevine red blotch disease, is widespread across the United States and causes a delay in ripening events in grapes. This study evaluates the effects of GRBV on Cabernet Sauvignon grape berry composition, grafted on two different rootstocks (110R and 420A) in two seasons (2016 and 2017). Total soluble solids, acidity, and anthocyanin concentrations were monitored through ripening and at harvest. Phenolic and volatile compounds were also analyzed at harvest to determine genotypic and environmental influences on disease outcome. Sugar accumulation through ripening was lower in diseased fruit (RB (+)) than healthy fruit across rootstock and season. GRBV impact was larger in 2016 than 2017, indicating a seasonal effect on disease expression. In general, anthocyanin levels and volatile compound accumulation was lower in RB (+) fruit than healthy fruit. Total phenolic composition and tannin content was higher in RB (+) fruit than healthy fruit in only 110R rootstock. Overall, GRBV impacted Cabernet Sauvignon grape composition crafted on rootstock 110R more than those crafted on rootstock 420A.

Sucrose Metabolism and Transport in Grapevines, with Emphasis on Berries and Leaves, and Insights Gained from a Cross-Species Comparison

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.

Crop Load and Plant Water Status Influence the Ripening Rate and Aroma Development in Berries of Grapevine (Vitis vinifera L.) cv. Cabernet Sauvignon

Wine made from grapes subjected to accelerated ripening, an increasingly frequent phenomenon occurring in many wine regions due to peaks of heat and water stress, displays higher alcohol levels and lacks balance with color and flavor compounds. Herein, the rate of sugar accumulation of grapes was manipulated by varying the crop load and irrigation regime and the development of secondary metabolites was monitored by gas chromatography-mass spectrometry (GC-MS) and high-performance liquid chromatography (HPLC). A 3-week delay in ripening correlated to an increase in the concentration of some monoterpenes and norisoprenoids and a greater decrease of green aroma compounds. Delayed ripening had a positive impact on the phenolic composition of grapes, displaying higher contents of total anthocyanins, total phenolics, quercetin glycosides, and polymeric pigments. A map of the chemical composition of grapes close to harvest allowed discrimination of compounds mainly responsive to delayed ripening from those driven by crop load or irrigation.

Comparative Metabolic Profiling of Grape Pulp during the Growth Process Reveals Systematic Influences under Root Restriction

The compositions and contents of metabolites in the pulp tissue play critical roles in the fruit quality for table grape. In this study, the effects of root restriction (RR) on the primary and secondary metabolites of pulp tissue at five developmental stages were studied at the metabolomics level, using “Red Alexandria” grape berry (Vitis vinifera L.) as materials. The main results were as follows: 283 metabolites were annotated by using ultra-high performance liquid chromatography-mass spectrometry (UPLC-MS); 28 and 16 primary metabolites contents were increased and decreased, and 11 and 19 secondary metabolites contents were increased and decreased, respectively, along the berry development; RR significantly decreased 12 metabolites (four amino acids and derivatives, three organic acids, four flavonoids and one other compound) contents, and improved 40 metabolites (22 amino acids and derivatives, six nucleotides, four carbohydrates, four cofactors, three cinnamic acids and one other compound) accumulation at the different developmental stages. Altogether, our study would be helpful to increase our understanding of grape berry’s responses to RR stress.

Vascular Connections Into the Grape Berry: The Link of Structural Investment to Seededness

Vascular bundles in the grape pedicel and berry contain the conduits, phloem and xylem, for transport of water, sugar, nutrients and signals into and through the grape berry and play a critical role in berry growth and composition. Here, we assess the vascular anatomy within the proximal region of the berry. Guided using a 3D berry model generated by micro-CT, differential staining of transverse sections of berries and receptacles was followed by fluorescent microscopy. Morphometric and vascular characteristics were analyzed within the central proximal region (brush zone, a fibrous extension from the pedicel vascular system into the berry) of the seeded cultivars Shiraz and Sauvignon Blanc, as well as the stenospermocarpic cultivars Ruby Seedless and Flame Seedless. Observations revealed a change in vascular arrangement from the receptacle into the berry brush zone and differences in xylem element size as well as xylem and phloem area relationships. Xylem anatomical and derived hydraulic parameters, as well as total tissue area of xylem and phloem varied between cultivars and in receptacle and berry components. Variation in vascular growth between grape pedicels and berries was independent of seededness. Differences in receptacle xylem vessel size and distribution could contribute to cultivar-dependent xylem backflow constraint.

Metabolomics of Photosynthetically Active Tissues in White Grapes: Effects of Light Microclimate and Stress Mitigation Strategies

The effects of climate change are becoming a real concern for the viticulture sector, with impacts on both grapevine physiology and the quality of the fresh berries and wine. Short-term mitigation strategies, like foliar kaolin application and smart irrigation regimes, have been implemented to overcome these problems. We previously showed that these strategies also influence the photosynthetic activity of the berries themselves, specifically in the exocarp and seed. In the present work, we assessed the modulating effects of both canopy-light microclimate, kaolin and irrigation treatments on the metabolic profiles of the exocarp and seed, as well as the potential role of berry photosynthesis herein. Berries from the white variety Alvarinho were collected at two contrasting light microclimate positions within the vine canopy (HL—high light and LL—low light) from both irrigated and kaolin-treated plants, and their respective controls, at three fruit developmental stages (green, véraison and mature). Untargeted liquid chromatography mass spectrometry (LCMS) profiling of semi-polar extracts followed by multivariate statistical analysis indicate that both the light microclimate and irrigation influenced the level of a series of phenolic compounds, depending on the ripening stage of the berries. Moreover, untargeted gas chromatography mass spectrometry (GCMS) profiling of polar extracts show that amino acid and sugar levels were influenced mainly by the interaction of irrigation and kaolin treatments. The results reveal that both photosynthetically active berry tissues had a distinct metabolic profile in response to the local light microclimate, which suggests a specific role of photosynthesis in these tissues. A higher light intensity within the canopy mainly increased the supply of carbon precursors to the phenylpropanoid/flavonoid pathway, resulting in increased levels of phenolic compounds in the exocarp, while in seeds, light mostly influenced compounds related to carbon storage and seed development. In addition, our work provides new insights into the influence of abiotic stress mitigation strategies on the composition of exocarps and seeds, which are both important tissues for the quality of grape-derived 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.

Update on the Roles of Polyamines in Fleshy Fruit Ripening, Senescence, and Quality

Ripening of fleshy fruits involves complex physiological, biochemical, and molecular processes that coincide with various changes of the fruit, including texture, color, flavor, and aroma. The processes of ripening are controlled by ethylene in climacteric fruits and abscisic acid (ABA) in non-climacteric fruits. Increasing evidence is also uncovering an essential role for polyamines (PAs) in fruit ripening, especially in climacteric fruits. However, until recently breakthroughs have been made in understanding PA roles in the ripening of non-climacteric fruits. In this review, we compare the mechanisms underlying PA biosynthesis, metabolism, and action during ripening in climacteric and non-climacteric fruits at the physiological and molecular levels. The PA putrescine (Put) has a role opposite to that of spermidine/spermine (Spd/Spm) in cellular metabolism. Arginine decarboxylase (ADC) is crucial to Put biosynthesis in both climacteric and non-climacteric fruits. S-adenosylmethionine decarboxylase (SAMDC) catalyzes the conversion of Put to Spd/Spm, which marks a metabolic transition that is concomitant with the onset of fruit ripening, induced by Spd in climacteric fruits and by Spm in non-climacteric fruits. Once PA catabolism is activated by polyamine oxidase (PAO), fruit ripening and senescence are facilitated by the coordination of mechanisms that involve PAs, hydrogen peroxide (H₂O₂), ABA, ethylene, nitric oxide (NO), and calcium ions (Ca²⁺). Notably, a signal derived from PAO5-mediated PA metabolism has recently been identified in strawberry, a model system for non-climacteric fruits, providing a deeper understanding of the regulatory roles played by PAs in fleshy fruit ripening.

Transcriptome Profiling During Muscadine Berry Development Reveals the Dynamic of Polyphenols Metabolism

Muscadine grapes accumulate higher amounts of bioactive phenolics compared with other grape species. To identify the molecular events associated with polyphenolic accumulation that influence antioxidant capacity, two contrasting muscadine genotypes (C5 and C6) with varied phenolic/flavonoid content and antioxidant activity were investigated via RNA-sequencing during berry development. The results showed that berry development is concomitant with transcriptome profile changes, which was more pronounced at the véraison (V) stage. Despite that the downregulation pattern of gene expression dominated the upregulation through berry development, the C5 genotype maintained higher expression levels. Comparative transcript profiling allowed the identification of 94 differentially expressed genes with potential relevance in regulating fruit secondary metabolism, including 18 transcription factors and 76 structural genes. The genes underlying the critical enzymes in the modification reactions of polyphenolics biosynthetic pathway, including hydroxylation, methylation, and glycosylation were more pronounced during the immature stages of prevéraison (PrV), V, and postvéraison (PoV) in the C5 genotype, resulting in more accumulation of biologically active phenolic/flavonoid derivatives. The results suggested that muscadine grapes, as in bunch grapes (Vitis sp.); possess a similar mechanism that organizes polyphenolics accumulation; however, the set of total flavonoids (TFs) and structural genes coordinating the pathway varies between the two species.

Tissue-Specific Hormonal Variations in Grapes of Irrigated and Non-irrigated Grapevines (Vitis vinifera cv. "Merlot") Growing Under Mediterranean Field Conditions

Agricultural practices in grapevines management include water restrictions due to its positive effect on wine quality, especially when applied at fruit ripening. Although the effects of water stress in some groups of phytohormones have already been described in leaves and whole grapes, information regarding tissue-specific variations in hormones during ripening in grapes is scarce. Field-grown grapevines from the cv. "Merlot" were subjected to two differential water supplies, including only rainfed, non-irrigated vines (T0) and vines additionally irrigated with 25Lweek^-1 vine^-1 (T1). Tissue-specific variations in the hormonal profiling of grapes [including changes in the contents of abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), the ethylene precursor 1-amino-cyclopropane-1-carboxylic acid (ACC), the auxin indole-3-acetic acid, gibberellins 1, 3, 4, and 7 (GA₁, GA₃, GA₄, and GA₇), the cytokinins trans-zeatin, and 2-isopentenyl adenine, including as well their respective ribosylated forms] were periodically evaluated from veraison to harvest. The hormonal profiling in leaves was also measured at the beginning and end of the season for comparison. Results showed that grape growth dynamics were transiently affected by the differences in water regimes, the increased water supply leading to an accelerated growth, slightly reduced accumulation of sugars, and transiently lowered pH, although grape quality did not differ between treatments at harvest. Hormonal profiling of whole berries did not reveal any difference in the endogenous contents of phytohormones between treatments, except for a transient decrease in GA₄ contents in T1 compared to T0 vines, which was not confirmed at the tissular level. Hormonal profiling at the tissue level highlighted a differential accumulation of phytohormones during ripening in berry tissues, with pulps being particularly poor in ABA, JA, and SA contents, seeds particularly accumulating ACC, gibberellins, and zeatin-type cytokinins, and the skin being particularly rich in auxin and active cytokinins. Changes in water supply led to very small and transient changes in the endogenous contents of phytohormones in the seeds, pulp, and skin of berries, the most remarkable variations being observed in cytokinin contents, which increased earlier [between 5 and 12days after veraison (DAV)] but later kept more constant in the skin from T1 compared to T0 vines and were also 3-fold higher at 40 DAV in seeds of T1 compared to T0 vines. It is concluded that small changes in water supply can trigger hormonal-driven physiological adjustments at the tissular level affecting the evolution of fruit growth and quality throughout grape berry ripening.

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

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

Exogenous allantoin improves anthocyanin accumulation in grape berry skin at early stage of ripening

Anthocyanin accumulation in grape berry skin is a crucial determinant of red/black grape berry quality. Recently, viticulture has been hampered by the issue of global warming, which has led to loss of anthocyanin accumulation in berry skin. The objectives of this study were to investigate the effect of allantoin on anthocyanin accumulation in berry skins of field-grown grapevines and to elucidate the molecular mechanism of the allantoin-induced anthocyanin accumulation in the berry skins. Allantoin enhanced anthocyanin accumulation in grape cultured cells and berry skins from field-grown grapevines at the early stage of ripening. MybA1 and UFGT, which encode the key transcription factor and enzyme in anthocyanin biosynthesis, were upregulated in allantoin-treated berry skins. Allantoin seems to increase the contents of delphinidin-based anthocyanin 3-glucosides in berry skins through the upregulation of F3'5'H gene that drives the synthesis of delphinidin-based anthocyanin 3-glucosides, compared with control berry skins. Allantoin increased soluble sugar contents in berries 10 days after treatment and upregulated abscisic acid (ABA)-responsible HT6 gene that encodes a key hexose transporter in sugar accumulation during ripening, in berry skins. These results suggested that physiological changes in allantoin-treated grape berries occurred in an ABA-dependent manner. Allantoin produced bioactive ABA through the β-glucosidase-catalyzed hydrolysis of glucose-conjugated ABA but not through the ABA biosynthesis by NCED, a key enzyme in ABA biosynthesis, in berry skins. Allantoin application in viticulture under global warming conditions is expected to contribute to mitigating loss of red/black berry skin color.

Novel stable QTLs identification for berry quality traits based on high-density genetic linkage map construction in table grape

BACKGROUND

Aroma, berry firmness and berry shape are three main quality traits in table grape production, and also the important target traits in grapevine breeding. However, the information about their genetic mechanisms is limited, which results in low accuracy and efficiency of quality breeding in grapevine. Mapping and isolation of quantitative trait locus (QTLs) based on the construction of genetic linkage map is a powerful approach to decipher the genetic determinants of complex quantitative traits.

RESULTS

In the present work, a final integrated map consisting of 3411 SLAF markers on 19 linkage groups (LGs) with an average distance of 0.98 cM between adjacent markers was generated using the specific length amplified fragment sequencing (SLAF-seq) technique. A total of 9 significant stable QTLs for Muscat flavor, berry firmness and berry shape were identified on two linkage groups among the hybrids analyzed over three consecutive years from 2016 to 2018. Notably, new stable QTLs for berry firmness and berry shape were found on LG 8 respectively for the first time. Based on biological function and expression profiles of candidate genes in the major QTL regions, 3 genes (VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350) related to berry firmness and 3 genes (VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200) linked to berry shape were highlighted. Overexpression of VIT_08s0032g01110 in transgenic Arabidopsis plants caused the change of pod shape.

CONCLUSIONS

A new high-density genetic map with total 3411 markers was constructed with SLAF-seq technique, and thus enabled the detection of narrow interval QTLs for relevant traits in grapevine. VIT_08s0007g00440, VIT_08s0040g02740 and VIT_08s0040g02350 were found to be related to berry firmness, while VIT_08s0032g01110, VIT_08s0032g01150 and VIT_08s0105g00200 were linked to berry shape.

Sugar Signaling During Fruit Ripening

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

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

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

Genome-wide identification and characterization of gibberellin metabolic and signal transduction (GA MST) pathway mediating seed and berry development (SBD) in grape (Vitis vinifera L.)

BACKGROUND

Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine.

RESULTS

In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed.

CONCLUSIONS

Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.

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

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

A Review of the Potential Climate Change Impacts and Adaptation Options for European Viticulture

Viticulture and winemaking are important socioeconomic sectors in many European regions. Climate plays a vital role in the terroir of a given wine region, as it strongly controls canopy microclimate, vine growth, vine physiology, yield, and berry composition, which together determine wine attributes and typicity. New challenges are, however, predicted to arise from climate change, as grapevine cultivation is deeply dependent on weather and climate conditions. Changes in viticultural suitability over the last decades, for viticulture in general or the use of specific varieties, have already been reported for many wine regions. Despite spatially heterogeneous impacts, climate change is anticipated to exacerbate these recent trends on suitability for wine production. These shifts may reshape the geographical distribution of wine regions, while wine typicity may also be threatened in most cases. Changing climates will thereby urge for the implementation of timely, suitable, and cost-effective adaptation strategies, which should also be thoroughly planned and tuned to local conditions for an effective risk reduction. Although the potential of the different adaptation options is not yet fully investigated, deserving further research activities, their adoption will be of utmost relevance to maintain the socioeconomic and environmental sustainability of the highly valued viticulture and winemaking sector in Europe.

Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis

BACKGROUND

Leaves of the medicinal plant Ampelopsis grossedentata, which is commonly known as vine tea, are used widely in the traditional Chinese beverage in southwest China. The leaves contain a large amount of dihydromyricetin, a compound with various biological activities. However, the transcript profiles involved in its biosynthetic pathway in this plant are unknown.

RESULTS

We conducted a transcriptome analysis of both young and old leaves of the vine tea plant using Illumina sequencing. Of the transcriptome datasets, a total of 52.47 million and 47.25 million clean reads were obtained from young and old leaves, respectively. Among 471,658 transcripts and 177,422 genes generated, 7768 differentially expressed genes were identified in leaves at these two stages of development. The phenylpropanoid biosynthetic pathway of vine tea was investigated according to the transcriptome profiling analysis. Most of the genes encoding phenylpropanoid biosynthesis enzymes were identified and found to be differentially expressed in different tissues and leaf stages of vine tea and also greatly contributed to the biosynthesis of dihydromyricetin in vine tea.

CONCLUSIONS

To the best of our knowledge, this is the first formal study to explore the transcriptome of A. grossedentata. The study provides an insight into the expression patterns and differential distribution of genes related to dihydromyricetin biosynthesis in vine tea. The information may pave the way to metabolically engineering plants with higher flavonoid content.

Distinct Metabolic Signals Underlie Clone by Environment Interplay in "Nebbiolo" Grapes Over Ripening

Several research studies were focused to understand how grapevine cultivars respond to environment; nevertheless, the biological mechanisms tuning this phenomenon need to be further deepened. Particularly, the molecular processes underlying the interplay between clones of the same cultivar and environment were poorly investigated. To address this issue, we analyzed the transcriptome of berries from three "Nebbiolo" clones grown in different vineyards, during two ripening seasons. RNA-sequencing data were implemented with analyses of candidate genes, secondary metabolites, and agronomical parameters. This multidisciplinary approach helped to dissect the complexity of clone × environment interactions, by identifying the molecular responses controlled by genotype, vineyard, phenological phase, or a combination of these factors. Transcripts associated to sugar signalling, anthocyanin biosynthesis, and transport were differently modulated among clones, according to changes in berry agronomical features. Conversely, genes involved in defense response, such as stilbene synthase genes, were significantly affected by vineyard, consistently with stilbenoid accumulation. Thus, besides at the cultivar level, clone-specific molecular responses also contribute to shape the agronomic features of grapes in different environments. This reveals a further level of complexity in the regulation of genotype × environment interactions that has to be considered for orienting viticultural practices aimed at enhancing the quality of grape productions.

Selection of candidate genes controlling veraison time in grapevine through integration of meta-QTL and transcriptomic data

BACKGROUND

High temperature during grape berry ripening impairs the quality of fruits and wines. Veraison time, which marks ripening onset, is a key factor for determining climatic conditions during berry ripening. Understanding its genetic control is crucial to successfully breed varieties more adapted to a changing climate. Quantitative trait loci (QTL) studies attempting to elucidate the genetic determinism of developmental stages in grapevine have identified wide genomic regions. Broad scale transcriptomic studies, by identifying sets of genes modulated during berry development and ripening, also highlighted a huge number of putative candidates.

RESULTS

With the final aim of providing an overview about available information on the genetic control of grapevine veraison time, and prioritizing candidates, we applied a meta-QTL analysis for grapevine phenology-related traits and checked for co-localization of transcriptomic candidates. A consensus genetic map including 3130 markers anchored to the grapevine genome assembly was compiled starting from 39 genetic maps. Two thousand ninety-three QTLs from 47 QTL studies were projected onto the consensus map, providing a comprehensive overview about distribution of available QTLs and revealing extensive co-localization especially across phenology related traits. From 141 phenology related QTLs we generated 4 veraison meta-QTLs located on linkage group (LG) 1 and 2, and 13 additional meta-QTLs connected to the veraison time genetic control, among which the most relevant were located on LG 14, 16 and 18. Functional candidates in these intervals were inspected. Lastly, taking advantage of available transcriptomic datasets, expression data along berry development were integrated, in order to pinpoint among positional candidates, those differentially expressed across the veraison transition.

CONCLUSION

Integration of meta-QTLs analysis on available phenology related QTLs and data from transcriptomic dataset allowed to strongly reduce the number of candidate genes for the genetic control of the veraison transition, prioritizing a list of 272 genes, among which 78 involved in regulation of gene expression, signal transduction or development.

Identification and characterization of cherry (Cerasus pseudocerasus G. Don) genes responding to parthenocarpy induced by GA3 through transcriptome analysis

Background

Fruit set after successful pollination is key for the production of sweet cherries, and a low fruit-setting rate is the main problem in production of this crop. As gibberellin treatment can directly induce parthenogenesis and satisfy the hormone requirement during fruit growth and development, such treatment is an important strategy for improving the fruit-setting rate of sweet cherries. Previous studies have mainly focused on physiological aspects, such as fruit quality, fruit size, and anatomical structure, whereas the molecular mechanism remains clear.

Results

In this study, we analyzed the transcriptome of ‘Meizao’ sweet cherry fruit treated with gibberellin during the anthesis and hard-core periods to identify genes associated with parthenocarpic fruit set. A total of 25,341 genes were identified at the anthesis and hard-core stages, 765 (681 upregulated, 84 downregulated) and 186 (141 upregulated, 45 downregulated) of which were significant differentially expressed genes (DEGs) at the anthesis and the hard-core stages after gibberellin 3 (GA3) treatment, respectively. Based on DEGs between the control and GA3 treatments, the GA3 response mainly involves parthenocarpic fruit set and cell division. Exogenous gibberellin stimulated sweet cherry fruit parthenocarpy and enlargement, as verified by qRT-PCR results of related genes as well as the parthenocarpic fruit set and fruit size. Based on our research and previous studies in Arabidopsis thaliana, we identified key genes associated with parthenocarpic fruit set and cell division. Interestingly, we observed patterns among sweet cherry fruit setting-related DEGs, especially those associated with hormone balance, cytoskeleton formation and cell wall modification.

Conclusions

Overall, the result provides a possible molecular mechanism regulating parthenocarpic fruit set that will be important for basic research and industrial development of sweet cherries.

Electronic supplementary material

The online version of this article (10.1186/s12863-019-0746-8) contains supplementary material, which is available to authorized users.

Peach ethylene response factor PpeERF2 represses the expression of ABA biosynthesis and cell wall degradation genes during fruit ripening

Ethylene response factors (ERFs) are known to regulate fruit ripening. However, the ERF regulatory networks are not clear. In this study, we have shown that peach (Prunus persica) PpeERF2 regulates fruit ripening through suppressing the expression of two ABA biosynthesis genes (PpeNCED2, PpeNCED3) and a cell wall degradation gene (PpePG1). The transcript levels of PpeERF2 in fruit were opposite to that of PpeNCED2, PpeNCED3 and PpePG1 during ripening and in response to various ripening treatments. PpeERF2 was found to bind to the PpeNCED2, PpeNCED3 and PpePG1 promotors as demonstrated by yeast one-hybrid (Y1H) and EMSA assays; and further found to repress the promoter activities of the three genes in tobacco leaf tissues after Agrobacterium infiltration. Taken together, these results provide new information for a better understanding of the crosstalk network between ethylene signaling, cell wall degradation and ABA biosynthesis during fruit ripening.