Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries (Vitis vinifera L.) Exposed to Water Deficit

Different frequencies of water deficit irrigation treatments improve fruit quality of Zitian seedless grapes under on-tree storage

In this study, we assessed the impact of varied water deficit irrigation frequencies (T1: 2.5 L/4 days; T2: 5 L/8 days; CK: 5 L/4 days) on Zitian Seedless grapes from veraison to post-ripening. Notably, total soluble solids increased during on-tree storage compared to at maturity, while total anthocyanin content decreased, particularly in CK (60.16%), T1 (62.35%), and less in T2 (50.54%). Glucose and fructose levels increased significantly in T1 and T2, more so in T2, but slightly declined in CK. Tartaric acid content increased by 41.42% in T2. Moreover, compared to regular irrigation, water deficit treatments enhanced phenolic metabolites and volatile compounds, including chlorogenic acid, various flavonoids, viniferin, hexanal, 2-nonenal, 2-hexen-1-ol, (E)-, 3-hydroxy-dodecanoic acid, and 1-hexanol, etc. Overall, the T2 treatment outperformed T1 and CK in maintaining grape quality. This study reveals that combining on-tree storage with water deficit irrigation not only improves grape quality but also water efficiency.

Appropriate mowing can promote the growth of Anabasis aphylla through the auxin metabolism pathway

Anabasis aphylla (A. aphylla), a species of the Amaranthaceae family, is widely distributed in northwestern China and has high pharmacological value and ecological functions. However, the growth characteristics are poorly understood, impeding its industrial development for biopesticide development. Here, we explored the regenerative capacity of A. aphylla. To this end, different lengths of the secondary branches of perennial branches were mowed at the end of March before sprouting. The four treatments were no mowing (M0) and mowing 1/3, 2/3, and the entire length of the secondary branches of perennial branches (M1-M3, respectively). Next, to evaluate the compensatory growth after mowing, new assimilate branches' related traits were recorded every 30 days, and the final biomass was recorded. The mowed plants showed a greater growth rate of assimilation branches than un-mowed plants. Additionally, with the increasing mowing degree, the growth rate and the final biomass of assimilation branches showed a decreasing trend, with the greatest growth rate and final biomass in response to M1. To evaluate the mechanism of the compensatory growth after mowing, a combination of dynamic (0, 1, 5, and 8 days after mowing) plant hormone-targeted metabolomics and transcriptomics was performed for the M0 and M1 treatment. Overall, 26 plant hormone metabolites were detected, 6 of which significantly increased after mowing compared with control: Indole-3-acetyl-L-valine methyl ester, Indole-3-carboxylic acid, Indole-3-carboxaldehyde, Gibberellin A24, Gibberellin A4, and cis (+)-12-oxo-phytodienoic acid. Additionally, 2,402 differentially expressed genes were detected between the mowed plants and controls. By combining clustering analysis based on expression trends after mowing and gene ontology analysis of each cluster, 18 genes related to auxin metabolism were identified, 6 of which were significantly related to auxin synthesis. Our findings suggest that appropriate mowing can promote A. aphylla growth, regulated by the auxin metabolic pathway, and lays the foundation for the development of the industrial value of A. aphylla.

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.

NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine

During late- and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes involved in berry ripening progression. NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression of NAC61 in Nicotiana benthamiana leaves resulted in low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressing NAC61 and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulator MYB14, the osmotic stress-related gene DHN1b, the Botrytis cinerea susceptibility gene WRKY52, and NAC61 itself was validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation of MYB14 and NAC61 expression. Overall, our findings establish NAC61 as a key player in a regulatory network that governs stilbenoid metabolism and osmotic, oxidative, and biotic stress responses that are the hallmark of late- and post-ripening grape stages.

High-Resolution Mass Spectrometry-Based Metabolomics for Increased Grape Juice Metabolite Coverage

The composition of the juice from grape berries is at the basis of the definition of technological ripeness before harvest, historically evaluated from global sugar and acid contents. If many studies have contributed to the identification of other primary and secondary metabolites in whole berries, deepening knowledge about the chemical composition of the sole flesh of grape berries (i.e., without considering skins and seeds) at harvest is of primary interest when studying the enological potential of widespread grape varieties producing high-added-value wines. Here, we used non-targeted DI-FT-ICR-MS and RP-UHPLC-Q-ToF-MS analyses to explore the extent of metabolite coverage of up to 290 grape juices from four Vitis vinifera grape varieties, namely Chardonnay, Pinot noir, Meunier, and Aligoté, sampled at harvest from 91 vineyards in Europe and Argentina, over three successive vintages. SPE pretreatment of samples led to the identification of more than 4500 detected C,H,O,N,S-containing elemental compositions, likely associated with tens of thousands of distinct metabolites. We further revealed that a major part of this chemical diversity appears to be common to the different juices, as exemplified by Pinot noir and Chardonnay samples. However, it was possible to build significant models for the discrimination of Chardonnay from Pinot noir grape juices, and of Chardonnay from Aligoté grape juices, regardless of the geographical origin or the vintage. Therefore, this metabolomic approach opens access to a remarkable holistic molecular description of the instantaneous composition of such a biological matrix, which is the result of complex interplays among environmental, biochemical, and vine growing practices.

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

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

Impact of Climate Change on Altered Fruit Quality with Organoleptic, Health Benefit, and Nutritional Attributes

As a consequence of global climate change, acute water deficit conditions, soil salinity, and high temperature have been on the rise in their magnitude and frequency, which have been found to impact plant growth and development negatively. However, recent evidence suggests that many fruit plants that face moderate abiotic stresses can result in beneficial effects on the postharvest storage characters of the fruits. Salinity, drought, and high temperature conditions stimulate the synthesis of abscisic acid (ABA), and secondary metabolites, which are vital for fruit quality. The secondary metabolites like phenolic acids and anthocyanins that accumulate under abiotic stress conditions have antioxidant activity, and therefore, such fruits have health benefits too. It has been noticed that fruits accumulate more sugar and anthocyanins owing to upregulation of phenylpropanoid pathway enzymes. The novel information that has been generated thus far indicates that the growth environment during fruit development influences the quality components of the fruits. But the quality depends on the trade-offs between productivity, plant defense, and the frequency, duration, and intensity of stress. In this review, we capture the current knowledge of the irrigation practices for optimizing fruit production in arid and semiarid regions and enhancement in the quality of fruit with the application of exogenous ABA and identify gaps that exist in our understanding of fruit quality under abiotic stress conditions.

Effects of Vine Water Status on Malate Metabolism and γ-Aminobutyric Acid (GABA) Pathway-Related Amino Acids in Marselan (Vitis vinifera L.) Grape Berries

Malic acid is the predominant organic acid in grape berries, and its content is affected by abiotic factors such as temperature (fruit zone microclimate) and water (vine water status). The objectives of this study were to explore the potential mechanisms behind the effects of vine water status on the biosynthesis and degradation of berry malic acid and the potential downstream effects on berry metabolism. This study was conducted over two growing seasons in 2021 and 2022, comprising three watering regimes: no water stress (CK), light water stress (LWS), and moderate water stress (MWS). Compared to CK, a significantly higher level of malic acid was found in berries from the MWS treatment when the berry was still hard and green (E-L 33) in both years. However, water stress reduced the malic acid content at the ripe berry harvest (E-L 38) stage. The activities of NAD-malate dehydrogenase (NAD-MDH) and pyruvate kinase (PK) were enhanced by water stress. Except for the E-L 33 stage, the activity of phosphoenolpyruvate carboxylase (PEPC) was reduced by water stress. The highest phosphoenolpyruvate carboxykinase (PEPCK) activity was observed at the berry veraison (E-L 35) stage and coincided with the onset of a decrease in the malate content. Meanwhile, the expression of VvPEPCK was consistent with its enzyme activity. This study showed that water stress changed the content of some free amino acids (GABA, proline, leucine, aspartate, and glutamate), two of which (glutamate and GABA) are primary metabolites of the GABA pathway.

Advances in detecting fruit aroma compounds by combining chromatography and spectrometry

Fruit aroma is produced by volatile compounds, which can significantly enhance fruit flavor. These compounds are highly complex and have remarkable pharmacological effects. The synthesis, concentration, type, and quantity of fruit aroma substances are affected by various factors, both abiotic and biotic. To fully understand the aroma substances of various fruits and their influencing factors, detection technology can be used. Many methods exist for detecting aroma compounds, and approaches combining multiple instruments are widely used. This review describes and compares each detection technology and discusses the potential use of combined technologies to provide a comprehensive understanding of fruit aroma compounds and the factors influencing their synthesis. These results can inform the development and utilization of fruit aroma substances. © 2023 Society of Chemical Industry.

Multi-omics quantitative data of tomato fruit unveils regulation modes of least variable metabolites

BACKGROUND

The composition of ripe fruits depends on various metabolites which content evolves greatly throughout fruit development and may be influenced by the environment. The corresponding metabolism regulations have been widely described in tomato during fruit growth and ripening. However, the regulation of other metabolites that do not show large changes in content have scarcely been studied.

RESULTS

We analysed the metabolites of tomato fruits collected on different trusses during fruit development, using complementary analytical strategies. We identified the 22 least variable metabolites, based on their coefficients of variation. We first verified that they had a limited functional link with the least variable proteins and transcripts. We then posited that metabolite contents could be stabilized through complex regulations and combined their data with the quantitative proteome or transcriptome data, using sparse partial-least-square analyses. This showed shared regulations between several metabolites, which interestingly remained linked to early fruit development. We also examined regulations in specific metabolites using correlations with individual proteins and transcripts, which revealed that a stable metabolite does not always correlate with proteins and transcripts of its known related pathways.

CONCLUSIONS

The regulation of the least variable metabolites was then interpreted regarding their roles as hubs in metabolic pathways or as signalling molecules.

Impact of heat stress, water stress, and their combined effects on the metabolism and transcriptome of grape berries

Recurring heat and drought episodes present challenges to the sustainability of grape production worldwide. We investigated the impacts of heat and drought stress on transcriptomic and metabolic responses of berries from two wine grape varieties. Cabernet Sauvignon and Riesling grapevines were subjected to one of four treatments during early fruit ripening: (1) drought stress only, (2) heat stress only, (3) simultaneous drought and heat stress, (4) no drought or heat stress (control). Berry metabolites, especially organic acids, were analyzed, and time-course transcriptome analysis was performed on samples before, during, and after the stress episode. Both alone and in conjunction with water stress, heat stress had a much more significant impact on berry organic acid content, pH, and titratable acidity than water stress. This observation contrasts with previous reports for leaves, which responded more strongly to water stress, indicating that grape berries display a distinct, organ-specific response to environmental stresses. Consistent with the metabolic changes, the global transcriptomic analysis revealed that heat stress had a more significant impact on gene expression in grape berries than water stress in both varieties. The differentially expressed genes were those associated with the tricarboxylic acid cycle and glyoxylate cycle, mitochondrial electron transport and alternative respiration, glycolysis and gluconeogenesis, carbohydrate allocation, ascorbate metabolism, and abiotic stress signaling pathways. Knowledge regarding how environmental stresses, alone and in combination, impact the berry metabolism of different grape varieties will form the basis for developing recommendations for climate change mitigation strategies and genetic improvement.

A multiomics integrative analysis of color de-synchronization with softening of 'Hass' avocado fruit: A first insight into a complex physiological disorder

Exocarp color de-synchronization with softening of 'Hass' avocado is a relevant recurrent problem for the avocado supply chain. This study aimed to unravel the mechanisms driving this de-synchronization integrating omics datasets from avocado exocarp of different storage conditions and color phenotypes. In addition, we propose potential biomarkers to predict color synchronized/de-synchronized fruit. Integration of transcriptomics, proteomics and metabolomics and network analysis revealed eight transcription factors associated with differentially regulated genes between regular air (RA) and controlled atmosphere (CA) and twelve transcription factors related to avocado fruit color de-synchronization control in ready-to-eat stage. CA was positively correlated to auxins, ethylene, cytokinins and brassinosteroids-related genes, while RA was characterized by enrichment of cell wall remodeling and abscisic acid content associated genes. At ready-to-eat higher contents of flavonoids, abscisic acid and brassinosteroids were associated with color-softening synchronized avocados. In contrast, de-synchronized fruit revealed increases of jasmonic acid, salicylic acid and auxin levels.

Grapevine genome analysis demonstrates the role of gene copy number variation in the formation of monoterpenes

Volatile organic compounds such as terpenes influence the quality parameters of grapevine through their contribution to the flavour and aroma profile of berries. Biosynthesis of volatile organic compounds in grapevine is relatively complex and controlled by multiple genes, the majority of which are unknown or uncharacterised. To identify the genomic regions that associate with modulation of these compounds in grapevine berries, volatile metabolic data generated via GC-MS from a grapevine mapping population was used to identify quantitative trait loci (QTLs). Several significant QTLs were associated with terpenes, and candidate genes were proposed for sesquiterpene and monoterpene biosynthesis. For monoterpenes, loci on chromosomes 12 and 13 were shown to be associated with geraniol and cyclic monoterpene accumulation, respectively. The locus on chromosome 12 was shown to contain a geraniol synthase gene (VvGer), while the locus on chromosome 13 contained an α-terpineol synthase gene (VvTer). Molecular and genomic investigation of VvGer and VvTer revealed that these genes were found in tandemly duplicated clusters, displaying high levels of hemizygosity. Gene copy number analysis further showed that not only did VvTer and VvGer copy numbers vary within the mapping population, but also across recently sequenced Vitis cultivars. Significantly, VvTer copy number correlated with both VvTer gene expression and cyclic monoterpene accumulation in the mapping population. A hypothesis for a hyper-functional VvTer allele linked to increased gene copy number in the mapping population is presented and can potentially lead to selection of cultivars with modulated terpene profiles. The study highlights the impact of VvTPS gene duplication and copy number variation on terpene accumulation in grapevine.

Benzothiadiazole Affects Grape Polyphenol Metabolism and Wine Quality in Two Greek Cultivars: Effects during Ripening Period over Two Years

Grape berries are one of the most important sources of phenolic compounds, either consumed fresh or as wine. A pioneer practice aiming to enrich grape phenolic content has been developed based on the application of biostimulants such as agrochemicals initially designed to induce resistance against plant pathogens. A field experiment was conducted in two growing seasons (2019-2020) to investigate the effect of benzothiadiazole on polyphenol biosynthesis during grape ripening in Mouhtaro (red-colored) and Savvatiano (white-colored) varieties. Grapevines were treated at the stage of veraison with 0.3 mM and 0.6 mM benzothiadiazole. The phenolic content of grapes, as well as the expression level of genes involved in the phenylpropanoid pathway were evaluated and showed an induction of genes specifically engaged in anthocyanins and stilbenoids biosynthesis. Experimental wines deriving from benzothiadiazole-treated grapes exhibited increased amounts of phenolic compounds in both varietal wines, as well as an enhancement in anthocyanin content of Mouhtaro wines. Taken together, benzothiadiazole can be utilized to induce the biosynthesis of secondary metabolites with oenological interest and to improve the quality characteristics of grapes produced under organic conditions.

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

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

From Classical to Modern Computational Approaches to Identify Key Genetic Regulatory Components in Plant Biology

The selection of plant genotypes with improved productivity and tolerance to environmental constraints has always been a major concern in plant breeding. Classical approaches based on the generation of variability and selection of better phenotypes from large variant collections have improved their efficacy and processivity due to the implementation of molecular biology techniques, particularly genomics, Next Generation Sequencing and other omics such as proteomics and metabolomics. In this regard, the identification of interesting variants before they develop the phenotype trait of interest with molecular markers has advanced the breeding process of new varieties. Moreover, the correlation of phenotype or biochemical traits with gene expression or protein abundance has boosted the identification of potential new regulators of the traits of interest, using a relatively low number of variants. These important breakthrough technologies, built on top of classical approaches, will be improved in the future by including the spatial variable, allowing the identification of gene(s) involved in key processes at the tissue and cell levels.

Big Data in Gastroenterology Research

Studying individual data types in isolation provides only limited and incomplete answers to complex biological questions and particularly falls short in revealing sufficient mechanistic and kinetic details. In contrast, multi-omics approaches to studying health and disease permit the generation and integration of multiple data types on a much larger scale, offering a comprehensive picture of biological and disease processes. Gastroenterology and hepatobiliary research are particularly well-suited to such analyses, given the unique position of the luminal gastrointestinal (GI) tract at the nexus between the gut (mucosa and luminal contents), brain, immune and endocrine systems, and GI microbiome. The generation of 'big data' from multi-omic, multi-site studies can enhance investigations into the connections between these organ systems and organisms and more broadly and accurately appraise the effects of dietary, pharmacological, and other therapeutic interventions. In this review, we describe a variety of useful omics approaches and how they can be integrated to provide a holistic depiction of the human and microbial genetic and proteomic changes underlying physiological and pathophysiological phenomena. We highlight the potential pitfalls and alternatives to help avoid the common errors in study design, execution, and analysis. We focus on the application, integration, and analysis of big data in gastroenterology and hepatobiliary research.

Overhead photoselective shade films mitigate effects of climate change by arresting flavonoid and aroma composition degradation in wine

INTRODUCTION

Overhead photoselective shade films installed in vineyards improve berry composition in hot grape-growing regions. The aim of the study was to evaluate the flavonoid and aroma profiles and composition of wines from Cabernet Sauvignon grapes (Vitis vinifera L.) treated with partial solar radiation exclusion.

METHODS

Experimental design consisted in a randomized experiment with four shade films (D1, D3, D4, D5) with differing solar radiation spectra transmittance and compared to an uncovered control (C0) performed over two seasons (2021 and 2022) in Oakville (CA, USA). Berries were collected by hand at harvest and individual vinifications for each treatment and season were conducted in triplicates. Then, wine chemical composition, flavonoid and aromatic profiles were analyzed.

RESULTS

The wines from D4 treatment had greater color intensity and total phenolic index due to co-pigmentation with anthocyanins. Shade film wines D5 and D1 from the 2020 vintage demonstrated increased total anthocyanins in the hotter of the two experimental years. In 2021, reduced cluster temperatures optimized total anthocyanins in D4 wines. Reduced cluster temperatures modulated anthocyanin acylation, methylation and hydroxylation in shade film wines. Volatile aroma composition was analyzed using gas chromatography mass spectroscopy (GCMS) and D4 wines exhibited a more fruity and pleasant aroma profile than C0 wines.

DISCUSSION

Results provided evidence that partial solar radiation exclusion in the vineyard using overhead shade films directly improved flavonoid and aroma profiles of resultant wines under hot vintage conditions, providing a tool for combatting air temperatures and warmer growing conditions associated with climate change.

Unlocking grapevine in vitro regeneration: Issues and perspectives for genetic improvement and functional genomic studies

In vitro plant regeneration is a pivotal process in genetic engineering to obtain large numbers of transgenic, cisgenic and gene edited plants in the frame of functional gene or genetic improvement studies. However, several issues emerge as regeneration is not universally possible across the plant kingdom and many variables must be considered. In grapevine (Vitis spp.), as in other woody and fruit tree species, the regeneration process is impaired by a recalcitrance that depends on numerous factors such as genotype and explant-dependent responses. This is one of the major obstacles in developing gene editing approaches and functional genome studies in grapevine and it is therefore crucial to understand how to achieve efficient regeneration across different genotypes. Further issues that emerge in regeneration need to be addressed, such as somaclonal mutations which do not allow the regeneration of individuals identical to the original mother plant, an essential factor for commercial use of the improved grapevines obtained through the New Breeding Techniques. Over the years, the evolution of protocols to achieve plant regeneration has relied mainly on optimizing protocols for genotypes of interest whilst nowadays with new genomic data available there is an emerging opportunity to have a clearer picture of its molecular regulation. The goal of this review is to discuss the latest information available about different aspects of grapevine in vitro regeneration, to address the main factors that can impair the efficiency of the plant regeneration process and cause post-regeneration problems and to propose strategies for investigating and solving them.

Decoding the Proanthocyanins Profile of Italian Red Wines

The Italian wine appellations system is organized in hundreds of origin wines, with unique characteristics that are protected with many denominations of origin. The aim of this work was to analyze and compare the proanthocyanin profile of 12 single-cultivar and single-vintage Italian red wine groups (Aglianico from Campania, Cannonau from Sardinia, Corvina from Veneto, Montepulciano from Abruzzo, Nebbiolo from Piedmont, Nerello Mascalese from Sicily, Primitivo from Apulia, Raboso Piave from Veneto, Sagrantino from Umbria, Sangiovese from Tuscany and Romagna, and Teroldego from Trentino), each one produced in their terroirs under ad hoc legal frameworks to guarantee their quality and origin. All wines were analyzed with a protocol that combined the phloroglucinolysis reaction with an LC-MS/MS instrument. The results underlined Sagrantino wines as the richest in proanthocyanins. Sangiovese, Montepulciano, Nerello, and Teroldego were the richest in B-ring trihydroxylated flavan-3-ols, and especially Nerello was the richest in prodelphinidins. Cannonau, Raboso Piave, Nerello, and Corvina were characterized by C-ring trans conformation flavan-3-ols. Nebbiolo and Corvina had high percentages of galloylated flavan-3-ols. Aglianico and Primitivo had the lowest percentages of B-ring trihydroxylated and C-ring trans conformation flavan-3-ols. This information should be useful in better understanding the Italian red wines and valorize them.

Berry flavonoids are differently modulated by timing and intensities of water deficit in Vitis vinifera L. cv. Sangiovese

In this work, we tested the effect of different regulated deficit irrigation (RDI) regimes on berry flavonoid content and its relative biosynthetic pathways. Vines were subjected to six irrigation regimes over two consecutive years: a) full irrigation during the entire irrigation period (FI); b) moderate (RDI-1M) or c) severe (RDI-1S) water deficit between berry pea-size and veraison; d) severe water deficit during the lag-phase (RDI-LS); and e) moderate (RDI-2M) or f) severe (RDI-2S) water deficit from veraison through harvest. Berries from both RDI-1 treatments showed the highest accumulation of anthocyanins, upregulating the expression of many genes of the flavonoid pathway since the beginning of veraison until harvest, far after the water deficit was released. Although to a lesser degree than RDI-1, both post-veraison water deficit treatments increased anthocyanin concentration, particularly those of the tri-substituted forms, overexpressing the F3'5'H hydroxylases. The moderate deficit irrigation treatments enhanced anthocyanin accumulation with respect to the severe ones regardless of the period when they were applied (pre- or post-veraison). The water deficit imposed during the lag-phase downregulated many genes throughout the flavonoid pathway, showing a slight reduction in anthocyanin accumulation. The measurements of cluster temperature and light exposure highlighted that under deficit irrigation conditions, the effects induced by water stress prevailed over that of light and temperature in regulating anthocyanin biosynthesis. Flavonol concentration was higher in RDI-1S berries due to the upregulation of the flavonol synthases and the flavonol-3-O-glycosyltransferases. In this case, the higher cluster light exposure induced by water deficit in RDI-1S berries had a major role in flavonol accumulation. We conclude that the timing and intensity of water stress strongly regulate the berry flavonoid accumulation and that proper management of deficit irrigation can modulate the phenylpropanoid and flavonoid pathways.

Prospecting the Resilience of Several Spanish Ancient Varieties of Red Grape under Climate Change Scenarios

BACKGROUND

Climate change results in warmer air temperatures and an uncertain amount and distribution of annual precipitations, which will directly impact rainfed crops, such as the grapevine. Traditionally, ancient autochthones grapevine varieties have been substituted by modern ones with higher productivity. However, this homogenization of genotypes reduces the genetic diversity of vineyards which could make their ability to adapt to challenges imposed by future climate conditions difficult. Therefore, this work aimed to assess the response of four ancient grapevine varieties to high temperatures under different water availabilities, focusing on plant water relations, grape technological and phenolic maturity, and the antioxidant capacity of the must.

METHODS

The study was conducted on fruit-bearing cuttings grown in pots in temperature-gradient greenhouses. A two-factorial design was established where two temperature regimes, ambient and elevated (ambient + 4 °C), were combined with two water regimes, full irrigation and post-veraison deficit irrigation, during fruit ripening.

RESULTS

There were significant differences among the ancient varieties regarding plant water relations and fruit quality.

CONCLUSION

This research underlines the importance of evaluating the behavior of ancient grapevine varieties that could offer good options for the adaptation of viticulture to future climate conditions.

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.

Non-destructive fluorescence sensing for assessing microclimate, site and defoliation effects on flavonol dynamics and sugar prediction in Pinot blanc grapes

In an era of growing international competition in modern viticulture, the study and implementation of innovative technologies to increase the production of high-quality grapes and wines are of critical importance. In this study, the non-destructive portable sensor Multiplex, based on fluorescence sensing technique, was applied to evaluate grape maturity parameters and flavonol content of the understudied Pinot blanc variety. The effects of environmental and agronomical factors on flavonol content of Pinot blanc grapes were investigated in eight vineyards characterised by different microclimatic and agronomic conditions. Furthermore, the direct impact of canopy management treatment on the flavonol dynamics of the grapes oriented in the four cardinal directions was assessed. Results highlight the positive role of moderate temperatures and direct sunlight exposure on Pinot blanc flavonol content; however, no direct vineyard-elevation effect was observed. The ability to modulate and evaluate the flavonol content in field represent crucial factors because of their potential effect on flavonoids-dependent wine characteristics, such as stability and ageing. In the present study, for the first time, two calibration curves were reported for pre- and post-veraison periods between flavonol indices and the berry skin flavonol content and a good correlation was observed between Multiplex measurement and the total polyphenolic content of grape juice. Moreover, the strong correlation between the chlorophyll index with grape juice sugar content and titratable acidity revealed the practical application of non-destructive sensors to predict the optimal harvest time for Pinot blanc grapes. In conclusion, the non-destructive fluorescence sensor Multiplex is a high-potential tool for innovative viticulture, for evaluating grape skin composition variables in white grape varieties.

Improving the Phenolic Content of Tempranillo Grapes by Sustainable Strategies in the Vineyard

Wine phenolics are of considerable interest due to their implication in the organoleptic appreciation of wines and due to their bioactive functions as antioxidants. In this work, the effects of sustainable strategies in the vineyard, regulated deficit irrigation treatments (RDI) and crop load level (CL) on Tempranillo grape phenolics over two seasons was studied. Rainfed (T), early (EDI) and late (LDI) regulated deficit irrigation was applied. Cluster thinning (TH) and control (C) without cluster removal were also applied under each irrigation treatment. The effect of CL remained independent of RDI for all compounds, except for phenolic acids. The RDI influence on the grape skin phenolic profile was higher than CL in the dry season (2009); however, in 2010, the effect of CL was greater. In 2009, a tendency to increase anthocyanin and hydroxycinnamic acid content in grape skins was registered in EDI with respect to T. However, significant decreases in hydroxycinnamic and flavanol compounds were found in LDI. In 2010, the wettest year, CL increased all phenolic families’ content. Thus, it can be concluded that the effects of RDI and cluster thinning treatments depend on the family of compounds considered and the meteorological conditions of the year.

Vine Irrigation through Two Shoot Densities in Flavonoid and Non-Flavonoid Compounds in ‘Tempranillo’ Grapes

This study aims to analyze the effects of non-limiting irrigation (I) vs. rainfed (R) through two different shoot densities, high-load (H) and low-load (L), on vegetative growth, agronomic parameters, flavonoid and non-flavonoid polyphenol substances of cv. Tempranillo grown in a semi-arid climate during three consecutive seasons (2014–2016). Under these conditions, in the 2015 and 2016 seasons, irrigation showed significant increases in berry weight (14.7% and 13.4% in H and L, respectively, in 2015, and 35.6% and 23.5% in the same treatments in 2016) and yield (66.7% and 48.5 in 2015; 27.9% and 177.5% in 2016). Additionally, a general decreasing trend is observed in anthocyanins with the exception of peonidin derivates, almost all flavonol compounds, cinnamic acid and resveratrol values with different degrees and statistical significance depending on the shoot density of the vines. A slight variation is observed in 2014 in these parameters. On the other hand, no general trends are established either in flavanol compounds or hydroxybenzoic acid. Thus, the effect of irrigation depends on the parameter considered, the shoot density of the vine and the season considered.

Influence of Climate Change on Metabolism and Biological Characteristics in Perennial Woody Fruit Crops in the Mediterranean Environment

The changes in the state of the climate have a high impact on perennial fruit crops thus threatening food availability. Indeed, climatic factors affect several plant aspects, such as phenological stages, physiological processes, disease-pest frequency, yield, and qualitative composition of the plant tissues and derived products. To mitigate the effects of climatic parameters variability, plants implement several strategies of defense, by changing phenological trends, altering physiology, increasing carbon sequestration, and metabolites synthesis. This review was divided into two sections. The first provides data on climate change in the last years and a general consideration on their impact, mitigation, and resilience in the production of food crops. The second section reviews the consequences of climate change on the industry of two woody fruit crops models (evergreen and deciduous trees). The research focused on, citrus, olive, and loquat as evergreen trees examples; while grape, apple, pear, cherry, apricot, almond, peach, kiwi, fig, and persimmon as deciduous species. Perennial fruit crops originated by a complex of decisions valuable in a long period and involving economic and technical problems that farmers may quickly change in the case of annual crops. However, the low flexibility of woody crops is balanced by resilience in the long-life cycle.

Shifts in the phenolic composition and aromatic profiles of Cabernet Sauvignon (Vitis vinifera L.) wines are driven by different irrigation amounts in a hot climate

Wine final color, taste and aroma are closely related to the accumulation of secondary metabolites that may be affected by deficit irrigation applied in viticulture. A two-year study was conducted to assess the different fractions of crop evapotranspiration (ET_c) irrigation replacement on wine composition, addressing the analysis of flavonoids and volatiles under context of global warming. Irrigating with 100% ET_c (full grapevine demand) enhanced wine hue, antioxidant capacity, and some aromas; however, it came with a diminution of flavonoids and a less stable flavonoid profile. Replacing 25 and 50% ET_c in wine grape improved wine color intensity, concentration of flavonoids, and shifted the aromatic profiles. These treatments increased some terpenes and esters which may enhance the desirable aromas for Cabernet Sauvignon, and decreased C6 alcohols related to unpleasant ones. Therefore, despite the warming trends in Mediterranean climates, 100% ET_c irrigation would be not advisable to improve or maintain wine quality, and 50% ET_c was sufficient.

Multi-Omics Landscape of DNA Methylation Regulates Browning in “Fuji” Apple

Browning seriously affects the quality of fresh-cut fruits, and its mechanism was thought to be polyphenol oxidase (PPO) in the past. A way of non-different PPO browning was found in our previous studies. However, the landscape of this browning way is still unclear in “Fuji” apples. Multi-omics (methylomics, transcriptomics, and proteomics) methods were performed to the global profiles of DNA methylation and gene and protein expression. We employed two natural bud mutation varieties of apple as materials and found a positive correlation between browning index (BI) and methylation (5mC%, MdCMT3, and MdCMT3c) and a negative correlation between BI and demethylation (MdROS1 and MdDME). DNA methylation inhibitor 5-azacytidine can delay apple browning. Further analysis showed that methylated-NCA1 and OMT1 increased significantly in apple browning. Methylated-NCA1 might inhibit NCA1 gene expression and resulted in the decline of catalase activity, thereafter significantly increased apple browning. These findings insight into a new pathway and landscape that DNA hypermethylation significantly accelerated the browning in “Fuji” apple.

The Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement

Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important, Vitis vinifera species has driven the need for a standardised collection of genes within the grapevine community. In an effort led by the Integrape COST Action CA17111, we have recently developed the first grape gene reference catalogue, where genes are ascribed to functional data, including their accession identifiers from different genome-annotation versions (https://integrape.eu/resources/genes-genomes/). We present and discuss this gene repository together with a validation-level scheme based on varied supporting evidence found in current literature. The catalogue structure and online submission form provided permits community curation. Finally, we present the Gene Cards tool, developed within the Vitis Visualization (VitViz) platform, to visualize the data collected in the catalogue and link gene function with tissue-specific expression derived from public transcriptomic data. This perspective article aims to present these resources to the community as well as highlight their potential use, in particular for plant-breeding applications.

Biogenic volatile organic compounds in the grapevine response to pathogens, beneficial microorganisms, resistance inducers, and abiotic factors

The synthesis of volatile organic compounds (VOCs) in plants is triggered in response to external stimuli, and these compounds can migrate to distal tissues and neighbouring receivers. Although grapevine VOCs responsible for wine aroma and plant-insect communications are well characterized, functional properties of VOCs produced in response to phytopathogens, beneficial microorganisms, resistance inducers, and abiotic factors have been less studied. In this review, we focused on the emission patterns and potential biological functions of VOCs produced by grapevines in response to stimuli. Specific grapevine VOCs are emitted in response to the exogenous stimulus, suggesting their precise involvement in plant defence response. VOCs with inhibitory activities against pathogens and responsible for plant resistance induction are reported, and some of them can also be used as biomarkers of grapevine resistance. Likewise, VOCs produced in response to beneficial microorganisms and environmental factors are possible mediators of grapevine-microbe communications and abiotic stress tolerance. Although further functional studies may improve our knowledge, the existing literature suggests that VOCs have an underestimated potential application as pathogen inhibitors, resistance inducers against biotic or abiotic stresses, signalling molecules, membrane stabilizers, and modulators of reactive oxygen species. VOC patterns could also be used to screen for resistant traits or to monitor the plant physiological status.

Multi-dimensional leaf phenotypes reflect root system genotype in grafted grapevine over the growing season

BACKGROUND

Modern biological approaches generate volumes of multi-dimensional data, offering unprecedented opportunities to address biological questions previously beyond reach owing to small or subtle effects. A fundamental question in plant biology is the extent to which below-ground activity in the root system influences above-ground phenotypes expressed in the shoot system. Grafting, an ancient horticultural practice that fuses the root system of one individual (the rootstock) with the shoot system of a second, genetically distinct individual (the scion), is a powerful experimental system to understand below-ground effects on above-ground phenotypes. Previous studies on grafted grapevines have detected rootstock influence on scion phenotypes including physiology and berry chemistry. However, the extent of the rootstock's influence on leaves, the photosynthetic engines of the vine, and how those effects change over the course of a growing season, are still largely unknown.

RESULTS

Here, we investigate associations between rootstock genotype and shoot system phenotypes using 5 multi-dimensional leaf phenotyping modalities measured in a common grafted scion: ionomics, metabolomics, transcriptomics, morphometrics, and physiology. Rootstock influence is ubiquitous but subtle across modalities, with the strongest signature of rootstock observed in the leaf ionome. Moreover, we find that the extent of rootstock influence on scion phenotypes and patterns of phenomic covariation are highly dynamic across the season.

CONCLUSIONS

These findings substantially expand previously identified patterns to demonstrate that rootstock influence on scion phenotypes is complex and dynamic and underscore that broad understanding necessitates volumes of multi-dimensional data previously unmet.

Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

Grapevine and Wine Metabolomics-Based Guidelines for FAIR Data and Metadata Management

In the era of big and omics data, good organization, management, and description of experimental data are crucial for achieving high-quality datasets. This, in turn, is essential for the export of robust results, to publish reliable papers, make data more easily available, and unlock the huge potential of data reuse. Lately, more and more journals now require authors to share data and metadata according to the FAIR (Findable, Accessible, Interoperable, Reusable) principles. This work aims to provide a step-by-step guideline for the FAIR data and metadata management specific to grapevine and wine science. In detail, the guidelines include recommendations for the organization of data and metadata regarding (i) meaningful information on experimental design and phenotyping, (ii) sample collection, (iii) sample preparation, (iv) chemotype analysis, (v) data analysis (vi) metabolite annotation, and (vii) basic ontologies. We hope that these guidelines will be helpful for the grapevine and wine metabolomics community and that it will benefit from the true potential of data usage in creating new knowledge being revealed.

Precipitation before Flowering Determined Effectiveness of Leaf Removal Timing and Irrigation on Wine Composition of Merlot Grapevine

Grapevine productivity, and berry and wine flavonoid concentration, depend on the interactions of cultivar, environment, and applied cultural practices. We characterized the effects that mechanical leaf removal and irrigation treatments had on the flavonoid concentration of ‘Merlot’ (Vitis vinifera, L.) grape berries and wines in a hot climate over two growing seasons with contrasting precipitation patterns. Leaves were removed by machine, either at prebloom (PBLR), or at post-fruit-set (PFLR), or not removed (control) and irrigation was either applied as sustained deficit irrigation (SDI) at 0.8 of crop evapotranspiration (ET_c) from budbreak to fruit set, or regulated deficit irrigation (RDI) at 0.8 ET_c from bud break to fruit set, 0.5 ET_c from fruit set to veraison, and 0.8 ET_c from veraison to harvest, of ET_c In 2014, PFLR reduced the leaf area index (LAI) compared to control. The RDI decreased season-long leaf water potential (Ψ_Int) compared to SDI. However, in 2015, none of the treatments affected LAI or Ψ_Int. In 2014, berry flavonoid concentrations were reduced by PBLR as well as SDI. SDI increased the flavonoid concentrations in wine, and PFLR increased some wine flavonols in one season. No factor affected the concentrations of wine proanthocyanidins or mean degree of polymerization. Thus, mechanical PFLR and RDI may increase berry flavonoid accumulation without yield reduction, in red wine grapes cultivars grown in hot climates when precipitation after bud break is lacking. However, spring precipitation may influence the effectiveness of these practices as evidenced by this work in a changing climate.

Effects of Irrigation at Different Fractions of Crop Evapotranspiration on Water Productivity and Flavonoid Composition of Cabernet Sauvignon Grapevine

Climate change models predict lower precipitation and higher air temperatures that will negatively affect viticultural regions. Irrigation of vineyards will be crucial for mitigating abiotic stress during the growing season. However, the environmental impact of irrigation requires consideration for ensuring its sustainability in the future. We evaluated the standard irrigation practices on grapevine water use efficiency, berry flavonoid composition, vineyard water footprint, and arbuscular mycorrhizal fungi-grapevine symbiosis in two seasons with contrasting amounts of precipitation. The irrigation treatments consisted of weekly replacement of 25, 50, and 100% of crop evapotranspiration (ET_c) during two growing seasons. Irrigation in grapevine vineyards mitigated the water scarcity when precipitation during the dormant season was not sufficient. The results provided field data supporting that despite the low rainfall recorded in one of the seasons, increasing the amount of irrigation was not advised, and replacing 50% ET_c was sufficient. In this treatment, berry composition was improved with increased contents of total soluble solids, anthocyanins, and flavonols, and a stable flavonoid profile without an economic decrease in yield. In addition, with 50% ET_c, the mycorrhizal symbiosis was not compromised and water resources were not highly impacted. Altogether, our results provide fundamental knowledge for viticulturists to design an appropriate irrigation schedule under the future warming scenarios with minimal environmental impact in semi-arid regions facing warming trends.

A Synchronized Increase of Stilbenes and Flavonoids in Metabolically Engineered Vitis vinifera cv. Gamay Red Cell Culture

Stilbenes and flavonoids are two major health-promoting phenylpropanoid groups in grapes. Attempts to promote the accumulation of one group usually resulted in a decrease in the other. This study presents a unique strategy for simultaneously increasing metabolites in both groups in V. vinifera cv. Gamay Red grape cell culture, by overexpression of flavonol synthase (FLS) and increasing Phe availability. Increased Phe availability was achieved by transforming the cell culture with a second gene, the feedback-insensitive E. coli DAHP synthase (AroG*), and feeding them with Phe. A combined metabolomic and transcriptomic analysis reveals that the increase in both phenylpropanoid groups is accompanied by an induction of many of the flavonoid biosynthetic genes and no change in the expression levels of stilbene synthase. Furthermore, FLS overexpression with increased Phe availability resulted in higher anthocyanin levels, mainly those derived from delphinidin, due to the induction of F3'5'H. These insights may contribute to the development of grape berries with increased health benefits.

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.

Influence of Non-Saccharomyces on Wine Chemistry: A Focus on Aroma-Related Compounds

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

Impact of Environmental Factors on Stilbene Biosynthesis

Stilbenes are a small family of polyphenolic secondary metabolites that can be found in several distantly related plant species. These compounds act as phytoalexins, playing a crucial role in plant defense against phytopathogens, as well as being involved in the adaptation of plants to abiotic environmental factors. Among stilbenes, trans-resveratrol is certainly the most popular and extensively studied for its health properties. In recent years, an increasing number of stilbene compounds were subjected to investigations concerning their bioactivity. This review presents the most updated knowledge of the stilbene biosynthetic pathway, also focusing on the role of several environmental factors in eliciting stilbenes biosynthesis. The effects of ultraviolet radiation, visible light, ultrasonication, mechanical stress, salt stress, drought, temperature, ozone, and biotic stress are reviewed in the context of enhancing stilbene biosynthesis, both in planta and in plant cell and organ cultures. This knowledge may shed some light on stilbene biological roles and represents a useful tool to increase the accumulation of these valuable compounds.

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

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

The influence of soil drought stress on the leaf transcriptome of faba bean (Vicia faba L.) in the Qinghai-Tibet Plateau

Water deficit has a significant impact on growth, development and yield of fava bean (Vicia fava L.) in arid and semi-arid climates. The aim of this study was to identify differentially expressed genes in the Qinghai 13 genotype under soil drought through leaf transcriptome analysis. A total of 256.95 M clean reads were obtained and assembled into 176334 unigenes, with an average length of 766 bp. A total of 9126 (4439 upregulated and 4687 downregulated) differentially expressed genes (DEGs) were identified in faba bean leaves under soil drought. In total, 324 putative transcription factors were identified and classified as belonging to different transcription factor families. According to GO and KEGG analysis, the soil drought stress-inducible DEGs encoded proteins mainly involved in regulating photosynthesis, osmotic adjustment, detoxification, autophagy and other functions. In addition, a large portion of DEGs appeared to be novel because they could not be annotated in any functional databases, therefore, suggesting a specific response to soil drought in faba bean. Finally, RNA-seq analysis was validated by quantitative reverse-transcription PCR analysis. This work provides comprehensive and valuable information for understanding the molecular mechanisms which faba bean uses to respond to soil drought.

Characterization of Sub-Regional Variation in Saccharomyces Populations and Grape Phenolic Composition in Pinot Noir Vineyards of a Canadian Wine Region

Wine is a product of grape juice fermentation by yeast. Terroir is a term that encompasses all environmental factors and interactions at a specific geographical site, resulting in the development of regional-specific microbial strains and grape metabolites. In this study we determine the distribution of vineyard-associated wine yeast strains and characterize the flavonoid profile of Pinot Noir grapes among 3 sub-regions in the Okanagan Valley (OV), a major wine region in British Columbia, Canada. Pinot Noir grape samples were collected from 13 vineyards among 3 sub-regions of the OV, namely Kelowna (KE), Naramata-Penticton (NP) and Oliver-Osoyoos (OO), within a week prior to the winery harvesting date in 2016 and 2017. A total of 156 spontaneous Pinot Noir fermentations were conducted and vineyard-associated Saccharomyces strains were isolated from fermentations that reached two-thirds sugar depletion. Using microsatellite genotyping, we identified 103 Saccharomyces cerevisiae strains and 9 Saccharomyces uvarum strains. We also identified Saccharomyces paradoxus in one vineyard using ITS sequencing. We developed a microsatellite database of 160 commercial S. cerevisiae strains to determine the identity of the isolated strains and we include the database herein. Commercial strains were widely distributed across the three sub-regions. Forty-two of our 103 S. cerevisiae strains were equivalent or highly similar to commercial strains whereas the remaining 61 were considered as ‘unknown’ strains. Two S. uvarum strains were previously isolated in other OV studies and none matched the S. uvarum commercial strain BMV58. S. cerevisiae population structure was driven by sub-region, although S. cerevisiae populations did not differ significantly across vintages. S. uvarum and S. paradoxus were only identified in the 2017 vintage, demonstrating dynamic wine yeast populations between vintages. We found that the flavonoid profile of Pinot Noir grapes from the same 13 vineyards was also affected by sub-regional terroir. The anthocyanin content was lower and the proportion of methoxylated anthocyanins and flavonols was higher in Pinot Noir grapes from OO, the warmer sub-region as compared to KE, the cooler sub-region. Our study demonstrates that both yeast populations and metabolites associated with the Pinot Noir variety have sub-regional variation within a viticultural area.

The physiology of drought stress in grapevine: towards an integrative definition of drought tolerance

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

Two-omics data revealed commonalities and differences between Rpv12- and Rpv3-mediated resistance in grapevine

Plasmopara viticola is the causal agent of grapevine downy mildew (DM). DM resistant varieties deploy effector-triggered immunity (ETI) to inhibit pathogen growth, which is activated by major resistance loci, the most common of which are Rpv3 and Rpv12. We previously showed that a quick metabolome response lies behind the ETI conferred by Rpv3 TIR-NB-LRR genes. Here we used a grape variety operating Rpv12-mediated ETI, which is conferred by an independent locus containing CC-NB-LRR genes, to investigate the defence response using GC/MS, UPLC, UHPLC and RNA-Seq analyses. Eighty-eight metabolites showed significantly different concentration and 432 genes showed differential expression between inoculated resistant leaves and controls. Most metabolite changes in sugars, fatty acids and phenols were similar in timing and direction to those observed in Rpv3-mediated ETI but some of them were stronger or more persistent. Activators, elicitors and signal transducers for the formation of reactive oxygen species were early observed in samples undergoing Rpv12-mediated ETI and were paralleled and followed by the upregulation of genes belonging to ontology categories associated with salicylic acid signalling, signal transduction, WRKY transcription factors and synthesis of PR-1, PR-2, PR-5 pathogenesis-related proteins.

Network aggregation improves gene function prediction of grapevine gene co-expression networks

Aggregation across multiple networks highlights robust co-expression interactions and improves the functional connectivity of grapevine gene co-expression networks. In recent years, the rapid accumulation of transcriptome datasets from diverse experimental conditions has enabled the widespread use of gene co-expression network (GCN) analysis in plants. In grapevine, GCN analysis has shown great promise for gene function prediction, however, measurable progress is currently lacking. Using accumulated microarray datasets from the grapevine whole-genome array (33 experiments, 1359 samples), we explored how meta-analysis through aggregation influences the functional connectivity (performance) of derived networks using guilt-by-association neighbor voting. Two annotation schemes, i.e. MapMan BIN and Pfam, at two sparsity thresholds, i.e. top 100 (stringent) and 300 (relaxed) ranked genes were evaluated. We observed that aggregating across multiple networks improves performance dramatically, with the aggregate outperforming the majority of functional terms across individual networks. Network sparsity and size (i.e. the number of samples and aggregates) were key factors influencing performance while the choice of annotation scheme had little. Systematic comparison with various state-of-the-art microarray and RNA-seq networks was also performed, however, none outperformed the aggregate microarray network despite having good predictive performance. Repeating these series of tests using a functional enrichment-based performance metric also showed remarkably consistent findings with guilt-by-association neighbor voting. To demonstrate its functionality, we explore the function and transcriptional regulation of grapevine EXPANSIN genes. We envisage that network aggregation will offer new and unique opportunities for gene function prediction in future grapevine functional genomics studies. To this end, we make the aggregate networks and associated metadata publicly available at VTC-Agg (https://sites.google.com/view/vtc-agg).

Systematic Multi-Omics Integration (MOI) Approach in Plant Systems Biology

Across all facets of biology, the rapid progress in high-throughput data generation has enabled us to perform multi-omics systems biology research. Transcriptomics, proteomics, and metabolomics data can answer targeted biological questions regarding the expression of transcripts, proteins, and metabolites, independently, but a systematic multi-omics integration (MOI) can comprehensively assimilate, annotate, and model these large data sets. Previous MOI studies and reviews have detailed its usage and practicality on various organisms including human, animals, microbes, and plants. Plants are especially challenging due to large poorly annotated genomes, multi-organelles, and diverse secondary metabolites. Hence, constructive and methodological guidelines on how to perform MOI for plants are needed, particularly for researchers newly embarking on this topic. In this review, we thoroughly classify multi-omics studies on plants and verify workflows to ensure successful omics integration with accurate data representation. We also propose three levels of MOI, namely element-based (level 1), pathway-based (level 2), and mathematical-based integration (level 3). These MOI levels are described in relation to recent publications and tools, to highlight their practicality and function. The drawbacks and limitations of these MOI are also discussed for future improvement toward more amenable strategies in plant systems biology.

Drought stress modulates cuticular wax composition of the grape berry

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

Phytohormone profiles are strongly altered during induction and symptom development of the physiological ripening disorder berry shrivel in grapevine

The process of grape berry ripening follows three phases with distinct metabolic processes and complex regulations via phytohormones. The physiological ripening disorder berry shrivel (BS) is characterized by reduced sugar accumulation, low anthocyanin contents, and high acidity in affected berries. The processes leading to BS induction are unknown, but recent transcriptional data on reduced expression of switch genes hint towards a disturbed ripening onset. Herein we investigated the phytohormone composition throughout grape berry ripening in healthy and BS berries in Vitis vinifera L. cultivar Blauer Zweigelt. Thereby we hypothesize that phytohormones are key players for BS induction and suppress the expression of switch genes at veraison. The presented metabolomics and RNAseq data describe two distinct phytohormone profiles in BS berries, differing between pre- and post-veraison with a clear ethylene precursor (aminocyclopropane-1-carboxylic acid, ACC) peak before veraison. Exogenous application of ACC led to BS symptoms, while ethephone application led to berry abscission. During post-veraison, we observed high ABA-glucose ester (ABA-GE) and low indole-3-acetate aspartate (IAA-Asp) and isopentenyladenine (iP) contents in BS berries and the transcriptional induction of several phytohormone pathways. The presented descriptive data provide valuable knowledge to further decipher the role of phytohormones in BS induction and BS symptom development.

Can metabolic tightening and expansion of co-expression network play a role in stress response and tolerance?

Plants respond and adapt to changes in their environment by employing a wide variety of genetic, molecular, and biochemical mechanisms. When so doing, they trigger large-scale rearrangements at the metabolic and transcriptional levels. The dynamics and patterns of these rearrangements and how they govern a stress response is not clear. In this opinion, we discuss a plant's response to stress from the perspective of the metabolic gene co-expression network and its rearrangement upon stress. As a case study, we use publicly available expression data of Arabidopsis thaliana plants exposed to heat and drought stress to evaluate and compare the co-expression networks of metabolic genes. The analysis highlights that stress conditions can lead to metabolic tightening and expansion of the co-expression network. We argue that this rearrangement could play a role in a plant's response to stress and thus may be an additional tool to assess and understand stress tolerance/sensitivity. Additional studies are needed to evaluate the metabolic network in response to multiple stresses at various intensities and across different genetic backgrounds (e.g., intra- and inter-species, sensitive and tolerant eco/genotypes).