Grapevine field experiments reveal the contribution of genotype, the influence of environment and the effect of their interaction (G×E) on the berry transcriptome

Study of red vine phenotypic plasticity across central-southern Italy sites: an integrated analysis of the transcriptome and weather indices through WGCNA

The grapevine (Vitis spp., family Vitaceae) is characterized by marked phenotypic plasticity. Its ability to withstand specific environmental conditions depends on the activation of highly coordinated responses resulting from interactions among genotypes (G) and environmental factors (E). In this study, the transcriptomes of commercially ripe berries of the Cabernet Sauvignon and Aglianico genotypes grown in open fields at three different sites in central-southern Italy (Campania, Molise and Sicily) were analyzed with RNA sequencing. These transcriptomic data were integrated with a comprehensive set of weather course indices through weighted gene co-expression network analysis (WGCNA). A total of 11,887 differentially expressed genes (DEGs) were retrieved, most of which were associated with the Aglianico genotype. The plants from the Sicilian site presented the greatest number of DEGs for both genotypes. Most of the weather course data (daily maximum air temperature, relative humidity, air pressure, dew point, and hours of sun radiation) were significantly correlated with the "lightcyan1" module, confirming WGCNA as a powerful method for identifying genes of high biological interest. Within this module, the gene encoding the ACA10 cation transporter was highly expressed in plants of both genotypes from Campania, where the lowest anthocyanin content was recorded. The transcriptome was also correlated with quality traits, such as total soluble solids and polyphenol content. This approach could lead to the identification of a transcriptomic profile that may specifically identify a genotype and its growing site and to the discovery of hub genes that might function as markers of wine quality.

Grapevine varieties show different sensitivities to flavonoid alterations caused by high temperatures under two irrigation conditions

This study aimed to assess the response of four red grapevine (Vitis vinifera L.) varieties to elevated temperature, drought and their combination, focusing on the concentration and profile of grape flavonoids. Fruit-bearing cuttings of Tempranillo, Cabernet Sauvignon, Merlot and Grenache grew in greenhouses under, either ambient temperature (T) or ambient temperature + 4 °C (T+4). Plants also received either full irrigation (FI, substrate field capacity) or deficit irrigation (DI, 50 % substrate field capacity). In general, T+4 decreased the concentration of anthocyanins, but DI mitigated this effect. T+4 and DI increased the abundance of methylated anthocyanins and flavonols with additive effects. Grapes under T+4 had higher abundance of acylated anthocyanins, while DI increased the proportion of tri-hydroxylated anthocyanins and flavonols. The impact of interacting elevated temperature and drought on grape composition was genotype dependent. In terms of anthocyanin concentration and profile, Tempranillo was the most affected variety, whereas Grenache was less sensitive.

NERD-seq: a novel approach of Nanopore direct RNA sequencing that expands representation of non-coding RNAs

Non-coding RNAs (ncRNAs) are frequently documented RNA modification substrates. Nanopore Technologies enables the direct sequencing of RNAs and the detection of modified nucleobases. Ordinarily, direct RNA sequencing uses polyadenylation selection, studying primarily mRNA gene expression. Here, we present NERD-seq, which enables detection of multiple non-coding RNAs, excluded by the standard approach, alongside natively polyadenylated transcripts. Using neural tissues as a proof of principle, we show that NERD-seq expands representation of frequently modified non-coding RNAs, such as snoRNAs, snRNAs, scRNAs, srpRNAs, tRNAs, and rRFs. NERD-seq represents an RNA-seq approach to simultaneously study mRNA and ncRNA epitranscriptomes in brain tissues and beyond.

Effects of Wind Exposure and Deficit Irrigation on Vegetative Growth, Yield Components and Berry Composition of Malbec and Cabernet Sauvignon

The impact of global warming on Argentine viticulture may result in a geographical shift, with wine-growing regions potentially moving towards the southwest, known as one of the windiest regions in the world. Deficit irrigation is a widely used strategy to control the shoot growth and improve fruit quality attributes, such as berry skin polyphenols. The present study aimed to assess the effects of different wind intensities and irrigation levels, as well as their interactions, on field-grown Vitis vinifera L. cvs. Malbec and Cabernet Sauvignon. The experiment was conducted during two growing seasons with two wind treatments (sheltered and exposed) and two irrigation treatments (well-watered and moderate deficit irrigation) in a multifactorial design. Vegetative growth, stomatal conductance, shoot biomass partition, fruit yield components and berry skin phenolics were evaluated. Our study found that, generally, wind exposure reduced vegetative growth, and deficit irrigation increased the proportion of smaller berries within the bunches. Meanwhile, deficit irrigation and wind exposure additively increased the concentration of berry skin phenolics. Combined stressful conditions enhance biomass partition across the shoot to fruits in Malbec, increasing the weight of bunches and the number of berries. Our findings offer practical implications for vineyard managers in windy regions, providing actionable insights to optimize grapevine cultivation and enhance wine quality.

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.

Metabolite profiling reveals the influence of grapevine genetic distance on the chemical signature of juices

BACKGROUND

Yield, disease tolerance, and climate adaptation are important traits in grapevine genetic breeding programs. Selection for these characteristics causes unpredictable changes in primary and specialized metabolism, affecting the physicochemical properties and chemical composition of the berries and their processed products, juice, and wine. In this study, we investigated the influence of the genetic distance between grapevine genotypes on the chemical signatures of the juices, by integrating comprehensive metabolic profiling to genetic analyses.

RESULTS

The studied grapevine cultivars exhibited low genetic diversity. Breeding for agronomic traits promoted higher contents of soluble sugars, total phenolics, and anthocyanins in the juices. Untargeted juice metabolomics identified a total of 147 metabolites, consisting of 30 volatiles, 21 phenolics, and 96 ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) features. Juices from grapes of the most recent cultivars exhibited increased levels of trans-resveratrol, catechin, and luteolin. The blend of volatiles from juices of later cultivars was also more complex, consisting of 29 distinct metabolites in 'BRS Magna'. Grapes from 'BRS Carmem', an intermediate cultivar, gave the most divergent UHPLC-MS juice profile.

CONCLUSION

Contents of soluble solids, total phenolics, and anthocyanins in grape juices were increased by controlled crosses and hybrid selection. Integrative analyses demonstrated that the juices' metabolic profiles accurately represent the cultivars' genetic distances. Juices from 'BRS Violeta' and 'BRS Magna' show relevant positive association with health-related phenolics and a distinct set of odor volatiles, although these characteristics were specifically sought by breeding. © 2023 Society of Chemical Industry.

The Role of Terroir on the Ripening Traits of V. vinifera cv 'Glera' in the Prosecco Area

The grapevine (Vitis vinifera L.) is widely cultivated worldwide owing to the substantial commercial value of the grapes and other products derived from their processing, wines in particular. The grapevine is characterized by a remarkable phenotypic plasticity within the same variety, which shapes the final berry quality attributes hence reflecting the complex interactions between the plant and the environment leading to the expression of wine typicity. In this study, we explored the metabolomic and transcriptomic basis of the plasticity of Glera, a white berry grapevine variety particularly renowned for the production of wine Prosecco. The two selected vineyards varied for site altitude and pedoclimatic conditions. We highlighted that these environments determined different berry ripening dynamics at the level of both technological parameters and the total abundance and intrafamily distribution of phenolic compounds. Moreover, a clear impact on the grape aroma profile was observed. The genome-wide gene expression analysis of the berries revealed remarkable differences in the ripening transcriptomic program, reflecting the differences in water status, light exposure, and temperature experienced by the plants while growing at the two sites. Overall, this survey portrayed how the quality attributes of the cv 'Glera' grape berries may be affected by different environmental conditions within the typical area of Prosecco wine production.

Genetic and Epigenetic Responses of Autochthonous Grapevine Cultivars from the 'Epirus' Region of Greece upon Consecutive Drought Stress

Within the framework of preserving and valorizing the rich grapevine germplasm of the Epirus region of Greece, indigenous grapevine (Vitis vinifera L.) cultivars were characterized and assessed for their resilience to abiotic stresses in the context of climate change. The cultivars 'Debina' and 'Dichali' displayed significant differences in their response to drought stress as judged by morpho-physiological analysis, indicating higher drought tolerance for Dichali. Hence, they were selected for further study aiming to identify genetic and epigenetic mechanisms possibly regulating drought adaptability. Specifically, self-rooted and heterografted on 'Richter 110' rootstock plants were subjected to two phases of drought with a recovery period in between. Gene expression analysis was performed for two stress-related miRNAs and their target genes: (a) miRNA159 and putative targets, VvMYB101, VvGATA-26-like, VvTOPLESS-4-like and (b) miRNA156 and putative target gene VvCONSTANS-5. Overall, grafted plants exhibited a higher drought tolerance than self-rooted plants, suggesting beneficial rootstock-scion interactions. Comparative analysis revealed differential gene expression under repetitive drought stresses between the two cultivars as well as between the self-rooted and grafted plants. 'Dichali' exhibited an up-regulation of most of the genes examined, which may be associated with increased tolerance. Nevertheless, the profound down-regulation of VvTOPLESS-4-like (a transcriptional co-repressor of transcription factors) upon drought and the concomitant up-regulation of miRNA159 highlights the importance of this 'miRNA-target' module in drought responsiveness. DNA methylation profiling using MSAP analysis revealed differential methylation patterns between the two genotypes in response to drought. Further investigations of gene expression and DNA methylation will contribute to our understanding of the epigenetic mechanisms underlying grapevine tolerance to drought stress.

Genetic independence between traits separated by metamorphosis is widespread but varies with biological function

Why is metamorphosis so pervasive? Does it facilitate the independent (micro)evolution of quantitative traits in distinct life stages, similarly to how it enables some limbs and organs to develop at specific life stages? We tested this hypothesis by measuring the expression of 6400 genes in 41 Drosophila melanogaster inbred lines at larval and adult stages. Only 30% of the genes showed significant genetic correlations between larval and adult expression. By contrast, 46% of the traits showed some level of genetic independence between stages. Gene ontology terms enrichment revealed that across stages correlated traits were often involved in proteins synthesis, insecticide resistance and innate immunity, while a vast number of genes expression traits associated with energy metabolism were independent between life stages. We compared our results to a similar case: genetic constraints between males and females in gonochoric species (i.e. sexual antagonism). We expected selection for the separation between males and females to be higher than between juvenile and adult functions, as gonochorism is a more common strategy in the animal kingdom than metamorphosis. Surprisingly, we found that inter-stage constraints were lower than inter-sexual genetic constraints. Overall, our results show that metamorphosis enables a large part of the transcriptome to evolve independently at different life stages.

Investigating the impact of pedoclimatic conditions on the oenological performance of two red cultivars grown throughout southern Italy

The cultivated grapevine, Vitis vinifera subsp. vinifera, possesses a rich biodiversity with numerous varieties. Each variety adapts differently to varying pedoclimatic conditions, which greatly influence the terroir expression of wine regions. These conditions impact vine growth, physiology, and berry composition, ultimately shaping the unique characteristics and typicity of the wines produced. Nowadays, the potential of the different adaptation capacities of grape varieties has not yet been thoroughly investigated. We addressed this issue by studying two grape varieties, Aglianico and Cabernet Sauvignon, in two different pedoclimatic conditions of Southern Italy. We evaluated and compared the effect of different pedoclimatic conditions on plant physiology, the microbial quality of grapes using Next-Generation Sequencing (NGS) technology, the expression trends of key genes in ripe berries and the concentration of phenolic compounds in grapes and wines by HPLC-MS, HPLC-DAD, NMR and spectrophotometric analyses. Metabolomic and microbiome data were integrated with quantitative gene expression analyses to examine varietal differences and plasticity of genes involved in important oenological pathways. The data collected showed that the phenotypic response of studied grapes in terms of vigor, production, and fruit quality is strongly influenced by the pedoclimatic conditions and, in particular, by soil physical properties. Furthermore, Aglianico grape variety was more influenced than the Cabernet Sauvignon by environmental conditions. In conclusion, the obtained findings not only reinforce the terroir concept and our comprehension of grape's ability to adapt to climate variations but can also have implications for the future usage of grape genetic resources.

Secondary metabolites in grapevine: crosstalk of transcriptional, metabolic and hormonal signals controlling stress defence responses in berries and vegetative organs

Abiotic stresses, such as temperature, heat waves, water limitation, solar radiation and the increase in atmospheric CO₂ concentration, significantly influence the accumulation of secondary metabolites in grapevine berries at different developmental stages, and in vegetative organs. Transcriptional reprogramming, miRNAs, epigenetic marks and hormonal crosstalk regulate the secondary metabolism of berries, mainly the accumulation of phenylpropanoids and of volatile organic compounds (VOCs). Currently, the biological mechanisms that control the plastic response of grapevine cultivars to environmental stress or that occur during berry ripening have been extensively studied in many worlds viticultural areas, in different cultivars and in vines grown under various agronomic managements. A novel frontier in the study of these mechanisms is the involvement of miRNAs whose target transcripts encode enzymes of the flavonoid biosynthetic pathway. Some miRNA-mediated regulatory cascades, post-transcriptionally control key MYB transcription factors, showing, for example, a role in influencing the anthocyanin accumulation in response to UV-B light during berry ripening. DNA methylation profiles partially affect the berry transcriptome plasticity of different grapevine cultivars, contributing to the modulation of berry qualitative traits. Numerous hormones (such as abscisic and jasmomic acids, strigolactones, gibberellins, auxins, cytokynins and ethylene) are involved in triggering the vine response to abiotic and biotic stress factors. Through specific signaling cascades, hormones mediate the accumulation of antioxidants that contribute to the quality of the berry and that intervene in the grapevine defense processes, highlighting that the grapevine response to stressors can be similar in different grapevine organs. The expression of genes responsible for hormone biosynthesis is largely modulated by stress conditions, thus resulting in the numeourous interactions between grapevine and the surrounding environment.

A molecular phenology scale of grape berry development

Fruit growth and development consist of a continuous succession of physical, biochemical, and physiological changes driven by a genetic program that dynamically responds to environmental cues. Establishing recognizable stages over the whole fruit lifetime represents a fundamental requirement for research and fruit crop cultivation. This is especially relevant in perennial crops like grapevine (Vitis vinifera L.) to scale the development of its fruit across genotypes and growing conditions. In this work, molecular-based information from several grape berry transcriptomic datasets was exploited to build a molecular phenology scale (MPhS) and to map the ontogenic development of the fruit. The proposed statistical pipeline consisted of an unsupervised learning procedure yielding an innovative combination of semiparametric, smoothing, and dimensionality reduction tools. The transcriptomic distance between fruit samples was precisely quantified by means of the MPhS that also enabled to highlight the complex dynamics of the transcriptional program over berry development through the calculation of the rate of variation of MPhS stages by time. The MPhS allowed the alignment of time-series fruit samples proving to be a complementary method for mapping the progression of grape berry development with higher detail compared to classic time- or phenotype-based approaches.

Dissecting the effect of soil on plant phenology and berry transcriptional plasticity in two Italian grapevine varieties (Vitis vinifera L.)

Grapevine embodies a fascinating species as regards phenotypic plasticity and genotype-per-environment interactions. The terroir, namely the set of agri-environmental factors to which a variety is subjected, can influence the phenotype at the physiological, molecular, and biochemical level, representing an important phenomenon connected to the typicality of productions. We investigated the determinants of plasticity by conducting a field-experiment where all terroir variables, except soil, were kept as constant as possible. We isolated the effect of soils collected from different areas, on phenology, physiology, and transcriptional responses of skin and flesh of a red and a white variety of great economic value: Corvina and Glera. Molecular results, together with physio-phenological parameters, suggest a specific effect of soil on grapevine plastic response, highlighting a higher transcriptional plasticity of Glera in respect to Corvina and a marked response of skin compared to flesh. Using a novel statistical approach, we identified clusters of plastic genes subjected to the specific influence of soil. These findings could represent an issue of applicative value, posing the basis for targeted agricultural practices to enhance the desired characteristics for any soil/cultivar combination, to improve vineyards management for a better resource usage and to valorize vineyards uniqueness maximizing the terroir-effect.

Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification

The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.

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.

Physiological and Transcriptional Responses to Saline Irrigation of Young 'Tempranillo' Vines Grafted Onto Different Rootstocks

The use of more salt stress-tolerant vine rootstocks can be a sustainable strategy for adapting traditional grapevine cultivars to future conditions. However, how the new M1 and M4 rootstocks perform against salinity compared to conventional ones, such as the 1103-Paulsen, had not been previously assessed under real field conditions. Therefore, a field trial was carried out in a young 'Tempranillo' (Vitis vinifera L.) vineyard grafted onto all three rootstocks under a semi-arid and hot-summer Mediterranean climate. The vines were irrigated with two kinds of water: a non-saline Control with EC of 0.8 dS m-1 and a Saline treatment with 3.5 dS m-1. Then, various physiological parameters were assessed in the scion, and, additionally, gene expression was studied by high throughput sequencing in leaf and berry tissues. Plant water relations evidenced the osmotic effect of water quality, but not that of the rootstock. Accordingly, leaf-level gas exchange rates were also reduced in all three rootstocks, with M1 inducing significantly lower net photosynthesis rates than 1103-Paulsen. Nevertheless, the expression of groups of genes involved in photosynthesis and amino acid metabolism pathways were not significantly and differentially expressed. The irrigation with saline water significantly increased leaf chloride contents in the scion onto the M-rootstocks, but not onto the 1103P. The limitation for leaf Cl- and Na+ accumulation on the scion was conferred by rootstock. Few processes were differentially regulated in the scion in response to the saline treatment, mainly, in the groups of genes involved in the flavonoids and phenylpropanoids metabolic pathways. However, these transcriptomic effects were not fully reflected in grape phenolic ripeness, with M4 being the only one that did not cause reductions in these compounds in response to salinity, and 1103-Paulsen having the highest overall concentrations. These results suggest that all three rootstocks confer short-term salinity tolerance to the scion. The lower transcriptomic changes and the lower accumulation of potentially phytotoxic ions in the scion grafted onto 1103-Paulsen compared to M-rootstocks point to the former being able to maintain this physiological response in the longer term. Further agronomic trials should be conducted to confirm these effects on vine physiology and transcriptomics in mature vineyards.

Bioinformatic approach for the discovery of cis-eQTL signals during fruit ripening of a woody species as grape (Vitis vinifera L.)

Expression quantitative trait loci (eQTLs) are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetic variance of gene expression of complex phenotypes. eQTLs analyses are common in biomedical models but are scarce in woody crop species such as fruit trees or grapes. In this study, a comprehensive bioinformatic analysis was conducted leveraging with expression data from two different growth stages, around ripening onset, of 10 genotypes of grape (Vitis vinifera L.). A total of 2170 cis-eQTL were identified in 212 gene modulated at ripening onset. The 48% of these DEGs have a known function. Among the annotated protein-coding genes, terpene synthase, auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and flavonol synthase were noted. This new inventory of cis-eQTLs influencing gene expression during fruit ripening will be an important resource to examine variation for this trait and will help to elucidate the complex genetic architecture underlying this process in grape.

Developmental Regulation of Transcription in Touriga Nacional Berries under Deficit Irrigation

Grapevine (Vitis vinifera L.) is one of the most economically important crops worldwide, especially due to the economic relevance of wine production. Abiotic stress, such as drought, may contribute to low yield, shifts in quality, and important economic loss. The predicted climate change phenomena point to warmer and dryer Mediterranean environmental conditions; as such, it is paramount to study the effects of abiotic stress on grapevine performance. Deficit irrigation systems are applied to optimize water use efficiency without compromising berry quality. In this research, the effect of two deficit irrigation strategies, sustained deficit irrigation (SDI) and regulated deficit irrigation (RDI), in the grape berry were assessed. The effects of different levels of drought were monitored in Touriga Nacional at key stages of berry development (pea size, véraison, and full maturation) through RNA-Seq transcriptome analysis and by specific differentially expressed genes (DEGs) monitoring through RT-qPCR. Handy datasets were obtained by bioinformatics analysis of raw RNA-Seq results. The dominant proportion of transcripts was mostly regulated by development, with véraison showing more upregulated transcripts. Results showed that primary metabolism is the functional category more severely affected under water stress. Almost all DEGs selected for RT-qPCR were significantly upregulated in full maturation and showed the highest variability at véraison and the lowest gene expression values in the pea size stage.

Stress responses and epigenomic instability mark the loss of somatic embryogenesis competence in grapevine

Somatic embryogenesis (SE) represents the most appropriate tool for next-generation breeding methods in woody plants such as grapevine (Vitis vinifera L.). However, in this species, the SE competence is strongly genotype-dependent and the molecular basis of this phenomenon is poorly understood. We explored the genetic and epigenetic basis of SE in grapevine by profiling the transcriptome, epigenome, and small RNAome of undifferentiated, embryogenic, and non-embryogenic callus tissues derived from two genotypes differing in competence for SE, Sangiovese and Cabernet Sauvignon. During the successful formation of embryonic callus, we observed the upregulation of epigenetic-related transcripts and short interfering RNAs in association with DNA hypermethylation at transposable elements in both varieties. Nevertheless, the switch to nonembryonic development matched the incomplete reinforcement of transposon silencing, and the evidence of such effect was more apparent in the recalcitrant Cabernet Sauvignon. Transcriptomic differences between the two genotypes were maximized already at early stage of culture where the recalcitrant variety expressed a broad panel of genes related to stress responses and secondary metabolism. Our data provide a different angle on the SE molecular dynamics that can be exploited to leverage SE as a biotechnological tool for fruit crop breeding.

The grapevine (Vitis vinifera L.) floral transcriptome in Pinot noir variety: identification of tissue-related gene networks and whorl-specific markers in pre- and post-anthesis phases

The comprehension of molecular processes underlying the development and progression of flowering in plants is a hot topic, not only because that often the products of interest for human and animal nutrition are linked to the development of fruits or seeds, but also because the processes of gametes formation occurring in sexual organs are at the basis of recombination and genetic variability which constitutes the matter on which evolution acts, whether understood as natural or human driven. In the present study, we used an NGS approach to produce a grapevine flower transcriptome snapshot in different whorls and tissues including calyx, calyptra, filament, anther, stigma, ovary, and embryo in both pre- and post-anthesis phases. Our investigation aimed at identifying hub genes that unequivocally distinguish the different tissues providing insights into the molecular mechanisms that are at the basis of floral whorls and tissue development. To this end we have used different analytical approaches, some now consolidated in transcriptomic studies on plants, such as pairwise comparison and weighted-gene coexpression network analysis, others used mainly in studies on animals or human's genomics, such as the tau (τ) analysis aimed at isolating highly and absolutely tissue-specific genes. The intersection of data obtained by these analyses allowed us to gradually narrow the field, providing evidence about the molecular mechanisms occurring in those whorls directly involved in reproductive processes, such as anther and stigma, and giving insights into the role of other whorls not directly related to reproduction, such as calyptra and calyx. We believe this work could represent an important genomic resource for functional analyses of grapevine floral organ growth and fruit development shading light on molecular networks underlying grapevine reproductive organ determination.

Evidence of differential spreading events of grapevine pinot Gris virus in Italy using datamining as a tool

Since its identification in 2003, grapevine Pinot gris virus (GPGV, Trichovirus) has now been detected in most grape-growing countries. So far, little is known about the epidemiology of this newly emerging virus. In this work, we used datamining as a tool to monitor in-silico the sanitary status of three vineyards in Italy. All data used in the study were recovered from a work that was already published and for which data were publicly available as SRA (Sequence Read Archive, NCBI) files. While incomplete, knowledge gathered from this work was still important, with evidence of differential accumulation of the virus in grapevine according to year, location, and variety-rootstock association. Additional data regarding GPGV genetic diversity were collected. Some advantages and pitfalls of datamining are discussed.

VviNAC33 promotes organ de-greening and represses vegetative growth during the vegetative-to-mature phase transition in grapevine

Plants undergo several developmental transitions during their life cycle. In grapevine, a perennial woody fruit crop, the transition from vegetative/green-to-mature/woody growth involves transcriptomic reprogramming orchestrated by a small group of genes encoding regulators, but the underlying molecular mechanisms are not fully understood. We investigated the function of the transcriptional regulator VviNAC33 by generating and characterizing transgenic overexpressing grapevine lines and a chimeric repressor, and by exploring its putative targets through a DNA affinity purification sequencing (DAP-seq) approach combined with transcriptomic data. We demonstrated that VviNAC33 induces leaf de-greening, inhibits organ growth and directly activates the expression of STAY-GREEN PROTEIN 1 (SGR1), which is involved in Chl and photosystem degradation, and AUTOPHAGY 8f (ATG8f), which is involved in the maturation of autophagosomes. Furthermore, we show that VviNAC33 directly inhibits AUXIN EFFLUX FACILITATOR PIN1, RopGEF1 and ATP SYNTHASE GAMMA CHAIN 1T (ATPC1), which are involved in photosystem II integrity and activity. Our results show that VviNAC33 plays a major role in terminating photosynthetic activity and organ growth as part of a regulatory network governing the vegetative-to-mature phase transition.

Comparative transcriptome analyses between cultivated and wild grapes reveal conservation of expressed genes but extensive rewiring of co-expression networks

The transcriptomes of wild and cultivated grapes consists of similar expressed genes but distinct wiring of co-expressed modules associated with environmental conditions. Grapevine is an important fruit crop worldwide, with high economic value and widespread distribution. Commercial production is based on Vitis vinifera, and, to a lesser extent, on hybrids with American grapes, such as V. labrusca. Wild grape relatives are important sources of resistance against biotic and abiotic factors; however, their global gene expression patterns remain poorly characterized. We associated genome-wide transcript profiling to phenotypic analyses to investigate the responses of cultivated and wild vines to vineyard conditions. The expressed genes in the Vitis reference transcriptome are largely shared by wild grapes, V. labrusca hybrids and vinifera cultivars. In contrast, significant differential regulation between wild and vinifera genotypes represents 80% of gene expression variation, regardless of the environment. In wild grapes, genes associated to regulatory processes are downregulated, whereas those involved in metabolic pathways are upregulated, in comparison to vinifera. Photosynthesis-related ontologies are overrepresented in the induced genes, in agreement with higher contents of chlorophyll in wild grapes. Co-regulated gene network analyses provide evidence of more complex transcriptome organization in vinifera. In wild grapes, genes involved in signaling pathways of stress-related hormones are overrepresented in modules associated with the environment. Consensus network analyses revealed high preservation within co-regulated gene modules between cultivated and wild grapes, but divergent relationships among the expression clusters. In conclusion, the distinct phenotypes of wild and cultivated grapes are underlain by differences in gene expression, but also by distinct higher-order organization of the transcriptome and contrasting association of co-expressed gene clusters with the environment.

Secondary Metabolism and Defense Responses Are Differently Regulated in Two Grapevine Cultivars during Ripening

Vitis vinifera ‘Nebbiolo’ is one of the most important wine grape cultivars used to produce prestigious high-quality wines known throughout the world, such as Barolo and Barbaresco. ‘Nebbiolo’ is a distinctive genotype characterized by medium/high vigor, long vegetative and ripening cycles, and limited berry skin color rich in 3′-hydroxylated anthocyanins. To investigate the molecular basis of these characteristics, ‘Nebbiolo’ berries collected at three different stages of ripening (berry pea size, véraison, and harvest) were compared with V. vinifera ‘Barbera’ berries, which are rich in 3′,5′-hydroxylated anthocyanins, using transcriptomic and analytical approaches. In two consecutive seasons, the two genotypes confirmed their characteristic anthocyanin profiles associated with a different modulation of their transcriptomes during ripening. Secondary metabolism and response to stress were the functional categories that most differentially changed between ‘Nebbiolo’ and ‘Barbera’. The profile rich in 3′-hydroxylated anthocyanins of ‘Nebbiolo’ was likely linked to a transcriptional downregulation of key genes of anthocyanin biosynthesis. In addition, at berry pea size, the defense metabolism was more active in ‘Nebbiolo’ than ‘Barbera’ in absence of biotic attacks. Accordingly, several pathogenesis-related proteins, WRKY transcription factors, and stilbene synthase genes were overexpressed in ‘Nebbiolo’, suggesting an interesting specific regulation of defense pathways in this genotype that deserves to be further explored.

Somatic variants for seed and fruit set in grapevine

BACKGROUND

Grapevine reproductive development has direct implications on yield. It also impacts on berry and wine quality by affecting traits like seedlessness, berry and bunch size, cluster compactness and berry skin to pulp ratio. Seasonal fluctuations in yield, fruit composition and wine attributes, which are largely driven by climatic factors, are major challenges for worldwide table grape and wine industry. Accordingly, a better understanding of reproductive processes such as gamete development, fertilization, seed and fruit set is of paramount relevance for managing yield and quality. With the aim of providing new insights into this field, we searched for clones with contrasting seed content in two germplasm collections.

RESULTS

We identified eight variant pairs that seemingly differ only in seed-related characteristics while showing identical genotype when tested with the GrapeReSeq_Illumina_20K_SNP_chip and several microsatellites. We performed multi-year observations on seed and fruit set deriving from different pollination treatments, with special emphasis on the pair composed by Sangiovese and its seedless variant locally named Corinto Nero. The pollen of Corinto Nero failed to germinate in vitro and gave poor berry set when used to pollinate other varieties. Most berries from both open- and cross-pollinated Corinto Nero inflorescences did not contain seeds. The genetic analysis of seedlings derived from occasional Corinto Nero normal seeds revealed that the few Corinto Nero functional gametes are mostly unreduced. Moreover, three genotypes, including Sangiovese and Corinto Nero, were unexpectedly found to develop fruits without pollen contribution and occasionally showed normal-like seeds. Five missense single nucleotide polymorphisms were identified between Corinto Nero and Sangiovese from transcriptomic data.

CONCLUSIONS

Our observations allowed us to attribute a seedlessness type to some variants for which it was not documented in the literature. Interestingly, the VvAGL11 mutation responsible for Sultanina stenospermocarpy was also discovered in a seedless mutant of Gouais Blanc. We suggest that Corinto Nero parthenocarpy is driven by pollen and/or embryo sac defects, and both events likely arise from meiotic anomalies. The single nucleotide polymorphisms identified between Sangiovese and Corinto Nero are suitable for testing as traceability markers for propagated material and as functional candidates for the seedless phenotype.

The study of VvMybA1 allele status of the indigenous grapevine varieties with non-colored berries

In the present work we describe preliminary results on a partial VvMybA1 locus sequencing of rear indigenous grapevine varieties. Obtained sequences were mostly conservative and have matches in NCBI GenBank. As expected, most of them have a sequence that is typical for varieties with non-colored berries. Surprisingly, however, cultivar Jaj izium biely demonstrated structure typical for varieties with colored berries, which implies another reason for the loss of color. Obviously, Tavlinskii pozdnii and Sypun chernyj varieties had typical for colored cultivars allele structure. Some nucleotide substitutions and differences in structure of sequences were found. Furthemore, we submitted our sequences to the NCBI and here we present their accession numbers: Unji bely (MW633123), Voskeat (MW633125), Tsolikauri (MW633126), Shabash (MW633127), Terbash (MW633130), Bajan Shirei (MW633131), Katta Kurgan (MW633132), Sirgula (MW633135), Khatmi (MW633136), Jaj izium biely (N/A), Tavlinskii pozdnii (MW633139), Sypun chernyj (MW633151). All sequences, excluding Jaj izium biely genotype, were submitted to the GenBank and will be available to the public as soon as possible.

How Do Novel M-Rootstock (Vitis Spp.) Genotypes Cope with Drought?

Most of the vineyards around the world are in areas characterized by seasonal drought, where water deficits and high temperatures represent severe constraints on the regular grapevine growth cycle. Although grapevines are well adapted to arid and semi-arid environments, water stress can cause physiological changes, from mild to irreversible. Screening of available Vitis spp. genetic diversity for new rootstock breeding programs has been proposed as a way for which new viticulture challenges may be faced. In 2014, novel genotypes (M-rootstocks) were released from the University of Milan. In this work, the behavior of M1, M3 and M4 in response to decreasing water availabilities (80%, 50% and 20% soil water content, SWC) was investigated at the physiological and gene expression levels, evaluating gas exchange, stem water potential and transcript abundances of key genes related to ABA (abscisic acid) biosynthesis (VvZEP, VvNCED1 and VvNCED2) and signaling (VvPP2C4, VvSnRK2.6 and VvABF2), and comparing them to those of cuttings of nine commercial rootstocks widely used in viticulture. M-rootstocks showed a change at physiological levels in severe water-stressed conditions (20% soil water content, SWC), reducing the stomatal conductance and stem water potential, but maintaining high photosynthetic activity. Water use efficiency was high in water-limiting conditions. The transcriptional changes were observed at 50% SWC, with an increment of transcripts of VvNCED1 and VvNCED2 genes. M-rootstocks showed similar behavior to 1103P and 110R rootstocks, two highly tolerant commercial genotypes. These rootstocks adopted a tolerant strategy to face water-stressed conditions.

Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus

BACKGROUND

With the expanding ash dieback epidemic that has spread across the European continent, an improved functional understanding of the disease development in afflicted hosts is needed. The study investigated whether differences in necrosis extension between common ash (Fraxinus excelsior) trees with different levels of susceptibility to the fungus Hymenoscyphus fraxineus are associated with, and can be explained by, the differences in gene expression patterns. We inoculated seemingly healthy branches of each of two resistant and susceptible ash genotypes with H. fraxineus grown in a common garden.

RESULTS

Ten months after the inoculation, the length of necrosis on the resistant genotypes were shorter than on the susceptible genotypes. RNA sequencing of bark samples collected at the border of necrotic lesions and from healthy tissues distal to the lesion revealed relatively limited differences in gene expression patterns between susceptible and resistant genotypes. At the necrosis front, only 138 transcripts were differentially expressed between the genotype categories while 1082 were differentially expressed in distal, non-symptomatic tissues. Among these differentially expressed genes, several genes in the mevalonate (MVA) and iridoid pathways were found to be co-regulated, possibly indicating increased fluxes through these pathways in response to H. fraxineus. Comparison of transcriptional responses of symptomatic and non-symptomatic ash in a controlled greenhouse experiment revealed a relatively small set of genes that were differentially and concordantly expressed in both studies. This gene-set included the rate-limiting enzyme in the MVA pathway and a number of transcription factors. Furthermore, several of the concordantly expressed candidate genes show significant similarity to genes encoding players in the abscisic acid- or Jasmonate-signalling pathways.

CONCLUSIONS

A set of candidate genes, concordantly expressed between field and greenhouse experiments, was identified. The candidates are associated with hormone signalling and specialized metabolite biosynthesis pathways indicating the involvement of these pathways in the response of the host to infection by H. fraxineus.

Rapid dehydration of grape berries dampens the post-ripening transcriptomic program and the metabolite profile evolution

The postharvest dehydration of grape berries allows the concentration of sugars and other solutes and promotes the synthesis of metabolites and aroma compounds unique to high-quality raisin wines such as the passito wines made in Italy. These dynamic changes are dependent on environmental parameters such as temperature and relative humidity, as well as endogenous factors such as berry morphology and genotype, but the contribution of each variable is not well understood. Here, we compared berries subjected to natural or accelerated dehydration, the latter driven by forced air flow. We followed the evolution of transcript and metabolite profiles and found that accelerated dehydration clearly dampened the natural transcriptomic and metabolomic programs of postharvest berries. We found that slow dehydration over a prolonged duration is necessary to induce gene expression and metabolite accumulation associated with the final quality traits of dehydrated berries. The accumulation of key metabolites (particularly stilbenoids) during postharvest dehydration is inhibited by rapid dehydration conditions that shorten the berry life time.

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.

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

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

VviERF6Ls: an expanded clade in Vitis responds transcriptionally to abiotic and biotic stresses and berry development

Background

VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress responses. To better understand this highly duplicated, conserved clade, additional members of the clade were identified in four Vitis genotypes. A meta-data analysis was performed on publicly available microarray and RNA-Seq data (confirmed and expanded with RT-qPCR), and Vitis VviERF6L1 overexpression lines were established and characterized with phenotyping and RNA-Seq.

Results

A total of 18 PN40024 VviERF6Ls were identified; additional VviERF6Ls were identified in Cabernet Sauvignon, Chardonnay, and Carménère. The amino acid sequences of VviERF6Ls were found to be highly conserved. VviERF6L transcripts were detected in numerous plant organs and were differentially expressed in response to numerous abiotic stresses including water deficit, salinity, and cold as well as biotic stresses such as red blotch virus, N. parvum, and E. necator. VviERF6Ls were differentially expressed across stages of berry development, peaking in the pre-veraison/veraison stage and retaining conserved expression patterns across different vineyards, years, and Vitis cultivars. Co-expression network analysis identified a scarecrow-like transcription factor and a calmodulin-like gene with highly similar expression profiles to the VviERF6L clade. Overexpression of VviERF6L1 in a Seyval Blanc background did not result in detectable morphological phenotypes. Genes differentially expressed in response to VviERF6L1 overexpression were associated with abiotic and biotic stress responses.

Conclusions

VviERF6Ls represent a large and distinct clade of ERF transcription factors in grapevine. The high conservation of protein sequence between these 18 transcription factors may indicate these genes originate from a duplication event in Vitis. Despite high sequence similarity and similar expression patterns, VviERF6Ls demonstrate unique levels of expression supported by similar but heterogeneous promoter sequences. VviERF6L gene expression differed between Vitis species, cultivars and organs including roots, leaves and berries. These genes respond to berry development and abiotic and biotic stresses. VviERF6L1 overexpression in Vitis vinifera results in differential expression of genes related to phytohormone and immune system signaling. Further investigation of this interesting gene family is warranted.

Slower development of lower canopy beans produces better coffee

The production of high-quality coffee is being challenged by changing climates in coffee-growing regions. The coffee beans from the upper and lower canopy at different development stages of the same plants were analyzed to investigate the impact of the microenvironment on gene expression and coffee quality. Compared with coffee beans from the upper canopy, lower canopy beans displayed more intense aroma with higher caffeine, trigonelline, and sucrose contents, associated with greater gene expression in the representative metabolic pathways. Global gene expression indicated a longer ripening in the lower canopy, resulting from higher expression of genes relating to growth inhibition and suppression of chlorophyll degradation during early bean ripening. Selection of genotypes or environments that enhance expression of the genes slowing bean development may produce higher quality coffee beans, allowing coffee production in a broader range of available future environments.

A key 'foxy' aroma gene is regulated by homology-induced promoter indels in the iconic juice grape 'Concord'

'Concord', the most well-known juice grape with a parentage of the North American grape species Vitis labrusca L., possesses a special 'foxy' aroma predominantly resulted from the accumulation of methyl anthranilate (MA) in berries. This aroma, however, is often perceived as an undesirable attribute by wine consumers and rarely noticeable in the common table and wine grape species V. vinifera. Here we discovered homology-induced promoter indels as a major genetic mechanism for species-specific regulation of a key 'foxy' aroma gene, anthraniloyl-CoA:methanol acyltransferase (AMAT), that is responsible for MA biosynthesis. We found the absence of a 426-bp and/or a 42-bp sequence in AMAT promoters highly associated with high levels of AMAT expression and MA accumulation in 'Concord' and other V. labrusca-derived grapes. These promoter variants, all with direct and inverted repeats, were further confirmed in more than 1,300 Vitis germplasm. Moreover, functional impact of these indels was validated in transgenic Arabidopsis. Superimposed on the promoter regulation, large structural changes including exonic insertion of a retrotransposon were present at the AMAT locus in some V. vinifera grapes. Elucidation of the AMAT genetic regulation advances our understanding of the 'foxy' aroma trait and makes it genetically trackable and amenable in grapevine breeding.

Cultivar, site or harvest date: the gordian knot of wine terroir

INTRODUCTION

The complex interactions of vine cultivars, and localised regional climate associated with specific vineyard sites are important attributes to the concept of terroir and significant contributors to grape maturity and wine sensory profiles. An improved understanding of the influence of each factor and their interactions is a challenging conundrum, and will enable more efficient production targeting specific wine styles.

OBJECTIVES

To characterise the metabolic flux of grape berries and resulting wines to characterise the relative impact of site specific climate, cultivar, and grape maturity based upon berry sugar accumulation models that consistently target specific wine styles.

METHODS

A spatial and temporal study of grape and wine composition was undertaken for two important cultivars in two distinct regions of New South Wales. Measures of composition and wine sensory ratings were simultaneously analysed using a multiblock algorithm taking advantage of the ANOVA framework to identify important contributions to wine style arising from grape maturity, vineyard site and cultivar.

RESULTS

A consistent flux of grape and wine constituents is evident for wine made from sequentially harvested grapes from the same vineyard with increasing levels of grape maturity. Contributions of region and vineyard site to wine style could also be elucidated. Differences in metabolite flux in grapes and resulting wines between cultivars growing in similar conditions are evident.

CONCLUSIONS

The combination of a metabolomics and multiblock data decomposition approach may be successfully used to profile and elucidate the contribution of abiotic factors to grape and wine composition and provide improved understanding of the terroir concept.

High Temperature and Elevated Carbon Dioxide Modify Berry Composition of Different Clones of Grapevine (Vitis vinifera L.) cv. Tempranillo

Tempranillo is a grapevine (Vitis vinifera L.) variety extensively used for world wine production which is expected to be affected by environmental parameters modified by ongoing global climate changes, i.e., increases in average air temperature and rise of atmospheric CO₂ levels. Apart from determining their effects on grape development and biochemical characteristics, this paper considers the intravarietal diversity of the cultivar Tempranillo as a tool to develop future adaptive strategies to face the impact of climate change on grapevine. Fruit-bearing cuttings of five clones (RJ43, CL306, T3, VN31, and 1084) were grown in temperature gradient greenhouses (TGGs), from fruit set to maturity, under two temperature regimes (ambient temperature vs. ambient temperature plus 4°C) and two CO₂ levels (ambient, ca. 400 ppm, vs. elevated, 700 ppm). Treatments were applied separately or in combination. The analyses carried out included berry phenological development, the evolution in the concentration of must compounds (organic acids, sugars, and amino acids), and total skin anthocyanins. Elevated temperature hastened berry ripening, sugar accumulation, and malic acid breakdown, especially when combined with high CO₂. Climate change conditions reduced the amino acid content 2 weeks after mid-veraison and seemed to delay amino acidic maturity. Elevated CO₂ reduced the decoupling effect of temperature on the anthocyanin to sugar ratio. The impact of these factors, taken individually or combined, was dependent on the clone analyzed, thus indicating certain intravarietal variability in the response of Tempranillo to these climate change-related factors.

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.

Effects of Ascophyllum nodosum extract on Vitis vinifera: Consequences on plant physiology, grape quality and secondary metabolism

Seaweed-based extracts have been recently employed as sustainable tools to improve abiotic stress tolerance and increase grape quality. However, the effect of these extracts on secondary metabolism compounds, that are fundamental for grape and wine quality, is still scarce. In the present study, the effects of foliar treatments with an Ascophyllum nodosum extract on physiological and biochemical parameters of Vitis vinifera (cv. Sangiovese) were investigated. We hypothesized an enhancement in the biosynthesis of secondary metabolites in berry skins and in leaves in response to these treatments, effective in improve grape quality and help vines to cope with abiotic stresses. Gas exchanges, chlorophyll fluorescence and midday stem water potential on leaves treated with A. nodosum extract and non-treated control leaves, were monitored over two growing seasons at three phenological stages: full véraison, mid maturation and full maturation. In addition, anthocyanins, flavonols and hydroxycinnamic acids were quantified both in berry skins and in leaves. The foliar treatments with A. nodosum increased photosynthesis and stomatal conductance in treated compared to control plants. Furthermore, extract-treated vines were able to maintain the potential efficiency of photosystem II close to the optimal value even during the hottest periods. No effect of A. nodosum extract treatments was observed on stem water potential. A. nodosum applications delayed berry ripening, leading to a lower sugar content and a higher anthocyanin content in treated berry skins. Interestingly, treatments also affected the content and the partitioning of secondary metabolites in berry skins, as anthocyanins and flavonols contents were higher in treated compared to control plants, while the ratio of methoxylated to non-methoxylated anthocyanins was lower in treated than in control vines. Furthermore, A. nodosum extract-treated plants also had higher content of flavonols and hydroxycinnamic acids both in berry skins and in leaves and showed a reduction in the biosynthesis of methoxylated anthocyanins, which are usually accumulated in grapes under environmental constraints. Considering the challenges posed by climate change in the Mediterranean basin, the use of seaweed extracts might represent a sustainable tool to mitigate the increasing severity of drought, often associated to heat-waves, on the viticulture sector.

The Rpv3-3 Haplotype and Stilbenoid Induction Mediate Downy Mildew Resistance in a Grapevine Interspecific Population

The development of new resistant varieties to the oomycete Plasmopara viticola (Berk.& Curt) is a promising way to combat downy mildew (DM), one of the major diseases threatening the cultivated grapevine (Vitis vinifera L.). Taking advantage of a segregating population derived from "Merzling" (a mid-resistant hybrid) and "Teroldego" (a susceptible landrace), 136 F1 individuals were characterized by combining genetic, phenotypic, and gene expression data to elucidate the genetic basis of DM resistance and polyphenol biosynthesis upon P. viticola infection. An improved consensus linkage map was obtained by scoring 192 microsatellite markers. The progeny were screened for DM resistance and production of 42 polyphenols. QTL mapping showed that DM resistance is associated with the herein named Rpv3-3 specific haplotype and it identified 46 novel metabolic QTLs linked to 30 phenolics-related parameters. A list of the 95 most relevant candidate genes was generated by specifically exploring the stilbenoid-associated QTLs. Expression analysis of 11 genes in Rpv3-3 +/- genotypes displaying disparity in DM resistance level and stilbenoid accumulation revealed significant new candidates for the genetic control of stilbenoid biosynthesis and oligomerization. These overall findings emphasized that DM resistance is likely mediated by the major Rpv3-3 haplotype and stilbenoid induction.

Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress

BACKGROUND

Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest.

RESULTS

The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca²⁺ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened.

CONCLUSIONS

The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program.

Cutting the Gordian Knot of abiotic stress in grapevine: From the test tube to climate change adaptation

In Mediterranean climate areas, the available scenarios for climate change suggest an increase in the frequency of heat waves and severe drought in summer. Grapevine (Vitis vinifera L.) is a traditional Mediterranean species and is the most valuable fruit crop in the world. Currently, viticulture must adjust to impending climate changes that are already pushing vine-growers toward the use of irrigation, with the concomitant losses in wine quality, and researchers to study tolerance to stress in existing genotypes. The viticulture and winemaking worlds are in demand to understand the physiological potential of the available genotypes to respond to climate changes. In this review, we will focus on the cross-talk between common abiotic stresses that currently affect grapevine productivity and that are prone to affect it deeper in the future. We will discuss results obtained under three experimental stress conditions and that call for specific responses: (1) acclimatization of in vitro plantlets, (2) stress combinations in controlled conditions for research purposes, (3) extreme events in the field that, driven by climate changes, are pushing Mediterranean species to the limit. The different levels of tolerance to stress put in evidence by the plasticity of phenotypic and genotypic response mechanisms, will be addressed. This information is relevant to understand varietal adaptation to impending climate changes and to assist vine growers in choosing genotypes and viticulture practices.

Towards the definition of a detailed transcriptomic map of berry development

The progress of the grapevine genomics and the development of high-throughput technologies for gene expression analysis stimulated the investigation of the physical, biochemical and physiological changes of grape berry growth and maturation at transcriptomic level. The molecular information generated in the last decade is however still fragmented since it relies upon detailed analysis of few stages and thus lacks continuity over grape development. To identify the molecular events associated with berry development at a higher temporal resolution and define a transcriptomic map, we performed RNA-seq analysis of berry samples collected every week from fruit-set to maturity in Pinot noir and Cabernet Sauvignon for three consecutive years, resulting in 219 samples. Using the most variable portion of the transcriptome, we built a preliminary transcriptomic model of berry development based on the Cabernet Sauvignon samples. The Pinot noir samples were then aligned onto this preliminary ripening map to investigate its performance in describing the development of another grape variety. A further step for testing the model was the projection of RNA-seq samples of fruit development of five red-skin Italian cultivars. For all these surveys, the transcriptomic route allowed a precise definition of the progression of berry development during both formation and ripening phases.

Multi-parameter characterization of water stress tolerance in Vitis hybrids for new rootstock selection

Drought in grapevine could be faced using tolerant rootstocks. The present work aims at the evaluation of 25 new genotypes potentially tolerant to drought by using recent methods of phenotypical screening (thermography and on-solid reaction spectroscopy). Plants were grown in well-watered and stressed field conditions. Proxi for transpiration, wood hydrophobicity and starch content were used to characterize and classify the genotypes. The predominant role of the environment was highlighted, nevertheless genotype and genotype × environment interaction showed significant variations as well. Hybrids were classified based on their steady, susceptible or adaptable behavior. The 14 most promising genotypes were identified, 5 of them showing two tolerance mechanisms. In the future, results from this experiment will support viticulture in water limited areas releasing new drought-tolerant interspecific hybrids to be tested after grafting with different scions.

Berry color variation in grapevine as a source of diversity

Even though it is one of the oldest perennial domesticated fruit crops in the world, grapevine (Vitis vinifera L.) cultivation today is the result of both conventional breeding practices (i.e. hybridizations adopted during the last century) and vegetative propagation. Human-assisted asexual propagation has allowed the maintenance of desired traits but has largely impacted the frequency of spontaneous somatic mutations observed in the field. Consequently, many grapevine fruit attributes to date have been artificially selected, including: fruit yield, compactness, size and composition, the latter being greatly diversified in the pursuit of altering berry skin coloration. The present review provides an overview of various aspects related to grapevine diversity, with a special emphasis on grape berry skin color variation and will discuss the current knowledge of how grape skin color variation is affected by the synthesis of phenolic compounds, particularly anthocyanins and their underlying genetic factors. We hope this knowledge will be useful in supporting the importance of the berry color trait diversity in cultivated grapevines, which is used as basis for selection during breeding programs because of its application for vine growers, winemakers and consumers.

Identification, characterization, and expression analysis of calmodulin and calmodulin-like genes in grapevine (Vitis vinifera) reveal likely roles in stress responses

Calcium (Ca²⁺) is an ubiquitous key second messenger in plants, where it modulates many developmental and adaptive processes in response to various stimuli. Several proteins containing Ca²⁺ binding domain have been identified in plants, including calmodulin (CaM) and calmodulin-like (CML) proteins, which play critical roles in translating Ca²⁺ signals into proper cellular responses. In this work, a genome-wide analysis conducted in Vitis vinifera identified three CaM- and 62 CML-encoding genes. We assigned gene family nomenclature, analyzed gene structure, chromosomal location and gene duplication, as well as protein motif organization. The phylogenetic clustering revealed a total of eight subgroups, including one unique clade of VviCaMs distinct from VviCMLs. VviCaMs were found to contain four EF-hand motifs whereas VviCML proteins have one to five. Most of grapevine CML genes were intronless, while VviCaMs were intron rich. All the genes were well spread among the 19 grapevine chromosomes and displayed a high level of duplication. The expression profiling of VviCaM/VviCML genes revealed a broad expression pattern across all grape organs and tissues at various developmental stages, and a significant modulation in biotic stress-related responses. Our results highlight the complexity of CaM/CML protein family also in grapevine, supporting the versatile role of its different members in modulating cellular responses to various stimuli, in particular to biotic stresses. This work lays the foundation for further functional and structural studies on specific grapevine CaMs/CMLs in order to better understand the role of Ca²⁺-binding proteins in grapevine and to explore their potential for further biotechnological applications.