Metabolic and RNA profiling elucidates proanthocyanidins accumulation in Aglianico grape

Distinct structural variants and repeat landscape shape the genomes of the ancient grapes Aglianico and Falanghina

Mounting evidence recognizes structural variations (SVs) and repetitive DNA sequences as crucial players in shaping the existing grape phenotypic diversity at intra- and inter-species levels. To deepen our understanding on the abundance, diversity, and distribution of SVs and repetitive DNAs, including transposable elements (TEs) and tandemly repeated satellite DNA (satDNAs), we re-sequenced the genomes of the ancient grapes Aglianico and Falanghina. The analysis of large copy number variants (CNVs) detected candidate polymorphic genes that are involved in the enological features of these varieties. In a comparative analysis of Aglianico and Falanghina sequences with 21 publicly available genomes of cultivated grapes, we provided a genome-wide annotation of grape TEs at the lineage level. We disclosed that at least two main clusters of grape cultivars could be identified based on the TEs content. Multiple TEs families appeared either significantly enriched or depleted. In addition, in silico and cytological analyses provided evidence for a diverse chromosomal distribution of several satellite repeats between Aglianico, Falanghina, and other grapes. Overall, our data further improved our understanding of the intricate grape diversity held by two Italian traditional varieties, unveiling a pool of unique candidate genes never so far exploited in breeding for improved fruit quality.

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

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

Antiviral Activity of Vitis vinifera Leaf Extract against SARS-CoV-2 and HSV-1

Vitis vinifera represents an important and renowned source of compounds with significant biological activity. Wines and winery bioproducts, such as grape pomace, skins, and seeds, are rich in bioactive compounds against a wide range of human pathogens, including bacteria, fungi, and viruses. However, little is known about the biological properties of vine leaves. The aim of this study was the evaluation of phenolic composition and antiviral activity of Vitis vinifera leaf extract against two human viruses: the Herpes simplex virus type 1 (HSV-1) and the pandemic and currently widespread severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). About 40 phenolic compounds were identified in the extract by HPLC-MS/MS analysis: most of them were quercetin derivatives, others included derivatives of luteolin, kaempferol, apigenin, isorhamnetin, myricetin, chrysoeriol, biochanin, isookanin, and scutellarein. Leaf extract was able to inhibit both HSV-1 and SARS-CoV-2 replication in the early stages of infection by directly blocking the proteins enriched on the viral surface, at a very low concentration of 10 μg/mL. These results are very promising and highlight how natural extracts could be used in the design of antiviral drugs and the development of future vaccines.

In vitro and in vivo antifungal activity of Cuminum cyminum essential oil against Aspergillus aculeatus causing bunch rot of postharvest grapes

Bunch rot in grapes is an aggressive disease and needs to be controlled during the postharvest period. We investigate the antifungal potential of Zanthoxylum bungeanum Maxim., Zanthoxylum rhetsa, Cuminum cyminum, Coriandrum sativum, and Zingiber montanum (J. Koenig) Link ex A. Dietr. essential oils against Aspergillus aculeatus that cause bunch rot disease on postharvest grapes. C. cyminum essential oil exhibited stronger significantly inhibition percentage of 95.08% than other treatments in in vitro assay. Cumin aldehyde (33.94%) and α-terpinen-7-al (32.20%) were identified as major volatile compounds in C. cyminum oil. Antifungal potential of C. cyminum oil was then tested in conidia germination and in vitro tests compared to cumin aldehyde and α-terpinen-7-al. Their EC₅₀ values against the conidial germination were also estimated. Significant reduction of conidia germination was also detected in C. cyminum essential oil and cumin aldehyde at a concentration of 1,000 and 100 μg/mL, respectively. EC₅₀ values of the C. cyminum essential oil, cumin aldehyde, and α-terpinen-7-al were 67.28 μg/mL, 9.31 μg/mL, and 13.23 μg/mL, respectively. In vivo assay, the decrease of the disease severity (0.69%) and incidence (1.48%) percentage of A. aculeatus on grape berries treated at 1,000 μg/mL of C. cyminum essential oil was significantly greater than that obtained from other treatments after 10 days incubation. In addition, grape berries treated with C. cyminum essential oil decreased weight loss and retained fruit firmness. The changing of total soluble solids, total phenolic content, and antioxidant activity are also delayed in treated fruits. Therefore, essential oil of C. cyminum may be applied as a biological antifungal agent to control A. aculeatus in postharvest grapes without any negative effects on its quality.

Dominance of S. cerevisiae Commercial Starter Strains during Greco di Tufo and Aglianico Wine Fermentations and Evaluation of Oenological Performances of Some Indigenous/Residential Strains

In order to evaluate dominance/implantation of starter cultures for wine fermentation, both commercial starters and wild strains were monitored during the fermentation of Greco di Tufo (GR) and Aglianico of Taurasi (AGL) musts. Preliminary characterization of commercial strains was carried out by several molecular markers. Five fermentations—four starter-inoculated and one spontaneous—were carried out in duplicates by using grapes from GR and AGL. Trials were monitored, and yeast cultures were isolated within the dominant microflora. Comparison of Interdelta patterns allowed to assess the real occurrence of both starters and indigenous strains. A high genetic diversity within S. cerevisiae strains was detected. In starter-led fermentations (except for few cases), in addition to the starter strains, indigenous S. cerevisiae biotypes were found, as well. Native strains isolated from replicates of the same fermentation showed different genetic profiles. Spontaneous fermentations were conducted, during the first 5 days, by non-Saccharomyces yeasts and, afterwards, by a high number (16 in the AGL and 20 in the GR) of S. cerevisiae biotypes. Indigenous biotypes isolated by GR revealed a high variability in oenological features and, in several cases, showed better performances than those recorded for commercial strains. The study further highlighted the low dominance of some commercial starter cultures. Moreover, autochthonous yeast strains proved to be sometimes more aggressive in terms of fermentation vigor in GR must, likely because better adapted to ecological and technological conditions occurring during winemaking. Finally, the use of such strains for production of autochthonous “pied de cuve” may be a useful strategy for lowering production cost of winemaking.

Genetic and epigenetic dynamics affecting anthocyanin biosynthesis in potato cell culture

Anthocyanins are antioxidant pigments widely used in drugs and food preparations. Flesh-coloured tubers of the cultivated potato Solanum tuberosum are important sources of different anthocyanins. Due to the high degree of decoration achieved by acylation, anthocyanins from potato are very stable and suitable for the food processing industry. The use of cell culture allows to extract anthocyanins on-demand, avoiding seasonality and consequences associated with land-based-tuber production. However, a well-known limit of cell culture is the metabolic instability and loss of anthocyanin production during successive subcultures. To get a general picture of mechanisms responsible for this instability, we explored both genetic and epigenetic regulation that may affect anthocyanin production in cell culture. We selected two clonally related populations of anthocyanin-producing (purple) and non-producing (white) potato cells. Through targeted molecular investigations, we identified and functionally characterized an R3-MYB, here named StMYBATV. This transcription factor can interact with bHLHs belonging to the MBW (R2R3-MYB, bHLH and WD40) anthocyanin activator complex and, potentially, may interfere with its formation. Genome methylation analysis revealed that, for several genomic loci, anthocyanin-producing cells were more methylated than clonally related white cells. In particular, we localized some methylation events in ribosomal protein-coding genes. Overall, our study explores novel molecular aspects associated with loss of anthocyanins in cell culture systems.

Extended Harvest Date Alter Flavonoid Composition and Chromatic Characteristics of Plavac Mali (Vitis vinifera L.) Grape Berries

This study delivers a comprehensive flavonoid fingerprint profile, physiochemical and external color characterization of Plavac Mali grapes through four harvest dates at two distinct vineyards (Split and Zadar) in the Eastern Adriatic region. The experimental harvest lasted 56 days, at total soluble solids content from 18.4 to 22.4°Brix in Split and 16.8 to 20.4°Brix in Zadar. Patterns of 27 skin and seed flavonoid compounds at each location indicate unique flavonoid composition of berries at each harvest date. Extended harvest increased six compounds in skin with maximum values of main anthocyanin malvidin-3-O-glucoside in H3 (4406.6 and 6389.5 mg kg⁻¹, Split and Zadar, respectively) followed by a decrease in October. Peak values of seed and skin catechins and galloylated flavan-3-ol subunits are seen in H1 and H2 at Split, while constantly high values are reported in the case of Zadar, with an incoherent pattern of those in skin extracts. Minimal values of epigallocatechin were detected with an extended harvest date at both locations. Berries of extended harvest dates underwent colorimetric improvements, trough decrease in L*, a*, b* and C characteristics and increase in skin color index for red grapes CIRG. The extended harvest date promotes flavonoid composition, and improves the quality of Plavac Mali grape berries.

New Insights into the Exploitation of Vitis vinifera L. cv. Aglianico Leaf Extracts for Nutraceutical Purposes

The leaves of Vitis vinifera L. have been used for a long time in traditional medicine for the treatment of many ailments. Grape polyphenols, indeed, have been demonstrated to be able to defend against oxidative stress, responsible for various disorders such as cancer, diabetes and neurodegenerative diseases. The effects of different extraction techniques, Soxhlet (SOX), Accelerated Solvent (ASE 40, ASE 50) and Ultrasound Assisted Extraction (UAE) were studied in this work to evaluate their impact on the chemical profile and bioactive potential of Vitis vinifera L. (cv. Aglianico) leaf extracts. The phytochemical profile was investigated by HPLC-DAD and 9 phenolic compounds were identified and quantified in the extract. Moreover, the antioxidant, anticholinesterase and antityrosinase activities were evaluated. In detail, the total polyphenol content and antioxidant activity (2,2-diphenyl-1-picrylhydrazyl, Oxygen Radical Absorbance Capacities and β-Carotene Bleaching assays) were evaluated and compared to assess the Relative Antioxidant Capacity Index (RACI). To test the inhibitory activity of extracts towards cholinesterases, acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibition assays were performed. SOX and ASE 50 have shown the highest value of RACI, 0.76 and 0.65, respectively. Regarding enzymatic inhibitory activity, ASE 50 (IC₅₀ = 107.16 ± 8.12 μg/mL) and SOX (IC₅₀ = 171.34 ± 12.12 μg/mL) extracts exhibited the highest AChE and BChE inhibitory activity, respectively, while UAE (IC₅₀ = 293.2 ± 25.6 μg/mL, followed by SOX (IC₅₀ = 302.5 ± 38.3 μg/mL) showed the highest tyrosinase inhibition value. Our results demonstrated for the first time that Aglianico leaves are important sources of phenols that could be used to prevent oxidative stress and be potentially helpful in diseases treatable with tyrosinase and cholinesterase inhibitors, like myasthenia gravis or Alzheimer’s.

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in wounding-response, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stress-responsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.

CIP elicitors on the defense response of A. macrocephala and its related gene expression analysis

Plant-derived elicitor is a new type of plant vaccine developed in the contemporary era, and it has safe and broad application prospects in organic agriculture. Research on defense mechanisms triggered by elicitor has become a hot topic in recent years. The Chrysanthemum indicum polysaccharide (CIP) obtained by separation and purification from Chrysanthemum indicum was used as an elicitor in this work. This elicitor has been shown to be effective in Atractylodes macrocephala Koidz (A. macrocephala) against Sclerotium rolfsii sacc (S. rolfsii) infection and soil-borne diseases. However, the mechanism of induced disease resistance has not been elucidated. In this research, we study the CIP-induced A. macrocephala defense response from the level of signal molecules and the defensive enzyme gene expression. Several defense responses to CIP treatment have been found in A. macrocephala, including early hydrogen peroxide (H₂O₂) production, accumulation of salicylic acid (SA) and increased phytoalexin (PA) content. In addition, CIP significantly increased the activity of related defense enzymes in A. macrocephala. RT-qPCR analysis showed that defense-related genes such as polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL) were up-regulated after CIP treatment. To obtain the sequence of the defense enzyme gene, we are the first to provide a public and comprehensive A. macrocephala database by transcriptome sequencing. These results together demonstrate that CIP triggers defense responses in A. macrocephala. Our research not only provides further research on immune mechanism between plant and elicitor, but also sheds new light on strategy for biocontrol in the future.

The Maize Class-I SUMO Conjugating Enzyme ZmSCE1d Is Involved in Drought Stress Response

Post-translational modification of cellular proteins by sumoylation plays a vital role in stress responses of plants. However, the mechanisms underlying the sumoylation’s involvement in stress responses in crop species remain largely unknown. Herein, a maize class-I SUMO conjugating enzyme gene (ZmSCE1d) was identified, whose expression was upregulated upon drought stress. Over-expression of ZmSCE1d in transgenic Arabidopsis plants increased SUMO conjugates and improved drought tolerance. The ZmSCE1d-transgenic plants showed higher antioxidant enzyme activities, but lower reactive oxygen species and lipid peroxidation upon drought stress. Furthermore, transcripts of several drought-responsive genes were significantly elevated, as revealed by qPCR in the transgenic lines. Taken together, these data have demonstrated that ZmSCE1d overexpression improved drought tolerance likely by regulating sumoylation levels, antioxidant capability, and drought-responsive gene expression in transgenic plants. This study may facilitate our understanding of the mechanisms underlying SCE-mediated sumoylation under drought stress and accelerate genetic improvement of crop plants tolerant to drought stress by manipulating the SUMO system.

Inferring RPW8-NLRs's evolution patterns in seed plants: case study in Vitis vinifera

Genomic and transcriptomic studies in plants and, more in deep, in grapevine reveal that the disease-resistance RNL gene family is highly variable. RNLs (RPW8-NLRs) are a phylogenetically distinct class of nucleotide oligomerization domain (NOD)-like receptors (NLRs) identified in plants. Two RNLs, namely, the NRG1 (N Requirement Gene 1) and the ADR1 (Activated Disease Resistance 1), have been characterized; however, little is known about the RNL evolutionary history in higher plants. To trace the diversification of RNL gene subfamily, we scanned the NLR proteins of 73 plant genomes belonging to 29 taxa, revealing a noticeable diversification across species and within the same genus or botanic family together with a conspicuous expansion in important crop species. To explore the RNL variability in Vitis vinifera and gain information with respect to their structure, evolutionary diversification of five grape genomes ('Aglianico', 'Falanghina', 'Sultanina', 'Tannat', and 'Nebbiolo') has been compared to the reference genome ('Pinot Noir'). The number of RNLs ranged from 6 ('Sultanina') to 14 ('Nebbiolo'), in contrast to the 10 'Pinot Noir' RNLs. The phylogenetic study on grapevine RNLs revealed that all collapsed into NRG1-clade, rather than four. To investigate more in depth the means of intraspecific variability of grape RNL copies, a transcriptomic profiling in response to powdery mildew (PM) infection was carried out through qRT-PCRs and public databases interrogation. The RNL expression variability identified in transcriptome data sets supports the hypothesis of a functional expansion/contraction in grapevine varieties. Although no direct correlations between grapevine PM-resistance and RNL expression was identified, our work can provide good candidates for functional studies able to elucidate the putative "helper" role of RNLs in grape immune signalling.

Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus

Brassica rapa and Raphanus sativus are two important edible vegetables that contain numerous nutritional ingredients. However, the agronomic traits and nutritional components of the intergeneric hybrid of B. rapa and R. sativus remain poorly understood. In this study, we used a stably inherited intergeneric hybrid of B. rapa and R. sativus as a model to study its metabolome and transcriptome profiles. Morphological and cytological analysis showed the intergeneric hybrid had the expected chromosome number and normal meiosis behavior. Moreover, the metabolome analysis showed multiple important secondary metabolites, including flavonoids and glucosinolates, were significantly upregulated in the hybrid. Furthermore, transcriptome data revealed that the expression level of the important genes involved in phenylpropanoid and flavonoid pathways was significantly upregulated in the hybrid. Ultimately, our data indicate the intergeneric hybrid will be a valuable bioengineering resource and promise to become a new-type hybrid vegetable with great medicinal value in future.