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California contains a broad geography over which climate conditions can be suitable for cultivating multiple varieties of winegrapes. However, climate change is projected to make winegrape cultivation more challenging across many of California's winegrowing regions. In order to understand the potential effects of climate change on winegrapes, this study models variety-specific phenology for six winegrape varieties and quantifies the change in phenology and viticulturally-important agroclimate metrics over 12 of California's American Viticultural Areas (AVAs) by the mid-21st century. Results show more rapid development for winegrapes with earlier budburst, flowering, veraison, and maturation across all varieties and AVAs. Cabernet Sauvignon shows the greatest change in phenology timing, while Chardonnay shows the least change. Likewise, the West Sonoma Coast AVA shows the greatest average change in phenology timing across varieties and development stages and Lodi AVA shows the least. Projected changes in agroclimatic metrics include an additional month of potentially damaging heat days (above 35 °C) in some AVAs, and decreases in frost days. These results have implications for numerous factors related to viticultural production, including water resources management and crop yield and quality, and underscore the need for California winegrape growers to improve their resilience to climate change by adopting strategies such as increasing soil health and water use efficiency and selecting cultivars suited for future climate conditions. By conducting climate effects analyses at the variety-specific and AVA scale, important information is provided to the winegrowing industry at a resolution that can support decision-making towards resilience.

Background and aimsMany agricultural areas are expected to face hotter, drier conditions from climate change. Understanding the mechanisms that crops use to mitigate these stresses can guide breeding for more tolerant plant material. We tested relationships between traits, physiological function in hot conditions and historical climate associations to evaluate these mechanisms for winegrapes. We expected a more negative leaf osmotic potential at full hydration (πo), which reduces leaf turgor loss during drought, and either a metabolically cheaper or more osmoprotectant leaf chemical composition, to allow cultivars associated with hot, dry regions to maintain greater gas exchange in hot growing conditions.MethodsWe measured πo, gas exchange and leaf chemistry for seven commercially important winegrape cultivars that vary widely in historical climate associations. Vines were grown in common-garden field conditions in a hot wine-growing region (Davis, CA, USA) and measured over the hottest period of the growing season (July-September).Key resultsThe value of πo varied significantly between cultivars, and all cultivars significantly reduced πo (osmotically adjusted) over the study period, although osmotic adjustment did not vary across cultivars. The value of πo was correlated with gas exchange and climate associations, but in the direction opposite to expected. Photosynthesis and πo were higher in the cultivars associated with hotter, less humid regions. Leaf chemical composition varied between cultivars but was not related to climate associations.ConclusionsThese findings suggest that maintenance of leaf turgor is not a primary limitation on grapevine adaptation to hot or atmospherically dry growing conditions. Thus, selecting for a more negative πo or greater osmotic adjustment is not a promising strategy to develop more climate-resilient grape varieties, contrary to findings for other crops. Future work is needed to identify the mechanisms increasing photosynthesis in the cultivars associated with hot, dry regions.

When grapes are exposed to wildfire smoke, certain smoke-related volatile phenols (VPs) can be absorbed into the fruit, where they can be then converted into volatile-phenol (VP) glycosides through glycosylation. These volatile-phenol glycosides can be particularly problematic from a winemaking standpoint as they can be hydrolyzed, releasing volatile phenols, which can contribute to smoke-related off-flavors. Current methods for quantitating these volatile-phenol glycosides present several challenges, including the requirement of expensive capital equipment, limited accuracy due to the molecular complexity of the glycosides, and the utilization of harsh reagents. To address these challenges, we proposed an enzymatic hydrolysis method enabled by a tailored enzyme cocktail of novel glycosidases discovered through genome mining, and the generated VPs from VP glycosides can be quantitated by gas chromatography-mass spectrometry (GC-MS). The enzyme cocktails displayed high activities and a broad substrate scope when using commercially available VP glycosides as the substrates for testing. When evaluated in an industrially relevant matrix of Cabernet Sauvignon wine and grapes, this enzymatic cocktail consistently achieved a comparable efficacy of acid hydrolysis. The proposed method offers a simple, safe, and affordable option for smoke taint analysis.

Smoke taint in wine has become a critical issue in the wine industry due to its significant negative impact on wine quality. Data-driven approaches including univariate analysis and predictive modeling are applied to a data set containing concentrations of 20 VOCs in 48 grape samples and 56 corresponding wine samples with a taster-evaluated smoke taint index. The resulting models for predicting the smoke taint index of wines are highly predictive when using as inputs VOC concentrations after log conversion in both grapes and wines (Pearson Correlation Coefficient PCC = 0.82; R2 = 0.68) and less so when only grape VOCs are used (Pearson Correlation Coefficient PCC = 0.76; R2 = 0.56), and the classification models also show the capacity for detecting smoke-tainted wines using both wine and grape VOC concentrations (Recall = 0.76; Precision = 0.92; F1 = 0.82) or using only grape VOC concentrations (Recall = 0.74; Precision = 0.92; F1 = 0.80). The performance of the predictive model shows the possibility of predicting the smoke taint index of the wine and grape samples before fermentation. The corresponding code of data analysis and predictive modeling of smoke taint in wine is available in the Github repository (https://github.com/IBPA/smoke_taint_prediction).

Societal Impact Statement Summary Grapevine leaves are emblematic of the strong visual associations people make with plants. Leaf shape is immediately recognizable at a glance, and therefore, this is used to distinguish grape varieties. In an era of computationally enabled machine learning‐derived representations of reality, we can revisit how we view and use the shapes and forms that plants display to understand our relationship with them. Using computational approaches combined with time‐honored methods, we can predict theoretical leaves that are possible, enabling us to understand the genetics, development, and environmental responses of plants in new ways. Grapevine leaves are a model morphometric system. Sampling over 10,000 leaves using dozens of landmarks, the genetic, developmental, and environmental basis of leaf shape has been studied and a morphospace for the genus Vitis predicted. Yet, these representations of leaf shape fail to capture the exquisite features of leaves at high resolution. We measure the shapes of 139 grapevine leaves using 1672 pseudo‐landmarks derived from 90 homologous landmarks with Procrustean approaches. From hand traces of the vasculature and blade, we have derived a method to automatically detect landmarks and place pseudo‐landmarks that results in a high‐resolution representation of grapevine leaf shape. Using polynomial models, we create continuous representations of leaf development in 10 Vitis spp. We visualize a high‐resolution morphospace in which genetic and developmental sources of leaf shape variance are orthogonal to each other. Using classifiers, Vitis vinifera, Vitis spp., rootstock and dissected leaf varieties as well as developmental stages are accurately predicted. Theoretical eigenleaf representations sampled from across the morphospace that we call synthetic leaves can be classified using models. By predicting a high‐resolution morphospace and delimiting the boundaries of leaf shapes that can plausibly be produced within the genus Vitis, we can sample synthetic leaves with realistic qualities. From an ampelographic perspective, larger numbers of leaves sampled at lower resolution can be projected onto this high‐resolution space, or, synthetic leaves can be used to increase the robustness and accuracy of machine learning classifiers. [ABSTRACT FROM AUTHOR]

Grapevine leaf rust (GLR) caused by Phakopsora euvitis is a serious disease that results in severe leaf necrosis and early plant defoliation. This study sought to understand the plant host response against GLR at the molecular level and select useful genes for the breeding of resistant grapes. Hence, transcriptome analysis was conducted in two pathogen-inoculated Korean wild grape genotypes, namely, Vitis coignetiae Pulliant (Vc) and V. flexuosa Thunb (Vf), resistant and susceptible to GLR, respectively. RNAs were extracted from uninfected and infected leaves 24 h post-inoculation (hpi). In transcriptome analysis, a total of differentially expressed genes (DEGs) were 3979 and 2436 in the resistant and susceptible genotypes, of which 1765 and 1162 were up-regulated, and 2214 and 1274 were down-regulated, respectively. The top five up-regulated genes in Vc compared to Vf were homolog of carrot EP3-3 chitinase, calcineurin B-like proteins (CBL)-interacting protein kinase 20 (CIPK20), chalcone and stilbene synthase family protein, osmotin 34, and major latex protein (MLP)-like protein 423 (MLP423). The five most down-regulated genes in Vc compared to Vf were RADIALIS (RAD)-like 1, flavonol synthase 1, glutamine synthetase 2, RAD-like 6, and GDSL-like lipase/acylhydrolase superfamily protein, which were validated for their expression by real-time PCR. According to the Gene Ontology (GO) analysis, most of the up-regulated genes in Vc were associated with metabolic processes, whereas, most of down-regulated genes in Vf were associated with catalytic activity. The down-regulated genes in Vc and up-regulated genes in Vf were mostly associated with metabolic processes and catalytic activity. Defense-related genes, including phenylalanine ammonia-lyase (PAL), pathogenesis-related (PR) proteins, and salicylic acid (SA)-dependent responses were differentially expressed against the infection by the pathogen. This is the first report on the transcriptome analysis of grapevines in response to GLR and provides a basis for further studies on the discovery of resistant genes and the development of GLR-resistant grapevine varieties. [ABSTRACT FROM AUTHOR]

Fusarium species are agriculturally important fungi with a broad host range and can be found as endophytic, pathogenic, or opportunistic parasites in many crop plants. This study aimed to identify Fusarium species in bare-rooted, dormant plants in Turkish grapevine nurseries using molecular identification methods and assess their pathogenicity. Asymptomatic dormant plants were sampled from grapevine nurseries (43) in different regions of the country, and fungi were isolated from plant roots and internal basal tissues. The Fusarium strains were identified by performing gene sequencing (TEF1-α, RPB2) and phylogenetic analyses. Pathogenicity tests were carried out by inoculating mycelial agar pieces of strains onto the stem or conidial suspensions into the rhizosphere of vines (1103 Paulsen rootstock). Laboratory tests revealed that Fusarium species were highly prevalent in Turkish grapevine nurseries (41 out of 43). Gene sequencing and phylogenetic analyses unraveled that 12 Fusarium species (F. annulatum, F. brachygibbosum, F. clavum, F. curvatum, F. falciforme, F. fredkrugeri, F. glycines, F. nanum, F. nematophilum, F. nirenbergiae, F. solani, and Fusarium spp.) existed in the ready-to-sale plants. Some of these species (F. annulatum, F. curvatum and F. nirenbergiae) consistently caused wood necrosis of seedling stems, rotting of the basal zone and roots, and reduced root biomass. Although the other nine species also caused some root rot and root reduction, their virulence was not as severe as the pathogenic ones, and they were considered opportunistic parasites or endophytic species. This study suggests that Fusarium species might play an important role in root-basal rot, wood canker symptoms, and young vine decline in Turkish grapevine nurseries and that these species need to be considered for healthy seedling production. [ABSTRACT FROM AUTHOR]

Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on plant phenotypic traits and local adaptation to abiotic and biotic stress. In this study, we employed woolly grape (Vitis retordii), a species native to the tropical and subtropical regions of East Asia with both coastal and inland habitats, as a valuable model for examining the impact of SVs on local adaptation. We assembled a haplotype‐resolved chromosomal reference genome for woolly grape, and conducted population genetic analyses based on whole‐genome sequencing (WGS) data from coastal and inland populations. The demographic analyses revealed recent bottlenecks in all populations and asymmetric gene flow from the inland to the coastal population. In total, 1,035 genes associated with plant adaptive regulation for salt stress, radiation, and environmental adaptation were detected underlying local selection by SVs and SNPs in the coastal population, of which 37.29% and 65.26% were detected by SVs and SNPs, respectively. Candidate genes such as FSD2, RGA1, and AAP8 associated with salt tolerance were found to be highly differentiated and selected during the process of local adaptation to coastal habitats in SV regions. Our study highlights the importance of SVs in local adaptation; candidate genes related to salt stress and climatic adaptation to tropical and subtropical environments are important genomic resources for future breeding programs of grapevine and its rootstocks. [ABSTRACT FROM AUTHOR]

Transient transformation is extremely useful for rapid in vivo assessment of gene function, especially for fruit-related genes. Grape berry, while an important fruit crop, is recalcitrant to transient transformation, due to the high turgor pressure in its mesocarp cells that limits the ability of Agrobacterium to penetrate into the tissue. It is urgent to establish a simple transient transformation system for rapid analysis of gene function. In this study, different injection methods, grape genotypes, and developmental stages were tested in order to develop a rapid and efficient Agrobacterium-mediated transient transformation methodology for grape berries. Two injection methods, namely punch injection and direct injection, were evaluated using the β-glucuronidase (GUS) gene and by x-gluc tissue staining and 4-methylumbelliferyl-β-D-glucuronide fluorescence analysis. The results indicated that there were no significant differences on transformation effects between the two methods, but the latter was more suitable because of its simplicity and convenience. Six grape cultivars ('Hanxiangmi', 'Moldova', 'Zijixin', 'Jumeigui', 'Shine-Muscat', and 'A17') were tested for transient transformation. 'Hanxiangmi', 'Moldova', and 'Zijixin' grape berries were not suitable for agroinfiltration due to frequently fruit cracking, browning, and formation of scar skin. The fruit integrity rates of 'Jumeigui', 'Shine-Muscat', and 'A17' berries were all above 80%, and GUS activity was detected in the berries of the three cultivars 3–14 days after injection with the Agrobacterium culture, while higher GUS activities were observed in the 'Jumeigui' berries. The levels of GUS activity in injected berries at 7–8 weeks after full blooming (WAFB) were more than twice at 6 WAFB. In subsequent assays, the over-expression of MYB transcription factor VvMYB44 via transient transformation accelerated the anthocyanin accumulation and fruit coloring through raising the expression levels of VvLAR1, VvUFGT, VvLDOX, VvANS, and VvDFR, which verified the effectiveness of this transformation system. These experiments finally identified the reliable grape cultivars and suitable operational approach for transient transformation and further indicated that this Agrobacterium-mediated transient transformation system was efficient and suitable for the elucidation of gene function in grape berries. [ABSTRACT FROM AUTHOR]

The grapevine was one of the earliest domesticated fruit crops and has been cultivated since ancient times. It is considered one of the most important fruit crops worldwide for wine and table grape production. The current grape varieties are the outcome of prolonged selection initiated during the domestication process of their wild relative. Recent genetic studies have shed light on the origins of the modern domestic grapevine in western Europe, suggesting that its origin stems from the introgression between eastern domestic grapes and western wild grapes. However, the origin of ancient grapevines remains largely unexplored. In this study, we conducted an extensive analysis of 2228 well-preserved waterlogged archaeological grape pips from two sites in Sardinia (Italy), dated to the Late Bronze Age (ca. 1300–1100 BC) and the Iron Age (4th and 3rd centuries BC). Using morphometrics and linear discriminant analyses, we compared the archaeological grape pips with modern reference collections to differentiate between wild and domestic grape types and to investigate similarities with 330 modern cultivars. Grape pips from the Late Bronze Age displayed a high percentage of similarity with domesticated grapevines, with a small percentage assigned to wild ones, while the majority of grape pips from the Iron Age were classified as domestic. Discriminant analyses revealed that both white and red grape varieties were cultivated during the Late Bronze and Iron Ages, suggesting a high level of diversification in grape cultivation. Furthermore, a high percentage of archaeological grape pips from both periods showed strong similarities with modern cultivars from the Caucasus and Balkans. This suggests that the great diversity of grapevines present in Sardinia could result from interbreeding between western Asian cultivars and local grapevines that began in the Late Bronze Age. Additionally, a substantial proportion of archaeological grape pips exhibited similar morphometric characteristics to two important Mediterranean grape cultivars: "Muscat à petits grains blancs" and "Garnacha". [ABSTRACT FROM AUTHOR]

BACKGROUND: Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. RESULTS: Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierces disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. CONCLUSIONS: This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.

Erysiphe necator is an obligate fungal pathogen that causes grape powdery mildew, globally the most important disease on grapevines. Previous attempts to obtain a quality genome assembly for this pathogen were hindered by its high repetitive DNA content. Here, chromatin conformation capture (Hi-C) with long-read PacBio sequencing was combined to obtain a chromosome-scale assembly and a high-quality annotation for E. necator isolate EnFRAME01. The resulting 81.1 Mb genome assembly is 98% complete and consists of 34 scaffolds, 11 of which represent complete chromosomes. All chromosomes contain large centromeric-like regions and lack synteny to the 11 chromosomes of the cereal PM pathogen Blumeria graminis. Further analysis of their composition showed that repeats and transposable elements (TEs) occupy 62.7% of their content. TEs were almost evenly interspersed outside centromeric and telomeric regions and massively overlapped with regions of annotated genes, suggesting that they could have a significant functional impact. Abundant gene duplicates were observed as well, particularly in genes encoding candidate secreted effector proteins. Moreover, younger in age gene duplicates exhibited more relaxed selection pressure and were more likely to be located physically close in the genome than older duplicates. A total of 122 genes with copy number variations among six isolates of E. necator were also identified and were enriched in genes that were duplicated in EnFRAME01, indicating they may reflect an adaptive variation. Taken together, our study illuminates higher-order genomic architectural features of E. necator and provides a valuable resource for studying genomic structural variations in this pathogen. IMPORTANCE Grape powdery mildew caused by the ascomycete fungus Erysiphe necator is economically the most important and recurrent disease in vineyards across the world. The obligate biotrophic nature of E. necator hinders the use of typical genetic methods to elucidate its pathogenicity and adaptation to adverse conditions, and thus comparative genomics has been a major method to study its genome biology. However, the current reference genome of E. necator isolate C-strain is highly fragmented with many non-coding regions left unassembled. This incompleteness prohibits in-depth comparative genomic analyses and the study of genomic structural variations (SVs) that are known to affect several aspects of microbial life, including fitness, virulence, and host adaptation. By obtaining a chromosome-scale genome assembly and a high-quality gene annotation for E. necator, we reveal the organization of its chromosomal content, unearth previously unknown features of its biology, and provide a reference for studying genomic SVs in this pathogen.

Wine cultivars are available to growers in multiple clonal selections with agronomic and enological differences. Phenotypic differences between clones originated from somatic mutations that accrued over thousands of asexual propagation cycles. Genetic diversity between grape cultivars remains unexplored, and tools to discriminate unequivocally clones have been lacking. This study aimed to uncover genetic variations among a group of clonal selections of 4 important Vitis vinifera cultivars: Cabernet sauvignon, Sauvignon blanc, Chardonnay, and Merlot, and use this information to develop genetic markers to discriminate the clones of these cultivars. We sequenced with short-read sequencing technology the genomes of 18 clones, including biological replicates for a total of 46 genomes. Sequences were aligned to their respective cultivars reference genome for variant calling. We used reference genomes of Cabernet sauvignon, Chardonnay, and Merlot and developed a de novo genome assembly of Sauvignon blanc using long-read sequencing. On average, 4 million variants were detected for each clone, with 74.2% being single nucleotide variants and 25.8% being small insertions or deletions (InDel). The frequency of these variants was consistent across all clones. From these variants, we validated 46 clonal markers using high-throughput amplicon sequencing for 77.7% of the evaluated clones, most of them small InDel. These results represent an advance in grapevine genotyping strategies and will benefit the viticulture industry for the characterization and identification of the plant material.

This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.

Abstract Background Downy mildew is a plant disease that affects all cultivated European grapevine varieties. The disease is caused by the oomycete Plasmopara viticola. The current strategy to control this threat relies on repeated applications of fungicides. The most eco-friendly and sustainable alternative solution would be to use bred-resistant varieties. During breeding programs, some wild Vitis species have been used as resistance sources to introduce resistance loci in Vitis vinifera varieties. To ensure the durability of resistance, resistant varieties are built on combinations of these loci, some of which are unfortunately already overcome by virulent pathogen strains. The development of a high-throughput machine learning phenotyping method is now essential for identifying new resistance loci. Results Images of grapevine leaf discs infected with P. viticola were annotated with OIV 452–1 values, a standard scale, traditionally used by experts to assess resistance visually. This descriptor takes two variables into account the complete phenotype of the symptom: sporulation and necrosis. This annotated dataset was used to train neural networks. Various encoders were used to incorporate prior knowledge of the scale’s ordinality. The best results were obtained with the Swin transformer encoder which achieved an accuracy of 81.7%. Finally, from a biological point of view, the model described the studied trait and identified differences between genotypes in agreement with human observers, with an accuracy of 97% but at a high-throughput 650% faster than that of humans. Conclusion This work provides a fast, full pipeline for image processing, including machine learning, to describe the symptoms of grapevine leaf discs infected with P. viticola using the OIV 452–1, a two-symptom standard scale that considers sporulation and necrosis. If symptoms are frequently assessed by visual observation, which is time-consuming, low-throughput, tedious, and expert dependent, the method developed sweeps away all these constraints. This method could be extended to other pathosystems studied on leaf discs where disease symptoms are scored with ordinal scales.

Background: Downy mildew is a plant disease that affects all cultivated European grapevine varieties. The disease is caused by the oomycete Plasmopara viticola. The current strategy to control this threat relies on repeated applications of fungicides. The most eco-friendly and sustainable alternative solution would be to use bred-resistant varieties. During breeding programs, some wild Vitis species have been used as resistance sources to introduce resistance loci in Vitis vinifera varieties. To ensure the durability of resistance, resistant varieties are built on combinations of these loci, some of which are unfortunately already overcome by virulent pathogen strains. The development of a high-throughput machine learning phenotyping method is now essential for identifying new resistance loci. Results: Images of grapevine leaf discs infected with P. viticola were annotated with OIV 452–1 values, a standard scale, traditionally used by experts to assess resistance visually. This descriptor takes two variables into account the complete phenotype of the symptom: sporulation and necrosis. This annotated dataset was used to train neural networks. Various encoders were used to incorporate prior knowledge of the scale's ordinality. The best results were obtained with the Swin transformer encoder which achieved an accuracy of 81.7%. Finally, from a biological point of view, the model described the studied trait and identified differences between genotypes in agreement with human observers, with an accuracy of 97% but at a high-throughput 650% faster than that of humans. Conclusion: This work provides a fast, full pipeline for image processing, including machine learning, to describe the symptoms of grapevine leaf discs infected with P. viticola using the OIV 452–1, a two-symptom standard scale that considers sporulation and necrosis. If symptoms are frequently assessed by visual observation, which is time-consuming, low-throughput, tedious, and expert dependent, the method developed sweeps away all these constraints. This method could be extended to other pathosystems studied on leaf discs where disease symptoms are scored with ordinal scales. [ABSTRACT FROM AUTHOR]

The chloroplast genome plays a crucial role in elucidating genetic diversity and phylogenetic relationships. Vitis vinifera L. (grapevine) is an economically important species, prompting exploration of wild genetic resources to enhance stress resilience. We meticulously assembled the chloroplast genomes of two Korean Vitis L. species, V. flexuosa Thunb. and V. amurensis Rupr., contributing valuable data to the Korea Crop Wild Relatives inventory. Through exhaustive specimen collection spanning diverse ecological niches across South Korea, we ensured comprehensive representation of genetic diversity. Our analysis, which included rigorous codon usage bias assessment and repeat analysis, provides valuable insights into amino acid preferences and facilitates the identification of potential molecular markers. The assembled chloroplast genomes were subjected to meticulous annotation, revealing divergence hotspots enriched with nucleotide diversity, thereby presenting promising candidates for DNA barcodes. Additionally, phylogenetic analysis reaffirmed intra-genus relationships and identified related crops, shedding light on evolutionary patterns within the genus. Comparative examination with chloroplast genomes of other crops uncovered conserved sequences and variable regions, offering critical insights into genetic evolution and adaptation. Our study advances the understanding of chloroplast genomes, genetic diversity, and phylogenetic relationships within Vitis species, thereby laying a foundation for enhancing grapevine genetic diversity and resilience to environmental challenges. [ABSTRACT FROM AUTHOR]

Understanding the origins and evolution of modern grapevine varieties in the Iberian Peninsula and western Europe necessitates an examination of the proportions of Vitis vinifera cultivars, their relationships with wild grapevine populations, and the utilization of seedless cultivars in al-Andalus. Employing morphometric studies, domestication indices, multivariate analysis, and Bayesian hypothesis testing, this study investigates several distinct seed types identified in materials from Roman and medieval deposits. These seeds exhibit a spectrum from highly domesticated to purely wild. Our findings reveal the predominance of Proles Occidentalis Negrul, and the presence of feral-like grapevines associated with Proles Euphratica. Additionally, we observe the continuous presence of wild grapevines related to Vitis sylvestris CC Gmelin throughout the studied period. Seeds exhibiting intermediate characteristics are documented, alongside the identification of "stenosperms", suggesting anomalies in seed formation. Notably, the presence of Vitis vinifera raisins "stenospermocarpics" of the sultana type is suggested, potentially elucidating the absence of table grapes and raisins of the Proles Orientalis Negrul in the archaeological record, despite frequent mentions by medieval agronomy writers from al-Andalus. [ABSTRACT FROM AUTHOR]

This paper focuses on the creation of an in vitro collection of grapevine hybrids from the breeding program of the Kazakh Scientific Research Institute of Fruit Growing and Viticulture and investigates the presence of Plasmopara viticola resistance mediated by Rpv3 and Rpv12 loci. We looked at the optimization of in vitro establishment using either shoots taken directly from field-grown plants or from budwood cuttings forced indoors. We further screened for the presence of endophyte contamination in the initiated explants and optimized the multiplication stage. Finally, the presence of the resistance loci against P. viticola was studied. The shoots initiated from the field-sourced explants were the more effective method of providing plant sources for in vitro initiation once all plant accessions met the goal of in vitro establishment. The concentration of phytohormones and the acidity of the culture medium have a great effect on the multiplication rate and the quality of in vitro stock cultures. Out of 17 grapevine accessions, 16 showed the presence of single or combined resistance loci against P. viticola. The grapevine accessions identified as carrying Rpv3 and Rpv12 alleles represent important genetic resources for disease resistance breeding programs. These accessions may further contribute to the creation of new elite cultivars of economic interest. [ABSTRACT FROM AUTHOR]

Grapevine is one of the most economically important fruit crops cultivated worldwide. However, grapevine is highly susceptible to virus infections and exposed to the most diverse forms of viral diseases compared to other fruit crops, and virus-induced incompatibility affects plant growth to different degrees ranging from decline to death. The influence of virus-induced incompatibility could be mitigated to an acceptable level by using appropriate rootstocks. However, the viral tolerance of various grapevine rootstocks with diverse genetic backgrounds remains unclear, along with the identification of the specific viral tolerance factors. In this study, the viral tolerance of 21 grapevine rootstocks was evaluated in a green grafting system. Cabernet Franc varieties infected with a single virus [grapevine leafroll associated virus-1 (GLRaV-1)], a co-infection of two viruses (GLRaV-1 plus grapevine virus A—GVA), and no infection were used as the scions, respectively. The vegetative growth and photosynthetic function of the grafts were analyzed 4 months after grafting. The results indicated that some rootstocks could alleviate the influence of the virus infection, with vegetative growth and photosynthetic function sustained at a normal level, whereas other rootstocks were susceptible to the virus infection, resulting in a decline in the growth and photosynthetic function of the grafts. Our research provides evidence for the existence and diversity of viral tolerance among grapevine rootstocks, offering important information for appropriate rootstock selection in the establishment of new vineyards and in the breeding of grapevine rootstocks with enhanced viral tolerance. [ABSTRACT FROM AUTHOR]

Graph representation learning methods opened new avenues for addressing complex, real-world problems represented by graphs. However, many graphs used in these applications comprise millions of nodes and billions of edges and are beyond the capabilities of current methods and software implementations. We present GRAPE (Graph Representation Learning, Prediction and Evaluation), a software resource for graph processing and embedding that is able to scale with big graphs by using specialized and smart data structures, algorithms, and a fast parallel implementation of random-walk-based methods. Compared with state-of-the-art software resources, GRAPE shows an improvement of orders of magnitude in empirical space and time complexity, as well as competitive edge- and node-label prediction performance. GRAPE comprises approximately 1.7 million well-documented lines of Python and Rust code and provides 69 node-embedding methods, 25 inference models, a collection of efficient graph-processing utilities, and over 80,000 graphs from the literature and other sources. Standardized interfaces allow a seamless integration of third-party libraries, while ready-to-use and modular pipelines permit an easy-to-use evaluation of graph-representation-learning methods, therefore also positioning GRAPE as a software resource that performs a fair comparison between methods and libraries for graph processing and embedding.

Xylella fastidiosa is a bacterium that infects crops like grapevines, coffee, almonds, citrus and olives. There is little understanding of the genes that contribute to plant resistance, the genomic architecture of resistance, and the potential role of climate in shaping resistance, in part because major crops like grapevines (Vitis vinifera) are not resistant to the bacterium. Here we study a wild grapevine species, V. arizonica, that segregates for resistance. Using genome-wide association, we identify candidate resistance genes. Resistance-associated kmers are shared with a sister species of V. arizonica but not with more distant species, suggesting that resistance evolved more than once. Finally, resistance is climate dependent, because individuals from low (

Development of efficient analytical techniques is required for effective interpretation of biological data to take novel hypotheses and finding the critical predictive patterns. Machine Learning algorithms provide a novel opportunity for development of low-cost and practical solutions in biology. In this study, we proposed a new integrated analytical approach using supervised machine learning algorithms and microsatellites data of worldwide vitis populations. A total of 1378 wild (V. vinifera spp. sylvestris) and cultivated (V. vinifera spp. sativa) accessions of grapevine were investigated using 20 microsatellite markers. Data cleaning, feature selection, and supervised machine learning classification models vis, Naive Bayes, Support Vector Machine (SVM) and Tree Induction methods were implied to find most indicative and diagnostic alleles to represent wild/cultivated and originated geography of each population. Our combined approaches showed microsatellite markers with the highest differentiating capacity and proved efficiency for our pipeline of classification and prediction of vitis accessions. Moreover, our study proposed the best combination of markers for better distinguishing of populations, which can be exploited in future germplasm conservation and breeding programs.

Parthenocarpy and stenospermocarpy are the two mechanisms underlying the seedless fruit set program. Seedless fruit occurs naturally and can be produced using hormone application, crossbreeding, or ploidy breeding. However, the two types of breeding are time-consuming and sometimes ineffective due to interspecies hybridization barriers or the absence of appropriate parental genotypes to use in the breeding process. The genetic engineering approach provides a better prospect, which can be explored based on an understanding of the genetic causes underlying the seedlessness trait. For instance, CRISPR/Cas is a comprehensive and precise technology. The prerequisite for using the strategy to induce seedlessness is identifying the crucial master gene or transcription factor liable for seed formation/development. In this review, we primarily explored the seedlessness mechanisms and identified the potential candidate genes underlying seed development. We also discussed the CRISPR/Cas-mediated genome editing approaches and their improvements.

Abstract Background In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake. This process was evaluated in a hydroponic experiment using two ungrafted grapevine rootstocks Fercal (Vitis berlandieri x V. vinifera) tolerant to deficiency induced Fe chlorosis and Couderc 3309 (V. riparia x V. rupestris) susceptible to deficiency induced Fe chlorosis. Results The results could differentiate Fe deficiency effects, N-forms effects, and rootstock effects. Interveinal chlorosis of young leaves appeared earlier on 3309 C from the second week of treatment with NO3 −/NH4 + (1:0)/-Fe, while Fercal leaves showed less severe symptoms after four weeks of treatment, corresponding to decreased chlorophyll concentrations lowered by 75% in 3309 C and 57% in Fercal. Ferric chelate reductase (FCR) activity was by trend enhanced under Fe deficiency in Fercal with both N combinations, whereas 3309 C showed an increase in FCR activity under Fe deficiency only with NO3 −/NH4 + (1:1) treatment. With the transcriptome analysis, Gene Ontology (GO) revealed multiple biological processes and molecular functions that were significantly regulated in grapevine rootstocks under Fe-deficient conditions, with more genes regulated in Fercal responses, especially when both forms of N were supplied. Furthermore, the expression of genes involved in the auxin and abscisic acid metabolic pathways was markedly increased by the equal supply of both forms of N under Fe deficiency conditions. In addition, changes in the expression of genes related to Fe uptake, regulation, and transport reflected the different responses of the two grapevine rootstocks to different N forms. Conclusions Results show a clear contribution of N forms to the response of the two grapevine rootstocks under Fe deficiency, highlighting the importance of providing both N forms (nitrate and ammonium) in an appropriate ratio in order to ease the rootstock responses to Fe deficiency.

The grapevine shoot meristem contains undifferentiated primordia known as anlagen, which can develop into either inflorescences or tendrils depending on vine age, growth status, hormone balance, and other factors. Interestingly, a gain-of-function mutation in the DELLA domain of VvDELLA1 in the dwarf mutant grape, Vitis vinifera L. cv. Pixie, virtually disrupts the normal developmental course of anlagen and reroutes tendril-bounded anlagen toward inflorescence development even at the juvenile stage. To understand the underlying mechanism(s), we compared the transcriptome profiles of V. vinifera cv. Pinot Meunier (from which Pixie was derived), Pixie, and three other V. vinifera grape cultivars (Dena, Gina, and Tia) which were derived from crosses involving Pixie and carry the same DELLA mutation. Our findings revealed significant mis-regulation of hundreds of genes, profoundly reshaping both transcriptome landscapes and regulatory pathways in the mutant grapes. Interestingly, VvAP1, a central positive flower regulator in annuals, was unexpectedly co-downregulated with VvTFL1a, a flowering repressor. We also found several other key flower regulators which were either upregulated (e.g., VvFT, VvLFY) or downregulated (e.g., VvSOC1s) in all mutant grapes, although the overall effect was moderate. These findings, along with the previous identification of tendril-specific expression of VvAP1 and inflorescence-specific expression of VvLFY, support that VvAP1 promotes anlagens to develop tendrils, whereas VvLFY favors inflorescences formation. The balance between these factors, particularly the abundance of VvAP1 transcripts, ultimately dictates whether anlagens develop into tendrils or inflorescences.

Spiders are the most abundant naturally occurring predators in vineyards and play a crucial role in natural pest control. However, vineyards are frequently sprayed with fungicides, which can harm spider communities. Fungus-resistant grape varieties can drastically reduce this fungicide input. The spiders on grape vines that were sprayed with a variable number of fungicide applications in 32 vineyards in different landscapes in Southwestern Germany were recorded. Vineyards received between 0 and 14 fungicidal sprays of varying toxicity (cumulated hazard quotients for honeybee up to 6). The majority of spiders benefited from a reduction in the number fungicide sprays, particularly Dictynidae, Philodromidae, Theridiidae and Thomisidae. Overall, space web weavers, orb web weavers and ambush hunters were most strongly affected by the frequency and toxicity of fungicide applications. The response of spiders to the landscape were highly variable and included both positive and negative effects of the percentage cover of woodland. In conclusion, reducing the cumulative hazard of fungicides by reducing the number of fungicide applications is a key element in fostering spiders in vineyards.

Background'Nebbiolo' is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection.ResultsWe employed a multiple platform approach to produce long-range genomic data for two different 'Nebbiolo' clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar 'Nebbiolo' (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines' reference genome and accounting for their functional implications. We performed variant calling analyses at three different organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between 'Nebbiolo' and 'Cabernet Sauvignon' assemblies and iii) between clones CVT 71 and CVT 185, representing different 'Nebbiolo' biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the first comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes.ConclusionsOur results suggest that SVs accumulation rate and their functional implications in 'Nebbiolo' genome are highly-dependent on the organizational level under study. SVs are abundant when comparing 'Nebbiolo' to a different cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed clones.

Grapevine red blotch virus (GRBV) is a recently identified virus. Previous research indicates primarily a substantial impact on berry ripening in all varieties studied. The current study analyzed grapes' primary and secondary metabolism across grapevine genotypes and seasons to reveal both conserved and variable impacts to GRBV infection. Vitis vinifera cv. Cabernet Sauvignon (CS) grapevines grafted on two different rootstocks (110R and 420A) were analyzed in 2016 and 2017. Metabolite profiling revealed a considerable impact on amino acid and malate acid levels, volatile aroma compounds derived from the lipoxygenase pathway, and anthocyanins synthesized in the phenylpropanoid pathway. Conserved transcriptional responses to GRBV showed induction of auxin-mediated pathways and photosynthesis with inhibition of transcription and translation processes mainly at harvest. There was an induction of plant-pathogen interactions at pre-veraison, for all genotypes and seasons, except for CS 110R in 2017. Lastly, differential co-expression analysis revealed a transcriptional shift from metabolic synthesis and energy metabolism to transcription and translation processes associated with a virus-induced gene silencing transcript. This plant-derived defense response transcript was only significantly upregulated at veraison for all genotypes and seasons, suggesting a phenological association with disease expression and plant immune responses.

Background: In viticulture, iron (Fe) chlorosis is a common abiotic stress that impairs plant development and leads to yield and quality losses. Under low availability of the metal, the applied N form (nitrate and ammonium) can play a role in promoting or mitigating Fe deficiency stresses. However, the processes involved are not clear in grapevine. Therefore, the aim of this study was to investigate the response of two grapevine rootstocks to the interaction between N forms and Fe uptake. This process was evaluated in a hydroponic experiment using two ungrafted grapevine rootstocks Fercal (Vitis berlandieri x V. vinifera) tolerant to deficiency induced Fe chlorosis and Couderc 3309 (V. riparia x V. rupestris) susceptible to deficiency induced Fe chlorosis. Results: The results could differentiate Fe deficiency effects, N-forms effects, and rootstock effects. Interveinal chlorosis of young leaves appeared earlier on 3309 C from the second week of treatment with NO3−/NH4+ (1:0)/-Fe, while Fercal leaves showed less severe symptoms after four weeks of treatment, corresponding to decreased chlorophyll concentrations lowered by 75% in 3309 C and 57% in Fercal. Ferric chelate reductase (FCR) activity was by trend enhanced under Fe deficiency in Fercal with both N combinations, whereas 3309 C showed an increase in FCR activity under Fe deficiency only with NO3−/NH4+ (1:1) treatment. With the transcriptome analysis, Gene Ontology (GO) revealed multiple biological processes and molecular functions that were significantly regulated in grapevine rootstocks under Fe-deficient conditions, with more genes regulated in Fercal responses, especially when both forms of N were supplied. Furthermore, the expression of genes involved in the auxin and abscisic acid metabolic pathways was markedly increased by the equal supply of both forms of N under Fe deficiency conditions. In addition, changes in the expression of genes related to Fe uptake, regulation, and transport reflected the different responses of the two grapevine rootstocks to different N forms. Conclusions: Results show a clear contribution of N forms to the response of the two grapevine rootstocks under Fe deficiency, highlighting the importance of providing both N forms (nitrate and ammonium) in an appropriate ratio in order to ease the rootstock responses to Fe deficiency. [ABSTRACT FROM AUTHOR]

Grapes are a globally important fruit with significant economic value, influenced by factors such as sugar content, organic acids, hormones, and antioxidants. Understanding the dynamics of these compounds during grape development and ripening is critical for optimizing berry quality and production. This study investigates the changes in sugar, organic acids, hormones, and antioxidants in two grape varieties, 'Italia' and 'Bronx Seedless', at various growth stages (BBCH-77, BBCH-79, BBCH-81, BBCH-83, BBCH-85, and BBCH-89). Regarding sugars, significant variations were observed due to grapevine cultivar and phenological stage. 'Bronx Seedless' grapes consistently displayed lower sugar content than 'Italia' grapes, regardless of the type of sugar being examined. The BBCH-77 stage consistently exhibited lower sugar levels compared to BBCH-89. The varieties 'Bronx Seedless' and 'Italia' exhibited distinct nutritional profiles, each with their unique advantages in terms of sugar content and organic acid composition. Both varieties were rich in the primary sugar glucose and fructose, with 'Bronx Seedless' displaying notably high levels of the beneficial tartaric acid, enhancing its nutritional value. On the other hand, 'Italia' stood out for its higher concentrations of fumaric, butyric, and oxalic acids, contributing to its unique taste and health benefits. Throughout their growth stages from BBCH-77 to BBCH-89, an increase in organic acid levels was observed, peaking at the BBCH-85 stage, except for maleic acid. In terms of hormonal content, 'Italia' exhibited higher levels compared to 'Bronx Seedless'. The predominant hormone, abscisic acid (ABA), alongside lower quantities of zeatin, indicated a strong physiological response to environmental and developmental cues in both varieties, with hormone levels increasing as the grapes approached maturity. Antioxidant profiles also varied between the two varieties, with 'Italia' consistently showing higher antioxidant levels than 'Bronx Seedless'. Antioxidant levels consistently increased from BBCH-77 to BBCH-89. This comprehensive analysis contributes to our understanding of the complex processes underlying grape berry development and ripening, with potential implications for enhancing grape quality and refining production strategies. [ABSTRACT FROM AUTHOR]

Spiders are the most abundant naturally occurring predators in vineyards and play a crucial role in natural pest control. However, vineyards are frequently sprayed with fungicides, which can harm spider communities. Fungus-resistant grape varieties can drastically reduce this fungicide input. The spiders on grape vines that were sprayed with a variable number of fungicide applications in 32 vineyards in different landscapes in Southwestern Germany were recorded. Vineyards received between 0 and 14 fungicidal sprays of varying toxicity (cumulated hazard quotients for honeybee up to 6). The majority of spiders benefited from a reduction in the number fungicide sprays, particularly Dictynidae, Philodromidae, Theridiidae and Thomisidae. Overall, space web weavers, orb web weavers and ambush hunters were most strongly affected by the frequency and toxicity of fungicide applications. The response of spiders to the landscape were highly variable and included both positive and negative effects of the percentage cover of woodland. In conclusion, reducing the cumulative hazard of fungicides by reducing the number of fungicide applications is a key element in fostering spiders in vineyards. [ABSTRACT FROM AUTHOR]

Stilbenes are a group of plant phenolic secondary metabolites, with trans-resveratrol (3,5,4′-trihydroxy-trans-stilbene) being recognized as the most prominent and studied member. Stilbenes have a great potential for use in agriculture and medicine, as they have significant activities against plant pathogens and have valuable beneficial effects on human health. In this study, we analyzed the effects of direct application of stilbenes, stilbene precursor, and stilbene-rich extract solutions to the plant foliar surface for increasing the resistance of Arabidopsis thaliana to various abiotic stresses (heat, cold, drought, and soil salinity). Exogenous treatment of A. thaliana with stilbenes (trans-resveratrol, piceid, and spruce bark extract) and phenolic precursor (p-coumaric acid or CA) during germination resulted in considerable growth retardation of A. thaliana plants: a strong delay in the root and stem length of 1-week-old seedlings (in 1.3–4.5 fold) and rosette diameter of 1-month-old plants (in 1.2–1.8 fold), while the 2-month-old treated plants were not significantly different in size from the control. Plant treatments with stilbenes and CA increased the resistance of A. thaliana to heat and, to a lesser extent, to soil salinity (only t-resveratrol and spruce extract) to drought (only CA), while cold resistance was not affected. Plant treatments with stilbenes and CA resulted in a significant increase in plant resistance and survival rates under heat, with plants showing 1.5–2.3 times higher survival rates compared to untreated plants. Thus, exogenous stilbenes and a CA are able to improve plant survival under certain abiotic stresses via specific activation of the genes involved in the biosynthesis of auxins, gibberellins, abscisic acid, and some stress-related genes. The present work provides new insights into the application of stilbenes to improve plant stress tolerance. [ABSTRACT FROM AUTHOR]

The domestic grape germination eco-physiology is a little studied aspect since reproduction occurs predominantly agamically, despite the sexual reproduction remains the main form for the selection of new cultivars. In this study, two international cultivars grown all over the world -Chardonnay and Syrah- were chosen as models of the domestic grape for the experiments in the ecophysiology of germination. The experimental design consisted of chemical, mechanical pre-treatments and combination of them as the bird ingestion pre-treatment that simulates the transit through the digestive tract of birds. Furthermore, seeds were submitted to different periods of cold stratification - 0, 15, 30, 60 and 90 days - to simulate the winter effect. Seeds were placed to germinate at different incubation temperatures, to find the optimal germination protocol. The results showed that domestic grapes retain the need for cold stratification, and the best germination temperature is represented by the fluctuating temperature that simulates spring conditions. Our results help to understand what the best germination conditions of domestic grapes are and offer a contribution to extend the knowledge on how the process of domestication may have affected the biology of Vitis vinifera L. subsp. vinifera. [ABSTRACT FROM AUTHOR]

Grapevine leaves have diverse shapes and sizes which are influenced by many factors including genetics, vine phytosanitary status, environment, leaf and vine age, and node position on the shoot. To determine the relationship between grapevine leaf shape or size and leaf canopy temperature, we examined five seedling populations grown in a vineyard in California, USA. The populations had one parent with compound leaves of the Vitis piasezkii type and a different second parent with non-compound leaves. In previous work, we had measured the shape and size of the leaves collected from these populations using 21 homologous landmarks. Here, we paired these morphological data with canopy temperature measurements made using a handheld infrared thermometer. After recording time of sampling and canopy temperature, we used a linear model between time of sampling and canopy temperature to estimate temperature residuals. Based on these residuals, we determined if the canopy temperature of each vine was cooler or warmer than expected, based on the time of sampling. We established a relationship between leaf size and canopy temperature: vines with larger leaves were cooler than expected. By contrast, leaf shape was not strongly correlated with variation in canopy temperature. Ultimately, these findings indicate that vines with larger leaves may contribute to the reduction of overall canopy temperature; however, further work is needed to determine whether this is due to variation in leaf size, differences in the openness of the canopy or other related traits.

Rootstocks are an important means of adapting grapevine to environmental conditions whilst conserving the typical features of scion genotypes. Rootstocks not only provide tolerance to Phylloxera, but also ensure the supply of water and mineral nutrients to the scion. We take advantage of the large diversity of rootstocks used worldwide to facilitate this adaptation. The aim of this study was to characterise rootstock regulation of scion mineral status and its relationship with scion development. Vitis vinifera cvs. Cabernet-Sauvignon, Pinot noir, Syrah and Ugni blanc were grafted onto 55 different rootstock genotypes and planted as three replicates of five plants in sandy gravelly soil near Bordeaux, France. In 2020 and 2021, petiolar concentrations of 13 mineral elements (N, P, K, S, Mg, Ca, Na, B, Zn, Mn, Fe, Cu and Al) were measured at veraison. Winter pruning weight, shoot vigour, leaf chlorophyll content, bud fertility and yield were measured. Magnesium deficiency severity was visually scored for each plant. Rootstocks were grouped according to their Vitis parentage background when at least 50 % of a Vitis species was present in order to determine whether the petiole mineral composition could be related to the rootstock genetic parentage. Scion, rootstock, and their interactions had a significant influence on petiole mineral content and explained the same proportion of phenotypic variance for most mineral elements. Rootstock effect explained 9, 28 and 45 % of the mineral content variance for N, Mg and S respectively. This unique experimental design showed that the rootstock effect was higher than the scion effect on the petiole concentration of a large majority of mineral elements. The genetic background V. riparia increased the probability of low petiolar P and Mg contents. The severity of Mg deficiency symptoms varied depending on the rootstock. The differences in mineral status conferred by rootstocks were not significantly correlated with vigour or fertility. The evaluation of Mg levels by petiole analysis and the intensity of deficiency symptoms showed for the first time the variability of the thresholds of satisfactory mineral nutrition between rootstocks. Therefore, fertiliser management should take the rootstock variety into account.

Muscadinia rotundifolia cv. Trayshed is a valuable source of resistance to grape powdery mildew. It carries 2 powdery mildew resistance-associated genetic loci, Run1.2 on chromosome 12 and Run2.2 on chromosome 18. The purpose of this study was to identify candidate resistance genes associated with each haplotype of the 2 loci. Both haplotypes of each resistance-associated locus were identified, phased, and reconstructed. Haplotype phasing allowed the identification of several structural variation events between haplotypes of both loci. Combined with a manual refinement of the gene models, we found that the heterozygous structural variants affected the gene content, with some resulting in duplicated or hemizygous nucleotide-binding leucine-rich repeat genes. Heterozygous structural variations were also found to impact the domain composition of some nucleotide-binding leucine-rich repeat proteins. By comparing the nucleotide-binding leucine-rich repeat proteins at Run1.2 and Run2.2 loci, we discovered that the 2 loci include different numbers and classes of nucleotide-binding leucine-rich repeat genes. To identify powdery mildew resistance-associated genes, we performed a gene expression profiling of the nucleotide-binding leucine-rich repeat genes at Run1.2b and Run2.2 loci with or without powdery mildew present. Several nucleotide-binding leucine-rich repeat genes were constitutively expressed, suggesting a role in powdery mildew resistance. These first complete, haplotype-resolved resistance-associated loci and the candidate nucleotide-binding leucine-rich repeat genes identified by this study are new resources that can aid the development of powdery mildew-resistant grape cultivars.

AbstractAphids (Hemiptera: Aphididae) are herbivorous insects which deprive plants of nutrients by feeding on the phloem sap and transmission of plant viruses. In the present study, the susceptibility of selected white-berried grapevine (Vitis spp.) cultivars “Aurora”, “Bianca”, “Muskat Letni” and “Solaris” to the black bean aphid (Aphis fabae Scop.) and the green peach aphid (Myzus persicae (Sulz.) was evaluated using the Electrical Penetration Graph (EPG) technique. The content of major flavonoids and stilbenoids in grapevine leaves and leaf anatomy parameters that might have affected aphid probing were also analyzed. Based on the success rate in reaching the phloem vessels and feeding on phloem sap, the studied grapevine cultivars can be assigned to various groups of susceptibility. Cultivars “Bianca” and “Muskalt Letni” are susceptible to A. fabae and M. persicae, respectively (aphids reach phloem phase and show short bouts of sap ingestion); “Muskat Letni” shows low susceptibility to A. fabae, while “Aurora” and “Bianca” to M. persicae (only 50% aphids reach phloem phase and no sap ingestion occurs); “Solaris” is resistant to A. fabae and M. persicae (no phloem phase present). Anatomical structure of leaves was similar in all cultivars and no mechanical barriers for aphid probing were observed. However, the content of individual flavonoids and silbenoids differed among cultivars. We hypothesize that the high content of piceid in the leaves of “Solaris” may be responsible for the rejection of this cultivar by both aphid species. The study demonstrated that the risk of the direct damage due to A. fabae and M. persicae feeding on grapevines is low. However, considering the intense aphid probing activity within leaf epidermis and mesophyll, A. fabae and M. persicae may pose a serious threat as vectors of non-persistent and semi-persistent viruses to white-berried grapevines.

The grapevine was one of the earliest domesticated fruit crops and has been cultivated since ancient times. It is considered one of the most important fruit crops worldwide for wine and table grape production. The current grape varieties are the outcome of prolonged selection initiated during the domestication process of their wild relative. Recent genetic studies have shed light on the origins of the modern domestic grapevine in western Europe, suggesting that its origin stems from the introgression between eastern domestic grapes and western wild grapes. However, the origin of ancient grapevines remains largely unexplored. In this study, we conducted an extensive analysis of 2228 well-preserved waterlogged archaeological grape pips from two sites in Sardinia (Italy), dated to the Late Bronze Age (ca. 1300–1100 BC) and the Iron Age (4th and 3rd centuries BC). Using morphometrics and linear discriminant analyses, we compared the archaeological grape pips with modern reference collections to differentiate between wild and domestic grape types and to investigate similarities with 330 modern cultivars. Grape pips from the Late Bronze Age displayed a high percentage of similarity with domesticated grapevines, with a small percentage assigned to wild ones, while the majority of grape pips from the Iron Age were classified as domestic. Discriminant analyses revealed that both white and red grape varieties were cultivated during the Late Bronze and Iron Ages, suggesting a high level of diversification in grape cultivation. Furthermore, a high percentage of archaeological grape pips from both periods showed strong similarities with modern cultivars from the Caucasus and Balkans. This suggests that the great diversity of grapevines present in Sardinia could result from interbreeding between western Asian cultivars and local grapevines that began in the Late Bronze Age. Additionally, a substantial proportion of archaeological grape pips exhibited similar morphometric characteristics to two important Mediterranean grape cultivars: “Muscat à petits grains blancs” and “Garnacha”.

The multifaceted nature of climate change is increasing the urgency to select resilient grapevine varieties, or generate new, fitter cultivars, to withstand a multitude of new challenging conditions. The attainment of this goal is hindered by the limiting pace of traditional breeding approaches, which require decades to result in new selections. On the other hand, markerassisted breeding has proved useful when it comes to traits governed by one or few genes with great effects on the phenotype, but its efficacy is still restricted for complex traits controlled by many loci. On these premises, innovative strategies are emerging which could help guide selection, taking advantage of the genetic diversity within the Vitis genus in its entirety. Multiple germplasm collections are also available as a source of genetic material for the introgression of alleles of interest via adapted and pioneering transformation protocols, which present themselves as promising tools for future applications on a notably recalcitrant species such as grapevine. Genome editing intersects both these strategies, not only by being an alternative to obtain focused changes in a relatively rapid way, but also by supporting a fine-tuning of new genotypes developed with other methods. A review on the state of the art concerning the available genetic resources and the possibilities of use of innovative techniques in aid of selection is presented here to support the production of climate-smart grapevine genotypes. [ABSTRACT FROM AUTHOR]

Aphids (Hemiptera: Aphididae) are herbivorous insects which deprive plants of nutrients by feeding on the phloem sap and transmission of plant viruses. In the present study, the susceptibility of selected white-berried grapevine (Vitis spp.) cultivars "Aurora", "Bianca", "Muskat Letni" and "Solaris" to the black bean aphid (Aphis fabae Scop.) and the green peach aphid (Myzus persicae (Sulz.) was evaluated using the Electrical Penetration Graph (EPG) technique. The content of major flavonoids and stilbenoids in grapevine leaves and leaf anatomy parameters that might have affected aphid probing were also analyzed. Based on the success rate in reaching the phloem vessels and feeding on phloem sap, the studied grapevine cultivars can be assigned to various groups of susceptibility. Cultivars "Bianca" and "Muskalt Letni" are susceptible to A. fabae and M. persicae, respectively (aphids reach phloem phase and show short bouts of sap ingestion); "Muskat Letni" shows low susceptibility to A. fabae, while "Aurora" and "Bianca" to M. persicae (only 50% aphids reach phloem phase and no sap ingestion occurs); "Solaris" is resistant to A. fabae and M. persicae (no phloem phase present). Anatomical structure of leaves was similar in all cultivars and no mechanical barriers for aphid probing were observed. However, the content of individual flavonoids and silbenoids differed among cultivars. We hypothesize that the high content of piceid in the leaves of "Solaris" may be responsible for the rejection of this cultivar by both aphid species. The study demonstrated that the risk of the direct damage due to A. fabae and M. persicae feeding on grapevines is low. However, considering the intense aphid probing activity within leaf epidermis and mesophyll, A. fabae and M. persicae may pose a serious threat as vectors of non-persistent and semi-persistent viruses to white-berried grapevines. [ABSTRACT FROM AUTHOR]

Aim: Eurasian grapevine (Vitis vinifera), one of the most important fruit crops worldwide, diverged from its wild and currently endangered relative (V. vinifera ssp. sylvestris) about 11,000 years ago. In the 19th century, detrimental phylloxera and disease outbreaks in Europe forced grapevine cultivation to use American Vitis species as rootstocks, which have now become naturalized in Europe and are starting to colonize similar habitats to the wild grapevine. Accordingly, wild grapevine now faces two additional threats: the expansion of vineyards and invasive rootstocks. Furthermore, climate change is expected to have significant impacts on the distribution of all grapevines in Europe. In this study, we quantified the distributional and bioclimatic overlap between grapewine's wild relative and the taxa associated with viticulture, under current and future climate. Location: Europe, North America. Methods: The distributions of wild Eurasian grapevine, cultivated Eurasian grapevine and five American grapevine species used in rootstock breeding programs were linked to climate variables to model their bioclimatic niches. These ecological niche models were used to quantify the spatial and bioclimatic overlap between these seven Vitis taxa in Europe. Results: Niche and spatial overlap is high between the wild, cultivated and rootstock grapevines, suggesting that existing conflicts between vineyards and wild grapevine conservation may be further complicated by naturalized rootstocks outcompeting the wild grapevine, especially under future scenarios of climate change. In the hottest scenario, only 76.1% of the current distribution of the Eurasian grapevine remains in suitable area. Main Conclusions: As wild grapevine may ultimately provide a valuable gene pool for adapting viticulture to a changing world, these findings demonstrate the need for improved management of the wild grapevine and its natural habitat, to counteract the harmful effects of global change on the wild relatives of viticulture. [ABSTRACT FROM AUTHOR]

This paper investigates the biodiversity of adult arthropods in two grapevine plantations influenced by two adjacent groves over a three-year period (2020–2022) in the viticultural center of Stefănești Argeș, located in southern Romania. The study holds significant implications for introducing parasitoid/predatory insect species into vineyards to control grapevine pests. A total of 164 arthropod species were identified, including 27 beneficial species. Additionally, two moth species, Lobesia botrana and Sparganothis pilleriana, were identified. L. botrana was consistently observed throughout the study, while S. pilleriana was only observed in 2022. The research reveals that the location with the highest number of identified species was in a grove near a black field, with 103 species. Other areas with notable species diversity included a vineyard maintained as a black field (89 species), a grove near permanent natural grassland (88 species), and a vineyard with intervals between rows of grapevines maintained as natural permanent grassland (81 species). Introducing beneficial organisms, such as the predator Crysoperla carnea, is recommended to control grapevine moths in this ecosystem. [ABSTRACT FROM AUTHOR]

Crop improvement by means of traditional or molecular breeding is a key strategy to accomplish the European Green Deal target of reducing pesticides by 50% by 2030. Regarding viticulture, this is exacerbated by the massive use of chemicals to control pathogen infections. Black rot is an emergent disease caused by the ascomycete Phyllosticta ampelicida, and its destructiveness is alarming vine growers. Implementing and improving effective phenotyping strategies are fundamental preliminary steps to breed disease resistant varieties and this work suggests good practices adopted for this purpose. Primarily, the pedigree of black rot resistance donors was reconstructed based on the collection of phenotypic historical data, highlighting unexplored sources of black rot resistance. Strains used for artificial infections were isolated, genetically characterized and mixed to avoid race-specific resistance selection. A new inoculation protocol based on the use of leaf mature lesions was developed. Ex vivo inoculation on detached leaves was effective for the evaluation of conidia germination and hyphal growth, but not for disease progression. Finally, the pedigree was used for the identification of 23 genotypes to be tested. Two breeding selections (NY39 and NY24) resulted symptomless in all assessments and a third one (F25P52) also showed very high resistance, although with a greater variability. Other two genotypes (F12P19 and 'Charvir') fell within the medium resistance category, making them good candidates in a regime of well-timed preventive treatments. In conclusion, this work was effective to a comprehensive parental line characterization and preparatory towards grapevine breeding programs for black rot resistance. [ABSTRACT FROM AUTHOR]

Evolutionary correlations between chemical defense and protection by mutualist bodyguards have been long predicted, but tests of these patterns remain rare. We use a phylogenetic framework to test for evolutionary correlations indicative of trade-offs or synergisms between direct defense in the form of plant secondary metabolism and indirect defense in the form of leaf domatia, across 33 species in the wild grape genus, Vitis. We also performed a bioassay with a generalist herbivore to associate our chemical phenotypes with herbivore palatability. Finally, we tested whether defensive traits correlated with the average abiotic characteristics of each species' contemporary range and whether these correlations were consistent with plant defense theory. We found a negative evolutionary correlation between domatia size and the diversity of secondary metabolites in Vitis leaf tissue across the genus, and also that leaves with a higher diversity and richness of secondary metabolites were less palatable to a generalist herbivore, consistent with a trade-off in chemical and mutualistic defense investment. Predictions from plant defense theory were not supported by associations between investment in defense phenotypes and abiotic variables. Our work demonstrates an evolutionary pattern indicative of a trade-off between indirect and direct defense strategies across the Vitis genus. [ABSTRACT FROM AUTHOR]

Grape (Vitis) production and fruit quality traits such as cluster size, berry shape, and timing of fruit development are key aspects when selecting cultivars for commercial production. Molecular markers for some, but not all, of these traits have been identified using biparental or association mapping populations. Previously identified markers were tested for transferability using a small (24 individual) test panel of commercially available grape cultivars. Markers had little to no ability to differentiate grape phenotypes based on the expected characteristics, except the marker for seedlessness. Using a biparental interspecific cross, 43 quantitative trait loci (QTLs) (previously identified and new genomic regions) associated with berry shape, number, size, cluster weight, cluster length, time to flower, veraison, and full color were detected. Kompetitive allele-specific polymerase chain reaction markers designed on newly identified QTLs were tested for transferability using the same panel. Transferability was low when use types were combined, but they were varied when use types were evaluated separately. A comparison of a 4-Mb region at the end of chromosome 18 revealed structural differences among grape species and use types. Table grape cultivars had the highest similarity in structure for this region (>75%) compared with other grape species and commodity types.

Background and aimsLiving root tissues significantly constrain plant water uptake under drought, but we lack functional traits to feasibly screen diverse plants for variation in the drought responses of these tissues. Water stress causes roots to lose volume and turgor, which are crucial to root structure, hydraulics and growth. Thus, we hypothesized that root pressure-volume (p-v) curve traits, which quantify the effects of water potential on bulk root turgor and volume, would capture differences in rootstock drought tolerance.MethodsWe used a greenhouse experiment to evaluate relationships between root p-v curve traits and gas exchange, whole-plant hydraulic conductance and biomass under drought for eight grapevine rootstocks that varied widely in drought performance in field trials (101-14, 110R, 420A, 5C, 140-Ru, 1103P, Ramsey and Riparia Gloire), grafted to the same scion variety (Vitis vinifera 'Chardonnay').Key resultsThe traits varied significantly across rootstocks, and droughted vines significantly reduced root turgor loss point (πtlp), osmotic potential at full hydration (πo) and capacitance (C), indicating that roots became less susceptible to turgor loss and volumetric shrinkage. Rootstocks that retained a greater root volume (i.e. a lower C) also maintained more gas exchange under drought. The rootstocks that previous field trials have classified as drought tolerant exhibited significantly lower πtlp, πo and C values in well-watered conditions, but significantly higher πo and πtlp values under water stress, than the varieties classified as drought sensitive.ConclusionsThese findings suggest that acclimation in root p-v curve traits improves gas exchange in persistently dry conditions, potentially through impacts on root hydraulics or root to shoot chemical signalling. However, retaining turgor and volume in previously unstressed roots, as these roots deplete wet soil to moderately negative water potentials, could be more important to drought performance in the deep, highly heterogenous rooting zones which grapevines develop under field conditions.