Cultivated Vitis Vinifera Research Articles

Wine metabolome and sensory analyses demonstrate the oenological potential of novel grapevine genotypes for sustainable viticulture in warm climates.

Genetic breeding is essential to develop grapevine genotypes adapted to warm climates and resistant to pathogens. Traditionally cultivated Vitis vinifera is susceptible to biotic and abiotic stresses. Winemakers and consumers, however, perceive wines from non-vinifera or hybrid cultivars as inferior. In this study, sensory analyses and comprehensive metabolite profiling by targeted and untargeted approaches were used to investigate the oenological potential of wines from grapes of genotypes developed throughout four breeding cycles to improve climate adaptation, sugar contents and berry color. Novel genotypes had higher yields and the wines exhibited increased contents of polyphenols, including anthocyanins. Volatile monoterpenes in the wines decreased throughout breeding cycles in the absence of selective pressure. Polyphenol contents were higher in intermediate wines, with hydroxytyrosol contents reaching up to three times reported values. Mouthfeel attributes astringency, leafy taste, flavor and body, and persistency showed significant correlation with untargeted features. Supervised model-based analyses of the metabolome effectively discriminate wines from distinct genetic origins. Taken together, the results demonstrate the potential of novel grapevine genotypes to a more sustainable viticulture and quality wine production in warm climates. Comprehensive metabolite profiling of the wines reveals that genotype clustering is dependent on the chemical class and that traits not submitted to selective pressure are also altered by breeding. Supervised multivariate models were effective to predict the genetic origin of the wines based on the metabolic profile, indicating the potential of the technique to identify biomarkers for wines from sustainable genotypes. © 2024 Society of Chemical Industry.

Genetic Diversity of Armenian Grapevine (Vitis vinifera L.) Germplasm: Molecular Characterization and Parentage Analysis.

Simple SummaryThe knowledge of genetic diversity and relatedness among grapevine varieties is important for recognizing gene pools. One of the major goals of the present large-scale study was to evaluate the level and relationships of existing genetic diversity across Armenia, aiming to identify genotypes that could provide genetic insights into the Armenian grapevine germplasm structure. A combination of nuclear microsatellite markers and ampelography proved useful to determine the identity of collected samples recovered from old vineyards and home gardens. Synonyms, homonyms, alternative spellings, and misnomers were clarified. First-degree genetic relationships between autochthonous varieties were partly uncovered. Missing parents might still exist in old vineyards but were not sampled yet or might have disappeared over time. The continuation of prospections to fill that gap is planned. The high number of new bred varieties included in the study reflects the enormous breeding activity in Armenia. The high number of alleles, high level of observed and effective heterozygosity, and presence of female APT3-allele 366, which is absent in western European cultivars, illustrate the huge diversity of the Armenian germplasm. Presumably, these findings are related to recurrent introgression of Vitis sylvestris into the cultivated compartment during domestication events. So far, the present study is the first most representative and comprehensive analysis of Armenian grape germplasm.Armenia is an important country of origin of cultivated Vitis vinifera subsp. vinifera and wild Vitis vinifera subsp. sylvestris and has played a key role in the long history of grape cultivation in the Southern Caucasus. The existence of immense grapevine biodiversity in a small territory is strongly linked with unique relief and diverse climate conditions assembled with millennium-lasting cultural and historical context. In the present in-depth study using 25 nSSR markers, 492 samples collected in old vineyards, home gardens, and private collections were genotyped. For verification of cultivar identity, the symbiotic approach combining genotypic and phenotypic characterization for each genotype was carried out. The study provided 221 unique varieties, including 5 mutants, from which 66 were widely grown, neglected or minor autochthonous grapevine varieties, 49 turned out to be new bred cultivars created within the national breeding programs mainly during Soviet Era and 34 were non-Armenian varieties with different countries of origin. No references and corresponding genetic profiles existed for 67 genotypes. Parentage analysis was performed inferring 62 trios with 53 out of them having not been previously reported and 185 half-kinships. Instability of grapevine cultivars was detected, showing allelic variants, with three and in rare cases four alleles at one loci. Obtained results have great importance and revealed that Armenia conserved an extensive grape genetic diversity despite geographical isolation and low material exchange. This gene pool richness represents a huge reservoir of under-explored genetic diversity.

Parentage Atlas of Italian Grapevine Varieties as Inferred From SNP Genotyping.

The Italian grape germplasm is characterized by a high level of richness in terms of varieties number, with nearly 600 wine grape varieties listed in the Italian National Register of Grapevine Varieties and with a plethora of autochthonous grapes. In the present study an extended SNP genotyping has been carried out on Italian germplasm of cultivated Vitis vinifera subsp. sativa and Vitis hybrids. Several hundred Italian varieties maintained in the repositories of scientific Institutions and about one thousand additional varieties derived from previous studies on European, Southern Italy, Magna Graecia and Georgian germplasm were considered. The large genotyping data obtained were used to check the presence of homonyms and synonyms, determine parental relationships, and identify the main ancestors of traditional Italian cultivars and closely-related accessions. The parentage among a set of 1,232 unique varieties has been assessed. A total of 92 new parent-offspring (PO) pairs and 14 new PO trios were identified. The resulted parentage network suggested that the traditional Italian grapevine germplasm originates largely from a few central varieties geographically distributed into several areas of genetic influence: “Strinto porcino” and its offspring “Sangiovese”, “Mantonico bianco” and “Aglianico” mainly as founder varieties of South-Western Italy (IT-SW); Italian Adriatic Coast (IT-AC); and Central Italy with most varieties being offsprings of “Visparola”, “Garganega” and “Bombino bianco”; “Termarina (Sciaccarello)” “Orsolina” and “Uva Tosca” as the main varieties of North-Western Italy (IT-NW) and Central Italy. The pedigree reconstruction by full-sib and second-degree relationships highlighted the key role of some cultivars, and, in particular, the centrality of “Visparola” in the origin of Italian germplasm appeared clear. An hypothetical migration of this variety within the Italian Peninsula from South to North along the eastern side, as well as of “Sangiovese” from South to Central Italy along the Western side might be supposed. Moreover, it was also highlighted that, among the main founders of muscat varieties, “Moscato bianco” and “Zibibbo (Muscat of Alexandria)” have spread over the whole Italy, with a high contribution by the former to germplasm of the North-Western of the peninsula.

Evaluation of the effectiveness of the fungicidal effect of drugs against pathogens of cultivated grapes (Vitis vinifera L.)

The Vitis vinifera L. cultural grape includes many varieties that are highly valued in winemaking and viticulture, as raw materials for the production of fresh and dried berries, for the production of wines. The fruits of cultural grapes play an important role in medicine, where they are used as a source of substances with high antioxidant activity. Grapes are often affected by phytopathogenic fungal infections. In recent years, a large number of reports have appeared in the literature about the acquisition of resistance of microorganisms to industrial pesticide preparations, which in turn leads to an increase in drug doses, the multiplicity of treatments and the accumulation of harmful substances in the environment and in the plants themselves. In this study, we evaluate the effectiveness of the fungicidal action of industrial preparations and plant extracts in relation to two native species of fungi (V1 and V2) isolated from the leaves of cultivated Vitis vinifera L. grapes, as well as against the phytopathogen Alternaria solani K-100054. Minimal inhibitory (MIC) and fungicidal concentrations (MFC) were detected for each sample. Ethanol extracts of plants showed low antimycotic activity in relation to fungi cultures isolated from grapes. Activity started from 0.0625%. The best result among industrial fungicides was shown by the drug “Maxim”, whose MIC values was 0.097 μg/mL, and the MFC varies between 3.125-12.5 μg/mL for pathogens V1 and V2, respectively.

Characterization of Stilbene Composition in Grape Berries from Wild Vitis Species in Year-To-Year Harvest.

Asian and American Vitis species possess a strong potential for crossbreeding programs, owing to their several resistance properties. Stilbenes are phenolic compounds present in grape berries and are well-known for their main role as phytoalexins and resistance to biotic stresses in plants. However, their identification and quantification in grape berries from wild Vitis remains unexplored. A mass spectrometry multiple reaction monitoring method combined with the analysis of pure standards allowed for the unambiguous characterization of 20 stilbenes in the grape berry skin extracts of nine native Vitis species and one cultivated Vitis vinifera species (cv. Cabernet Sauvignon). A main occurrence of monomeric (Z-piceid, E-piceid, E-isorhapontin, and E-astringin), dimeric (E-ε-viniferin, Z-ε-viniferin, and pallidol), and oligomeric (isohopeaphenol and r-viniferin) stilbenes was highlighted. Some stilbenes were clearly characterized for the first time in grape berries, such as the dimers ampelopsin A, E-vitisinol C, and parthenocissin A as well as the tetramers r2-viniferin and r-viniferin. Stilbene composition and content varied widely among several Vitis species and vintage years.

The wild grape genome sequence provides insights into the transition from dioecy to hermaphroditism during grape domestication

BackgroundA key step in domestication of the grapevine was the transition from separate sexes (dioecy) in wild Vitis vinifera ssp. sylvestris (V. sylvestris) to hermaphroditism in cultivated Vitis vinifera ssp. sativa (V. vinifera). It is known that V. sylvestris has an XY system and V. vinifera a modified Y haplotype (Yh) and that the sex locus is small, but it has not previously been precisely characterized.ResultsWe generate a high-quality de novo reference genome for V. sylvestris, onto which we map whole-genome re-sequencing data of a cross to locate the sex locus. Assembly of the full X, Y, and Yh haplotypes of V. sylvestris and V. vinifera sex locus and examining their gene content and expression profiles during flower development in wild and cultivated accessions show that truncation and deletion of tapetum and pollen development genes on the X haplotype likely causes male sterility, while the upregulation of a Y allele of a cytokinin regulator (APRT3) may cause female sterility. The downregulation of this cytokinin regulator in the Yh haplotype may be sufficient to trigger reversal to hermaphroditism. Molecular dating of X and Y haplotypes is consistent with the sex locus being as old as the Vitis genus, but the mechanism by which recombination was suppressed remains undetermined.ConclusionsWe describe the genomic and evolutionary characterization of the sex locus of cultivated and wild grapevine, providing a coherent model of sex determination in the latter and for transition from dioecy to hermaphroditism during domestication.

A Partially Phase-Separated Genome Sequence Assembly of the Vitis Rootstock 'Börner' (Vitis riparia × Vitis cinerea) and Its Exploitation for Marker Development and Targeted Mapping.

Grapevine breeding has become highly relevant due to upcoming challenges like climate change, a decrease in the number of available fungicides, increasing public concern about plant protection, and the demand for a sustainable production. Downy mildew caused by Plasmopara viticola is one of the most devastating diseases worldwide of cultivated Vitis vinifera. In modern breeding programs, therefore, genetic marker technologies and genomic data are used to develop new cultivars with defined and stacked resistance loci. Potential sources of resistance are wild species of American or Asian origin. The interspecific hybrid of Vitis riparia Gm 183 x Vitis cinerea Arnold, available as the rootstock cultivar ‘Börner,’ carries several relevant resistance loci. We applied next-generation sequencing to enable the reliable identification of simple sequence repeats (SSR), and we also generated a draft genome sequence assembly of ‘Börner’ to access genome-wide sequence variations in a comprehensive and highly reliable way. These data were used to cover the ‘Börner’ genome with genetic marker positions. A subset of these marker positions was used for targeted mapping of the P. viticola resistance locus, Rpv14, to validate the marker position list. Based on the reference genome sequence PN40024, the position of this resistance locus can be narrowed down to less than 0.5 Mbp on chromosome 5.

Evaluation of breeding potential of wild grape originating from Armenia

Crop wild relatives provide a useful source of genetic variation and represent a large pool of genetic diversity for new allelic variation required in breeding programs. Armenia is an important center of origin both for cultivatedVitis viniferassp. sativaand wildVitis viniferassp.sylvestris.Owing to recent prospection in Armenian woods and river floodplains many forms of wild grapevine were discovered and inventoried, which is an important prerequisite to unlock their breeding potential in the future. The fact that some genotypes ofV. sylvestriscan withstand the diseases is likely to be due to a more efficient basal immunity. The overall goal of the proposed research was to characterize the diversity ofV. sylvestrisfrom Armenia with respect to its capacity for stilbene biosynthesis, which might be exploited as genetic resource for resistance breeding. The realized research stimulates the recovery, characterization and preservation of wild grape germplasm, presently at risk of extinction. The recovery and characterization of wild genotypes will be the base of selection of genetic traits important in breeding programs for the generation of biotic and changing climate tolerant grapevine varieties and rootstocks, both necessary for the future of viticulture in Armenia and in Europe.

Vitis Flower Sex Specification Acts Downstream and Independently of the ABCDE Model Genes.

The most discriminating characteristic between the cultivated Vitis vinifera subsp. vinifera and the wild-form Vitis vinifera subsp. sylvestris is their sexual system. Flowers of cultivars are mainly hermaphroditic, whereas wild plants have female and male individuals whose flowers follow a hermaphroditic pattern during early stages of development and later develop non-functional reproductive organs. In angiosperms, the basic developmental system for floral organ identity is explained by the ABCDE model. This model postulates that regulatory gene functions work in a combinatorial way to confer organ identity in each whorl. In wild Vitis nothing is known about the function and expression profile of these genes. Here we show an overall view of the temporal and spatial expression pattern of the ABCDE genes as well as the pattern of VviSUPERMAN that establishes a boundary between the stamen and the carpel whorls, in the male, female and complete flower types. The results show a similar pattern in Vitis species suggesting that the pathway leading to unisexuality acts independently and/or downstream of B- and C- function genes.

Genomic signatures of different adaptations to environmental stimuli between wild and cultivated Vitis vinifera L

The application of population genetic methods in combination with gene mapping strategies can help to identify genes and mutations selected during the evolution from wild plants to crops and to explore the considerable genetic variation still maintained in natural populations. We genotyped a grapevine germplasm collection of 44 wild (Vitis vinifera subsp. sylvestris) and 48 cultivated (V. vinifera subsp. sativa) accessions at 54 K single-nucleotide polymorphisms (SNPs) to perform a whole-genome comparison of the main population genetic statistics. The analysis of Wright Fixation Index (FST) along the whole genome allowed us to identify several putative “signatures of selection” spanning over two thousand SNPs significantly differentiated between sativa and sylvestris. Many of these genomic regions included genes involved in the adaptation to environmental changes. An overall reduction of nucleotide diversity was observed across the whole genome within sylvestris, supporting a small effective population size of the wild grapevine. Tajima’s D resulted positive in both wild and cultivated subgroups, which may indicate an ongoing balancing selection. Association mapping for six domestication-related traits was performed in combination with population genetics, providing further evidence of different perception and response to environmental stresses between sativa and sylvestris.

Phased diploid genome assembly with single-molecule real-time sequencing.

While genome assembly projects have been successful in many haploid and inbred species, the assembly of noninbred or rearranged heterozygous genomes remains a major challenge. To address this challenge, we introduce the open-source FALCON and FALCON-Unzip algorithms (https://github.com/PacificBiosciences/FALCON/) to assemble long-read sequencing data into highly accurate, contiguous, and correctly phased diploid genomes. We generate new reference sequences for heterozygous samples including an F1 hybrid of Arabidopsis thaliana, the widely cultivated Vitis vinifera cv. Cabernet Sauvignon, and the coral fungus Clavicorona pyxidata, samples that have challenged short-read assembly approaches. The FALCON-based assemblies are substantially more contiguous and complete than alternate short- or long-read approaches. The phased diploid assembly enabled the study of haplotype structure and heterozygosities between homologous chromosomes, including the identification of widespread heterozygous structural variation within coding sequences.

Evidence of resistance to the downy mildew agent Plasmopara viticola in the Georgian Vitis vinifera germplasm

Grapevine downy mildew, caused by Plasmopara viticola , is one of the most important diseases at the international level. The mainly cultivated Vitis vinifera varieties are generally fully susceptible to P. viticola , but little information is available on the less common germplasm. The V. vinifera germplasm of Georgia (Caucasus) is characterized by a high genetic diversity and it is different from the main European cultivars. Aim of the study is finding possible sources of resistance in the Georgian autochthonous varieties available in a field collection in northern Italy. The resistance levels to P. viticola were estimated both by experimental inoculations and by disease assessment in field conditions in a multi-year activity. Of the 93 tested accessions, 'Mgaloblishvili N' showed a constant resistant behaviour, by reducing the disease severity and the pathogen sporulation. High levels of leaf hair density did not always associate with reduced disease gravity in experimental inoculations, confirming that this kind of preformed barrier is not completely efficient in preventing pathogen infections.

Hybridization of cultivated Vitis vinifera with wild V.californica and V.girdiana in California.

Hybridization of introduced domesticates and closely related natives is well documented in annual crops. The widespread introduction of the domesticated grapevine, Vitis vinifera, into California where it overlaps with two native congenerics, with which it is interfertile, provides opportunity to investigate hybridization between woody perennials. Although geographically widespread, the introduction over the past two centuries has been limited to a few elite clonal cultivars, providing a unique opportunity to study the effects of hybridization on the native species. The amount of hybridization with V. vinifera and the genetic diversity of wild‐growing Vitis californica and Vitis girdiana were examined using nineteen microsatellite markers. STRUCTURE analysis was used to define hybrid and introgressed individuals and to analyze genetic structure of the native species. FAMOZ software was used to identify which V. vinifera cultivars served as parents of F 1 hybrids. The three species were clearly distinguished by STRUCTURE analysis. Thirty percent of 119 V. californica vines were hybrids. The domesticated parent was identified for 16 F 1 hybrid vines; the original California cultivar, ‘Mission’, was the parent of eight. Backcrosses were also found, showing introgression into subsequent generations. Similar results were obtained for a small sample of V. girdiana. Removing hybrids greatly reduced the genetic variation of the presumed pure species, among which there was essentially no genetic structure. Limited genetic variability indicates the California natives may be threatened by genetic erosion. The discovery of F 1 hybrids of ‘Mission’, a cultivar not grown in the areas for ~100 years, suggests long generation times for wild vines that, often, grow into expansive liana and propagate by layering, all factors that limit recruitment in populations already disjunct by habitat lose. Hermaphroditic flowers and fruit that is more attractive to birds may favor the production of backcross seed and establishment of introgressed individuals.

Whole-genome genotyping of grape using a panel of microsatellite multiplex PCRs

The use of microsatellite markers in large-scale ge- netic studies islimited byits low throughputand highcostand labor requirements. Here, we provide a panel of 45 multiplex PCRs for fast and cost-efficient genome-wide fluorescence- based microsatellite analysis in grapevine. The developed multiplex PCRs panel (with upto 15-plex) enables the scoring of 270 loci covering all the grapevine genome (9 to 20 loci/chromosome) using only 45 PCRs and sequencer runs. The 45 multiplex PCRs were validated using a diverse grape- vinecollectionof207accessions,selectedtorepresentmostof the cultivated Vitis vinifera genetic diversity. Particular atten- tion was paid to quality control throughout the whole process (assay replication, null allele detection, ease of scoring). Genetic diversity summary statistics and features of electro- phoretic profiles for each studied marker are provided, as are the genotypes of 25 common cultivars that could be used as references in other studies.

Earliest evidence of a primitive cultivar of Vitis vinifera L. during the Bronze Age in Sardinia (Italy)

The discovery of the Nuragic culture settlement of Sa Osa, Cabras-Oristano, Sardinia, has made it possible to investigate the domestication status of waterlogged uncharred grape pips that were recovered from three wells dating from the Middle and Late Bronze Age (ca. 1350–1150 bc). Applying the stepwise linear discriminant analysis method, a morphological comparison of archaeological seeds and modern wild and cultivated Sardinian grapes pips was performed to determine the similarities between them. The results showed that the archaeological seeds from the Middle Bronze Age have intermediate morphological traits between modern wild and cultivated grape pips from Sardinia. In contrast, the analyses performed on the archaeological seeds from the Late Bronze Age showed a high degree of similarity with the modern cultivars in Sardinia. These results provide the first evidence of primitive cultivated Vitis vinifera in Sardinia during the Late Bronze Age (1286–1115 cal bc, 2σ). This evidence may support the hypothesis that Sardinia could have been a secondary domestication centre of the grapevine, due to the presence of ancient cultivars that still exhibit the phenotypic characteristics of wild grapes.

The effects of artificial selection on sugar metabolism and transporter genes in grape

Sugar content is a key feature of grape quality. The sugar content of grapes has been significantly improved after nearly a thousand years of artificial selection. However, the mechanism underlying the changes in the grape sugar content during the process of artificial selection remains largely unknown although several genes involved in sugar metabolism and transportation in grape have been identified. In this study, the genomes of 13 wild Vitis species and 14 cultivated Vitis vinifera accessions were resequenced to 2–5 X depth using the Illumina Hiseq2000 platform. Genetic variation of 138 genes involved in sugar biosynthesis and transport was investigated, and 7,690 and 12,717 single nucleotide polymorphisms/insertions and deletions (SNPs/InDel) were identified within the cultivated V. vinifera and wild Vitis species, respectively. The percentages of SNPs/InDels were 0.93 and 1.54 % in cultivated and wild species, respectively, and the wild Vitis species had 1.65-fold more SNPs/InDels than the cultivated V. vinifera. Moreover, the distribution of SNPs/InDels in gene regions was also investigated. Eight genes (HT4, PPFTK4, PPFTK6, PMT3, SPS1, HT8, HT15, SUSy1) showed low level of allelic diversity in cultivated species, suggesting they might have undergone purifying selection during the domestication process of grapes. Our genome DNA resequencing data provided a valuable resource for analyzing the effects of artificial selection on trait-related pathways in grape. The result that eight genes showed lower level of DNA variation in cultivated species than in wild species will be very helpful in understanding sugar accumulation in grapes.

Antispila oinophylla new species (Lepidoptera, Heliozelidae), a new North American grapevine leafminer invading Italian vineyards: taxonomy, DNA barcodes and life cycle.

A grapevine leafminer Antispila oinophylla van Nieukerken & Wagner, sp. n., is described both from eastern North America (type locality: Georgia) and as a new important invader in North Italian vineyards (Trentino and Veneto Region) since 2006. The species is closely related to, and previously confused with Antispila ampelopsifoliella Chambers, 1874, a species feeding on Virginia creeper Parthenocissus quinquefolia (L.) Planchon., and both are placed in an informal Antispila ampelopsifoliella group. Wing pattern, genitalia, and DNA barcode data all confirm the conspecificity of native North American populations and Italian populations. COI barcodes differ by only 0–1.23%, indicating that the Italian populations are recently established from eastern North America. The new species feeds on various wild Vitis species in North America, on cultivated Vitis vinifera L. in Italy, and also on Parthenocissus quinquefolia in Italy. North American Antispila feeding on Parthenocissus include at least two other species, one of which is Antispila ampelopsifoliella. Morphology and biology of the new species are contrasted with those of North American Antispila Hübner, 1825 species and European Holocacista rivillei (Stainton, 1855). The source population of the introduction is unknown, but cases with larvae or pupae, attached to imported plants, are a likely possibility. DNA barcodes of the three European grapevine leafminers and those of all examined Heliozelidae are highly diagnostic. North American Vitaceae-feeding Antispila form two species complexes and include several as yet unnamed taxa. The identity of three out of the four previously described North American Vitaceae-feeding species cannot be unequivocally determined without further revision, but these are held to be different from Antispila oinophylla. In Italy the biology of Antispila oinophylla was studied in a vineyard in the Trento Province (Trentino-Alto Adige Region) in 2008 and 2009. Mature larvae overwinter inside their cases, fixed to vine trunks or training stakes. The first generation flies in June. An additional generation occurs from mid-August onwards. The impact of the pest in this vineyard was significant with more than 90% of leaves infested in mid-summer. Since the initial discovery in 2006, the pest spread to several additional Italian provinces, in 2010 the incidence of infestation was locally high in commercial vineyards. Preliminary phylogenetic analyses suggest that Antispila is paraphyletic, and that the Antispila ampelopsifoliella group is related to Coptodisca Walsingham, 1895, Holocacista Walsingham & Durrant, 1909 and Antispilina Hering, 1941, all of which possess reduced wing venation. Vitaceae may be the ancestral hostplant family for modern Heliozelidae.