Collection and characterization of grapevine genetic resources (Vitis vinifera) in the Holy Land, towards the renewal of ancient winemaking practices

Setting the morphologic quality limits enabling accurate classification of charred archaeological grape seeds

This study investigates the morphological changes in grape pips resulting from various charring conditions. Employing high-resolution scanning combined with morphometric measurements for morphological analysis, we aimed to understand the effects of charring on grape pips. Our morphometric analysis demonstrated significant alterations in seed shape above 250 °C. The length-width ratio and the occurrence of cracks notably changed, providing a basis for assessing charring conditions. In addition, applying a machine learning classification method, we determined that accurate classification of grape varieties by the morphometric analysis method is feasible for seeds charred at up to 250 °C and 8 h. Integrating the morphometric changes and temperature ranges suitable for classification, we developed a sorting model for archaeological seeds. By projecting length-width ratios onto a curve calculated from controlled conditions, we estimated charring temperatures. Approximately 50% of archaeological seeds deviated from the model, indicating drastic charring conditions. This sorting model facilitates a stringent selection of seeds fit for classification, enhancing the accuracy of our machine learning-based methodology. In conclusion, combining machine learning with morphometric sorting enables the identification of charred grape seeds suitable for identification by the morphometric method. This comprehensive approach provides a valuable tool for future research for the identification of charred grape seeds found in archaeological contexts, enhancing our understanding of ancient viticulture practices and grape cultivation.

Integration of machine learning models with microsatellite markers: New avenue in world grapevine germplasm characterization

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.

A history of olive and grape cultivation in Southwest Asia using charcoal and seed remains

Evaluating archaeobotanical data from over 3.9 million seeds and 124,300 charcoal fragments across 330 archaeological site phases in Southwest Asia, we reconstruct the history of olive and grape cultivation spanning a period of 6,000 years. Combining charcoal and seed data enables investigation into both the production and consumption of olive and grape. The earliest indication for olive and grape cultivation appears in the southern Levant around ca. 5000 BC and 4th millennium BC respectively, although cultivation may have been practiced prior to these dates. Olive and grape cultivation in Southwest Asia was regionally concentrated within the Levant until 600 BC, although there were periodic pushes to the East. Several indications for climate influencing the history of olive and grape cultivation were found, as well as a correlation between periods of high population density and high proportions of olive and grape remains in archaeological sites. While temporal uncertainty prevents a detailed understanding of the causal mechanisms behind these correlations, we suggest that long distance trade in olives, grapes and their associated products was integral to the economic, social, and demographic trajectories of the region.

Boosting grapevine breeding for climate-smart viticulture: from genetic resources to predictive genomics

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, marker-assisted 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.

Influence of late pruning practice on two red skin grapevine cultivars in a semi-desert climate

Continually increasing global temperature could severely affect grape berry metabolite accumulation and ultimately wine polyphenol concentration and color intensity. To explore the effect of late shoot pruning on grape berry and wine metabolite composition, field trials were carried out on Vitis vinifera cv. Malbec and cv. Syrah grafted on 110 Richter rootstock. Fifty-one metabolites were detected and unequivocally annotated employing UPLC-MS based metabolite profiling. Integrating the data using hierarchical clustering showed a significant effect of late pruning treatments on must and wine metabolites. Syrah metabolite profiles were characterized by a general trend of higher metabolite content in the late shoot pruning treatments, while Malbec profiles did not show a consistent trend. In summary, late shoot pruning exerts a significant effect, though varietal specific, on must and wine quality-related metabolites, possibly related to enhanced photosynthetic efficiency, which should be taken into consideration when planning mitigating strategies in warm climates.

A Field Collection of Indigenous Grapevines as a Valuable Repository for Applied Research

The grapevine is an economically important plant, with a historical connection to the development of human culture. Currently, over 6000 accessions are known as individual grapevine varieties, some of which are important to national heritage, valuable for current viticultural practices, and as genetic resources to maintain plasticity under changing climatic conditions, environmental sustainability, and market demands. Recently, the diversity of cultivated grapevines has declined significantly, due to the increased focus of global wine industries on a few major cultivars. Moreover, due to biotic and abiotic stresses, the wild V. vinifera germplasm's genetic diversity has declined, with some varieties on the verge of extinction. Vitis germplasm conservation can be achieved via either in situ (e.g., protected areas) or Ex situ (e.g., field collections, seed banks, and tissue culture collections) methods. This study aims to highlight the importance of Vitis field bank collections. We demonstrate the research done in the Israeli indigenous Vitis vinifera collection. The multi-layer analysis of the varieties enabled the identification of drought stress-resistant varieties, and suggested a mechanism for this resistance through noting the dramatic phenological differences in foliage development between resistant and sensitive varieties. In addition, we show a general characterization of the varieties via major grape characteristics, including bunch and berry shape, as well as their possible utilization based on their aromatic and phenolic profiles.

The Rise of Wine among Ancient Civilizations across the Mediterranean Basin

The purpose of this work is to present the archaeological and historical background of viticulture and winemaking from ancient times to the present day in the Mediterranean basin. According to recent archaeological, archaeochemical and archaeobotanical data, winemaking emerged during the Neolithic period (c. 7th–6th millennium BC) in the South Caucasus, situated between the basins of the Black and Caspian Seas, and subsequently reached the Iberian Peninsula and Western Europe during the local beginning of Iron Age (c. 8th century BC), following the main maritime civilizations. This review summarises the most relevant findings evidencing that the expansion of wine production, besides depending on adequate pedo-climatic conditions and wine-growing practices, also required the availability of pottery vessels to properly ferment, store and transport wine without deterioration. The domestication of wild grapevines enabled the selection of more productive varieties, further sustaining the development of wine trade. Other fermented beverages such as mead and beer gradually lost their relevance and soon wine became the most valorised. Together with grapes, it became an object and a system of value for religious rituals and social celebrations throughout successive ancient Western civilizations. Moreover, wine was used for medicinal purposes and linked to a wide variety of health benefits. In everyday life, wine was a pleasant drink consumed by the elite classes and commoner populations during jubilee years, festivals, and banquets, fulfilling the social function of easy communication. In the present work, emphasis is put on the technical interpretation of the selected archaeological and historical sources that may explain present viticultural and oenological practices. Hopefully, this review will contribute to nurturing mutual understanding between archaeologists and wine professionals.

Accurate classification of fresh and charred grape seeds to the varietal level, using machine learning based classification method

Grapevine (Vitis vinifera L.) currently includes thousands of cultivars. Discrimination between these varieties, historically done by ampelography, is done in recent decades mostly by genetic analysis. However, when aiming to identify archaeobotanical remains, which are mostly charred with extremely low genomic preservation, the application of the genomic approach is rarely successful. As a result, variety-level identification of most grape remains is currently prevented. Because grape pips are highly polymorphic, several attempts were made to utilize their morphological diversity as a classification tool, mostly using 2D image analysis technics. Here, we present a highly accurate varietal classification tool using an innovative and accessible 3D seed scanning approach. The suggested classification methodology is machine-learning-based, applied with the Iterative Closest Point (ICP) registration algorithm and the Linear Discriminant Analysis (LDA) technique. This methodology achieved classification results of 91% to 93% accuracy in average when trained by fresh or charred seeds to test fresh or charred seeds, respectively. We show that when classifying 8 groups, enhanced accuracy levels can be achieved using a "tournament" approach. Future development of this new methodology can lead to an effective seed classification tool, significantly improving the fields of archaeobotany, as well as general taxonomy.

Demographic and ecogeographic factors limit wild grapevine spread at the southern edge of its distribution range

The spatial distribution of plants is constrained by demographic and ecogeographic factors that determine the range and abundance of the species. Wild grapevine (Vitis vinifera ssp. sylvestris) is distributed from Switzerland in the north to Israel in the south. However, little is known about the ecogeographic constraints of this species and its genetic and phenotypic characteristics, especially at the southern edge of its distribution range in the Levant region. In this study, we explore the population structure of southern Levantine wild grapevines and the correlation between demographic and ecogeographic characteristics. Based on our genetic analysis, the wild grapevine populations in this region can be divided into two major subgroups in accordance with a multivariate spatial and ecogeographical clustering model. The identified subpopulations also differ in morphological traits, mainly leaf hairiness which may imply adaptation to environmental stress. The findings suggest that the Upper Jordan River population was spread to the Sea of Galilee area and that a third smaller subpopulation at the south of the Golan Heights may represent a distinguished gene pool or a recent establishment of a new population. A spatial distribution model indicated that distance to water sources, Normalized difference vegetation index, and precipitation are the main environmental factors constraining V. v. sylvestris distribution at its southern distribution range. These factors in addition to limited gene flow between populations prevent further spread of wild grapevines southwards to semi-arid regions.

Population structure of Erysiphe necator on domesticated and wild vines in the Middle East raises questions on the origin of the grapevine powdery mildew pathogen

Plant pathogens usually originate and diversify in geographical regions where hosts and pathogens co-evolve. Erysiphe necator, the causal agent of grape powdery mildew, is a destructive pathogen of grapevines worldwide. Although Eastern US is considered the centre of origin and diversity of E. necator, previous reports on resistant native wild and domesticated Asian grapevines suggest Asia as another possible origin of the pathogen. By using multi-locus sequencing, microsatellites and a novel application of amplicon sequencing (AmpSeq), we show that the population of E. necator in Israel is composed of three genetic groups: Groups A and B that are common worldwide, and a new group IL, which is genetically differentiated from any known group in Europe and Eastern US. Group IL showed distinguished ecological characteristics: it was dominant on wild and traditional vines (95%); its abundance increased along the season; and was more aggressive than A and B isolates on both wild and domesticated vines. The low genetic diversity within group IL suggests that it has invaded Israel from another origin. Therefore, we suggest that the Israeli E. necator population was founded by at least two invasions, of which one could be from a non-East American source, possibly from Asian origin.

Differences between microbiota, phytochemical, antioxidant profile and dna fingerprinting of cabernet sauvignon grape from Slovakia and Macedonia

This study aimed to evaluate the microbiota, phytochemical, antioxidant profile and DNA fingerprinting of Cabernet Sauvignon grapes from Slovakia and R. North Macedonia. There were used two samples of grape berries (one sample from Slovakia and one from Macedonia). Each sample was analyzed in triplicate. The bacteria were cultivated on Plate count agar (PCA), microscopic filamentous fungi were cultivated on Malt extract agar (MEA). MALDI-TOF MS Biotyper mass spectrometry was used for the identification of microorganisms (bacteria and yeasts) and microscopic filamentous fungi with manuals. DPPH method was used to determine of antioxidant activity of grape berries. Phytochemical and antioxidant profiles were evaluated in grape berries samples. Total genomic DNA was extracted from mature grapes by GeneJET Plant Genomic DNA Purification Kit. The number of bacteria was higher in the sample of Macedonian grape (4.13 log CFU.g-1) in comparison to the grape from Slovakia as well as the number of yeasts was also higher in the Macedonian sample (2.57 log CFU.g-1). Antioxidant activity of Slovak grape berries was 0.55 mg TEAC.g-1 and of Macedonian grape, berries was 0.51 mg TEAC.g-1. Total polyphenol content was higher in grape from Slovakia (0.81 mg GAE.g-1) than in grape from Macedonia (0.77 mg GAE.g-1), while total flavonoid content was 0.57 and 0.17 mg QE.g-1 in Slovak grape and Macedonian grape, respectively. Total phenolic acid content was higher in the sample from Macedonia (0.40 mg CAE.g-1) compared to the grape from Slovakia (0.24 mg CAE.g-1). Total anthocyanin content was also higher in Macedonian grape (0.46 mg.g-1) compared to the Slovak sample (0.05 mg.g-1). The total polymorphism for all of the used primers of 87.5% was obtained for the Macedonian sample of Cabernet Sauvignon and 89.4% for the Slovak sample.

Population genetic analysis in old Montenegrin vineyards reveals ancient ways currently active to generate diversity in Vitis vinifera

Global viticulture has evolved following market trends, causing loss of cultivar diversity and traditional practices. In Montenegro, modern viticulture co-exists with a traditional viticulture that still maintains ancient practices and exploits local cultivars. As a result, this region provides a unique opportunity to explore processes increasing genetic diversity. To evaluate the diversity of Montenegrin grapevines and the processes involved in their diversification, we collected and analyzed 419 samples in situ across the country (cultivated plants from old orchards and vines growing in the wild), and 57 local varieties preserved in a grapevine collection. We obtained 144 different genetic profiles, more than 100 corresponding to cultivated grapevines, representing a surprising diversity for one of the smallest European countries. Part of this high diversity reflects historical records indicating multiple and intense introduction events from diverse viticultural regions at different times. Another important gene pool includes many autochthonous varieties, some on the edge of extinction, linked in a complex parentage network where two varieties (Razaklija and Kratošija) played a leading role on the generation of indigenous varieties. Finally, analyses of genetic structure unveiled several putative proto-varieties, likely representing the first steps involved in the generation of new cultivars or even secondary domestication events.

The Cypriot Indigenous Grapevine Germplasm Is a Multi-Clonal Varietal Mixture

Cypriot vineyards are considered as one among the earliest niches of viticulture and a pivotal hub for the domestication and dissemination of grapevine. The millennial presence of Vitis spp. in this Eastern Mediterranean island has given rise to a plethora of biotypes that have not been adequately characterized, despite their unique attributes and stress tolerance. This ancient germplasm also has an additional value since it survived the phylloxera outbreak; hence, it possesses a large amount of genetic diversity that has been unnoticed. In order to provide useful insights to the lineage of Cypriot vineyards, a two-year-spanning collection of centennial grapevine cultivars mostly regarded to belong to four indigenous variety clusters ("Mavro", "Xynisteri", "Maratheftiko", and "Veriko") was initiated. There were 164 accessions across the broader Commandaria wine zone sampled and characterized using a universal microsatellite primer set. Genetic analysis indicated that considered indigenous Cypriot germplasm has a polyclonal structure with a high level of heterozygosity. Moreover, several lineages or unexplored varieties may exist, since a larger than considered number of discrete genotypes was discovered. Furthermore, it was established that grapevine lineages in Cyprus were shaped across eras via clonal, as well as, sexual propagation. The special attributes of the Cypriot landscape are discussed.

Genetic analysis of the grapevine genotypes of the Russian Vitis ampelographic collection using iPBS markers

Cultivated grapevine (Vitis vinifera L. ssp. sativa D.C.) is one of the oldest agricultural crops, each variety comprising an array of clones obtained by vegetative propagation from a selected vine grown from a single seedling. Most clones within a variety are identical, but some show a different form of accession, giving rise to new divergent phenotypes. Understanding the associations among the genotypes within a variety is crucial to efficient management and effective grapevine improvement. Inter-primer binding-site (iPBS) markers may aid in determining the new clones inside closely related genotypes. Following this idea, iPBS markers were used to assess the genetic variation of 33 grapevine genotypes collected from Russia. We used molecular markers to identify the differences among and within five grapevine clonal populations and analysed the variation, using clustering and statistical approaches. Four of a total of 30 PBS primers were selected, based on amplification efficiency. Polymerase chain reaction (PCR) with PBS primers resulted in a total of 1412 bands ranging from 300 to 6000 bp, with a polymorphism ratio of 44%, ranging from 58 to 75 bands per group. In total, were identified seven private bands in 33 genotypes. Results of molecular variance analysis showed that 40% of the total variation was observed within groups and only 60% between groups. Cluster analysis clearly showed that grapevine genotypes are highly divergent and possess abundant genetic diversities. The iPBS PCR-based genome fingerprinting technology used in this study effectively differentiated genotypes into five grapevine groups and indicated that iPBS markers are useful tools for clonal selection. The number of differences between clones was sufficient to identify them as separate clones of studied varieties containing unique mutations. Our previous phenotypic and phenological studies have confirmed that these genotypes differ from those of maternal plants. This work emphasized the need for a better understanding of the genotypic differences among closely related varieties of grapevine and has implications for the management of its selection processes.

Identification of disease resistance-linked alleles in Vitis vinifera germplasm

Introgression of genetic resistance to fungal diseases from American and Asian Vitis species traditionally pursued in grape breeding programs, although facilitated by molecular tools, has an impact on wine quality that still slows down development of competitive varieties. A contribution to the genetic improvement of grapevines for resistance to pathogens may come from unexplored genetic resources of the Eurasian Vitis vinifera L. In the present study, a hundred grapevine accessions from Georgia, Armenia and Azerbaijan were genotyped with SSR markers linked to QTLs for resistance to downy and powdery mildew, and with 21 SSR markers widely used for genetic diversity and relationship analysis. Looking at population genetic structure, Armenian and Azerbaijani accessions fell within the same cluster and were included among the Central Asian grape varieties of a homogeneous dataset, while Georgian accessions formed a separate group. Pattern of SSR alleles flanking the locus Ren1 and associated with resistance to Erysiphe necator in 'Kishmish vatkana', 'Dzhandzhal kara' and other Central Asian cultivars were found in three varieties from the Azerbaijani population that reached very high scores when assessed for PM resistance.

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.

Development of a 3D seed morphological tool for grapevine variety identification, and its comparison with SSR analysis

Grapevine (Vitis vinifera L.) is one of the classical fruits of the Old World. Among the thousands of domesticated grapevine varieties and variable wild sylvestris populations, the range of variation in pip morphology is very wide. In this study we scanned representative samples of grape pip populations, in an attempt to probe the possibility of using the 3D tool for grape variety identification. The scanning was followed by mathematical and statistical analysis using innovative algorithms from the field of computer sciences. Using selected Fourier coefficients, a very clear separation was obtained between most of the varieties, with only very few overlaps. These results show that this method enables the separation between different Vitis vinifera varieties. Interestingly, when using the 3D approach to analyze couples of varieties, considered synonyms by the standard 22 SSR analysis approach, we found that the varieties in two of the considered synonym couples were clearly separated by the morphological analysis. This work, therefore, suggests a new systematic tool for high resolution variety discrimination.