Genetic Structure and Relationships among Wild and Cultivated Grapevines from Central Europe and Part of the Western Balkan Peninsula

Genetic relationships and introgression events between wild and cultivated grapevines (Vitis vinifera L.): focus on Italian Lambruscos

Research efforts on genomic structure and ecology of wild populations of Vitis vinifera L. offer insights on grape domestication processes and on the assortment evolution of the cultivated forms. Attention is also paid to the origin of traditional, long-cultivated varieties, often producing renowned and valuable wines. The genetic relationships between 283 Vitis vinifera cultivated varieties (subsp. sativa) and 65 individuals from 9 populations of the sylvestris subspecies mainly from northern Italy were explored by means of molecular markers (27 nuclear and 4 chloroplastic microsatellites). Several episodes of contamination of the wild germplasm by the pollen of specific grape cultivars were detected, implying concern for maintaining the purity of the wild form. At the same time, events of introgression from the wild subspecies resulted playing a crucial role in the emergence of several cultivated varieties with a clear admixed genome ancestry sativa-sylvestris. These included Lambruscos originated from the flat areas crossed by the Po and Adige rivers in northern Italy, while other cultivars still called Lambrusco but typical of hilly areas did not show the same admixed genome. Historical and ecological evidences suggesting an adaptative recent post-domestication process in the origin of several Italian Lambruscos are discussed.

Monitoring and Genotyping of Wild Grapevine (Vitis vinifera L. subsp. sylvestris) in Slovenia

Vitis vinifera L. subsp. sylvestris (sylvestris) is the only native wild grapevine in Eurasia (Europe and western Asia) and is the existing ancestor of the grapevine varieties (for wine and table grape production) belonging to the subsp. sativa. In Slovenia, the prevailing opinion has been that there are no Slovenian sylvestris habitats. This study describes sylvestris in Slovenia for the first time and aims to present an overview of the locations of the wild grapevine in the country. In this project, a sample set of 89 accessions were examined using 24 SSR and 2 SSR markers plus APT3 markers to determine flower sex. The accessions were found in forests on the left bank of the Sava River in Slovenia, on the border between alluvial soils and limestone and dolomite soils, five different sites, some of which are described for the first time. The proportion of female to male accessions differed between sites. At two sites, female plants dominated; at others, the ratio was balanced. The plants' genetic diversity and structure were compared with autochthonous and unique varieties of subsp. sativa from old vineyards in Slovenia and with rootstocks escaped from nature from abandoned vineyards. Sylvestris was clearly distinguishable from vinifera and the rootstocks. Based on genetic analyses, it was confirmed that Slovenian sylvestris is closest to the Balkan and German sylvestris groups. Meanwhile, a safety duplication of the wild grapevine accessions has been established at the University Centre of Viticulture and Enology Meranovo, Faculty of Agriculture and Life Sciences at the University of Maribor.

Biochemical Response and Gene Expression to Water Deficit of Croatian Grapevine Cultivars (Vitis vinifera L.) and a Specimen of Vitis sylvestris

The biochemical response and gene expression in different grapevine cultivars to water deficit are still not well understood. In this study, we investigated the performance of four traditional Croatian Vitis vinifera L. cultivars ('Plavac mali crni', 'Istrian Malvasia', 'Graševina', and 'Tribidrag'), and one wild (Vitis vinifera subsp. sylvestris) genotype exposed to water deficit (WD) for nine days under semi-controlled conditions in the greenhouse. Sampling for biochemical and gene expression analyses was performed at days six and nine from the beginning of WD treatment. The WD affected the accumulation of metabolites with a significant increase in abscisic acid (ABA), salicylic acid (SA), and proline in the leaves of the stressed genotypes when the WD continued for nine days. Lipid peroxidation (MDA) was not significantly different from that of the control plants after six days of WD, whereas it was significantly lower (297.40 nmol/g dw) in the stressed plants after nine days. The cultivar 'Istrian Malvasia' responded rapidly to the WD and showed the highest and earliest increase in ABA levels (1.16 ng mg-1 dw, i.e., 3.4-fold increase compared to control). 'Graševina' differed significantly from the other genotypes in SA content at both time points analyzed (six and nine days, 47.26 and 49.63 ng mg-1 dw, respectively). Proline level increased significantly under WD (up to 5-fold at day nine), and proline variation was not genotype driven. The expression of aquaporin genes (TIP2;1 and PIP2;1) was down-regulated in all genotypes, coinciding with the accumulation of ABA. The gene NCED1 (9-cis-epoxycarotenoid dioxygenase) related to ABA was up-regulated in all genotypes under stress conditions and served as a reliable marker of drought stress. This work suggests that the stress response in metabolite synthesis and accumulation is complex, treatment- and genotype-dependent.

Genetic structure of the population of wild-growing vines of the Utrish Nature Reserve

Grapes are one of the most common agricultural crops in the world. Currently, the analysis of genotypes directly at the DNA level is considered to be the most accurate method for studying the plant gene pool. The study of wild vines and ancient varieties in various regions of viticulture is an important direction of research in this field. The purpose of this work was to study the population of wild grapes growing on the territory of the Utrish Nature Reserve on the Black Sea coast of Krasnodar Region. The territory of the reserve is of interest as it is a site of ancient settlements, and the environmental conditions are suitable for the growth of wild grapes. During the survey of the territory, 24 samples of wild grapes were found, which were described according to the main morphological characteristics and analyzed by the molecular genetic method. The found vines were genotyped using 15 DNA markers, including nine commonly used for DNA fingerprinting (VVS2, VVMD5, VVMD7, VVMD25, VVMD27, VVMD28, VVMD32, VrZAG62, VrZAG79) and VVIb23, which allows determining hermaphrodite and dioecious vines. Statistical processing of microsatellite loci polymorphism data was carried out using the GenAlEx 6.5 program. The genetic relationships of the studied vines were evaluated using the PAST 2.17c program. The samples were found to be morphologically and genetically polymorphic. The number of alleles identified in the sample varied from 5 to 18 and averaged 8 alleles per locus. Statistical processing of DNA analysis data made it possible to identify two genetically different populations among the wild discovered vines. An assessment of genetic similarity of the found vines with some local varieties of geographically close viticulture regions, rootstocks and representatives of Vitis sylvestris from other territories was made. One of the populations found in the Utrish Nature Reserve is close to a number of V. sylvestris genotypes, the DNA profiles of which are presented in the Vitis International Variety Catalogue.

Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high-density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r² was between 0.45 and 0.2 and became flat when r² was 0.05. The average LD decay for the entire genome was 30 kb when r^2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.

Dual domestications and origin of traits in grapevine evolution

We elucidate grapevine evolution and domestication histories with 3525 cultivated and wild accessions worldwide. In the Pleistocene, harsh climate drove the separation of wild grape ecotypes caused by continuous habitat fragmentation. Then, domestication occurred concurrently about 11,000 years ago in Western Asia and the Caucasus to yield table and wine grapevines. The Western Asia domesticates dispersed into Europe with early farmers, introgressed with ancient wild western ecotypes, and subsequently diversified along human migration trails into muscat and unique western wine grape ancestries by the late Neolithic. Analyses of domestication traits also reveal new insights into selection for berry palatability, hermaphroditism, muscat flavor, and berry skin color. These data demonstrate the role of the grapevines in the early inception of agriculture across Eurasia.

SNP Diversity and Genetic Structure of "Rogosija", an Old Western Balkan Durum Wheat Collection

Durum wheat landraces represent a genetic resource for the identification and isolation of new valuable genes and alleles, useful to increase the crop adaptability to climate change. Several durum wheat landraces, all denominated "Rogosija", were extensively cultivated in the Western Balkan Peninsula until the first half of the 20th century. Within the conservation program of the Montenegro Plant Gene Bank, these landraces were collected, but without being characterized. The main goal of this study was to estimate the genetic diversity of the "Rogosija collection" consisting of 89 durum accessions, using 17 morphological descriptors and the 25K Illumina single nucleotide polymorphism (SNP) array. The genetic structure analysis of the Rogosija collection showed two distinguished clusters localized in two different Montenegro eco-geographic micro-areas, characterized by continental Mediterranean climate and maritime Mediterranean climate. Data suggest that these clusters could be composed of two different Balkan durum landrace collections evolved in two different eco-geographic micro-areas. Moreover, the origin of Balkan durum landraces is discussed.

Microstructure of Croatian Wild Grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) Pollen Grains Revealed by Scanning Electron Microscopy

Wild grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) is dioecious with male and female plants, whereas domesticated grapevine is mostly hermaphrodite with self-fertile hermaphrodite flowers. The pollen morphology of wild grapevine has been poorly studied. There is no detailed palynological study of V. sylvestris in Croatia and neighboring countries. Here, scanning electron microscopy (SEM) was used to analyze the pollen of V. sylvestris from male and female individuals growing at two natural sites in Croatia. The selective APT3 marker was used to confirm the flower phenotype with the genetic background. SEM analysis showed that the pollen grains of V. sylvestris were isopolar and radially symmetrical, with foveolate perforated ornamentation, regardless of the flower type of the individuals. All male flowers were 3-colporate and prolate in shape, whereas female individuals varied from subprolate to spheroidal and had inaperturate pollen grains. Pollen shape, dimensions and exine ornamentation proved very informative, and here we address the most polymorphic traits in the analyzed V. sylvestris individuals. Principal component analysis (PCA) and clustering based on pollen morphology variables clearly differentiated individuals by their flower type, and no grouping specific to population was observed, pointing to the conserved pollen structure of V. sylvestris. The results indicate the need to continue the palynological study of V. sylvestris and serve as a good phenotypic basis for functional genetic studies on genes involved in pollen morphology and function.

Identification of powdery mildew resistance in wild grapevine (Vitis vinifera subsp. sylvestris Gmel Hegi) from Croatia and Bosnia and Herzegovina

Wild grapevine (Vitis vinifera subsp. sylvestris) is widely recognized as an important source of resistance or tolerance genes for diseases and environmental stresses. Recent studies revealed partial resistance to powdery mildew (Erysiphe necator, PM) in V. sylvestris from Central Asia. Here, we report resistance to PM of V. sylvestris collected from different regions of Croatia and in seedling populations established from in situ V. sylvestris accessions. Ninety-one in situ individuals and 67 V. sylvestris seedlings were evaluated for PM resistance according to OIV 455 descriptor. Three SSR markers (SC47-18, SC8-071-0014, and UDV-124) linked to PM resistance locus Ren1 were used to decipher allelic structure. Nine seedlings showed resistance in in vivo evaluations while leaf disk assays revealed three PM-resistant accessions. One V. vinifera cultivar used as a control for PM evaluations also showed high phenotypic resistance. Based on the presence of one or two resistance alleles that are linked to the Ren1 locus, 32 resistant seedlings and 41 resistant in situ genotypes were identified in the investigated set. Eight seedlings showed consistent phenotypic PM resistance, of which seven carried one or two alleles at the tested markers. This study provides the first evidence of PM resistance present within the eastern Adriatic V. sylvestris germplasm.

History of Grape in Anatolia and Historical Sustainable Grape Production in Erzincan Agroecological Conditions in Turkey

The Anatolian peninsula has long been linked with the origins of viticulture and winemaking. Erzincan province in Anatolia hosted many civilizations in the past, and each civilization used grapes for different purposes. From past to present, viticulture carried out with the famous ‘Karaerik’ grape (Vitis vinifera L.) on old traditional Baran training system to avoid cold damage occurred in winter months. During the old civilizations, the cultivar was used only for wine production, but after the first period of the 1900s, this situation changed, and the cultivar was used for table consumption because wine is banned by Islam. The archaeological findings in Erzincan province revealed the cultivar has existed in the province for centuries, and in each historical period, the cultivar was used sustainably, added value to the region, and brought cultural heritage from generation to generation. Grape production in Erzincan province has been a symbol of abundance, fertility and productivity since mythological times. The historical facts indicated that viticulture and winemaking had been a dispensable part of the Erzincan economy and rural development. The vineyards apply the same sustainable management practices from which they receive their grapes. The traditional Baran training system is used for all vineyards. The viticulture in the province has been strongly committed to improving environmental and social sustainability throughout history.

The genomes of 204 Vitis vinifera accessions reveal the origin of European wine grapes

In order to elucidate the still controversial processes that originated European wine grapes from its wild progenitor, here we analyse 204 genomes of Vitis vinifera and show that all analyses support a single domestication event that occurred in Western Asia and was followed by numerous and pervasive introgressions from European wild populations. This admixture generated the so-called international wine grapes that have diffused from Alpine countries worldwide. Across Europe, marked differences in genomic diversity are observed in local varieties that are traditionally cultivated in different wine producing countries, with Italy and France showing the largest diversity. Three genomic regions of reduced genetic diversity are observed, presumably as a consequence of artificial selection. In the lowest diversity region, two candidate genes that gained berry–specific expression in domesticated varieties may contribute to the change in berry size and morphology that makes the fruit attractive for human consumption and adapted for winemaking.

Reports on the origin of European wine grapes are controversial. Here, the authors perform population genetics analyses on a large set of representative wine-making varieties and reveal a single domestication event at the origin of the entire germplasm followed by repeated introgression from wild populations.

‘Pinore’: The New Red Wine Variety Cross-Bred between ‘Pinot Noir’ and ‘Regent’ Vines

Renewed interest in varieties that are more tolerant to diseases has emerged, which is mainly due to increased awareness by producers and consumers regarding the impact of phytochemicals in the environment. This paper describes the first Slovenian grapevine variety ‘Pinore’ crossed between the Vitis vinifera L. ‘Pinot Noir’ clone Mf and ‘Regent’ vines. The aim was to create an early ripening grape cultivar that has a good tolerance to biotic stress (e.g., downy and powdery mildew, botrytis) combined with the benefits of established cultivars and their intense wine colors. Some ampelographic characteristics of young shoots, mature leaves, bunches, and berries are presented, and its major agronomic traits, ripening time, grape yield, quality performances, and disease resistance were evaluated over a three-year period (2014–2017). Wine sensory analyses were performed and compared with the international variety ‘Pinot Noir’. The examined genotype showed good agronomic performance and a high wine quality as far as the content of polyphenols is concerned, especially in terms of anthocyanins and tolerance to diseases (Ren3/9 and Rpv3.1); it is significantly different compared to the reference variety ‘Pinot Noir’. In terms of ampelographic characteristics, the main differences are in the number of leaf lobes, the depth of the lateral sinuses, and the content of anthocyanins in its flesh. The investigated genotype has been proposed to the Committee of new varieties in Slovenia for the variety recognition procedure, and completion of the procedure planned for the end of 2023.

Back to the Origins: Background and Perspectives of Grapevine Domestication

Domestication is a process of selection driven by humans, transforming wild progenitors into domesticated crops. The grapevine (Vitis vinifera L.), besides being one of the most extensively cultivated fruit trees in the world, is also a fascinating subject for evolutionary studies. The domestication process started in the Near East and the varieties obtained were successively spread and cultivated in different areas. Whether the domestication occurred only once, or whether successive domestication events occurred independently, is a highly debated mystery. Moreover, introgression events, breeding and intense trade in the Mediterranean basin have followed, in the last thousands of years, obfuscating the genetic relationships. Although a succession of studies has been carried out to explore grapevine origin and different evolution models are proposed, an overview of the topic remains pending. We review here the findings obtained in the main phylogenetic and genomic studies proposed in the last two decades, to clarify the fundamental questions regarding where, when and how many times grapevine domestication took place. Finally, we argue that the realization of the pan-genome of grapes could be a useful resource to discover and track the changes which have occurred in the genomes and to improve our understanding about the domestication.