SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

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.

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.

TaqMan® and HRM approaches for SNP genotyping in genetic traceability of musts and wines

The fight against fraud in the wine sector requires continuous improvements and validations of new technologies applicable to musts and wines. Starting from published data from the Vitis18kSNP array, a series of new specific single nucleotide polymorphism (SNP) markers have been identified for some important north-western Italian cultivars, such as Barbera, Dolcetto and Arneis (Vitis vinifera L.), used in the production of high-quality wines under Protected Denomination of Origin. A pair of new SNP markers for each grape variety were selected and validated using two real-time PCR techniques: TaqMan® genotyping assays and high-resolution melting analysis (HRM). The TaqMan® assay has proven to be more reliable and repeatable than HRM analysis because despite being an economical and versatile technique for the detection of different types of genomic mutations (SNPs, insertions or deletions), HRM has shown limitations in the presence of poor-quality DNA extracted from musts and wines. TaqMan® assays have successfully identified Barbera, Dolcetto and Arneis in their respective musts and experimental wines, and with good efficiency in commercial wines. Marked differences between genotypes were observed, varietal identification in Dolcetto-based musts/wines was more efficient than that in Arneis-based wines. Therefore, the TaqMan® assay has considerable potential for varietal identification in wines and the procedure described in the present work can be easily adapted to all wines with adequate setup of DNA extraction methods that should be adapted to different wines.

Genealogical Analyses of 3 Cultivated and 1 Wild Specimen of Vitis vinifera from Greece

Grapevine (Vitis vinifera) has been an important crop with considerable cultural and economic significance for over 2,500 years, and Greece has been an important entry point into Europe for lineages that were domesticated in Western Asia and the Caucasus. However, whole-genome-based investigation of the demographic history of Greek cultivars relative to other European lineages has only started recently. To understand how Greek cultivars relate to Eurasian domesticated and wild populations, we sequenced 3 iconic domesticated strains ('Xinomavro,' 'Agiorgitiko,' 'Mavrotragano') along with 1 wild accession (the vinetree of Pausanias-a historically important wild specimen) and analyzed their genomic diversity together with a large sample of publicly available domesticated and wild strains. We also reconstructed genealogies by leveraging the powerful tsinfer methodology which has not previously been used in this system. We show that cultivated strains from Greece differ genetically from other strains in Europe. Interestingly, all the 3 cultivated Greek strains clustered with cultivated and wild accessions from Transcaucasia, South Asia, and the Levant and are amongst the very few cultivated European strains belonging to this cluster. Furthermore, our results indicate that 'Xinomavro' shares close genealogical proximity with European elite cultivars such as 'Chardonnay,' 'Riesling,' and 'Gamay' but not 'Pinot.' Therefore, the proximity of 'Xinomavro' to Gouais/Heunisch Weiss is confirmed and the utility of ancestral recombination graph reconstruction approaches to study genealogical relationships in crops is highlighted.

Disentangling the origins of viticulture in the western Mediterranean

We present direct evidence of early grape domestication in southern Italy via a multidisciplinary study of pip assemblage from one site, shedding new light on the spread of viticulture in the western Mediterranean during the Bronze Age. This consist of 55 waterlogged pips from Grotta di Pertosa, a Middle Bronze Age settlement in the south of the Italian peninsula. Direct radiocarbon dating of pips was carried out, confirming the chronological consistency of the samples with their archaeological contexts (ca. 1450-1200 BCE). The extraordinary state of conservation of the sample allowed to perform geometric morphometric (GMM) and paleogenetic analyses (aDNA) at the same time. The combination of the two methods has irrefutably shown the presence of domestic grapevines, together with wild ones, in Southern Italy during the Middle/Late Bronze Age. The results converge towards an oriental origin of the domestic grapes, most likely arriving from the Aegean area through the Mycenaeans. A parent/offspring kinship was also recognised between a domestic/wild hybrid individual and a domestic clonal group. This data point out a little known aspect of the diffusion of the first viticulture in Italy, and therefore in the western Mediterranean, which involved the hybridization between imported domestic varieties with, likely local, wild vines.

Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties

Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.

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.

A high-density integrated map for grapevine based on three mapping populations genotyped by the Vitis18K SNP chip

We present a high-density integrated map for grapevine, allowing refinement and improved understanding of the grapevine genome, while demonstrating the applicability of the Vitis18K SNP chip for linkage mapping. The improvement of grapevine through biotechnology requires identification of the molecular bases of target traits by studying marker-trait associations. The Vitis18K SNP chip provides a useful genotyping tool for genome-wide marker analysis. Most linkage maps are based on single mapping populations, but an integrated map can increase marker density and show order conservation. Here we present an integrated map based on three mapping populations. The parents consist of the well-known wine cultivars 'Cabernet Sauvignon', 'Corvina' and 'Rhine Riesling', the lesser-known wine variety 'Deckrot', and a table grape selection, G1-7720. Three high-density population maps with an average inter-locus gap ranging from 0.74 to 0.99 cM were developed. These maps show high correlations (0.9965-0.9971) with the reference assembly, containing only 93 markers with large order discrepancies compared to expected physical positions, of which a third is consistent across multiple populations. Moreover, the genetic data aid the further refinement of the grapevine genome assembly, by anchoring 104 yet unanchored scaffolds. From these population maps, an integrated map was constructed which includes 6697 molecular markers and reduces the inter-locus gap distance to 0.60 cM, resulting in the densest integrated map for grapevine thus far. A small number of discrepancies, mainly of short distance, involve 88 markers that remain conflictual across maps. The integrated map shows similar collinearity to the reference assembly (0.9974) as the single maps. This high-density map increases our understanding of the grapevine genome and provides a useful tool for its further characterization and the dissection of complex traits.

Dissecting the susceptibility/resistance mechanism of Vitis vinifera for the future control of downy mildew

The Eurasian grapevine (Vitis vinifera), a species cultivated worldwide for high-quality wine production, is extremely susceptible to the agent of downy mildew, Plasmopara viticola. Nevertheless, germplasm from Georgia (Southern Caucasus, the first grapevine domestication centre), characterized by a high genetic variability, showed resistance traits to P. viticola. The cultivar Mgaloblishvili exhibited the most promising phenotype in terms of resistance against P. viticola. Its defence response results in: i) low disease intensity; ii) low sporulation; iii) damaged mycelium; iv) production of antimicrobial compounds such as volatile organic compounds (VOCs), whose effectiveness on the pathogen was evaluated by leafdisc assays. At the transcriptomic level, its resistance mechanism is determined by the differential expression of both resistance and susceptible genes. The resistance genes are related to: i) pathogen recognition through PAMP, DAMP and effector receptors; ii) ethylene signalling pathway; iii) synthesis of antimicrobial compounds (VOCs) and fungal wall degrading enzymes; iv) development of structural barriers (cell wall reinforcement). The first putative susceptible gene was the transcription factor VviLBDIf7 gene, whose validation was carried out by dsRNA (double-stranded RNA) assay. In this work, these unique results on plant-pathogen interaction are reviewed with the aim of developing new strategies to control the disease.

Grapevine Diversity and Genetic Relationships in Northeast Portugal Old Vineyards

More than 100 grapevine varieties are registered as suitable for wine production in “Douro” and “Trás-os-Montes” Protected Designations of Origin regions; however, only a few are actually used for winemaking. The identification of varieties cultivated in past times can be an important step to take advantage of all the potential of these regions grape biodiversity. The conservation of the vanishing genetic resources boosts greater product diversification, and it can be considered strategic in the valorisation of these wine regions. Hence, one goal of the present study was to prospect and characterise, through molecular markers, 310 plants of 11 old vineyards that constitute a broad representation of the grape genetic patrimony of “Douro” and “Trás-os-Montes” wine regions; 280 samples, grouped into 52 distinct known varieties, were identified through comparison of their genetic profiles generated via 6 nuclear SSR and 43 informative SNP loci amplification; the remaining 30 samples, accounting for 13 different genotypes, did not match with any profile in the consulted databases and were considered as new genotypes. This study also aimed at evaluating the population structure among the 65 non-redundant genotypes identified, which were grouped into two ancestral genetic groups. The mean probability of identity values of 0.072 and 0.510 (for the 6 SSR and 226 SNP sets, respectively) were determined. Minor differences were observed between frequencies of chlorotypes A and D within the non-redundant genotypes studied. Twenty-seven pedigrees were confirmed and nine new trios were established. Ancestors of eight genotypes remain unknown.

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

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.

Pervasive hybridization with local wild relatives in Western European grapevine varieties

Grapevine (Vitis vinifera L.) diversity richness results from a complex domestication history over multiple historical periods. Here, we used whole-genome resequencing to elucidate different aspects of its recent evolutionary history. Our results support a model in which a central domestication event in grapevine was followed by postdomestication hybridization with local wild genotypes, leading to the presence of an introgression signature in modern wine varieties across Western Europe. The strongest signal was associated with a subset of Iberian grapevine varieties showing large introgression tracts. We targeted this study group for further analysis, demonstrating how regions under selection in wild populations from the Iberian Peninsula were preferentially passed on to the cultivated varieties by gene flow. Examination of underlying genes suggests that environmental adaptation played a fundamental role in both the evolution of wild genotypes and the outcome of hybridization with cultivated varieties, supporting a case of adaptive introgression in grapevine.

Climate Change Impacts on Plant Phenology: Grapevine (Vitis vinifera) Bud Break in Wintertime in Southern Italy

The effects of global warming on plants are not limited to the exacerbation of summer stresses; they could also induce dormancy dysfunctions. In January 2020, a bud break was observed in an old poly-varietal vineyard. Meteorological data elaboration of the 1951–2020 period confirmed the general climatic warming of the area and highlighted the particular high temperatures of the last winter. Phenological records appeared to be significantly correlated to wood hydration and starch reserve consumption, demonstrating a systemic response of the plant to the warm conditions. The eight cultivars, identified by single-nucleotide polymorphism (SNP) profiles and ampelographic description, grown in this vineyard showed different behaviors. Among them, the neglected Sprino, Baresana, Bianco Palmento, and Uva Gerusalemme, as well as the interspecific hybrid Seyve Villard 12.375, appeared to be the most interesting. Among the adaptation strategies to climate changes, the cultivar selection should be considered a priority, as it reduces the inputs required for the plant management over the entire life cycle of the vineyard. Hot Mediterranean areas, such as Salento, are a battlefront against the climate change impacts, and, thus, they represent a precious source of biodiversity for viticulture.

Recovery, Molecular Characterization, and Ampelographic Assessment of Marginal Grapevine Germplasm from Southern Umbria (Central Italy)

The protection of grapevine biodiversity and the safeguarding of genetic variability are certainly primary and topical objectives for wine research, especially in territories historically devoted to viticulture. To assess the autochthonous germplasm of three different districts of Southern Umbria (Central Italy), the plant material of 70 grapevines retrieved from reforested land plots or old vineyards was collected, and their genetic identity was investigated using 13 microsatellite markers (SSR). The results revealed the presence of 39 unique genotypes, divided into 24 already-known cultivars and 15 never-reported SSR profiles. Most of the grapevine accessions were then vegetatively propagated and cultivated in a vineyard collection both to be protected from extinction and to be evaluated at the ampelographic level. Overall, this work emphasizes the need for recovering the threatened genetic variability that characterizes minor neglected grapevine cultivars or biotypes of Southern Umbria germplasm, and the requirement to revalue and exploit the more valuable genetic resources to enhance the local agri-food economy.

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.

Europe as a bridgehead in the worldwide invasion history of grapevine downy mildew, Plasmopara viticola

Europe is the historical cradle of viticulture, but grapevines (Vitis vinifera) have been increasingly threatened by pathogens of American origin. The invasive oomycete Plasmopara viticola causes downy mildew, one of the most devastating grapevine diseases worldwide. Despite major economic consequences, its invasion history remains poorly understood. We analyzed a comprehensive dataset of ∼2,000 samples, collected from the most important wine-producing countries, using nuclear and mitochondrial gene sequences and microsatellite markers. Population genetic analyses revealed very low genetic diversity in invasive downy mildew populations worldwide and little evidence of admixture. All the invasive populations originated from only one of the five native North American lineages, the one parasitizing wild summer grape (V. aestivalis). An approximate Bayesian computation-random forest approach allowed inferring the worldwide invasion scenario of P. viticola. After an initial introduction into Europe, invasive European populations served as a secondary source of introduction into vineyards worldwide, including China, South Africa, and twice independently, Australia. Only the invasion of Argentina probably represents a tertiary introduction, from Australia. Our findings provide a striking example of a global pathogen invasion resulting from secondary dispersal of a successful invasive population. Our study will also help designing quarantine regulations and efficient breeding for resistance against grapevine downy mildew.

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

Almond [Prunus dulcis Miller (D.A. Webb)] is the main tree nut species worldwide. Here, genotyping-by-sequencing (GBS) was applied to 149 almond cultivars from the ex situ collections of the Italian Council for Agricultural Research (CREA) and the Spanish National Research Council (CSIC), leading to the detection of 93,119 single-nucleotide polymorphisms (SNPs). The study of population structure outlined four distinct genetic groups and highlighted diversification between the Mediterranean and Californian gene pools. Data on SNP diversity and runs of homozygosity (ROHs) allowed the definition of kinship, inbreeding, and linkage disequilibrium (LD) decay in almond cultivated germplasm. Four-year phenotypic observations, gathered on 98 cultivars of the CREA collection, were used to perform a genome-wide association study (GWAS) and, for the first time in a crop species, homozygosity mapping (HM), resulting in the identification of genomic associations with nut, shell, and seed weight. Both GWAS and HM suggested that loci controlling nut and seed weight are mostly independent. Overall, this study provides insights on the almond cultivation history and delivers information of major interest for almond genetics and breeding. In a broader perspective, our results encourage the use of ROHs in crop science to estimate inbreeding, choose parental combinations minimizing the risk of inbreeding depression, and identify genomic footprints of selection for specific traits.

Georgian Grapevine Cultivars: Ancient Biodiversity for Future Viticulture

Grapevine (Vitis vinifera) is one of the most widely cultivated plant species of agricultural interest, and is extensively appreciated for its fruits and the wines made from its fruits. Considering the high socio-economic impact of the wine sector all over the world, in recent years, there has been an increase in work aiming to investigate the biodiversity of grapevine germplasm available for breeding programs. Various studies have shed light on the genetic diversity characterizing the germplasm from the cradle of V. vinifera domestication in Georgia (South Caucasus). Georgian germplasm is placed in a distinct cluster from the European one and possesses a rich diversity for many different traits, including eno-carpological and phenological traits; resistance to pathogens, such as oomycetes and phytoplasmas; resistance to abiotic stresses, such as sunburn. The aim of this review is to assess the potential of Georgian cultivars as a source of useful traits for breeding programs. The unique genetic and phenotypic aspects of Georgian germplasm were unraveled, to better understand the diversity and quality of the genetic resources available to viticulturists, as valuable resources for the coming climate change scenario.

Integrated Bayesian Approaches Shed Light on the Dissemination Routes of the Eurasian Grapevine Germplasm

The domestication and spreading of grapevine as well as the gene flow history had been described in many studies. We used a high-quality 7k SNP dataset of 1,038 Eurasian grape varieties with unique profiles to assess the population genetic diversity, structure, and relatedness, and to infer the most likely migration events. Comparisons of putative scenarios of gene flow throughout Europe from Caucasus helped to fit the more reliable migration routes around the Mediterranean Basin. Approximate Bayesian computation (ABC) approach made possible to provide a response to several questions so far remaining unsolved. Firstly, the assessment of genetic diversity and population structure within a well-covered dataset of ancient Italian varieties suggested the different histories between the Northern and Southern Italian grapevines. Moreover, Italian genotypes were shown to be distinguishable from all the other Eurasian populations for the first time. The entire Eurasian panel confirmed the east-to-west gene flow, highlighting the Greek role as a "bridge" between the Western and Eastern Eurasia. Portuguese germplasm showed a greater proximity to French varieties than the Spanish ones, thus being the main route for gene flow from Iberian Peninsula to Central Europe. Our findings reconciled genetic and archaeological data for one of the most cultivated and fascinating crops in the world.

DNA-based genealogy reconstruction of Nebbiolo, Barbera and other ancient grapevine cultivars from northwestern Italy

Northwestern Italy is a wine region of the world with the highest of reputations, where top quality wines of remarkable economic value are produced from traditional, long-cultivated varieties. Kinship analyses were performed using 32 microsatellite loci and more than 10 K single-nucleotide polymorphism markers on 227 traditional grapes mostly from Northwestern Italy—including those that have been neglected or are threatened. This was done to better understand the genetic grapevine origins and history of this reputable wine producing area, thus enhancing its cultural value and the marketing appeal of its wines. The work revealed a complex network of genetic relationships among varieties, with little contribution of genotypes from other areas. It revealed the major role played by a few ancient grape varieties as parents of numerous offspring, including some that are endangered today. The ancestry of many cultivars is proposed. Among these are Dolcetto, Barbera and Riesling italico. Through the inference of parent–offspring and sibling relations, marker profiles of ungenotyped putative parents were reconstructed, suggesting kinship relations and a possible parentage for Nebbiolo, one of the most ancient wine grapes worldwide. Historic and geographic implications from the resulting kinships are discussed.

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.

A transcriptomic variation map provides insights into the genetic basis of Pinus massoniana Lamb. evolution and the association with oleoresin yield

BACKGROUND

Masson pine (Pinus massoniana Lamb.), the dominant native coniferous species in southern China, is commercially important for supplying timber and oleoresin. However, knowledge of the genetic variability of masson pine germplasm is still limited. In this study, the genetic diversity and population structure of masson pine germplasm were assessed using 204 wild accessions from 10 main distribution regions using 94,194 core single-nucleotide polymorphisms (SNPs) obtained from transcriptome sequencing data.

RESULTS

The average expected heterozygosity was 0.2724, implying abundant genetic diversity within masson pine germplasm. Analysis of molecular variance (AMOVA) revealed that 3.29% of the variation was sourced from genetic differentiation. Structure analysis identified two geographically distinct groups. Discriminant analysis of principal components (DAPC) showed that one of those groups was further divided into two clusters. Sichuan and Chongqing provenance is the geographical origin, which diffused outward along two different lines. Oleoresin yield is reflected in the evolution of the two groups, and exhibits two different trends along the two lines of diffusion. The oleoresin yield may be associated with the genes of chitinase, CYP720B, cytochrome P450, ABC transporter, and AP2/ethylene-responsive transcription factor (ERF) based on SNPs and expression.

CONCLUSIONS

SNP markers from transcriptome sequencing are highly capable of evaluating genetic diversity within different species, as well as the genetic control of objective traits. The functions of these genes will be verified in future studies, and those genes strongly associated with oleoresin yield will be used to improve yields by means of early genotype selection and genetic engineering.

Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.

Correction to: SNP genotyping elucidates the genetic diversity of Magna Graecia grapevine germplasm and its historical origin and dissemination

An amendment to this paper has been published and can be accessed via the original article.

Genetic Diversity and Population Structure in a Vitis spp. Core Collection Investigated by SNP Markers

Single nucleotide polymorphism (SNP) genotyping arrays are powerful tools to measure the level of genetic polymorphism within a population. The coming of next-generation sequencing technologies led to identifying thousands and millions of SNP loci useful in assessing the genetic diversity. The Vitis genotyping array, containing 18k SNP loci, has been developed and used to detect genetic diversity of Vitis vinifera germplasm. So far, this array was not validated on non-vinifera genotypes used as grapevine rootstocks. In this work, a core collection of 70 grapevine rootstocks, composed of individuals belonging to Vitis species not commonly used in the breeding programs, was genotyped using the 18k SNP genotyping array. SNP results were compared to the established SSR (Simple Sequence Repeat) markers in terms of heterozygosity and genetic structure of the core collection. Genotyping array has proved to be a valuable tool for genotyping of grapevine rootstocks, with more than 90% of SNPs successfully amplified. Structure analysis detected a high degree of admixed genotypes, supported by the complex genetic background of non-vinifera germplasm. Moreover, SNPs clearly differentiated non-vinifera and vinifera germplasm. These results represent a first step in studying the genetic diversity of non-conventional breeding material that will be used to select rootstocks with high tolerance to limiting environmental conditions.

Genetic Relationships Among Portuguese Cultivated and Wild Vitis vinifera L. Germplasm

The domesticated grapevine spread along the Mediterranean basin from the primary Near East domestication area, where the greatest genetic diversity is found in its ancestor, the wild vine populations. Portuguese wild populations are on the southwestern fringe of the distribution of the Vitis vinifera L. ssp. sylvestris (C.C. Gmel.) Hegi in Europe. During the last Glacial Period they became isolated from the previous continuum that had been the territory of wild vine populations. Archaeological remains of domesticated vinifera grapevines in Portugal date back from 795 Before Common Era (BCE) in the lower Tagus river basin. In this work, 258 Portuguese vinifera varieties and sylvestris plants were characterized using 261 single nucleotide polymorphism (SNP) markers. The study of the genetic diversity of this local germplasm, its population structure and kinship, all framed in their historical and geographical backgrounds, revealed a complex network of first-degree relationships, where only Iberian varieties are involved. Some Iberian genotypes, like Alfrocheiro (Bruñal, in Spain), Sarigo (Cayetana Blanca), Mourisco Branco (Hebén), Amaral (Caiño Bravo), and Marufo (Moravia Dulce) are ancestors of a considerable fraction of all the autochthonous analyzed varieties. A part of the diversity developed was mostly local in some cases as shown by the closeness of several varieties (Vinhos Verdes) to the wild cluster in different analyses. Besides, several evidences of introgression of domesticated germplasm into wild vines was found, substantiating the high risk of genetic contamination of the sylvestris subspecies. All these findings together to the known matching between the wild maternal lineage of the Iberian Peninsula and an important number of Portuguese grapevine varieties (chlorotype A), point out that some of these varieties derive, directly or indirectly, from originally local wild populations, supporting the possible occurrence of secondary events of local domestication, or, at least, of an introgression process of wild into cultivated grapevines.

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.

Single-nucleotide polymorphism (SNP) genotyping assays for the varietal authentication of 'Nebbiolo' musts and wines

'Nebbiolo' (Vitis vinifera L.) is renowned for its use in producing monovarietal high-quality red wines, such Barolo and Barbaresco. The fight against fraud to safeguard high-quality productions requires an effective varietal identification system applicable in musts and wines. 'Nebbiolo'-specific single-nucleotide polymorphisms (SNPs) were identified starting from available databases and 260 genotypes analysed by Vitis18kSNP array. Two SNPs were sufficient to identify 'Nebbiolo' from 1157 genotypes. The SNP TaqMan® genotyping assays developed in this work successfully identified 'Nebbiolo' in all musts and wines collected at different experimental wine-making steps. The high sensitivity of the assays allowed identification of must mixtures at 1% and wine mixtures at 10-20% with non-'Nebbiolo' genotypes. In commercial wines, the amplification efficiency was limited by the low amount of grapevine DNA and the presence of PCR inhibitors. The TaqMan® genotyping assay is a rapid, highly sensitive and specific methodology with remarkable potential for varietal identification in wines.

Phylogenetic Relationship Among Wild and Cultivated Grapevine in Sicily: A Hotspot in the Middle of the Mediterranean Basin

Grapevine (Vitis vinifera ssp. sativa) is a perennial crop especially important for wine and fruit production. The species is highly polymorphic with thousands of different varieties selected by farmers and clonally propagated. However, it is still debated whether grapevine domestication from its wild ancestor (V. vinifera ssp. sylvestris) has been a single event or rather it occurred on multiple occasions during the diffusion of its cultivation across the Mediterranean. Located in the center of the Basin, Sicily is its largest island and has served as a hotspot for all civilizations that have crossed the Mediterranean throughout history. Hundreds of unique grapevine cultivars are still cultivated in Sicily and its surrounding minor islands, though most of them are menaced by extinction. Wild grapevine is also present with isolated populations thriving along riverbanks. With the aim to evaluate the phylogenetic relationships among Sicilian varieties, and to assess the possible contribution of indigenous wild populations to the genetic makeup of cultivated grapevine, we analyzed 170 domestic cultivars and 125 wild plants, collected from 10 different populations, with 23 SSR markers. We also compared our data with published dataset from Eurasia. Results show that Sicilian wild populations are related to the cultivated Sicilian and Italian germplasm, suggesting events of introgression and/or domestication of local varieties.