An extensive study of the genetic diversity within seven French wine grape variety collections

Identification of grapevine clones via high-throughput amplicon sequencing: a proof-of-concept study

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

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.

Linking breadfruit cultivar names across the globe connects histories after 230 years of separation

Every crop has a story. The story of breadfruit (Artocarpus altilis), an increasingly valued staple crop in tropical agroforestry systems, is filled with intrigue, oppression, and remains incomplete. The Caribbean is a major producer and consumer of breadfruit, yet most breadfruit there came from a single 1793 introduction aimed at providing a cheap food source for slaves forced to work on British plantations. St. Vincent was the first significant point of Caribbean introduction and played a vital role in subsequent breadfruit distribution throughout the region. Hundreds of cultivars are documented in breadfruit's native Oceania. It remains a mystery, however, which ones were introduced to the Caribbean 230 years ago-still comprising the vast diversity found there today. Integrating local knowledge, historical documents and specimens, morphological data, and DNA, we identify eight major global breadfruit lineages-five of which are found in the Caribbean and likely represent the original 1793 introduction. Genetic data were able to match two Caribbean cultivar names confidently to their Oceania counterparts. Genetics and morphology together enabled additional possible matches. Many other named cultivars within lineages are too genetically similar to differentiate, highlighting difficulties of defining and identifying variation among clonally propagated triploid crops. Breadfruit is important in resilient agroforestry in tropical islands predicted to be especially affected by climate change. Findings reveal global links, building upon collective knowledge that can be used to inform breadfruit management. Results are also summarized in a brochure about breadfruit history and diversity in St. Vincent, and the Caribbean more broadly.

Efficient Assessment and Large-Scale Conservation of Intra-Varietal Diversity of Ancient Grapevine Varieties: Case Study Portugal

There are thousands of ancient grapevine varieties in Europe, each one having a high level of intra-varietal diversity with regard to important economic traits (yield, soluble solids content, acidity, anthocyanins, and others). However, this potential has become exposed to a process of genetic erosion since the middle of the last century. The main objective of this work is to present experimental strategies for conservation and utilization of intra-varietal diversity. A concrete example is given about the actions performed in Portugal since 1978. Two main approaches for the conservation of intra-varietal diversity were performed: (1) strict conservation (in pots and in the field without experimental design) for future generations; and (2) conservation and, simultaneously, evaluation of the intra-varietal variability for selection to fulfil the immediate needs of the grape and wine sector (in the field with experimental design). More than 30,000 accessions of Portuguese autochthonous varieties are conserved. Using the theory of mixed models, intra-varietal diversity of the yield was found for the 59 varieties studied. The conservation and the evaluation of the intra-varietal diversity for quantitative traits will allow to extract high economic value, as well as to ensure its utilization to meet the objectives of the vine and wine sector.

Molecular Tools for Adapting Viticulture to Climate Change

Adaptation of viticulture to climate change includes exploration of new geographical areas, new training systems, new management practices, or new varieties, both for rootstocks and scions. Molecular tools can be defined as molecular approaches used to study DNAs, RNAs, and proteins in all living organisms. We present here the current knowledge about molecular tools and their potential usefulness in three aspects of grapevine adaptation to the ongoing climate change. (i) Molecular tools for understanding grapevine response to environmental stresses. A fine description of the regulation of gene expression is a powerful tool to understand the physiological mechanisms set up by the grapevine to respond to abiotic stress such as high temperatures or drought. The current knowledge on gene expression is continuously evolving with increasing evidence of the role of alternative splicing, small RNAs, long non-coding RNAs, DNA methylation, or chromatin activity. (ii) Genetics and genomics of grapevine stress tolerance. The description of the grapevine genome is more and more precise. The genetic variations among genotypes are now revealed with new technologies with the sequencing of very long DNA molecules. High throughput technologies for DNA sequencing also allow now the genetic characterization at the same time of hundreds of genotypes for thousands of points in the genome, which provides unprecedented datasets for genotype-phenotype associations studies. We review the current knowledge on the genetic determinism of traits for the adaptation to climate change. We focus on quantitative trait loci and molecular markers available for developmental stages, tolerance to water stress/water use efficiency, sugar content, acidity, and secondary metabolism of the berries. (iii) Controlling the genome and its expression to allow breeding of better-adapted genotypes. High-density DNA genotyping can be used to select genotypes with specific interesting alleles but genomic selection is also a powerful method able to take into account the genetic information along the whole genome to predict a phenotype. Modern technologies are also able to generate mutations that are possibly interesting for generating new phenotypes but the most promising one is the direct editing of the genome at a precise location.

Differential expression of transcription factor- and further growth-related genes correlates with contrasting cluster architecture in Vitis vinifera 'Pinot Noir' and Vitis spp. genotypes

Grapevine (Vitis vinifera L.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid fungal damage. Grapevine cultivars with loose cluster architecture enable reducing protective treatments due to their enhanced resilience against fungal infections, such as Botrytis cinerea-induced gray mold. A recent study identified transcription factor gene VvGRF4 as determinant of pedicel length, an important component of cluster architecture, in samples of two loose and two compact quasi-isogenic 'Pinot Noir' clones. Here, we extended the analysis to 12 differently clustered 'Pinot Noir' clones from five diverse clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons. Two phenotypically opposite clones were grown at all three locations and served for standardization. Data were correlated with the phenotypic variation of cluster architecture sub-traits. A set of 14 genes with consistent expression differences between loosely and compactly clustered clones-independent from season and location-was newly identified. These genes have annotations related to cellular growth, cell division and auxin metabolism and include two more transcription factor genes, PRE6 and SEP1-like. The differential expression of VvGRF4 in relation to loose clusters was exclusively found in 'Pinot Noir' clones. Gene expression studies were further broadened to phenotypically contrasting F1 individuals of an interspecific cross and OIV reference varieties of loose cluster architecture. This investigation confirmed PRE6 and six growth-related genes to show differential expression related to cluster architecture over genetically divergent backgrounds.

Assessment of genetic diversity of cultivated and wild Iranian grape germplasm using retrotransposon-microsatellite amplified polymorphism (REMAP) markers and pomological traits

Understanding the genetic diversity and relationships between genotypes is an effective step in designing effective breeding programs. Insertional polymorphisms of retrotransposons were studied in 75 cultivated and wild grape genotypes using retrotransposon-microsatellite amplified polymorphism (REMAP) technique. In the morphological part of work, seven pomological traits with a high breeding interest were also analyzed in the cultivated genotypes. A total of 328 markers were produced by 42 primer pairs, out of which 313 markers (95.43%) were polymorphic. Number of markers ranged from 4 in loci Tvv1Fa-873, Vine1-811, Gret1Ra-855 and Tvv1Fa-890 to 12 in locus Vine1Ra-841 with an average value of 7.45. Similarity values based on Dice's coefficient among all 75 grapevine genotypes varied from 0.41 to 0.77. Classification of genotypes using unweighted pair-group method using complete-linkage clustering led to six distinct groups. Some wild and cultivated varieties placed in the same groups. It seems there are close relationship between wild and cultivated genotypes and maybe wild genotypes are ancestor of native grapevines. Grouping of grapevine genotypes based on molecular marker data was not in agreement with clustering by agro-morphological data indicating that the most of multiplied sequences are confined to the non-coding regions of transposon elements. Results showed a substantial level of genetic diversity at molecular and pomological level and the potential of this diversity for future grape breeding programs.

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.

Unraveling the genetic origin of 'Glera', 'Ribolla Gialla' and other autochthonous grapevine varieties from Friuli Venezia Giulia (northeastern Italy)

'Glera' and 'Ribolla Gialla' are the most economically relevant local grapevine cultivars of Friuli Venezia Giulia region (north-eastern Italy). 'Glera' is used to produce the world-renowned Prosecco wine. 'Ribolla Gialla' cultivation is constantly increasing due to the strong demand for sparkling wine and is the most important variety in Brda (Slovenia). Knowledge of local varieties history in terms of migration and pedigree relationships has scientific and marketing appeal. Following prospections, genotyping and ampelographic characterization of minor germplasm in Friuli Venezia Giulia, a further research was developed to understand the parentage relationships among the grapevine varieties grown in this region. An integrated strategy was followed combining the analysis of nuclear and chloroplast microsatellites with the Vitis 18k SNP chip. Two main recurrent parents were found, which can be regarded as "founders": 'Vulpea', an Austrian variety parent-offspring related with at least ten Friuli Venezia Giulia cultivars, among them 'Glera', and 'Refosco Nostrano', first degree related with other six Friuli Venezia Giulia varieties. 'Ribolla Gialla' was shown to be another member of the impressively long list of offspring derived from the prolific 'Heunisch Weiss'. Combining molecular markers and historical references was a high-performance strategy for retracing and adjusting the history of cultivars.

Wild grapes of Kuban, their ecological and biological features of growth

The biodiversity of the Vitaceae Juss family is studied with more interest than before, but still not fully according to the current scientific literature. For example, indigenous varieties and wild forms of grapes are known in the Crimea, Dagestan, along the banks of the Don and in other regions, but there is practically no data about wild and autochthonic grapes in the Kuban. This work presents new data about wild grapes studied in the Krasnodar region in the forests of the “Red forest” reserve. The ecological and geographical conditions of their growth are studied in detail. The description of plant community where the studied plant forms grow is conducted. Isolated populations of wild grapes, presumably belonging to the species of Vitis vinifera ssp. silvestris Gmel. or its varieties - var. Tipica Negr. (typical wild forest grapes) were ampelographically studied. Samples were taken for further genetic analysis to identify the origin of these forms and identify promising donors of resistance to various environmental stressors for use in the breeding process.

Machado M. Differential genetic stability in vineyards of the cultivar ‘Italy’ (Vitis vinifera L.) cultivated in different regions of Southern and Southwestern Brazil

During more than 50 years the vegetative propagation has been the form of maintaining and multiplication of the cv. ’Italy’ vineyards, a ’Bicane’ x ’Muscat Hamburg’ hybrid. In the current study, polymorphism in 17 microsatellite loci was used to evaluate the genetic stability at DNA level in vineyards of cv. ’Italy’ planted in different regions of the states of Paraná and São Paulo, Brazil. Unchanged and equal allele frequency indicating genetic stability was reported in 47% of the microsatellite loci in vineyards of six localities, while allele frequency variation has been observed in Scu15vv, Udv44, Udv74, Udv96, Udv107, Udv108, Vvmd5, Vvmd6 and Vvs3 microsatellite loci. Alleles Udv96140 and Vvs3448, detected in vines in only one of the vineyards, evidenced somatic mutations at molecular level in cv. ’Italy’. Genetic diversity, as result of changes in the allele frequencies in 53% of microsatellite loci, was detected more frequently than somatic mutations due to new alleles. Polymorphism in microsatellite loci revealed different genetic stability in vineyards of cv. ’Italy’ cultivated in six different Brazilian regions and indicated vineyards with less genetic stability as a possible source of somatic mutants, showing traits of agronomic interest with a potential to generate new cultivars.

On-The-Go Hyperspectral Imaging Under Field Conditions and Machine Learning for the Classification of Grapevine Varieties

Grapevine varietal classification is an important plant phenotyping issue for grape growing and wine industry. This task has been achieved from destructive techniques like classic ampelography and DNA analysis under laboratory conditions. This work displays a new approach for the classification of a high number of grapevine (Vitis vinifera L.) varieties under field conditions using on-the-go hyperspectral imaging and different machine learning algorithms. On-the-go imaging was performed under natural illumination using a hyperspectral camera mounted on an all-terrain vehicle at 5 km/h. Spectra were acquired over two different leaf phenological stages on the canopy of 30 different varieties on a commercial vineyard located in La Rioja, Spain. A total of 1,200 spectral samples were generated. Support vector machines (SVM) and artificial neural networks (multilayer perceptrons, MLP) were used for the development of a large number of models, testing different algorithm parameters and spectral pre-processing techniques. Both classifiers yielded notable performance values and were able to train models with recall F1 scores and area under the receiver operating characteristic curve marks up to 0.99 for 5-fold cross validation. Statistical analyses supported that the best SVM kernel was linear and the best activation function for MLP was the hyperbolic tangent function. The prediction performance for individual varieties of MLP ranged from 0.94 to 0.99, displaying low levels of variability. In the case of SVM, slightly higher differences were obtained, ranging from 0.83 to 0.97 for individual varieties. These results support the possibility of deploying an on-the-go hyperspectral imaging system in the field capable of successfully classifying leaves from different grapevine varieties. This technology could thus be considered as a new useful non-destructive tool for plant phenotyping under field conditions.

The table grape 'Victoria' with a long shaped berry: a potential mutation with attractive characteristics for consumers

BACKGROUND

Puglia is the most important region in Italy for table grape production. Since consumers look for new products, the number of table grape varieties has greatly increased in recent years.

RESULTS

In a survey in the Puglia region, we identified several years ago a potential mutation of the cv. Victoria. We described this accession in comparison with the standard Victoria for some amphelographic traits. All the characteristics were very similar to the standard Victoria except for the berry shape, which was significantly more elongated. Moreover, the berry of the mutated Victoria showed higher firmness, lightness and chroma than the standard one, with a more intense yellow colour of the skin (appreciated by consumers). The molecular characterisation with 25 SSR markers showed that normal and mutant Victoria were genetically identical at all the analysed loci, thus suggesting that the two accessions could be considered as clones with the difference in berry shape probably due to a somatic mutation.

CONCLUSIONS

This mutation of the cv. Victoria may have interesting perspective for the market since consumers are always attracted by different shape and colour of the fruits (consumers buy with eyes). This accession can be an alternative clone of the already known standard Victoria. © 2017 Society of Chemical Industry.

Genetic diversity of Xanthoceras sorbifolium bunge germplasm using morphological traits and microsatellite molecular markers

Xanthoceras sorbifolium Bunge has great potential for producing biodiesel. In order to select and evaluate appropriate germplasm to produce biodiesel, we analyzed the genetic diversity of Xanthoceras sorbifolium Bunge germplasm based on morphological traits and simple sequence repeats (SSRs) in this study. Fifty-six germplasm samples were evaluated using nine morphological traits and 23 SSR loci. Significant differences among germplasms were observed in eight morphological characters. The SSR markers analysis showed high genetic diversity among the germplasms. All SSRs had polymorphisms, and we detected 77 alleles in total. The number of alleles at each locus ranged from two to six, averaging 3.35 per marker. The polymorphic information content values ranged from 0.36 to 0.61, averaging 0.49. Expected heterozygosity, observed heterozygosity, and Shannon's information index calculations detected large genetic variations among germplasms. The high average number of alleles per locus and the allelic diversity observed in the set of genotypes analyzed indicated that the genetic base of this species is relatively wide. Thus, microsatellite markers can be used to efficiently distinguish Xanthoceras sorbifolium Bunge germplasms and assess their genetic diversity. Hundred-grain weight and lateral diameter were positively correlated with monounsaturated fatty acids and depended on genotype. These results suggest that seeds with higher hundred-grain weight and lateral diameter could be more suitable to produce biodiesel. Our data will lay a foundation for selecting appropriate germplasm to produce biodiesel based on seed phenotype and will contribute to the conservation and management of this important plant genetic resource.

Data Mining and NIR Spectroscopy in Viticulture: Applications for Plant Phenotyping under Field Conditions

Plant phenotyping is a very important topic in agriculture. In this context, data mining strategies may be applied to agricultural data retrieved with new non-invasive devices, with the aim of yielding useful, reliable and objective information. This work presents some applications of machine learning algorithms along with in-field acquired NIR spectral data for plant phenotyping in viticulture, specifically for grapevine variety discrimination and assessment of plant water status. Support vector machine (SVM), rotation forests and M5 trees models were built using NIR spectra acquired in the field directly on the adaxial side of grapevine leaves, with a non-invasive portable spectrophotometer working in the spectral range between 1600 and 2400 nm. The ν-SVM algorithm was used for the training of a model for varietal classification. The classifiers’ performance for the 10 varieties reached, for cross- and external validations, the 88.7% and 92.5% marks, respectively. For water stress assessment, the models developed using the absorbance spectra of six varieties yielded the same determination coefficient for both cross- and external validations (R² = 0.84; RMSEs of 0.164 and 0.165 MPa, respectively). Furthermore, a variety-specific model trained only with samples of Tempranillo from two different vintages yielded R² = 0.76 and RMSE of 0.16 MPa for cross-validation and R² = 0.79, RMSE of 0.17 MPa for external validation. These results show the power of the combined use of data mining and non-invasive NIR sensing for in-field grapevine phenotyping and their usefulness for the wine industry and precision viticulture implementations.

Clonal differences and impact of defoliation on Sauvignon blanc (Vitis vinifera L.) wines: a chemical and sensory investigation

BACKGROUND

The aim of this study, performed on Sauvignon blanc clones SB11 and SB316, grafted on the same rootstock 101-14 Mgt (Vitis riparia × V. ruperstris) and grown at two adjacent vineyards, was two-fold: (1) to study wine chemical and sensory composition of both clones within an unaltered canopy; and (2) to determine the effect of defoliation (e.g. bunch microclimate) on wine chemical and sensory composition.

RESULTS

Orthogonal projection to latent structures discriminate analysis (OPLS-DA) was applied to the concentration profiles of volatile compounds derived from gas chromatography-mass spectrometry data. The loadings directions inferred that 3-isobutyl-2-methoxypyrazine (IBMP) discriminated control treatments (shaded fruit zone) of both clones from defoliation treatments (exposed fruit zone), whereas 3-sulfanyl-hexan-1-ol (3SH), 3-sulfanylhexyl acetate (3SHA), hexanol, hexyl hexanoate and some other esters discriminated defoliated treatments from the controls. The OPLS-DA indicated the importance of IBMP, higher alcohol acetates and phenylethyl esters, for discrimination of clone SB11 from clone SB316 irrespective of the treatment. Defoliation in the fruit zone significantly decreased perceived greenness in clone SB11 and elevated fruitier aromas, whereas in clone SB316 the effect of defoliation on wine sensory perception was less noticeable regardless the decrease in IBMP concentrations.

CONCLUSION

These findings highlight the importance of clone selection and bunch microclimate to diversify produced wine styles.

Support Vector Machine and Artificial Neural Network Models for the Classification of Grapevine Varieties Using a Portable NIR Spectrophotometer

The identification of different grapevine varieties, currently attended using visual ampelometry, DNA analysis and very recently, by hyperspectral analysis under laboratory conditions, is an issue of great importance in the wine industry. This work presents support vector machine and artificial neural network’s modelling for grapevine varietal classification from in-field leaf spectroscopy. Modelling was attempted at two scales: site-specific and a global scale. Spectral measurements were obtained on the near-infrared (NIR) spectral range between 1600 to 2400 nm under field conditions in a non-destructive way using a portable spectrophotometer. For the site specific approach, spectra were collected from the adaxial side of 400 individual leaves of 20 grapevine (Vitis vinifera L.) varieties one week after veraison. For the global model, two additional sets of spectra were collected one week before harvest from two different vineyards in another vintage, each one consisting on 48 measurement from individual leaves of six varieties. Several combinations of spectra scatter correction and smoothing filtering were studied. For the training of the models, support vector machines and artificial neural networks were employed using the pre-processed spectra as input and the varieties as the classes of the models. The results from the pre-processing study showed that there was no influence whether using scatter correction or not. Also, a second-degree derivative with a window size of 5 Savitzky-Golay filtering yielded the highest outcomes. For the site-specific model, with 20 classes, the best results from the classifiers thrown an overall score of 87.25% of correctly classified samples. These results were compared under the same conditions with a model trained using partial least squares discriminant analysis, which showed a worse performance in every case. For the global model, a 6-class dataset involving samples from three different vineyards, two years and leaves monitored at post-veraison and harvest was also built up, reaching a 77.08% of correctly classified samples. The outcomes obtained demonstrate the capability of using a reliable method for fast, in-field, non-destructive grapevine varietal classification that could be very useful in viticulture and wine industry, either global or site-specific.

Genomics and the Contrasting Dynamics of Annual and Perennial Domestication

Plant domestication modifies a wild species genetically for human use. Among thousands of domesticated plants, a major distinction is the difference between annual and perennial life cycles. The domestication of perennials is expected to follow different processes than annuals, with distinct genetic outcomes. Here we examine domestication from a population genetics perspective, with a focus on three issues: genetic bottlenecks during domestication, introgression as a source of local adaptation, and genetic load. These three issues have been studied nominally in major annual crops but even less extensively in perennials. Here we highlight lessons from annual plants, motivations to study these issues in perennial plants, and new approaches that may lead to further progress.

Genetic variability and geographic typicality of Italian former Prosecco grape variety using PCR-derived molecular markers

This study uses PCR-derived marker systems to investigate the extent and distribution of genetic variability of 80 Italian Prosecco accessions coming from Prosecco DOC area (north-east area of Italy). The studied samples include genotypes from Veneto and Friuli Venezia Giulia region. In order to verify the varietal identity of the samples, analyses based on 22 SSR loci were performed, and two grape varieties were found: Prosecco tondo and Prosecco lungo. In addition to microsatellite analysis, intra-varietal variability study was performed using AFLP, SAMPL, ISSR, and M-AFLP molecular markers. This molecular approach could discriminate different Prosecco tondo accessions coming from Treviso hills, from Veneto plain, from Friuli Venezia Giulia region, and from Padua hills (Serprina samples). As concerning Prosecco lungo variety, it was possible to discriminate molecularly the accessions from Veneto region and those from Friuli Venezia Giulia region. The molecular analysis allowed a distinction of the Prosecco genotypes on the basis of their geographic origins with plant-specific markers able to differentiate all Prosecco accessions. In this paper, the studied grape variety is termed Prosecco and not Glera (which is the present name) because the sampled vineyards were established many years ago when the name of the variety was Prosecco.

A forensic perspective on the genetic identification of grapevine (Vitis vinifera L.) varieties using STR markers

The grapevine (Vitis vinifera subsp. vinifera) is one of the most important agricultural crops worldwide. A long interest in the historical origins of ancient and cultivated current grapevines, as well as the need to establish phylogenetic relationships and parentage, solve homonymies and synonymies, fingerprint cultivars and clones, and assess the authenticity of plants and wines has encouraged the development of genetic identification methods. STR analysis is currently the most commonly used method for these purposes. A large dataset of grapevines genotypes for many cultivars worldwide has been produced in the last decade using a common set of recommended dinucleotide nuclear STRs. This type of marker has been replaced by long core-repeat loci in standardized state-of-the-art human forensic genotyping. The first steps toward harmonized grapevine genotyping have already been taken to bring the genetic identification methods closer to human forensic STR standards by previous authors. In this context, we bring forward a set of basic suggestions that reinforce the need to (i) guarantee trueness-to-type of the sample; (ii) use the long core-repeat markers; (iii) verify the specificity and amplification consistency of PCR primers; (iv) sequence frequent alleles and use these standardized allele ladders; (v) consider mutation rates when evaluating results of STR-based parentage and pedigree analysis; (vi) genotype large and representative samples in order to obtain allele frequency databases; (vii) standardize genotype data by establishing allele nomenclature based on repeat number to facilitate information exchange and data compilation.

Genetic diversity and population structure assessed by SSR and SNP markers in a large germplasm collection of grape

BACKGROUND

The economic importance of grapevine has driven significant efforts in genomics to accelerate the exploitation of Vitis resources for development of new cultivars. However, although a large number of clonally propagated accessions are maintained in grape germplasm collections worldwide, their use for crop improvement is limited by the scarcity of information on genetic diversity, population structure and proper phenotypic assessment. The identification of representative and manageable subset of accessions would facilitate access to the diversity available in large collections. A genome-wide germplasm characterization using molecular markers can offer reliable tools for adjusting the quality and representativeness of such core samples.

RESULTS

We investigated patterns of molecular diversity at 22 common microsatellite loci and 384 single nucleotide polymorphisms (SNPs) in 2273 accessions of domesticated grapevine V. vinifera ssp. sativa, its wild relative V. vinifera ssp. sylvestris, interspecific hybrid cultivars and rootstocks. Despite the large number of putative duplicates and extensive clonal relationships among the accessions, we observed high level of genetic variation. In the total germplasm collection the average genetic diversity, as quantified by the expected heterozygosity, was higher for SSR loci (0.81) than for SNPs (0.34). The analysis of the genetic structure in the grape germplasm collection revealed several levels of stratification. The primary division was between accessions of V. vinifera and non-vinifera, followed by the distinction between wild and domesticated grapevine. Intra-specific subgroups were detected within cultivated grapevine representing different eco-geographic groups. The comparison of a phenological core collection and genetic core collections showed that the latter retained more genetic diversity, while maintaining a similar phenotypic variability.

CONCLUSIONS

The comprehensive molecular characterization of our grape germplasm collection contributes to the knowledge about levels and distribution of genetic diversity in the existing resources of Vitis and provides insights into genetic subdivision within the European germplasm. Genotypic and phenotypic information compared in this study may efficiently guide further exploration of this diversity for facilitating its practical use.

Transposable elements are a major cause of somatic polymorphism in Vitis vinifera L

Through multiple vegetative propagation cycles, clones accumulate mutations in somatic cells that are at the origin of clonal phenotypic diversity in grape. Clonal diversity provided clones such as Cabernet-Sauvignon N°470, Chardonnay N° 548 and Pinot noir N° 777 which all produce wines of superior quality. The economic impact of clonal selection is therefore very high: since approx. 95% of the grapevines produced in French nurseries originate from the French clonal selection. In this study we provide the first broad description of polymorphism in different clones of a single grapevine cultivar, Pinot noir, in the context of vegetative propagation. Genome sequencing was performed using 454 GS-FLX methodology without a priori, in order to identify and quantify for the first time molecular polymorphisms responsible for clonal variability in grapevine. New generation sequencing (NGS) was used to compare a large portion of the genome of three Pinot noir clones selected for their phenotypic differences. Reads obtained with NGS and the sequence of Pinot noir ENTAV-INRA® 115 sequenced by Velasco et al., were aligned on the PN40024 reference sequence. We then searched for molecular polymorphism between clones. Three types of polymorphism (SNPs, Indels, mobile elements) were found but insertion polymorphism generated by mobile elements of many families displayed the highest mutational event with respect to clonal variation. Mobile elements inducing insertion polymorphism in the genome of Pinot noir were identified and classified and a list is presented in this study as potential markers for the study of clonal variation. Among these, the dynamic of four mobile elements with a high polymorphism level were analyzed and insertion polymorphism was confirmed in all the Pinot clones registered in France.