The parentage of a classic wine grape, Cabernet Sauvignon

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.

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.

Sub-Regional Variation and Characteristics of Cabernet Sauvignon Wines in the Eastern Foothills of the Helan Mountain: A Perspective from Phenolics, Visual Properties and Mouthfeel

As one of the most promising wine regions in China, the eastern foothills of the Helan Mountain (EFHM) in the Ningxia Hui Autonomous Region has attracted great attention recently. Geographically, EFHM is divided into six sub-regions, namely Shizuishan, Xixia, Helan, Qingtongxia, Yongning and Hongsipu. However, there have been few reports on the character and differences between wines in the six sub-regions. In this experiment, a total of 71 commercial Cabernet Sauvignon wines from six sub-regions were collected, and their phenolic compounds, visual properties and mouthfeel were investigated. The results showed that wines from the six sub-regions of EFHM showed distinctive phenolic profiles and could be distinguished through the OPLS-DA mode using 32 potential markers. In terms of color, Shizuishan wines showed higher a* values and lower b* values. The sensory evaluation showed that Hongsipu wines had higher astringency strength and lower tannin texture. The overall results implied that the phenolic compounds of wines in different sub-regions were affected by terroir conditions. To the best of our knowledge, this is the first time that a wide coverage of phenolic compounds has been analysed for wines from the sub-regions of EFHM, which could provide valuable information in deciphering the terroir of EFHM.

Analysis of Wine-Producing Vitis vinifera L. Biotypes, Autochthonous to Crete (Greece), Employing Ampelographic and Microsatellite Markers

Vitis vinifera ssp. vinifera (domesticated grapevine) includes thousands of cultivars, which are classified according to their main uses, as wines, fresh fruits or dried raisins and sultanas since ancient times. Evidence showed that Crete grapevine cultivars and winemaking date back to 2300 BC. In this study, fifty-one genotypes belonging to seven different traditional Vitis vinifera cultivars, presumed autochthonous to the island of Crete, were selected for their wine-producing potential and classified by 51 ampelographic descriptors. In addition, five genotypes belonging to two non-autochthonous cultivars were included as out-group controls. Subsequently, in order to characterize genetic diversity, establish genetic relationships within and between cultivars and solve accession-labeling problems, genotypes were fingerprinted employing Simple Sequence Repeat (SSR or microsatellite) markers. Four of the autochthonous cultivars namely 'Vidiano', 'Vilana', 'Plyto', and 'Moschato Spinas' are used in the local economy for blanc (white) wine production while the rest, namely 'Kotsifali', 'Liatiko' and 'Mantilari' for Noir (red) wines. The two cultivars employed as out-group were 'Moschato Samou' and 'Moschato Alexandrias': both white wine producers. Ampelography-based clustering grouped the majority of genotypes along cultivar-specific clusters. All three Moschato cultivars formed a distinct clade pointing to the non-autochthonous origin of 'Moschato Spinas'. A total of one hundred and thirteen (113) SSR alleles were amplified from thirteen (13) SSR loci, with an average number of alleles per locus equal to 10.23 revealing ample genetic polymorphism. The cumulative probability of identity was also quite high (3.389 × 10-16). The overall observed heterozygosity was 0.837 while for twenty-nine of the examined genotypes, at least one private SSR allele was detected. The majority of genotypes were grouped in cultivar-specific clusters. The results of this paper pave the way for the certification and registration of clones of some of the most important wine-producing cultivars in Crete.

Photoprotection Is Achieved by Photorespiration and Modification of the Leaf Incident Light, and Their Extent Is Modulated by the Stomatal Sensitivity to Water Deficit in Grapevines

Absorbed energy in excess of that used by photosynthesis induces photoinhibition, which is common in water deficit conditions, resulting in reductions in stomatal conductance. In grapevines, controlled water deficit is a common field practice, but little is known about the impact of a given water shortage on the energy transduction processes at the leaf level in relation to contrasting stomatal sensitivities to drought. Here, we assessed the effect of a nearly similar water deficit condition on four grapevine varieties: Cabernet Sauvignon (CS) and Sauvignon Blanc (SB), which are stomatal sensitive, and Chardonnay (CH) and Carménère (CM), which are less stomatal sensitive, grown in 20 L pots outdoors. Plants were maintained to nearly 94% of field capacity (WW) and 83% field capacity (WD). We have assessed plant water status, photosynthesis (A_N), photorespiration, A_N vs. PAR, AC_i curves, photochemical (qP) and non-photochemical (qN) fluorescence quenching vs. PAR, the photoprotective effectiveness of NPQ (qPd) and light interception by leaves. Photorespiration is important under WD, but to a different extent between varieties. This is related to stomatal sensitivity, maintaining a safe proportion of PSII reaction centres in an open state. Additionally, the capacity for carboxylation is affected by WD, but to a greater extent in more sensitive varieties. As for qN, in WD it saturates at 750 μmol PAR m⁻²s⁻¹, irrespective of the variety, which coincides with PAR, from which qN photoprotective effectiveness declines, and qP is reduced to risky thresholds. Additionally, that same PAR intensity is intercepted by WD leaves from highly stomatal-sensitive varieties, likely due to a modification of the leaf angle in those plants. Pigments associated with qN, as well as chlorophylls, do not seem to be a relevant physiological target for acclimation.

Genome-wide SSR markers in bottle gourd: development, characterization, utilization in assessment of genetic diversity of National Genebank of India and synteny with other related cucurbits

Lagenaria siceraria (Molina) Standley is an important cultivated crop with its immense importance in pharmaceutical industry and as vegetable. Its seed, root, stem, leaves, flower, and fruit are used as an ointment for ailment of various diseases throughout Asia. Despite its worldwide importance, informative co-dominant microsatellite markers in the bottle gourd crop are very restricted, impeding genetic improvement, cultivar identification, and phylogenetic studies. Next-generation sequencing has revolutionized the approaches for discovery, assessment, and validation of molecular markers. We conducted a genome-wide analysis, for developing SSR markers by utilizing restriction site-associated DNA sequencing (RAD-Seq) data obtained from NCBI. By performing in silico mining of microsatellite repeat motifs, we developed 45,066 perfect SSR markers. Of which 207 markers were successfully validated and 120 (57.97%) polymorphic primer pairs were utilized for an in-depth genetic diversity and population structure analysis of 96 accessions from the National Genebank of India. Tetranucleotide repeats (∼34.3%) were the most prevalent followed by trinucleotide repeats (∼30.73%), further 21.03%, 9.6%, and 4.3% of di-, penta-, and hexa-nucleotide repeats in the bottle gourd genome, respectively. Synteny of SSR markers on 11 bottle gourd linkage groups was correlated with the 7 chromosomes of cucumber (93.2%), 12 chromosomes of melon (87.4%), and 11 of watermelon (90.8%). The generated SSR markers provide a valuable tool for germplasm characterization, genetic linkage map construction, studying synteny, gene discovery, and for breeding in bottle gourd and other cucurbits species. KEY MESSAGE: Development of 45,066 perfect microsatellite markers as a valuable tool for marker assisted selection (MAS) in plant breeding.

State of Crop Landraces in Arcadia (Greece) and In-Situ Conservation Potential

Genetic erosion of landraces is increasing worldwide, however there are still regions rich in landrace biodiversity, such as islands and mountainous isolated areas. Defining the reasons of landrace abandonment in these areas, as well as collecting and preserving landraces, is of outmost importance. In this context, the Agricultural University of Athens organized missions in 53 villages of Arcadia, a prefecture rich in floral biodiversity and variable climatic conditions and topography. The aim was to collect samples of the on-farm (in-situ) conserved annual crop landraces and record the location of perennial crop local varieties. Since traditional knowledge and practices have been playing a vital role in the survival of landraces and local varieties, information was obtained through personal interviews with locals using semi-structured questionnaires. Even though the number of accessions collected from Arcadia has been reduced (141 samples) compared to previous collections and genetic erosion is advancing dramatically for cereals and pulses, a significant number of landraces is still cultivated by the locals. The reasons of landrace abandonment were other sources of occupation than agriculture, such as public service jobs, mechanization, and commercialization of agriculture. Gastronomic and agro-tourism along with European Union trademarks and policies can support locals in landrace/local varieties in-situ conservation.

Succession of Fungal Communities at Different Developmental Stages of Cabernet Sauvignon Grapes From an Organic Vineyard in Xinjiang

Fungi present on grape surface considerably impact grape growth and quality. However, information of the fungal community structures and dynamics on the worldwide cash crop, the Cabernet Sauvignon grape, from the budding to ripening stages remains limited. Here, we investigated the succession of fungal communities on Cabernet Sauvignon grapes from an organic vineyard in Xinjiang, China at different developmental stages via high-throughput sequencing combined with multivariate data analysis. In total, 439 fungal amplicon sequence variants (ASVs) from six phyla were identified. The fungal communities differed over the budding to the berry stages. Moreover, Aspergillus, Malassezia, Metschnikowia, and Udeniomyces were predominant during the unripe stage, whereas Erysiphe, Cryptococcus, Vishniacozyma, and Cladosporium were dominant in the ripe stages. Notably, Vishniacozyma was the most abundant genus, conserved in all development stages. Moreover, network analysis resulted in 171 edges—96 negative and 75 positive. Moreover, fungal genera such as Vishniacozyma, Sporobolomyces, Aspergillus, Alternaria, Erysiphe, Toxicodendron, and Metschnikowia were present in the hubs serving as the main connecting nodes. Extensive mutualistic interactions potentially occur among the fungi on the grape surface. In conclusion, the current study expounded the characteristics of the Cabernet Sauvignon grape fungal community during the plant growth process, and the results provided essential insights into the potential impacts of fungal communities on grape growth and health.

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.

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.

Introgression Among Cultivated and Wild Grapevine in Tuscany

Wild grapevine, Vitis vinifera L. subsp. sylvestris (Gmelin, Hegi) is spontaneous to Europe and common in Tuscany. In this study, wild grapevines were identified in 22 populations from eight locations in Tuscan Maremma (Grosseto and Siena province). The plants were propagated by cuttings, collected in a vineyard, genotyped by nuclear simple sequence repeats (SSRs), chloroplast SSRs and single nucleotide polymorphisms (SNPs), and compared to locally cultivated varieties (Vitis vinifera L. subsp. sativa) and to non-vinifera and non-vitis genotypes. The identity analysis revealed that some individuals were redundant genotypes, suggesting natural vegetative propagation. In addition, four of the supposed V.v. sylvestris were in fact naturalized V.v. sativa. The majority of putative sylvestris genotypes had chlorotype A, while the remainder had chlorotype D, as the majority of Vitis vinifera subsp. sativa cultivated in Italy. Some of the recovered sylvestris genotypes appeared to be natural crosses with cultivated grapevine varieties in Tuscany, and their chlorotype suggests a higher pollen flow from sativa to the sylvestris genotypes than in the opposite direction. In addition, other genotypes appeared to be crosses within sylvestris, sylvestris-sativa or sylvestris-sylvestris siblings, or equivalent relationships. These relationships suggest a noticeably level of sexual reproductive activities among sylvestris and sylvestris-sativa genotypes. A cluster and structure analysis clearly differentiated the true sylvestris from the sativa, and the non-vinifera or non-vitis genotypes, and also highlighted a possible introgression of sylvestris into some Italian and French cultivated varieties. The results therefore suggest that, in addition to the primary ancient center of domestication from the Near East to Central Asia, the introgression among cultivated and wild grapevine occurred in other centers of diversification along the migration routes, contributing to the domestication processes, and suggesting that these processes are still ongoing despite the reduction in populations of sylvestris. The results also highlight that the GrapeReSeq 18K Vitis genotyping chip are suitable for non-vitis genotyping and that the range of SNPs heterozygosity in sylvestris appears to be up to 6% less and does not overlap the heterozygosity range of sativa genotypes.

Using Rapid Chlorophyll Fluorescence Transients to Classify Vitis Genotypes

When a dark-adapted leaf is illuminated with saturating light, a fast polyphasic rise of fluorescence emission (Kautsky effect) is observed. The shape of the curve is dependent on the molecular organization of the photochemical apparatus, which in turn is a function of the interaction between genotype and environment. In this paper, we evaluate the potential of rapid fluorescence transients, aided by machine learning techniques, to classify plant genotypes. We present results of the application of several machine learning algorithms (k-nearest neighbors, decision trees, artificial neural networks, genetic programming) to rapid induction curves recorded in different species and cultivars of vine grown in the same environmental conditions. The phylogenetic relations between the selected Vitis species and Vitis vinifera cultivars were established with molecular markers. Both neural networks (71.8%) and genetic programming (75.3%) presented much higher global classification success rates than k-nearest neighbors (58.5%) or decision trees (51.6%), genetic programming performing slightly better than neural networks. However, compared with a random classifier (success rate = 14%), even the less successful algorithms were good at the task of classifying. The use of rapid fluorescence transients, handled by genetic programming, for rapid preliminary classification of Vitis genotypes is foreseen as feasible.

Geographical origin traceability of Cabernet Sauvignon wines based on Infrared fingerprint technology combined with chemometrics

Mid-infrared (MIR) and near-infrared (NIR) spectroscopy combined with chemometrics were explored to classify Cabernet Sauvignon wines from different countries (Australia, Chile and China). Commercial wines (n = 540) were scanned in transmission mode using MIR and NIR, and their characteristic fingerprint bands were extracted at 1750-1000 cm⁻¹ and 4555-4353 cm⁻¹. Through the identification system of Tri-step infrared spectroscopy, the correlation between macroscopic chemical fingerprints and geographical regions was explored more deeply. Furthermore, Principal component analysis (PCA), soft independent modelling of class analogy (SIMCA) and discriminant analysis (DA) based on MIR and NIR spectra were used to visualize or discriminate differences between samples and to realize geographical origin traceability of Cabernet Sauvignon wines. Through “external test set (n = 157)” validation, SIMCA models correctly classified 97%, 97% and 92% of Australian, Chilean and Chinese Cabernet Sauvignon wines, while the DA models correctly classified 86%, 85% and 77%, respectively. Based on unique digital fingerprints of spectroscopy (FT-MIR and FT-NIR) associated with chemometrics, geographical origin traceability was achieved in a more comprehensive, effective and rapid manner. The developed database models based on IR fingerprint spectroscopy with chemometrics could provide scientific basis and reference for geographical origin traceability of Cabernet Sauvignon wines (Australia, Chile and China).

Diploid Genome Assembly of the Wine Grape Carménère

In this genome report, we describe the sequencing and annotation of the genome of the wine grape Carménère (clone 02, VCR-702). Long considered extinct, this old French wine grape variety is now cultivated mostly in Chile where it was imported in the 1850s just before the European phylloxera epidemic. Genomic DNA was sequenced using Single Molecule Real Time technology and assembled with FALCON-Unzip, a diploid-aware assembly pipeline. To optimize the contiguity and completeness of the assembly, we tested about a thousand combinations of assembly parameters, sequencing coverage, error correction and repeat masking methods. The final scaffolds provide a complete and phased representation of the diploid genome of this wine grape. Comparison of the two haplotypes revealed numerous heterozygous variants, including loss-of-function ones, some of which in genes associated with polyphenol biosynthesis. Comparisons with other publicly available grape genomes and transcriptomes showed the impact of structural variation on gene content differences between Carménère and other wine grape cultivars. Among the putative cultivar-specific genes, we identified genes potentially involved in aroma production and stress responses. The genome assembly of Carménère expands the representation of the genomic variability in grapes and will enable studies that aim to understand its distinctive organoleptic and agronomical features and assess its still elusive extant genetic variability. A genome browser for Carménère, its annotation, and an associated blast tool are available at http://cantulab.github.io/data.

Iso-Seq Allows Genome-Independent Transcriptome Profiling of Grape Berry Development

Transcriptomics has been widely applied to study grape berry development. With few exceptions, transcriptomic studies in grape are performed using the available genome sequence, PN40024, as reference. However, differences in gene content among grape accessions, which contribute to phenotypic differences among cultivars, suggest that a single reference genome does not represent the species' entire gene space. Though whole genome assembly and annotation can reveal the relatively unique or "private" gene space of any particular cultivar, transcriptome reconstruction is a more rapid, less costly, and less computationally intensive strategy to accomplish the same goal. In this study, we used single molecule-real time sequencing (SMRT) to sequence full-length cDNA (Iso-Seq) and reconstruct the transcriptome of Cabernet Sauvignon berries during berry ripening. In addition, short reads from ripening berries were used to error-correct low-expression isoforms and to profile isoform expression. By comparing the annotated gene space of Cabernet Sauvignon to other grape cultivars, we demonstrate that the transcriptome reference built with Iso-Seq data represents most of the expressed genes in the grape berries and includes 1,501 cultivar-specific genes. Iso-Seq produced transcriptome profiles similar to those obtained after mapping on a complete genome reference. Together, these results justify the application of Iso-Seq to identify cultivar-specific genes and build a comprehensive reference for transcriptional profiling that circumvents the necessity of a genome reference with its associated costs and computational weight.

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

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

Nanostructured TiO2-induced photocatalytic stress enhances the antioxidant capacity and phenolic content in the leaves of Vitis vinifera on a genotype-dependent manner

Over the past decades, nanotechnology has received great attention and brought revolutionary solutions for a number of challenges in scientific fields. Industrial, agricultural and medical applications of engineered nanomaterials have increased intensively. The ability of titanium dioxide nanoparticles (TiO₂ NPs) to produce reactive oxygen species (ROS), when excited by ultra-violet (UV) light, makes them useful for effectively inactivate various pathogens. It is known that ROS also have signalling role in living organisms, therefore, TiO₂ NPs-induced ROS can influence both enzymatic and non-enzymatic defence systems, and could play a role in the resistance of plants to pathogens. Herein, we studied the photocatalytic stress responses of grapevine (Vitis vinifera L.) as model plant, when exposed to a well-known photocatalyst, Degussa P25 TiO₂ NPs. The photocatalytically produced ROS such as superoxide anion, hydroxyl radical and singlet oxygen were confirmed by electron paramagnetic resonance spectroscopy. Foliar exposure of five red cultivars (Cabernet sauvignon, Cabernet franc, Merlot, Kékfrankos and Kadarka) was carried out in blooming phenophase under field condition where plants are exposed to natural sunlight with relatively high UV radiation (with a maximum of ~ 45 W m^-2). After two weeks of exposure, the effects of photogenerated ROS on the total phenolic content, antioxidant capacity, flavonol profile and the main macro-, microelements of the leaves were studied in detail. We found that foliar application of TiO₂ NPs boosted the total phenolic content and biosynthesis of the leaf flavonols depending on the grapevine variety. Photocatalytically active TiO₂ NPs also increased K, Mg, Ca, B and Mn levels in the leaves as shown by ICP-AES measurements.

Berry color variation in grapevine as a source of diversity

Even though it is one of the oldest perennial domesticated fruit crops in the world, grapevine (Vitis vinifera L.) cultivation today is the result of both conventional breeding practices (i.e. hybridizations adopted during the last century) and vegetative propagation. Human-assisted asexual propagation has allowed the maintenance of desired traits but has largely impacted the frequency of spontaneous somatic mutations observed in the field. Consequently, many grapevine fruit attributes to date have been artificially selected, including: fruit yield, compactness, size and composition, the latter being greatly diversified in the pursuit of altering berry skin coloration. The present review provides an overview of various aspects related to grapevine diversity, with a special emphasis on grape berry skin color variation and will discuss the current knowledge of how grape skin color variation is affected by the synthesis of phenolic compounds, particularly anthocyanins and their underlying genetic factors. We hope this knowledge will be useful in supporting the importance of the berry color trait diversity in cultivated grapevines, which is used as basis for selection during breeding programs because of its application for vine growers, winemakers and consumers.

Bioavailability of potentially toxic elements in soil-grapevine (leaf, skin, pulp and seed) system and environmental and health risk assessment

Monitoring of potentially toxic elements in agricultural soil represents the first measure of caution regarding food safety, while research into element bioavailability should be a step forward in understanding the element transportation chain. This study was conducted in the grapevine growing area ("Oplenac Wine Route") for investigating element bioavailability in the soil-grapevine system accompanied by an assessment of the ecological implications and human health risk. Single extraction procedures (CH₃COOH, Na₂EDTA, CaCl₂, NH₄NO₃ and deionised H₂O) and digestion were performed to estimate the bioavailability of 22 elements (Al, As, B, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Na, Ni, Pb, Sb, Sr, V and Zn) from the topsoil (0-30 cm) and subsoil (30-60 cm) to the grapevine parts (leaf, skin, pulp and seed) and wine. The extractants were effective comparing to the pseudo-total concentrations in following order Na₂EDTA ˃ CH₃COOH ˃ NH₄NO₃ ˃ CaCl₂, H₂O 2 h and 16 h. The most suitable extractants for assessing the bioavailability of the elements from the soil to the grapevine parts were CaCl₂, NH₄NO₃ and Na₂EDTA, but deionised H₂O could be suitable, as well. The results showed that Ba was the most bioavailable element in the soil-grapevine system. Contamination factor implied a moderate contamination (1 < CF < 3) of the soil. The concentrations of Cr, Ni and Cd in the soil were above the maximum allowed concentrations. According to the biological accumulation coefficient (BAC), the grape seeds and grapevine leaves mostly accumulated Cu and Zn from the soil, respectively. Based on ratio factor (RF > 1), the influence of atmospheric deposition on the aerial grapevine parts (leaves and grape skin) was observed. Nevertheless, low adverse health risk effects (HI < 1 and R ≤ 1 × 10^-6) were estimated for farmers and grape and wine consumers.

Free Monoterpene Isomer Profiles of Vitis Vinifera L. cv. White Wines

Monoterpene compounds contribute floral and fruity characters to wine and are desired by grape growers and winemakers for many white wines. However, monoterpene isomers, especially monoterpene enantiomers, have been little explored. It is possible to identify and quantitate 17 monoterpene isomers in 148 varietal wines from eight grape varieties; Chardonnay, Gewürztraminer, Muscat, Pinot gris, Riesling, Sauvignon blanc, Torrontes, and Viognier in two vintages by Headspace solidphase microextraction multidimensional gas chromatography mass spectrometry (HS-SPME-MDGC-MS). Results obtained from general linear models and discriminant analysis showed significant differences for the isomer profiles and enantiomer fractions among the eight grape varieties and four wine styles. The high R² values from the fitted line show low variation in enantiomeric differences based on variety. These results provide an overview of the monoterpene isomers of wide varietal wines, and support that isomer profiles and enantiomer fractions could differentiate our wines by varietal and wine style.

Proton Nuclear Magnetic Resonance-Spectroscopic Discrimination of Wines Reflects Genetic Homology of Several Different Grape (V. vinifera L.) Cultivars

Background and Aims

Proton nuclear magnetic resonance spectroscopy coupled multivariate analysis (¹H NMR-PCA/PLS-DA) is an important tool for the discrimination of wine products. Although ¹H NMR has been shown to discriminate wines of different cultivars, a grape genetic component of the discrimination has been inferred only from discrimination of cultivars of undefined genetic homology and in the presence of many confounding environmental factors. We aimed to confirm the influence of grape genotypes in the absence of those factors.

Methods and Results

We applied ¹H NMR-PCA/PLS-DA and hierarchical cluster analysis (HCA) to wines from five, variously genetically-related grapevine (V. vinifera) cultivars; all grown similarly on the same site and vinified similarly. We also compared the semi-quantitative profiles of the discriminant metabolites of each cultivar with previously reported chemical analyses. The cultivars were clearly distinguishable and there was a general correlation between their grouping and their genetic homology as revealed by recent genomic studies. Between cultivars, the relative amounts of several of the cultivar-related discriminant metabolites conformed closely with reported chemical analyses.

Conclusions

Differences in grape-derived metabolites associated with genetic differences alone are a major source of ¹H NMR-based discrimination of wines and ¹H NMR has the capacity to discriminate between very closely related cultivars.

Significance of the Study

The study confirms that genetic variation among grape cultivars alone can account for the discrimination of wine by ¹H NMR-PCA/PLS and indicates that ¹H NMR spectra of wine of single grape cultivars may in future be used in tandem with hierarchical cluster analysis to elucidate genetic lineages and metabolomic relations of grapevine cultivars. In the absence of genetic information, for example, where predecessor varieties are no longer extant, this may be a particularly useful approach.

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.

Pedigree reconstruction of the Italian grapevine Aglianico (Vitis vinifera L.) from Campania

A total of 41 accessions of Aglianico belonging to three different biotypes (Taburno, Taurasi, and Vulture) and 9 accessions of Sirica grapes were sampled from diverse areas of Campania (Italy). All accessions were first genotyped using 21 microsatellite markers (SSR) to evaluate possible homonymies, synonymies, and the genetic structure of each group. A larger dataset was then constructed adding Italian and International cultivars. On the basis of results obtained analyzing the first dataset, further investigations were carried out enlarging the number of investigated loci (up to 43). The addition of 22 SSRs was useful in the definition of likely genetic relationships linking Aglianico biotypes, Sirica and Syrah. According to their SSR allelic profiles, the monophyletic origin of the three Aglianico biotypes was confirmed. Among Aglianico Taburno accessions, eight samples (called Aglianico like-to-type) performed a different SSR allelic profile from Aglianico true-to-type. Sirica and Syrah proved to be synonyms. This work allowed to determine the genetic relationship between Aglianico and the cultivars supposed to be related. The parentage analysis was investigated. The most likely pedigree has been reconstructed; revealing a second-degree relationship between the worldwide cultivated Syrah from the Rhone Valley and Aglianico. Aglianico like-to-type appeared related to Aglianico in a parent-offspring fashion.

A methyltransferase essential for the methoxypyrazine-derived flavour of wine

Methoxypyrazines are a family of potent volatile compounds of diverse biological significance. They are used by insects and plants in chemical defence, are present in many vegetables and fruit and, in particular, impart herbaceous/green/vegetal sensory attributes to wines of certain varieties, including Cabernet Sauvignon. While pathways for methoxypyrazine biosynthesis have been postulated, none of the steps have been confirmed genetically. We have used the F2 progeny of a cross between a rapid flowering grapevine dwarf mutant, which does not produce 3-isobutyl-2-methoxypyrazine (IBMP), and Cabernet Sauvignon to identify the major locus responsible for accumulation of IBMP in unripe grape berries. Two candidate methyltransferase genes within the locus were identified and one was significantly associated with berry IBMP levels using association mapping. The enzyme encoded by this gene (VvOMT3) has high affinity for hydroxypyrazine precursors of methoxypyrazines. The gene is not expressed in the fruit of Pinot varieties, which lack IBMP, but is expressed in Cabernet Sauvignon at the time of accumulation of IBMP in the fruit. The results suggest that VvOMT3 is responsible for the final step in methoxypyrazine synthesis in grape berries and is the major determinant of IBMP production.

Bioarchaeological insights into the process of domestication of grapevine (Vitis vinifera L.) during Roman times in Southern France

Grapevine (Vitis vinifera), one of the most important fruit species in the Classical Mediterranean world, is thought to have been domesticated first in South-Western Asia, during the Neolithic. However, the domestication process remains largely unknown. Crucial unanswered questions concern the duration of the process (rapid or slow?) and the related geographical area (single or multiple-origins?). Seeds from domesticated grapevine and from its wild ancestor are reported to differ according to shape. Our work aims, first, to confirm this difference and secondly to identify the extent of domestication in the grapes cultivated by Romans in Southern France during the period 50 BCE–500 CE. We had the opportunity to analyze uncharred waterlogged grape pips from 17 archaeological sites. Based on an extended reference sample of modern wild grapevines and cultivars our work shows that both subspecies can be discriminated using simple measurements. The elongation gradient of the pip’s body and stalk may be regarded as an indicator of the strength of the selection pressures undergone by domesticated grapes. Grapevines cultivated during the Roman period included a mix of morphotypes comprising wild, intermediate and moderately selected domesticated forms. Our data point to a relative shift towards more selected types during the Roman period. Domestication of the grapevine appears to have been a slow process. This could result from the recurrent incorporation into cultivation of plants originating from sexual reproduction, when grape cultivation essentially relies on vegetative propagation.

DNA profiling of pineapple cultivars in Japan discriminated by SSR markers

We developed 18 polymorphic simple sequence repeat (SSR) markers in pineapple (Ananas comosus) by using genomic libraries enriched for GA and CA motifs. The markers were used to genotype 31 pineapple accessions, including seven cultivars and 11 breeding lines from Okinawa Prefecture, 12 foreign accessions and one from a related species. These SSR loci were highly polymorphic: the 31 accessions contained three to seven alleles per locus, with an average of 4.1. The values of expected heterozygosity ranged from 0.09 to 0.76, with an average of 0.52. All 31 accessions could be successfully differentiated by the 18 SSR markers, with the exception of 'N67-10' and 'Hawaiian Smooth Cayenne'. A single combination of three markers TsuAC004, TsuAC010 and TsuAC041, was enough to distinguish all accessions with one exception. A phenogram based on the SSR genotypes did not show any distinct groups, but it suggested that pineapples bred in Japan are genetically diversed. We reconfirmed the parentage of 14 pineapple accessions by comparing the SSR alleles at 17 SSR loci in each accession and its reported parents. The obtained information will contribute substantially to protecting plant breeders' rights.

A 48 SNP set for grapevine cultivar identification

BACKGROUND

Rapid and consistent genotyping is an important requirement for cultivar identification in many crop species. Among them grapevine cultivars have been the subject of multiple studies given the large number of synonyms and homonyms generated during many centuries of vegetative multiplication and exchange. Simple sequence repeat (SSR) markers have been preferred until now because of their high level of polymorphism, their codominant nature and their high profile repeatability. However, the rapid application of partial or complete genome sequencing approaches is identifying thousands of single nucleotide polymorphisms (SNP) that can be very useful for such purposes. Although SNP markers are bi-allelic, and therefore not as polymorphic as microsatellites, the high number of loci that can be multiplexed and the possibilities of automation as well as their highly repeatable results under any analytical procedure make them the future markers of choice for any type of genetic identification.

RESULTS

We analyzed over 300 SNP in the genome of grapevine using a re-sequencing strategy in a selection of 11 genotypes. Among the identified polymorphisms, we selected 48 SNP spread across all grapevine chromosomes with allele frequencies balanced enough as to provide sufficient information content for genetic identification in grapevine allowing for good genotyping success rate. Marker stability was tested in repeated analyses of a selected group of cultivars obtained worldwide to demonstrate their usefulness in genetic identification.

CONCLUSIONS

We have selected a set of 48 stable SNP markers with a high discrimination power and a uniform genome distribution (2-3 markers/chromosome), which is proposed as a standard set for grapevine (Vitis vinifera L.) genotyping. Any previous problems derived from microsatellite allele confusion between labs or the need to run reference cultivars to identify allele sizes disappear using this type of marker. Furthermore, because SNP markers are bi-allelic, allele identification and genotype naming are extremely simple and genotypes obtained with different equipments and by different laboratories are always fully comparable.

2-Methoxy-3-isobutylpyrazine in grape berries and its dependence on genotype

2-Methoxy-3-isobutylpyrazine (MIBP) contributes a bell pepper aroma to many grape cultivars and has a reported aroma threshold of ∼2 ng L(-1) in water. The purpose of this study was twofold: (1) develop a procedure using headspace solid phase micro-extraction combined with GC-MS in the selected ion monitoring mode (HS-SPME-GC-MS-SIM) for analysis of MIBP in grape berries, and (2) determine the location of MIBP biosynthesis in grapevines by approach grafting clusters of Vitis vinifera L. cvs Cabernet Sauvignon and Muscat blanc onto each other. The soluble solids and pH of the grape juice/homogenate matrix from different grape berry developmental stages influenced the method precision; therefore, quantification via the method of standard addition was used. Using our developed method, the limit of detection (LOD) and limit of quantitation (LOQ) of MIBP were 0.1 ng L(-1) and 2 ng L(-1), respectively, measured in a model juice and non-MIBP containing Chardonnay juice. Spiked recoveries averaged between 91% and 112% in Cabernet Sauvignon and Pinot noir homogenates and the overall relative standard deviation was less than 10%. The method was used to analyze MIBP in 29 grape cultivars and in fruit from clusters grafted to Cabernet Sauvignon or Muscat vines. Quantifiable levels were found only in Cabernet franc, Cabernet Sauvignon, Merlot, Sauvignon blanc and Semillon, providing information on the genetic connection for the occurrence of MIBP in grapes. No MIBP was detected in the berries of Muscat blanc clusters grafted onto Cabernet Sauvignon vines when sampled at fruit maturity. MIBP was detected in all berries of Cabernet Sauvignon regardless the graft configuration. The data indicate that MIBP or its precursors originate in the berry and its formation depends upon grape genotype.

The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin

A collection of 1005 grapevine accessions was genotyped at 34 microsatellite loci (SSR) with the aim of analysing genetic diversity and exploring parentages. The comparison of molecular profiles revealed 200 groups of synonymy. The removal of perfect synonyms reduced the database to 745 unique genotypes, on which population genetic parameters were calculated. The analysis of kinship uncovered 74 complete pedigrees, with both parents identified. Many of these parentages were not previously known and are of considerable historical interest, e.g. Chenin blanc (Sauvignon × Traminer rot), Covè (Harslevelu selfed), Incrocio Manzoni 2-14 and 2-15 (Cabernet franc × Prosecco), Lagrein (Schiava gentile × Teroldego), Malvasia nera of Bolzano (Perera × Schiava gentile), Manzoni moscato (Raboso veronese × Moscato d'Amburgo), Moscato violetto (Moscato bianco × Duraguzza), Muscat of Alexandria (Muscat blanc à petit grain × Axina de tres bias) and others. Statistical robustness of unexpected pedigrees was reinforced with the analysis of an additional 7-30 SSRs. Grouping the accessions by profile resulted in a weak correlation with their geographical origin and/or current area of cultivation, revealing a large admixture of local varieties with those most widely cultivated, as a result of ancient commerce and population flow. The SSRs with tri- to penta-nucleotide repeats adopted for the present study showed a great capacity for discriminating amongst accessions, with probabilities of identity by chance as low as 1.45 × 10(-27) and 9.35 × 10(-12) for unrelated and full sib individuals, respectively. A database of allele frequencies and SSR profiles of 32 reference cultivars are provided.

Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

Background

Cucumber, Cucumis sativus L. is an important vegetable crop worldwide. Until very recently, cucumber genetic and genomic resources, especially molecular markers, have been very limited, impeding progress of cucumber breeding efforts. Microsatellites are short tandemly repeated DNA sequences, which are frequently favored as genetic markers due to their high level of polymorphism and codominant inheritance. Data from previously characterized genomes has shown that these repeats vary in frequency, motif sequence, and genomic location across taxa. During the last year, the genomes of two cucumber genotypes were sequenced including the Chinese fresh market type inbred line '9930' and the North American pickling type inbred line 'Gy14'. These sequences provide a powerful tool for developing markers in a large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequences, representing 55% of its nuclear genome, and in cucumber EST sequences. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber.

Results

A total of 112,073 perfect repeats were detected in the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites in genomic DNA sequence, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length. Coding regions (ESTs) of the cucumber genome had fewer microsatellites compared to its genomic sequence, with trinucleotides predominating in EST sequences. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.

Conclusions

The cucumber genome is rich in microsatellites; AT and AAG are the most abundant repeat motifs in genomic and EST sequences of cucumber, respectively. Considering all the species investigated, some commonalities were noted, especially within the monocot and dicot groups, although the distribution of motifs and the frequency of certain repeats were characteristic of the species examined. The large number of SSR markers developed from this study should be a significant contribution to the cucurbit research community.

Parental relationships among three grape varieties studied by MALDI of grape seed protein profiles

Two Raboso cultivars, i.e. Raboso Veronese and Raboso Piave, are two black Vitis vinifera varieties. A genetic study suggested that Raboso Veronese is the progeny of a spontaneous cross between Raboso Piave and Marzemina Bianca cultivars. Parental relationships are usually investigated by genetic studies, which are effective to establish genetic links among different cultivars. Considering that proteome is the genome expression, in this article we evaluated the power of seed protein profiles obtained by matrix-assisted laser desorption/ionization (MALDI)/MS for parentage investigation. The three cultivars lead to very similar spectra with differences in the relative intensity of the most abundant species and the presence of very weak specific ions. In order to evaluate the analytical significance of these aspects, the variability due to instrumental factors and due to different harvesting areas and years of the same cultivars have been considered and measured by the calculation of discrepancy factor values. On one hand, the results obtained can be considered a valid confirmation of the genomic findings, whereas on the other hand, the results provide evidence for the ability of MALDI/MS to individuate minor differences in protein profiles of complex protein mixtures.

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

The process of vegetative propagation used to multiply grapevine varieties produces, in most cases, clones genetically identical to the parental plant. Nevertheless, spontaneous somatic mutations can occur in the regenerative cells that give rise to the clones, leading to consider varieties as populations of clones that conform to a panel of phenotypic traits. Using two sets of nuclear microsatellite markers, the present work aimed at evaluating and comparing the intravarietal genetic diversity within seven wine grape varieties: Cabernet franc, Cabernet Sauvignon, Chenin blanc, Grolleau, Pinot noir, Riesling, Savagnin, comprising a total number of 344 accessions of certified clones and introductions preserved in French repositories. Ten accessions resulted in being either self-progeny, possible offspring of the expected variety or misclassified varieties. Out of the 334 remaining accessions, 83 displayed genotypes different from the varietal reference, i.e., the microsatellite profile shared by the larger number of accessions. They showed a similarity value ranging from 0.923 to 0.992, and thus were considered as polymorphic monozygotic clones. The fraction of polymorphic clones ranged from 2 to 75% depending on the variety and the set of markers, the widest clonal diversity being observed within the Savagnin. Among the 83 polymorphic clones, 29 had unique genotype making them distinguishable; others were classified in 21 groups sharing the same genotype. All microsatellite markers were not equally efficient to show diversity within clone collections and a standard set of five microsatellite markers (VMC3a9, VMC5g7, VVS2, VVMD30, and VVMD 32) relevant to reveal clonal polymorphism is proposed.

Evolution and history of grapevine (Vitis vinifera) under domestication: new morphometric perspectives to understand seed domestication syndrome and reveal origins of ancient European cultivars

BACKGROUND AND AIMS

In spite of the abundance of archaeological, bio-archaeological, historical and genetic data, the origins, historical biogeography, identity of ancient grapevine cultivars and mechanisms of domestication are still largely unknown. Here, analysis of variation in seed morphology aims to provide accurate criteria for the discrimination between wild grapes and modern cultivars and to understand changes in functional traits in relation to the domestication process. This approach is also used to quantify the phenotypic diversity in the wild and cultivated compartments and to provide a starting point for comparing well-preserved archaeological material, in order to elucidate the history of grapevine varieties.

METHODS

Geometrical analysis (elliptic Fourier transform method) was applied to grapevine seed outlines from modern wild individuals, cultivars and well-preserved archaeological material from southern France, dating back to the first to second centuries.

KEY RESULTS AND CONCLUSIONS

Significant relationships between seed shape and taxonomic status, geographical origin (country or region) of accessions and parentage of varieties are highlighted, as previously noted based on genetic approaches. The combination of the analysis of modern reference material and well-preserved archaeological seeds provides original data about the history of ancient cultivated forms, some of them morphologically close to the current 'Clairette' and 'Mondeuse blanche' cultivars. Archaeobiological records seem to confirm the complexity of human contact, exchanges and migrations which spread grapevine cultivation in Europe and in Mediterranean areas, and argue in favour of the existence of local domestication in the Languedoc (southern France) region during Antiquity.

A multidisciplinary study of archaeological grape seeds

We report here the first integrated investigation of both ancient DNA and proteins in archaeobotanical samples: medieval grape (Vitis vinifera L.) seeds, preserved by anoxic waterlogging, from an early medieval (seventh–eighth century A.D.) Byzantine rural settlement in the Salento area (Lecce, Italy) and a late (fourteenth–fifteenth century A.D.) medieval site in York (England). Pyrolysis gas chromatography mass spectrometry documented good carbohydrate preservation, whilst amino acid analysis revealed approximately 90% loss of the original protein content. In the York sample, mass spectrometry-based sequencing identified several degraded ancient peptides. Nuclear microsatellite locus (VVS2, VVMD5, VVMD7, ZAG62 and ZAG79) analysis permitted a tentative comparison of the genetic profiles of both the ancient samples with the modern varieties. The ability to recover microsatellite DNA has potential to improve biomolecular analysis on ancient grape seeds from archaeological contexts. Although the investigation of five microsatellite loci cannot assign the ancient samples to any geographic region or modern cultivar, the results allow speculation that the material from York was not grown locally, whilst the remains from Supersano could represent a trace of contacts with the eastern Mediterranean.

Molecular and cellular mechanisms of diversity within grapevine varieties

A grapevine variety consists of an array of clones descended by vegetative propagation from a single selected vine grown from a single seedling. A majority of the clones within a variety are identical, but some can show divergent genotypes and, to some extent, divergent phenotypes. Polymorphism results mainly from somatic mutations that occur naturally during plant growth. Various types of mutations were shown to be responsible for genetic diversity among clones: point mutations, large deletions, illegitimate recombination or variable number of repeats in microsatellite sequences. In most cases, somatic mutations do not affect the whole plant; rather, they affect only one cell layer, leading to periclinal chimeras. Such structures do not threaten the plant's fitness and are stable through vegetative propagation. Occasionally, cellular rearrangements in the chimera lead to homogenization of the genotype of the whole plant. Through these molecular and cellular mechanisms, the genotypes of clones drift over time and grapevine varieties evolve.

Water deficit alters differentially metabolic pathways affecting important flavor and quality traits in grape berries of Cabernet Sauvignon and Chardonnay

BACKGROUND

Water deficit has significant effects on grape berry composition resulting in improved wine quality by the enhancement of color, flavors, or aromas. While some pathways or enzymes affected by water deficit have been identified, little is known about the global effects of water deficit on grape berry metabolism.

RESULTS

The effects of long-term, seasonal water deficit on berries of Cabernet Sauvignon, a red-wine grape, and Chardonnay, a white-wine grape were analyzed by integrated transcript and metabolite profiling. Over the course of berry development, the steady-state transcript abundance of approximately 6,000 Unigenes differed significantly between the cultivars and the irrigation treatments. Water deficit most affected the phenylpropanoid, ABA, isoprenoid, carotenoid, amino acid and fatty acid metabolic pathways. Targeted metabolites were profiled to confirm putative changes in specific metabolic pathways. Water deficit activated the expression of numerous transcripts associated with glutamate and proline biosynthesis and some committed steps of the phenylpropanoid pathway that increased anthocyanin concentrations in Cabernet Sauvignon. In Chardonnay, water deficit activated parts of the phenylpropanoid, energy, carotenoid and isoprenoid metabolic pathways that contribute to increased concentrations of antheraxanthin, flavonols and aroma volatiles. Water deficit affected the ABA metabolic pathway in both cultivars. Berry ABA concentrations were highly correlated with 9-cis-epoxycarotenoid dioxygenase (NCED1) transcript abundance, whereas the mRNA expression of other NCED genes and ABA catabolic and glycosylation processes were largely unaffected. Water deficit nearly doubled ABA concentrations within berries of Cabernet Sauvignon, whereas it decreased ABA in Chardonnay at véraison and shortly thereafter.

CONCLUSION

The metabolic responses of grapes to water deficit varied with the cultivar and fruit pigmentation. Chardonnay berries, which lack any significant anthocyanin content, exhibited increased photoprotection mechanisms under water deficit conditions. Water deficit increased ABA, proline, sugar and anthocyanin concentrations in Cabernet Sauvignon, but not Chardonnay berries, consistent with the hypothesis that ABA enhanced accumulation of these compounds. Water deficit increased the transcript abundance of lipoxygenase and hydroperoxide lyase in fatty metabolism, a pathway known to affect berry and wine aromas. These changes in metabolism have important impacts on berry flavor and quality characteristics. Several of these metabolites are known to contribute to increased human-health benefits.

Grape variety effect on proanthocyanidin composition and sensory perception of skin and seed tannin extracts from bordeaux wine grapes (Cabernet Sauvignon and Merlot) for two consecutive vintages (2006 and 2007)

Grape variety [Cabernet Sauvignon (CS) and Merlot (M)] effect on the proanthocyanidin composition and sensory perception of wine grapes from Bordeaux vineyards for two successive vintages (2006 and 2007) is reported. The flavan-3-ol monomers [(+)-catechin = C, (-)-epicatechin = EC, (-)-epicatechin-O-gallatte = ECG] and the proanthocyanidin oligomers [dimers B1, B2, B3, and B4 and trimer Cat-Cat-Epi (T)] in grape seed and skin tannin extracts were identified and quantified at harvest. Proanthocyanidin subunit compositions, percentage of galloylation (%G), and percentage of prodelphinidins (%P) as well as mean degree of polymerization (mDP) of the proanthocyanidin fraction were determined. Sensory analysis concerning the astringency and bitterness intensity of the proanthocyanidins of skin and seed tannin extracts was also performed. The results showed that proanthocyanidin composition can be greatly affected by grape variety. For both vintages between CS and M, significant differences were found on mDP (p < 0.05) in seed tannin extracts, whereas in skin tannin extracts, significant differences were observed for %G and %P (p < 0.05). Sensory analysis showed that grape variety influenced neither astringency nor bitterness intensity perception for both skin and seed tannin extracts for the two successive vintages studied. A positive correlation was found between astringency intensity, mDP, and B3 content in skin tannin extracts.

Gene pool variation and phylogenetic relationships of an indigenous northeast Italian grapevine collection revealed by nuclear and chloroplast SSRs

A germplasm safeguard programme was set up with 19 grapevine varieties considered as indigenous to northeastern Italy. To better estimate how genetic structure can be used to obtain a conservation perspective of local varieties, genetic variability was examined at 30 nuclear and 3 chloroplast polymorphic microsatellite loci in the native varieties plus 7 European cultivars taken as reference. The genetic profiles of all the cultivars were searched for possible parentage relationships and several suspected cases of the same variety having different names were investigated. The alleles shared at the loci suggest a parent-offspring relationship between Merlot and Cabernet Franc, 'Gruaja' and 'Negrara Veronese', and Marzemina Nera and Marzemina Bianca. Alleles at the 30 nuclear loci are consistent with Raboso Veronese being the progeny of Marzemina Bianca and Raboso Piave. Chloroplast-specific haplotypes were singled out for the first time in this indigenous germplasm and should be considered typical of the region. It is hypothesized that there are many specific haplotypes for the local varieties due to a past contribution of wild grapevine to the cultivated gene pool. The majority of investigated cultivars were demonstrated to constitute an independent source of genetic variation, and therefore a possible valuable resource of genetic traits for breeders.

A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping

BACKGROUND

Individual fingerprinting based on molecular markers has become a popular tool for studies of population genetics and analysis of genetic diversity in germplasm collections, including the solution of synonymy/homonymy and analysis of paternity and kinship. Genetic profiling of individuals is nowadays based on SSR (Simple Sequence Repeat) markers, which have a number of positive features that make them superior to any other molecular marker developed so far. In humans, SSRs with core repeats three to five nucleotides long are preferred because neighbour alleles are more easily separated and distinguished from each other; while in plants, SSRs with shorter repeats, namely two-nucleotides long, are still in use although they suffer lower separation of neighbour alleles and uncomfortable stuttering.

RESULTS

New microsatellite markers, containing tri-, tetra-, and penta-nucleotide repeats, were selected from a total of 26,962 perfect microsatellites in the genome sequence of nearly homozogous grapevine PN40024, assembled from reads covering 8.4 X genome equivalents. Long nucleotide repeats were selected for fingerprinting, as previously done in many species including humans. The new grape SSR markers were tested for their reproducibility and information content in a panel of 48 grape cultivars. Allelic segregation was tested in progenies derived from two controlled crosses.

CONCLUSION

A list of 38 markers with excellent quality of peaks, high power of discrimination, and uniform genome distribution (1-3 markers/chromosome), is proposed for grape genotyping. The reasons for exclusion are given for those that were discarded. The construction of marker-specific allelic ladders is also described, and their use is recommended to harmonise allelic calls and make the data obtained with different equipment and by different laboratories fully comparable.

A physical map of the heterozygous grapevine 'Cabernet Sauvignon' allows mapping candidate genes for disease resistance

BACKGROUND

Whole-genome physical maps facilitate genome sequencing, sequence assembly, mapping of candidate genes, and the design of targeted genetic markers. An automated protocol was used to construct a Vitis vinifera 'Cabernet Sauvignon' physical map. The quality of the result was addressed with regard to the effect of high heterozygosity on the accuracy of contig assembly. Its usefulness for the genome-wide mapping of genes for disease resistance, which is an important trait for grapevine, was then assessed.

RESULTS

The physical map included 29,727 BAC clones assembled into 1,770 contigs, spanning 715,684 kbp, and corresponding to 1.5-fold the genome size. Map inflation was due to high heterozygosity, which caused either the separation of allelic BACs in two different contigs, or local mis-assembly in contigs containing BACs from the two haplotypes. Genetic markers anchored 395 contigs or 255,476 kbp to chromosomes. The fully automated assembly and anchorage procedures were validated by BAC-by-BAC blast of the end sequences against the grape genome sequence, unveiling 7.3% of chimerical contigs. The distribution across the physical map of candidate genes for non-host and host resistance, and for defence signalling pathways was then studied. NBS-LRR and RLK genes for host resistance were found in 424 contigs, 133 of them (32%) were assigned to chromosomes, on which they are mostly organised in clusters. Non-host and defence signalling genes were found in 99 contigs dispersed without a discernable pattern across the genome.

CONCLUSION

Despite some limitations that interfere with the correct assembly of heterozygous clones into contigs, the 'Cabernet Sauvignon' physical map is a useful and reliable intermediary step between a genetic map and the genome sequence. This tool was successfully exploited for a quick mapping of complex families of genes, and it strengthened previous clues of co-localisation of major NBS-LRR clusters and disease resistance loci in grapevine.

Structural variability of Tvv1 grapevine retrotransposons can be caused by illegitimate recombination

Structural variability of Tvv1, a grapevine retrotransposon Ty1 copia-like family, was investigated within the grape genome and the canonical sequence of Tvv1 determined. Then, two remarkable elements, Tvv1-Delta3001 and Tvv1-Delta3640, which had suffered large deletions 3,001 bp and 3,460 bp in length of their coding sequences were compared to the canonical copy. In both deleted elements, the deletion breakpoint was characterized by a stretch 13 bp-long in Tvv1-Delta3001 and 11 bp-long in Tvv1-Delta3640 found duplicated in the canonical copy at each bound of the deleted regions. Tvv1-Delta3001 and Tvv1-Delta3460 were both shown to be unique copies fixed at a single locus in the grapevine genome. Their presence was very variable in a set of 58 varieties and wild vines. These elements have most likely been dispersed through natural intermixing after their initial insertion whose chronology was estimated. The model that we propose to explain the structure of Tvv1-Delta3001 and Tvv1-Delta3640, implies illegitimate recombination involving template switching between two RNA molecules co-packaged in the VLP prior to the integration of the deleted daughter copy into the host genome.