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Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analysing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from eastern North America: Vitis aestivalis, V. cinerea and V. riparia using different marker types. Vitis aestivalis and V. cinerea showed higher diversity than V. riparia. The two former species are less differentiated, confirming an earlier divergence of V. riparia. V. aestivalis and V. riparia exhibited different genetic groups on both sides of the Appalachian Mountains that could mirror different recolonization routes from southern refugia. Genetic structure was stronger in V. cinerea, for which two varieties (var. berlandieri and var. cinerea) are morphologically recognized. Our results confirm this distinction and suggest the existence of three other lineages within var. cinerea. These discontinuities appear linked to adaptation of var. berlandieri to dry and limy areas of Texas and partially to the Mississippi River Valley. Rapid range expansions from refugia upon climate warming are also suggested by the low linkage disequilibrium values observed. Furthermore, large variation for downy mildew resistance was observed in the three species. Our findings appeared consistent with the vegetation history of eastern North America.

To cope with the challenges facing agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennial species such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait loci in bi-parental crosses, we exploited a diversity panel of 279 Vitis vinifera L. cultivars planted in 5 blocks in the vineyard. This panel was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms by combining an 18K microarray and genotyping-by-sequencing. The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via genotyping-by-sequencing markedly increased the proportion of genetic variance explained by single nucleotide polymorphisms, and 2 multi-single nucleotide polymorphism models identified quantitative trait loci not found by a single nucleotide polymorphism-by-single nucleotide polymorphism model. Overall, 489 reliable quantitative trait loci were detected for 41% more response variables than by a single nucleotide polymorphism-by-single nucleotide polymorphism model with microarray-only single nucleotide polymorphisms, many new ones compared with the results from bi-parental crosses. A prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as quantitative trait locus and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application into breeding are discussed.

Breeding new cultivars is an important lever to cope with the various challenges facing viticulture. As a prerequisite, it is necessary to assess how much genetic variation is available for the traits of interest, and to understand their genetic architecture. To go beyond quantitative trait locus (QTL) mapping in biparental crosses, we exploited the panel of 279 cultivars capturing most of the genetic and phenotypic diversity of Vitis vinifera L. present within the French collection of genetic resources (INRA Vassal). This panel was planted in the vineyard in five randomized complete blocks and numerous traits (berry weight, cluster weight, length and compactness, organic acids, δ13C, polyphenols, etc.) were phenotyped over several years. In parallel, the panel was genotyped with the GrapeReSeq microarray as well as with restriction-assisted DNA sequencing. This allowed us to conduct a genome-wide association study per trait, either by testing each single-nucleotide polymorphism (SNP) separately or by modeling all SNPs jointly. Focusing here on berry weight, we showed that genotyping by sequencing provided enough SNPs to explain most of the genetic variance, and that, compared with SNP-by-SNP approaches, a multi-SNP statistical model led to a gain in power. Several significant associations were detected, some being new compared with the QTLs detected in biparental crosses. Future prospects include setting up an international consortium to plant the panel on various sites to help to decipher genotype-environment interactions.

To cope with the challenges faced by agriculture, speeding-up breeding programs is a worthy endeavor, especially for perennials such as grapevine, but requires understanding the genetic architecture of target traits. To go beyond the mapping of quantitative trait locus (QTL) in bi-parental crosses, we exploited a diverse panel of 279 Vitis vinifera L. cultivars. This panel planted in five blocks in the vineyard was phenotyped over several years for 127 traits including yield components, organic acids, aroma precursors, polyphenols, and a water stress indicator. The panel was genotyped for 63k single nucleotide polymorphisms (SNPs) by combining an 18K microarray and genotyping-by-sequencing (GBS). The experimental design allowed to reliably assess the genotypic values for most traits. Marker densification via GBS markedly increased the proportion of genetic variance explained by SNPs, and two multi-SNP models identified QTLs not found by a SNP-by-SNP model. Overall, 489 reliable QTLs were detected for 41% more response variables than by a SNP-by-SNP model with microarray-only SNPs, many new ones compared to the results from bi-parental crosses. Prediction accuracy higher than 0.42 was obtained for 50% of the response variables. Our overall approach as well as QTL and prediction results provide insights into the genetic architecture of target traits. New candidate genes and the application in breeding are discussed.

Double-stranded RNAs and total RNAs purified from grapevine (Vitis vinifera) phloem scrapings of two varieties held in the INRAE (France) grapevine germplasm collection were analyzed by high-throughput sequencing. BLAST annota-tion revealed contigs with homology to Polerovirus genus members. The full genome sequence of one isolate (KT) was determined (5651 nucleotides [nt]), and a partial sequence representing about half of the genome was assembled for a second isolate (KS) that was found to share 95% nt sequence identity with the KT isolate. The genome has a typical polerovirus organization, containing six open reading frames (ORFs) as well as a putative additional ORF3a. Based on genome organization and phylogenetic relationships, the new virus belongs to the genus Polerovirus but, similar to the recently described persimmon polerovirus 1, is characterized by a highly divergent coat-protein/readthrough domain. Considering the species demarcation criteria for the family Luteoviridae, these two isolates, together with a closely related sequence recently deposited in the GenBank database (LC507098), represent a new Polerovirus species for which the name “Grapevine polerovirus 1” is proposed.

To characterize their virome, double stranded RNAs extracted from scrapings of two Iranian grapevine varieties held in the Vassal-Montpellier Grapevine Biological Resources Center were analysed by high-throughput sequencing. In addition to several well-known grapevine viruses, divergent isolates of the newly described grapevine Kizil Sapak virus were identified in both accessions. Four complete genome sequences were determined, as well as two additional partial sequences (1,580 and 3,849 nucleotides long). These genomic sequences highlight the molecular diversity of this poorly known virus. In view of the absence of amplification of the GKSV isolates characterized here using the published primer pair, novel degenerate, polyvalent primers were designed, providing a more robust diagnosis.

International audience; Simon de Rojas Clemente y Rubio (1777 to 1827) is considered the father of modern ampelography. He developed the first scientific method for describing grapevine varieties through the examination of material he collected in Andalusia between 1802 and 1804. The Royal Botanical Garden in Madrid conserves the material he collected and preserved (leaves and shoots). This herbarium, the oldest of all grapevine variety herbaria, is invaluable for ampelographic and other studies (such as genetic diversity, molecular characterization, or viticultural history studies) and provides unique insight into early 19th century (the pre-phylloxera era) grapevine cultivation. The present work reports a DNA extraction protocol and a redefining of the simple sequence repeat primers routinely used in grapevine characterization, which allowed successful amplification of the ancient DNA extracted from Clemente's herborized material.

The Spanish botanist Simon de Rojas Clemente y Rubio (1777-1827) did the groundwork for modern ampelography, the discipline that focuses on the characterization of Vitis vinifera L. He developed his methods through the examination of material he himself collected in Andalusia in 1803-04. The material that Clemente herborized (leaves and shoots) is preserved among the collections held in the Royal Botanical Garden herbaria. Clemente's herbarium contains 186 specimens, all in an excellent state of preservation, and it is the world's oldest collection of herborized grapevine cultivars, as it was collected before the arrival of phylloxera in Spain. For these reasons, this herbarium is a remarkable source of information for the study of ancient grapevine cultivars and the history of ampelography and viticulture in general. Despite its clear relevance for research in viticulture, not much attention has been paid to it, and it had never been fully studied before. The present work reports the successful isolation and amplification of ancient nuclear DNA extracted from Clemente's herborized material, allowing the molecular identification of two cultivars.

International audience; Key message The maternal and paternal parentage of 36 rootstocks was determined and verified. The results of this study indicate that existing grape rootstocks are closely related to each other and have a narrow genetic background. Abstract Rootstocks are used to protect grapevines from biotic and abiotic stresses including phylloxera, nematodes, viruses, limestone-based soils, salinity and drought. The most important rootstocks were developed from three grape species between the 1890s and the 1930s in European breeding programs. In this report, we developed nuclear and chloroplast SSR fingerprint data from rootstock selections maintained in germplasm collections, compared them to develop a reference dataset, and carried out parentage analysis to resolve previously reported, and determine new, breeding records. We refined and updated the parentage of 26 rootstocks based on 21 nuclear and 14 chloroplast markers. Results indicate that 39% of the genetic background of analyzed rootstocks originated from only three accessions of three grape species: Vitis berlandieri cv. Resseguier 2, V. rupestris cv. du Lot and V. riparia cv. Gloire de Montpellier. Results determined that Resseguier 2 is the maternal parent for 14 commercial rootstocks, 9 of which are full-sibs with Gloire de Montpellier as the paternal parent. Similarly, du Lot is the paternal parent of nine rootstocks. The pedigree information for 28 rootstocks was determined or corrected in this study. The previously reported pedigree information for eight of the rootstocks was correct. The results found that the world's existing rootstocks have a narrow genetic base derived from only a few American grape species. Future rootstock breeding efforts should use a more diverse array of species to combat a changing climate and pest pressure.

VITIRAMA: A program to characterize disease susceptibility in French ampelographic collections. 12. International Conference on Grapevine Breeding and Genetics

Since 1997, many studies have been performed based on the inheritance of nuclear microsatellite markers to verify or uncover the parentage of several grapevine cultivars. The aim of the present study was to undertake an extended analysis using a large sample of Vitis vinifera cultivars held in the INRA ?Domaine de Vassal? Grape Germplasm Repository (F-34340 Marseillan-Plage, France). We genotyped 5,516 accessions with 20 nuclear SSR markers and checked their identity. The dataset of 2,332 single genotypes identified (without synonyms, clones and mutants) was analyzed using FaMoz software. Parentages showing a LOD score higher than 18 were validated in relation to historical data available. The parentage analysis first permitted the identification of 284 genotypes showing no direct relationship with any other cultivar in the collection. Second, in approx. 1,150 genotypes, only incomplete parentages could be determined due to the absence of complementary parents in the cultivar sample. Last, the full-parentage of approx. 700 genotypes was revealed resulting in i) confirmations of the pedigree as stated by the breeder (180) or in previously published studies (80), ii) partial or complete invalidations of published pedigree (90), or iii) original discoveries (390). Compiling these parentage results improves our knowledge of the genetic constitution of the population of V. vinifera cultivars and the identification of the main genitors involved in varietal assortment evolution and grapevine breeding.

16 pages; International audience; tUnderstanding differences in phenology for varieties of a given species is important for making informeddecisions on variety choice in the context of climate change and breeding new cultivars. Phenologicalmodels that incorporate temperature as a key environmental factor can be used to describe the differencesin phenological timing between cultivars. This paper outlines a methodology, based on a phenologicalmodel, for classifying the timing of flowering and veraison for a substantial number of varieties of thegrapevine (Vitis vinifera L.). 95 varieties were characterized for flowering and 104 varieties for veraison.Various statistical measures were used to assess the performance and predictions of the model at thevarietal level: model efficiency, root mean squared error and confidence intervals. The methodologymight be used to understand varietal differences for other species in future studies. Model outputs canbe used in combination with predicted climate change scenarios to assess the suitability of varietiesunder climate conditions of the future.

Afin de contribuer au developpement des connaissances sur lepatrimoine ampelographique et les ressources genetiques viticoles de la Grece, nous avons caracterise la vigne dite “de Pausanias” au niveau ampelographique et moleculaire. Cette vigne se trouve dans le centre du Peloponnese (village de Pagrati, Prefecture d’Achaia). Elle est denommee et repertoriee sous le nom de “Vigne de Pausanias”, geographe grec du iie siecle apres J.-C., meme si son origine et son âge reel ne sont pas veritablement connus. Les resultats des analyses montrent qu’il ne s’agit pas d’unancien cepage grec mais d’une lambrusque (Vitis vinifera subsp. sylvestris), dont la specificite reside dans le fait que la souche s’est maintenue naturellement depuis tres longtemps, et vraisemblablement depuis plusieurs siecles, sans intervention humaine particuliere. A cet egard, et par son developpement spectaculaire, c’est certainement un exemplaire unique et tout a fait exceptionnel.

Two new datasets were created for the evaluation of plant varieties recognition.An experimental study was conducted with today's best performing techniques.Recognizing rice seeds variety appears to be feasible in controlled environment.Recognizing grape varieties from their leaves is still an open problem.Results show that convolutional neural networks perform the best on such problems. This paper addresses the problem of categorizing plant images at the variety level, i.e. at a finer taxonomic grain than state-of-the-art studies usually working at the species level. It therefore introduces two new evaluation datasets of agro-biodiversity interest, each being related to concrete scenarios on large-scale plant resources. They have been chosen so as to involve very different acquisition protocols and visual patterns in order to evaluate if state-of-the-art image classification techniques can generalize to such specific contexts and avoid the cost of building specific ad-hoc solutions. The first one is a collection of 2071 pictures of loose rice seeds built from 95 accessions kept in a bank of seeds. The second one is a collection of 2037 pictures of grape leaves taken in the fields and belonging to 34 varieties among the most commonly ones used in viticulture. Both datasets exhibit a very low inter-class variability resulting in two challenging fine-grained classification tasks, even for expert human operators. A baseline experimental study was conducted on the two datasets using the two most effective families of classification techniques in the state-of-the-art, i.e. convolutional neural networks on one side and fisher vectors-based discriminant models on the other side. It shows that the achieved classification performance is very different between the two problems. It is actually pretty bad for the grape leaves collection but much better in the case of the rice seeds collection for which the acquisition protocol was much more constrained and the morphological variability more visible. The conclusion is that automatically identifying plant varieties might already be feasible for some specific scenarios and in controlled environments but that it is still an open problem in the general case.

Currently, many monovarietal vineyards present a minority of mixed cultivars. Some of these cultivars are unknown and could represent an opportunity to discover new and potentially useful genotypes both for research and production purposes. In a ‘Carmenere’ vineyard planted in 1994 in Palmilla (Colchagua Valley, Chile), a minority presence of other cultivars was found. The present work covers for the first time the identification and characterization of one of these cultivars, which presented a very poor fruit set. Through classic ampelography, it was not possible to associate the studied cultivar with any known cultivar in Chile. However, through a simple sequence repeats (SSR) comparison against the database of the INRA Germplasm Repository “Domaine de Vassal” in France, the cultivar was identified as a triploid accession named ‘Folle Blanche Faux’ ( Vitis vinifera L.) that was previously found in Chile during the season of 1950-1951. This cultivar presents earlier bud breaking than ‘Carmenere’, has morphologically complete flowers, and shows a physiological disorder around the fruit set, leading to partial or complete bunch necrosis under the environmental conditions of Palmilla. This cultivar contributes to the genotypic richness present in Chile and might be an interesting tool for physiological and molecular studies. It also could become productive under other environmental conditions (i.e., environmental conditions that favor a good fruit set) or by the application of adequate vineyard practices, such as cane girdling at bloom time. Actualmente, muchos vinedos monovarietales presentan mezclas de otros cultivares en proporciones menores. Algunos de estos cultivares son desconocidos y podrian representar una oportunidad para descubrir genotipos nuevos y potencialmente utiles en investigacion y/o produccion. En un vinedo cv. ‘Carmenere’, plantado en 1994 en la comuna de Palmilla (Valle de Colchagua, Chile), se determino la presencia minoritaria de otros cultivares. El presente trabajo cubre por primera vez la identificacion y caracterizacion de uno de estos cultivares, el cual presento una muy pobre fructificacion. A traves de ampelografia clasica, no fue posible asociar el cultivar en estudio a ningun cultivar conocido en Chile. Sin embargo, a traves de una comparacion de marcadores moleculares microsatelites con la base de datos del Repositorio de Germoplasma de Vid del INRA “Domaine de Vassal” en Francia, fue identificado como un acceso triploide llamado ‘Folle Blanche Faux’ ( Vitis vinifera L.), el cual habia sido descubierto en Chile previamente durante la temporada 1950-1951. Este cultivar presenta una brotacion mas precoz que la del cv. ‘Carmenere’, posee flores morfologicamente completas y muestra un notorio desorden fisiologico en su fructificacion, el cual se manifiesta a traves de una necrosis de racimo parcial o completa, bajo las condiciones ambientales de Palmilla. Este cultivar contribuye a la riqueza genotipica presente en Chile y eventualmente podria llegar a ser una herramienta interesante para estudios fisiologicos y moleculares. Adicionalmente, podria volverse productiva bajo otras condiciones ambientales ( i.e. condiciones ambientales que favorezcan una buena cuaja frutal) o por la aplicacion de practicas viticolas adecuadas, como el anillamiento de cargadores durante la floracion.

We propose here a decision support system for vine growers to assess the quality of a vineyard to be planted. The quality of a vineyard is defined by the probability of possible profitability of the wine sales he is able to produce. The model, based on a Bayesian network (BN), takes into account environment and the parameters defining vineyard status with their associated interactions. BN are widely used for knowledge representation and reasoning under uncertainty in natural resource management. There is a rising interest in BN as tools for ecological and agronomic modelling. Data were collected from knowledge of vine-growing experts. We developed a C# computer program predicting the likely quality of a vineyard. The model has been validated on existing vineyards with prediction ability around 75 %. This system should ease assessments of the likely impact of the choices and decisions of vine growers on the quality of new vineyards to be planted in any part of the world. No such model has been developed before for vine growers.

Une discussion entre les reviewers a donné lieu à une publication (The requested discussion paper has a corresponding peer-reviewed final revised paper.) :Yiou, P. (Auteur de correspondance), Garcia De Cortazar Atauri, I., Chuine, I., Daux, V., Garnier, E., Viovy, N., Van Leeuwen, C., Parker, A., Boursiquot, J.-M. (2011). Continental atmospheric circulation over Europe during Little Ice Age inferred from grape harvest dates. Discussions. Climate of the past, 7 (5), 3023-3048. DOI : 10.5194/cpd-7-3023-2011; Estimates of climate conditions before the 19th century are based on proxy data reconstructions or sparse meteorological measurements. The reconstruction of the atmospheric circulation that prevailed during the European Little Ice Age (∼1500–1850) has fostered many efforts. This study illustrates a methodology, combining historical proxies and modern datasets to obtain detailed information on the atmospheric circulation that prevailed over the North Atlantic region during the Little Ice Age. We used reconstructions of temperature gradients over France based on grape harvest dates to infer the atmospheric circulation. We found that blocking situations were more likely in summer, inducing a continental atmospheric flow. This study advocates that the reconstructions of the past atmospheric circulation should take this regime into account.

Aim : Vitis subg. Vitis provides an example of a plant disjunction occurring in the Northern Hemisphere. It shows broad morphological variation but is assumed to be a species complex with limited genetic differentiation. Based on a comprehensive sampling of taxa and polymorphism in both chloroplast and nuclear DNA, we assessed genetic variation within this subgenus. Our aims were to clarify the relationships among species and to examine their historical biogeography. Location: Asia, Europe, North America. Methods: We analysed a total of 30 species and putative hybrids from subgenus Vitis and examined the infra-specific variation in some species. Polymorphism in chloroplast DNA was assessed in trnL and trnH-psbA-trnK sequences (c. 2170 bp) and in 15 microsatellite loci. We also obtained nuclear data for size variation at 24 microsatellite loci. Phylogenetic inference was performed with Bayesian analyses. A maximum parsimony network was constructed to depict the evolutionary relationships among haplotypes, and microsatellite data were also subjected to hierarchical clustering analysis using the Ward distance. In addition, we assessed size homoplasy by sequencing both chloroplast and nuclear microsatellite loci. Results Chloroplast polymorphisms resolved subgenus Vitis as a monophyletic group with limited genetic variation. The ancestral haplotypes were found in Eurasia. American taxa all harboured derived haplotypes. Most of them formed a monophyletic group that did not include Vitis californica. The four main haplotypes in Vitis vinifera corresponded to two different origins. Nuclear microsatellites indicated that genetic variation was especially large in North America. Asian species exhibited a lower level of nuclear divergence and the European V. vinifera corresponded to a differentiated nuclear lineage. Main conclusions: We obtained some evidence that subgenus Vitis has an Asian origin and then dispersed to Europe and North America. Geographic separation was followed by diversification, presumably during the Pleistocene, resulting in phylogeographic patterns similar to other biota. In contrast to chloroplast DNA, nuclear DNA shows a larger than expected genetic variation. Our molecular data also highlight the need to re-examine certain aspects of the current subgeneric classification

[An assessment of error sources when using grape harvest date for past climate reconstruction]; Several studies have used grape harvest date (GHD) as a proxy for temperature variations of the last centuries in Europe. However, the use of grape harvest dates to reconstruct climate is not straightforward, with four possible causes of major flaws. In this study we identify and evaluate the accuracy of GHD as a proxy to past temperature anomalies, uncertainties in the model used to relate temperature to GHD, identity of the grape varieties cultivated in the past, type of wine produced in the past and cultural practices used in the past. Our analyses are based on several phenological and crop models, and on the most complete data set on grape vine phenology and harvest quality. We show that the two methodologies currently used — linear regression models and process-based phenological models — can be accurate, but process-based phenological models ascertain robustness to be applied confidently in different vineyards and different periods. However, we show that several factors can induce a bias in temperature reconstructions using process-based models. We demonstrate the importance of historical information on the studied areas such as the varieties cultivated, the style of wine produced, the quality sought, the agricultural practices, in order to build the most robust model.

ADDITIONAL INDEX WORDS. ampelography, microsatellite, pedigree, genetic structure, Vitis vinifera ABSTRACT. Genetic structuring and parentage analysis were performed on a very large database comprising 2786 unique multilocus genotypes (20 nuclear simple sequence repeats (nSSRs)) of Vitis vinifera L. ssp. sativa (DC.) Hegi with a special focus on Tuscan cultivars to reveal the parentage and history of the cultivar Sangiovese, the most important cultivar of Italy. For this cultivar, the authors also analyzed clones and synonyms, investigating its genetic origin and intracultivar diversity. Known synonyms of 'Sangiovese' were confirmed and new ones were revealed with cultivars outside Tuscany. Some synonyms were invalidated, and unexpected homonyms were identified. The absence of true intracultivar variability leads to the rejection of a polyclonal origin for 'Sangiovese'. The existence of an Italian genetic pool composed of ancient cultivars including Sangiovese was demonstrated by analyzing the entire set of 2786 cultivars. Ten individuals compose the kin group of 'Sangiovese', including two offspring: 'Ciliegiolo' and 'Catarratto bianco faux'. Despite the large presence and long history of 'Sangiovese' in the Tyrrenian area, its kin group is unexpectedly composed of a majority of ancient cultivars that are largely diffused in far southern Italy, which leads to the hypothesis of a Sicilian origin for 'Sangiovese'. Analysis of the Tuscan pool revealed large kin groups for cultivars Mammolo and Garganega, demonstrating their contribution to the genetic diversification in the Tyrrenian area. This work contributes to the understanding of grapevine diversification, evolution, and history in Italy and Europe.

222 cultivated (Vitis vinifera) and 22 wild (V. vinifera ssp. sylvestris) grape accessions were analysed for genetic diversity and differentiation at eight microsatellite loci. A total of 94 alleles were detected, with extensive polymorphism among the accessions. Multivariate relationships among accessions revealed 16 genetic groups structured into three clusters, supporting the classical eco-geographic grouping of grape cultivars: occidentalis, pontica and orientalis. French cultivars appeared to be distinct and showed close affinity to the wild progenitor, ssp. sylvestris from south-western France (Pyrenees) and Tunisia, probably reflecting the origin and domestication history of many of the old wine cultivars from France. There was appreciable level of differentiation between table and wine grape cultivars, and the Muscat types were somewhat distinct within the wine grapes. Contingency χ2 analysis indicated significant heterogeneity in allele frequencies among groups at all loci. The observed heterozygosities for different groups ranged from 0·625 to 0·9 with an overall average of 0·771. Genetic relationships among groups suggested hierarchical differentiation within cultivated grape. The gene diversity analysis indicated narrow divergence among groups and that most variation was found within groups (∼85%). Partitioning of diversity suggested that the remaining variation is somewhat structured hierarchically at different levels of differentiation. The overall organization of genetic diversity suggests that the germplasm of cultivated grape represents a single complex gene pool and that its structure is determined by strong artificial selection and a vegetative mode of reproduction.

In total, 25 clones of Vitis vinifera 'Pinot noir' and 22 clones of 'Chardonnay' were analyzed with 100 microsatellite markers, selected from an initial screening of 228 markers. Of the 100 markers, 17 detected polymorphism within one or both of the cultivars. In 'Pinot noir', 15 polymorphic markers detected 15 different genotypes, uniquely distinguished 12 clones out of the 25 and separated the remaining 13 clones into 3 groups. In 'Chardonnay', 9 polymorphic markers detected 9 genotypes and uniquely distinguished 6 clones out of the 22. The remaining 16 clones were separated into 3 groups. For markers that were polymorphic in 'Pinot noir' and 'Chardonnay', none of the variant alleles were common to both cultivars. It is inferred from this result that the natural cross that produced 'Chardonnay' probably occurred when 'Pinot' was still relatively young. Many of the variant genotypes were expressed as three alleles. Further analysis revealed the presence of chimeras in which the third allele was present in leaf but not root or wood tissues, confirming that the grape apical meristem is functionally two-layered. Some clones that share the same microsatellite genotype are documented to have originated in the same locality, suggesting that the origins of undocumented clones may be traced by comparing their microsatellite genotypes with those of well-documented clones. Because clones of 'Pinot noir' and 'Chardonnay' are often visually indistinguishable, microsatellite genotyping may also be useful to detect identification errors in collections and nurseries. Because winemakers have strong preferences for certain clones, it has become increasingly important to be able to identify them. Morphological differences between clones are slight at best and are often obscured by environmental variables and cultural practices. An objective means by which to distinguish them has long been sought.

Fernandez, Lucie et al., [Background] Interaction between TERMINAL FLOWER 1 (TFL1) and LEAFY (LFY) seem to determine the inflorescence architecture in Arabidopsis. In a parallel way, overexpression of VvTFL1A, a grapevine TFL1 homolog, causes delayed flowering and production of a ramose cluster in the reiterated reproductive meristem (RRM) somatic variant of cultivar Carignan. To analyze the possible contribution of this gene to cluster phenotypic variation in a diversity panel of cultivated grapevine (Vitis vinifera L. subsp. vinifera) its nucleotide diversity was characterized and association analyses among detected sequence polymorphisms and phenology and cluster traits was carried out., [Results] A total of 3.6 kb of the VvTFL1A gene, including its promoter, was sequenced in a core collection of 140 individuals designed to maximize phenotypic variation at agronomical relevant traits. Nucleotide variation for VvTFL1A within this collection was higher in the promoter and intron sequences than in the exon regions; where few polymorphisms were located in agreement with a high conservation of coding sequence. Characterization of the VvTFL1A haplotype network identified three major haplogroups, consistent with the geographic origins and the use of the cultivars that could correspond to three major ancestral alleles or evolutionary branches, based on the existence of mutations in linkage disequilibrium. Genetic association studies with cluster traits revealed the presence of major INDEL polymorphisms, explaining 16%, 13% and 25% of flowering time, cluster width and berry weight, respectively, and also structuring the three haplogroups., [Conclusions] At least three major VvTFL1A haplogroups are present in cultivated grapevines, which are defined by the presence of three main polymorphism LD blocks and associated to characteristic phenotypic values for flowering time, cluster width and berry size. Phenotypic differences between haplogroups are consistent with differences observed between Eastern and Western grapevine cultivars and could result from the use of different genetic pools in the domestication process as well as different selection pressures on the development of table and wine cultivars, respectively. Altogether, these results are coherent with previous classifications of grapevine phenotypic diversity mainly based on cluster and berry morphotypes as well as with recent results on the structure of genetic diversity in cultivated grapevine. © 2014 Fernandez et al., This work was funded by grant BIO2008-03892 and BIO2011-026229 from the MICINN and MINECO of Spain to JMM-Z. Networking activities were also funded by COST Action FA1003 “East–west Collaboration for Grapevine Diversity Exploration and Mobilization of Adaptive Traits for Breeding”. JT was recipient of a fellowship from the MICINN.

Grapevines were propagated from cuttings up until the late 19th century when the soil-borne aphid phylloxera (Daktulosphaira vitifoliae [Fitch]) destroyed Vitis vinifera L. vines grown on their own roots. The damaging import of grape phylloxera to France in 1868 led to extensive international research and collaboration to save European viticulture. Numerous growers, breeders and scientists played important roles in the historic campaign against the grape phylloxera and in finding the solution to this problem, which ultimately lay in grafting European vines on American rootstocks. Nowadays, more than 80% of the vineyards worldwide use grafted plants: a scion of V. vinifera grafted onto a rootstock of single American Vitis species or interspecific hybrids of Vitis species that combine desirable features of their parentage. The majority of rootstocks used today were bred at the end of the 19th century or at the turn of the 20th century. They are mainly hybrids of four species: V. berlandieri, V. riparia, V. rupestris and V. vinifera, but secondary species have also been used. In addition to phylloxera, rootstocks contribute to the control of other soil-borne pests such as nematodes and to various abiotic constraints such as drought, salinity, limestone and mineral nutrition problems. They also strongly interact with scion genotypes and modify whole plant development, biomass accumulation and repartition, and phenology. In the context of climate change, they may be considered as a key element of adaptation. Rootstock breeding programs in the main grape growing countries around the world aim to improve pest resistance and adaptation to abiotic stresses. This article will give an overview of the history of rootstock use in the world, a brief description of the main rootstocks cultivated and some details on current breeding programs.

UMR AGAP - Equipe Diversité, Adaptation et Amélioration de la Vigne; The study of accessions from Argentina may provide a valuable testimony on the origins of thedifferent genetic resources and varieties which were sought and used to develop the vineyard of this country. 54accessions introduced in the Vassal collection were analyzed using 20 microsatellite markers and ampelographicdescriptors. Among them, 43 distinct varieties have been identified: 22 correspond to old traditional wine ortable grape varieties from Europe and Middle East, 12 are probably varieties selected in Argentina or SouthAmerica and are mostly descendants of Muscat of Alexandria and Mission, 4 are seedlings obtained in Italy,USA and Bulgaria, 2 are specific mutants and 3 are still currently original and of undetermined origin. Theseresults highlight the links and help to trace the flows that have existed between the ancient world and Argentina.They are a particularly good example of the interest of the 2 traditional ways of multiplication which may existfor the vine, cuttings and seedlings. Some of these resources are now also highly original and rare and must bepreserved

All protocols for Next Generation Sequencers (NGS) start with the preparation of a DNA library from extracted DNA. Quality, number, and length of the sequences produced by NGS all depend on the quality of the library that was prepared, itself dependent on the DNA quality. Generally, when using NGS, one would wish to obtain the genomic information contained in the nucleus without an excessive proportion of cytoplasmic DNA. Multiple copies of cytoplasmic genomes are present in every cell (11 to 70 copies, depending on the developmental stage and/or physiological status) ( Tymms et al., 1983 ). The chloroplast DNA of plants, therefore, represents 17 - 23% of their total DNA ( Boffey and Leech, 1982 ). In this study, we developed a protocol that strongly reduces the amount of cytoplasmic DNA. The improvement in quality makes the method perfectly adapted to library construction for NGS. We applied this extraction method to the grapevine ( Vitis vinifera L.) and coffee tree ( Coffea canephora Pierre ex A. Froehner). These species are known to contain many secondary metabolites, which can generate diffi culties for DNA extraction ( Peterson et al., 1997 ; Mattivi et al., 2006 ). To establish the protocol, we were partially inspired by a classic protocol for nuclear DNA plant extraction destined for the construction of BAC (Bacterial Artifi cial Chromosome) libraries ( Peterson et al., 1997 ). The two stages of the protocol are: (i) isolation of nuclei and (ii) nuclear DNA extraction. Nuclear DNA obtained with this protocol was then sequenced using 454/GS-FLX technology (Roche, Basel, Switzerland) with the Titanium kit. All protocols for Next Generation Sequencers (NGS) start with the preparation of a DNA library from extracted DNA. Quality, number, and length of the sequences produced by NGS all depend on the quality of the library that was prepared, itself dependent on the DNA quality. Generally, when using NGS, one would wish to obtain the genomic information contained in the nucleus without an excessive proportion of cytoplasmic DNA. Multiple copies of cytoplasmic genomes are present in every cell (11 to 70 copies, depending on the developmental stage and/or physiological status) ( Tymms et al., 1983 ). The chloroplast DNA of plants, therefore, represents 17 - 23% of their total DNA ( Boffey and Leech, 1982 ). In this study, we developed a protocol that strongly reduces the amount of cytoplasmic DNA. The improvement in quality makes the method perfectly adapted to library construction for NGS. We applied this extraction method to the grapevine ( Vitis vinifera L.) and coffee tree ( Coffea canephora Pierre ex A. Froehner). These species are known to contain many secondary metabolites, which can generate diffi culties for DNA extraction ( Peterson et al., 1997 ; Mattivi et al., 2006 ). To establish the protocol, we were partially inspired by a classic protocol for nuclear DNA plant extraction destined for the construction of BAC (Bacterial Artifi cial Chromosome) libraries ( Peterson et al., 1997 ). The two stages of the protocol are: (i) isolation of nuclei and (ii) nuclear DNA extraction. Nuclear DNA obtained with this protocol was then sequenced using 454/GS-FLX technology (Roche, Basel, Switzerland) with the Titanium kit.

`Albariño' (Vitis vinifera L.) is an important grape cultivar in Spain, morphologically diverse but subject to much misnaming. The objectives of the present work were to correct some of the more common misnamings concerning `Albariño' and to evaluate the genetic variability within this cultivar by analyzing DNA polymorphisms using randomly amplified polymorphic DNA (RAPD) markers and microsatellite techniques. Several accessions of `Albariño' (16 accessions from Misión Biológica de Galicia, one accession from El Encin, one accession from Rancho de la Merced), related cultivars (`Alvarinho', `Caíño blanco', `Cainho branco', `Loureiro'), and cultivars presumably identical to misnomers (`Savagnin blanc' and `Gewürztraminer') were analyzed using 20 RAPD markers and six microsatellite loci. Both techniques revealed polymorphism among `Albariño', `Caíño blanco', `Albariño' from Rancho de la Merced and `Loureiro'. No polymorphism was detected among the 16 `Albariño' accessions from Galicia, the `Albariño' accession from El Encin and `Alvarinho', nor among the `Albariño' accession from Rancho de la Merced, `Savagnin blanc' and `Gewürztraminer', nor between `Caíño blanco' and `Cainho branco'. These results enabled us to clarify the main misnomers concerning these cultivars. The absence of polymorphism among the true `Albariño' accessions did not allow the detection of any clonal variation. The suitability of both techniques for defining the cultivar level for grapevine is discussed.

To obtain a broader variability of the Grenache N grapevine, somaclones were produced from anther calli and placed in two different environments: a poor sandy soil (Espiguette) and a richer silty clay soil (Chapitre). To evaluate the observed variations at the foliage level, an ampelometric study was conducted over three consecutive years. Various biometrical analyses revealed that (i) leaf size varies in relationship with the environment: in the poor soil, leaves are smaller than in the rich soil for the control clone as well as the somaclones; (ii) whatever the environment, indentation is deeper in somaclone leaves than in control leaves, even 10 years after outplanting; (iii) some somaclones with deeply or barely indented leaves have a more stable behaviour, while others have a leaf morphology changing with the year and the environment; (iv) leaf indentation parameters defined by the authors allow for a fairly good characterization among somaclones and control: indentation index X5, (S1 + S2)/(L + L1), appears to have the highest discrimination potential; vein length and angle parameters do not allow for discrimination. Representation of the somaclones based on a "theoretical leaf", obtained from the different measurements, gives interesting supplementary information for the interpretation of the results. Principal component analysis leads to more information on the parameters as well as on individuals. This method was therefore retained for further analyses. In conclusion, this study shows that before commercial introduction of a somaclone, one must ensure that the morphology always corresponds to the grapevine type. Key words: in vitro, somatic embryos, variability, morphology, indenting, principal component analysis, discriminant analysis. [Journal translation]

Background - Grapevine (Vitis vinifera subsp. vinifera) is one of the most important and ancient horticultural plants in the world. Domesticated about 8--10,000 years ago in the Eurasian region, grapevine evolved from its wild relative (V. vinifera subsp. sylvestris) into very diverse and heterozygous cultivated forms. In this work we study grapevine genetic structure in a large sample of cultivated varieties, to interpret the wide diversity at morphological and molecular levels and link it to cultivars utilization, putative geographic origin and historical events. Results - We analyzed the genetic structure of cultivated grapevine using a dataset of 2,096 multi-locus genotypes defined by 20 microsatellite markers. We used the Bayesian approach implemented in the STRUCTURE program and a hierarchical clustering procedure based on Ward's method to assign individuals to sub-groups. The analysis revealed three main genetic groups defined by human use and geographic origin: a) wine cultivars from western regions, b) wine cultivars from the Balkans and East Europe, and c) a group mainly composed of table grape cultivars from Eastern Mediterranean, Caucasus, Middle and Far East countries. A second structure level revealed two additional groups, a geographic group from the Iberian Peninsula and Maghreb, and a group comprising table grapes of recent origins from Italy and Central Europe. A large number of admixed genotypes were also identified. Structure clusters regrouped together a large proportion of family-related genotypes. In addition, Ward's method revealed a third level of structure, corresponding either to limited geographic areas, to particular grape use or to family groups created through artificial selection and breeding. Conclusions - This study provides evidence that the cultivated compartment of Vitis vinifera L. is genetically structured. Genetic relatedness of cultivars has been shaped mostly by human uses, in combination with a geographical effect. The finding of a large portion of admixed genotypes may be the trace of both large human-mediated exchanges between grape-growing regions throughout history and recent breeding.

Background Cultivated grapevines, Vitis vinifera subsp. sativa, evolved from their wild relative, V. vinifera subsp. sylvestris. They were domesticated in Central Asia in the absence of the powdery mildew fungus, Erysiphe necator, which is thought to have originated in North America. However, powdery mildew resistance has previously been discovered in two Central Asian cultivars and in Chinese Vitis species. Results A set of 380 unique genotypes were evaluated with data generated from 34 simple sequence repeat (SSR) markers. The set included 306 V. vinifera cultivars, 40 accessions of V. vinifera subsp. sylvestris, and 34 accessions of Vitis species from northern Pakistan, Afghanistan and China. Based on the presence of four SSR alleles previously identified as linked to the powdery mildew resistance locus, Ren1, 10 new mildew resistant genotypes were identified in the test set: eight were V. vinifera cultivars and two were V. vinifera subsp. sylvestris based on flower and seed morphology. Sequence comparison of a 620 bp region that includes the Ren1-linked allele (143 bp) of the co-segregating SSR marker SC8-0071-014, revealed that the ten newly identified genotypes have sequences that are essentially identical to the previously identified mildew resistant V. vinifera cultivars: ‘Kishmish vatkana’ and ‘Karadzhandal’. Kinship analysis determined that three of the newly identified powdery mildew resistant accessions had a relationship with ‘Kishmish vatkana’ and ‘Karadzhandal’, and that six were not related to any other accession in this study set. Clustering procedures assigned accessions into three groups: 1) Chinese species; 2) a mixed group of cultivated and wild V. vinifera; and 3) table grape cultivars, including nine of the powdery mildew resistant accessions. Gene flow was detected among the groups. Conclusions This study provides evidence that powdery mildew resistance is present in V. vinifera subsp. sylvestris, the dioecious wild progenitor of the cultivated grape. Four first-degree parent progeny relationships were discovered among the hermaphroditic powdery mildew resistant cultivars, supporting the existence of intentional grape breeding efforts. Although several Chinese grape species are resistant to powdery mildew, no direct genetic link to the resistance found in V. vinifera could be established.

Twenty highly polymorphic nuclear microsatellite markers were used to assess genetic relationships among 181 grapevine accessions traditionally grown in different geographical region of the species’ range and 21 wild Tunisian samples. A total of 330 alleles were detected and extensive genetic polymorphisms were recorded either in the cultivated or in the wild compartment. A genetic structure according to accessions taxonomic status and cultivars geographical origin was revealed by multivariate analysis and F st values. However, a considerable overlap was observed in the majority of distinguished groups. The highest level of differentiation between wild and cultivated accessions is recorded between Tunisian wild accessions and North African cultivars which are confirmed by multivariate analysis. Thus the occurrence of local domestication event of grapevines in the North African region is unlikely. North African cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced probably from East region or derived from crosses between them. A genetic affinity between wild gene pool and cultivars of West Europe was brought to light by multivariate and F st analysis. Pattern structure of genetic diversity in the analyzed material presents an additional proof of the occurrence of secondary grapevine domestication events in West Europe region which contributed to the evolution of the species, a hypothesis supported by recent archeobiological and molecular studies.

Chantier qualité GA; 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.

Background Stenospermocarpy is a mechanism through which certain genotypes of Vitis vinifera L. such as Sultanina produce berries with seeds reduced in size. Stenospermocarpy has not yet been characterized at the molecular level. Results Genetic and physical maps were integrated with the public genomic sequence of Vitis vinifera L. to improve QTL analysis for seedlessness and berry size in experimental progeny derived from a cross of two seedless genotypes. Major QTLs co-positioning for both traits on chromosome 18 defined a 92-kb confidence interval. Functional information from model species including Vitis suggested that VvAGL11, included in this confidence interval, might be the main positional candidate gene responsible for seed and berry development. Characterization of VvAGL11 at the sequence level in the experimental progeny identified several SNPs and INDELs in both regulatory and coding regions. In association analyses performed over three seasons, these SNPs and INDELs explained up to 78% and 44% of the phenotypic variation in seed and berry weight, respectively. Moreover, genetic experiments indicated that the regulatory region has a larger effect on the phenotype than the coding region. Transcriptional analysis lent additional support to the putative role of VvAGL11's regulatory region, as its expression is abolished in seedless genotypes at key stages of seed development. These results transform VvAGL11 into a functional candidate gene for further analyses based on genetic transformation. For breeding purposes, intragenic markers were tested individually for marker assisted selection, and the best markers were those closest to the transcription start site. Conclusion We propose that VvAGL11 is the major functional candidate gene for seedlessness, and we provide experimental evidence suggesting that the seedless phenotype might be caused by variations in its promoter region. Current knowledge of the function of its orthologous genes, its expression profile in Vitis varieties and the strong association between its sequence variation and the degree of seedlessness together indicate that the D-lineage MADS-box gene VvAGL11 corresponds to the Seed Development Inhibitor locus described earlier as a major locus for seedlessness. These results provide new hypotheses for further investigations of the molecular mechanisms involved in seed and berry development.

Genome-wide association (GWA) genetics is potentially of great interest in grapevine to find much more rapidly and efficiently the main loci (QTLs) and alleles involved in the variation of traits of interest to breeding, compared to searches based on individual segregating progenies. Knowledge of the structure of genetic diversity and linkage disequilibrium (LD) is a necessary prerequisite to design association genetics studies. Vitis vinifera genetic diversity and structure are already well characterized, but LD in this species has not been thoroughly estimated yet. Other Vitis species are a large potential source of resistance to biotic and abiotic stresses for introgression into V. vinifera, but relatively few genetic resources are available in germplasm repositories and the genetic diversity of these species is hardly known. The objectives of the DL-Vitis project (ANR 2009-2011) are to assess genetic structure and linkage disequilibrium in V. vinifera and 3 American species (V. riparia, V. cinerea, V. aestivalis). For V. vinifera, 3 samples of 93 cultivars were defined, based on available SSR data, by minimizing structure and kinship and maximizing genetic distances. An additional sample of 93 accessions of wild V. vinifera (subsp. silvestris) was also defined. For each American species, 150-200 seeds were collected in natura last autumn. Genetic diversity and structure will be assessed this year using SSRs, and a sample of 93 accessions will be defined for each species. Four genomic regions of 2 Mb each were chosen to estimate LD between specific SNPs in ca. 1 gene out of 3 in each sample of 93 individuals described above. Novel estimates of LD taking structure and kinship into account were developed. The first results obtained in V. vinifera in 2 genomic regions showed differences in the rate of LD decay between samples and regions, suggesting past occurrence of differential selection.

Contact: valerie.laucou@supagro.inra.fr; Using 20 SSR markers well scattered across the 19 grape chromosomes, we analyzed 4,370 accessions of the INRA grape repository at Vassal, mostly cultivars of Vitis vinifera subsp. sativa (3,727), but also accessions of V. vinifera subsp. sylvestris (80), interspecific hybrids (364), and rootstocks (199). The analysis revealed 2,836 SSR single profiles: 2,323 sativa cultivars, 72 wild individuals (sylvestris), 306 interspecific hybrids, and 135 rootstocks, corresponding to 2,739 different cultivars in all. A total of 524 alleles were detected, with a mean of 26.20 alleles per locus. For the 2,323 cultivars of V. vinifera, 338 alleles were detected with a mean of 16.9 alleles per locus. The mean genetic diversity (GDI) was 0.797 and the level of heterozygosity was 0.76, with broad variation from 0.20 to 1. Interspecific hybrids and rootstocks were more heterozygous and more diverse (GDI = 0.839 and 0.865, respectively) than V. vinifera cultivars (GDI = 0.769), Vitis vinifera subsp. sylvestris being the least divergent with GDI = 0.708. Principal coordinates analysis distinguished the four groups. Slight clonal polymorphism was detected. The limit between clonal variation and cultivar polymorphism was set at four allelic differences out of 40. SSR markers were useful as a complementary tool to traditional ampelography for cultivar identification. Finally, a set of nine SSR markers was defined that was sufficient to distinguish 99.8% of the analyzed accessions. This set is suitable for routine characterization and will be valuable for germplasm management

Equipe DAVEM = Diversité et Adaptation de la Vigne et des Espèces Méditerranéennes Contact : ai.oualkadi@gmail.com; Grape diversity present in Morocco and the part of this diversity used nowadays are poorly documented. In order to choose diversified genotypes, to select them so that their agronomic interest will be tested, a group of 21 autochthonous cultivars preserved in the germplasm collections of SODEA and 18 Moroccan cultivars from "Domaine de Vassal" INRA grape collection was compared to a group of cultivars from neighbouring countries (Algeria and Tunisia), and from a core collection optimizing simple sequence repeat (SSR) allelic diversity of grape. Data from 20 nuclear and 3 chloroplastic SSR markers were obtained for this set of 211 cultivars. A total of 156 alleles (mean of 7.8 alleles per locus) were detected for the nSSRs and 7 alleles for the cpSSR in the Moroccan group. Chlorotype diversity in Moroccan and Algerian group were similar, but slightly lower than in the Tunisian group and the core collection. Similarly, the nSSR diversity was high in the core collection and low in the Moroccan and the Algerian groups compared to the two other groups. Clustering of cultivars based on nSSR data reflected their geographical origin and, to a certain extent, the use of the cultivars. The specificity of the Moroccan plant material was attested by the Bayesian analysis using Structure, while differences of the core collection were clearly revealed both by the Bayesian and a multivariate analysis. These results confirm the differentiation of the material from Maghreb and more specifically of Moroccan material, having evolved independently from Europe.

International audience; In the past decade, thanks to an important international effort, our understanding of grape nuclear diversity greatly improved, in particular through European Programs such as GenRes81 and GrapeGen06 leading to the standardization of SSR analysis. Our knowledge of grape diversity in genes, is however still limited. A precise knowledge of gene diversity will be highly beneficial in order to improve our understanding of quantitative important traits. Since the publication of the grape sequence, we have now the possibility to study gene diversity in grape at a large scale. In the present work, SSR diversity in the INRA grape collection (2300 cultivars) enabled the definition of a highly diverse sample of 27 V. vinifera accessions. This set was completed by 7 accessions of V. vinifera subsp. sylvestris and several accessions of Vitis species from Asia or America. Analysis of gene diversity over this sample of 47 accessions was thus performed for a set of 900 genes scattered through the grape genome. Through bioinformatics developments, diversity maps of the grape genome have been drawn at different levels. This data will be very useful in order to select markers for mapping, for comparison of diversity between Vitis species and for the search of selective sweeps in grape. It will also be very useful in the assessment of DL in grape, a prerequisite for Whole Genome Association studies.

Contact: riahi.0311@yahoo.fr; International audience; Three gene pools representative of Vitis vinifera L. subsp. vinifera (=subsp. sativa Beger) growing in the Maghreb regions (North Africa) from Tunisia (44), Algeria (31) and Morocco (18) and 16 wild grape accessions (Vitis vinifera L. subsp. sylvestris (Gmelin) Beger) from Tunisia were analysed for genetic diversity and differentiation at twenty nuclear microsatellites markers distributed throughout the 19 grape chromosomes. 203 alleles with a mean number of 10.15 alleles per locus were observed in a total of 109 accessions. Genetic diversities were high in all populations with values ranging from 0.6775 (Moroccan cultivars) to 0.7254 (Tunisian cultivars). F (st) pairwise values between cultivated grapevine populations were low but found to be significantly different from zero. High F (st) pairwise values were shown between wild and cultivated compartments. Two parent offspring relationships, two synonyms and two clones of the same cultivar were detected. The rate of gene flow caused by vegetative dissemination of cultivated grapevine plants was not sufficient to genetically homogenise the pools of cultivars grown in different regions. The Neighbour Joining cluster analysis showed a clear separation according to geographical origins for the cultivated grapevines gene pools and revealed a high dissimilarity between cultivated and wild grapevine. However, three cultivars (Plant d'Ouchtata 1, Plant de Tabarka 3 and Plant d'Ouchtata 3) are very close to wild accessions and may result from a hybridisation between cultivated and wild accessions. The high level of differentiation between cultivated and wild accessions indicates that the cultivated accessions do not derive directly from local wild populations but could mostly correspond to imported materials introduced from others regions during historical times or derived from crossing between them

Correspondence: Dr P This, UMR Diversité et adaptation des plantes cultivées, INRA, 2 place Viala, Montpellier 34060, France. E-mail: this@supagro.inra.fr; International audience; Polymorphisms in the grape transcription factor family VvMybA are responsible for variation in anthocyanin content in the berries of cultivated grapevine (Vitis vinifera L. subsp. sativa). Previous study has shown that white grapes arose through the mutation of two adjacent genes: a retroelement insertion in VvMybA1 and a single-nucleotide polymorphism mutation in VvMybA2. The purpose of this study was to understand how these mutations emerged and affected genetic diversity at neighbouring sites and how they structured the genetic diversity of cultivated grapevines. We sequenced a total of 3225 bp of these genes in a core collection of genetic resources, and carried out empirical selection tests, phylogenetic- and coalescence-based demographic analyses. The insertion in the VvMybA1 promoter was shown to have occurred recently, after the mutation of VvMybA2, both mutations followed by a selective sweep. The mutational pattern for these colour genes is consistent with progressively relaxed selection from constrained ancestral coloured haplotypes to light coloured and finally white haplotypes. Dynamics of population size in the VvMybA genes showed an initial exponential growth, followed by population size stabilization. Most ancestral haplotypes are found in cultivars from western region, whereas recent haplotypes are essentially present in table cultivars from eastern regions where intense breeding practices may have replaced the original diversity. Finally, the emergence of the white allele was followed by a recent strong exponential growth, showing a very fast diffusion of the initial white allele.