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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.

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.

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.

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

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.

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.

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.

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.

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.

International audience; Background and Aims: Based on parentage analysis of a large nuclear simple sequence repeat (SSR) marker database of grapevine genotypes, we propose the pedigree of several cultivars from southwestern France including Merlot, one of the world's major black winegrapes.Methods and Results: The putative mother of Merlot, deduced from inheritance at 55 nuclear and three chloroplast microsatellite loci, is a non-referenced and previously unknown cultivar, first sampled some years ago in northern Brittany where vines were cultivated at the end of the Middle Ages, and then identified in four places in Charentes. Considering both the name used by the growers of this grape and the literature, we have named it Magdeleine Noire des Charentes. The putative father of Merlot is Cabernet Franc, already involved in the parentage of Cabernet-Sauvignon. Further analysis of genetic relationships leads us to propose the kinship group of Merlot composed, among others, of Carmenere (Gros Cabernet x Cabernet Franc), Merlot Blanc (Merlot x Folle Blanche), Cot (Magdeleine Noire des Charentes Prunelard) and Mourtes (Magdeleine Noire des Charentes x Penouille).Conclusions: These results shed new light on the origin of Merlot and on the relationships among several cultivars from southwestern France.Significance of the Study: Our discovery of the key genetic role of a previously unknown cultivar in the origins of some significant cultivars reinforces the importance of deep exploration, before it is too late, to discover original genotypes which have not yet been collected or referenced

Background The first high quality draft of the grape genome sequence has just been published. This is a critical step in accessing all the genes of this species and increases the chances of exploiting the natural genetic diversity through association genetics. However, our basic knowledge of the extent of allelic variation within the species is still not sufficient. Towards this goal, we constructed nested genetic core collections (G-cores) to capture the simple sequence repeat (SSR) diversity of the grape cultivated compartment (Vitis vinifera L. subsp. sativa) from the world's largest germplasm collection (Domaine de Vassal, INRA Hérault, France), containing 2262 unique genotypes. Results Sub-samples of 12, 24, 48 and 92 varieties of V. vinifera L. were selected based on their genotypes for 20 SSR markers using the M-strategy. They represent respectively 58%, 73%, 83% and 100% of total SSR diversity. The capture of allelic diversity was analyzed by sequencing three genes scattered throughout the genome on 233 individuals: 41 single nucleotide polymorphisms (SNPs) were identified using the G-92 core (one SNP for every 49 nucleotides) while only 25 were observed using a larger sample of 141 individuals selected on the basis of 50 morphological traits, thus demonstrating the reliability of the approach. Conclusion The G-12 and G-24 core-collections displayed respectively 78% and 88% of the SNPs respectively, and are therefore of great interest for SNP discovery studies. Furthermore, the nested genetic core collections satisfactorily reflected the geographic and the genetic diversity of grape, which are also of great interest for the study of gene evolution in this species.

Contact: francesco.emanuelli@iasma.it Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Background: The sweet, floral flavor typical of Muscat varieties (Muscats), due to high levels of monoterpenoids (geraniol, linalool and nerol), is highly distinct and has been greatly appreciated both in table grapes and in wine since ancient times. Muscat flavor determination in grape (Vitis vinifera L.) has up to now been studied by evaluating monoterpenoid levels through QTL analysis. These studies have revealed co-localization of 1-deoxy-D-xylulose 5-phosphate synthase (VvDXS) with the major QTL positioned on chromosome 5. Results: We resequenced VvDXS in an ad hoc association population of 148 grape varieties, which included muscat-flavored, aromatic and neutral accessions as well as muscat-like aromatic mutants and non-aromatic offsprings of Muscats. Gene nucleotide diversity and intragenic linkage disequilibrium (LD) were evaluated. Structured association analysis revealed three SNPs in moderate LD to be significantly associated with muscat-flavored varieties. We identified a putative causal SNP responsible for a predicted non-neutral substitution and we discuss its possible implications for flavor metabolism. Network analysis revealed a major star-shaped cluster of reconstructed haplotypes unique to muscat-flavored varieties. Moreover, muscat-like aromatic mutants displayed unique non-synonymous mutations near the mutated site of Muscat genotypes. Conclusions: This study is a crucial step forward in understanding the genetic regulation of muscat flavor in grapevine and it also sheds light on the domestication history of Muscats. VvDXS appears to be a possible human-selected locus in grapevine domestication and post-domestication. The putative causal SNP identified in Muscat varieties as well as the unique mutations identifying the muscat-like aromatic mutants under study may be immediately applied in marker-assisted breeding programs aimed at enhancing fragrance and aroma complexity respectively in table grape and wine cultivars

Equipe " Diversité, Génétique et Génomique Vigne ". Contact: boursiqu@supagro.inra.fr; International audience; Aims: This study aims to characterize the SODEA ampelographic collection in Meknes, the only germplasm repository in Morocco. To assess the usefulness of this germplasm, a study was conducted to verify the trueness to type of the genotypes and to provide the first database for a reference collection in Morocco. A core collection was then established to define a small sample easier to handel further characterization. Methods and results: Ninety-four grapevine samples from the collection were analyzed using 20 nuclear SSR markets. From these samples. we identified 67 grapevine genotypes. The nuclear SSRs revealed a high diversity within the SODEA collection: 202 alleles were detected with a mean of 10.1 alleles per locus. Analysis of molecular data with the software DARwin was used to classify the genotypes into six groups according to their origin or their genetic relatedness. The 18 autochthonous cultivars were differentiated according to geographical origin (North vs. South). We established a core collection among this germplasm using MSTRAT: the complete diversity present in the collection was captured with only 34 individuals. Nevertheless,an optimal core collection representing 89% of the diversity was constituted by only 17 cultivars. Among these 17 individuals, 5 are autochthonous. Conclusion: The collection of SODEA represents a unique resources of grapevines for Morocco. It contains several important autochthonous cultivars in terms of diversity and agronomic utilisation. Significance and impact of the study: The study showed potential and interest of the cultivars present in the collection of SODEA, suggesting that their utilisation may be important for the farmers; Objectifs : cette étude a pour objectif de caractériser la collection ampélographique de la SODEA à Meknès, l’unique conservatoire de ressources génétiques vignes existant au Maroc. Pour évaluer l’intérêt de ce conservatoire, une étude a été conduite afin de vérifier l’identité exacte des génotypes et d’établir la première base de données relative à cette collection de référence. Une core collection a ensuite été établie afin de définir un sous-échantillon restreint, plus facile à gérer pour de futures analyses. Méthodes et résultats : quatre-vingt quatorze échantillons de vigne prélevés dans la collection ont été analysés en utilisant 20 marqueurs microsatellites. A partir de ces échantillons, nous avons identifié 67 génotypes distincts. L’analyse de ces marqueurs a révélé une grande diversité au sein de la collection de la SODEA : 202 allèles ont été détectés avec une moyenne de 10,1 allèles par locus. Les données moléculaires ont été analysées avec le programme DARwin. Les génotypes ont pu être répartis en 6 groupes, en relation avec leur origine ou leur relation génétique. Les 18 cultivars autochtones ont été différenciés en fonction de leur origine géographique (Nord vs. Sud). Nous avons établi une core collection à partir de ces ressources génétiques en utilisant le logiciel MSTRAT : la diversité totale présente dans ce conservatoire peut être représentée par 34 individus. Toutefois, une core collection optimisée et constituée seulement de 17 cultivars permet de représenter 89 % de la diversité. Parmi ces 17 individus, 5 sont autochtones. Conclusion : la collection de la SODEA représente plusieurs cépages autochtones importants en termes de diversité et d’intérêt agronomique. Signification et impact de l’étude : l’étude a permis de montrer le potentiel et l’intérêt des cultivars présents dans la collection de la SODEA et suggère que leur utilisation pourrait être importante pour les agriculteurs.