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Simón 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.

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 'Carmenère' 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 'Carmenère', 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 viñedos monovarietales presentan mezclas de otros cultivares en proporciones menores. Algunos de estos cultivares son desconocidos y podrían representar una oportunidad para descubrir genotipos nuevos y potencialmente útiles en investigación y/o producción. En un viñedo cv. 'Carmenère', plantado en 1994 en la comuna de Palmilla (Valle de Colchagua, Chile), se determinó la presencia minoritaria de otros cultivares. El presente trabajo cubre por primera vez la identificación y caracterización de uno de estos cultivares, el cual presentó una muy pobre fructificación. A través de ampelografía clásica, no fue posible asociar el cultivar en estudio a ningún cultivar conocido en Chile. Sin embargo, a través de una comparación de marcadores moleculares microsatélites 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 había sido descubierto en Chile previamente durante la temporada 1950-1951. Este cultivar presenta una brotación más precoz que la del cv. 'Carmenère', posee flores morfológicamente completas y muestra un notorio desorden fisiológico en su fructificación, el cual se manifiesta a través de una necrosis de racimo parcial o completa, bajo las condiciones ambientales de Palmilla. Este cultivar contribuye a la riqueza genotípica presente en Chile y eventualmente podría llegar a ser una herramienta interesante para estudios fisiológicos y moleculares. Adicionalmente, podría volverse productiva bajo otras condiciones ambientales (i.e. condiciones ambientales que favorezcan una buena cuaja frutal) o por la aplicación de prácticas vitícolas adecuadas, como el anillamiento de cargadores durante la floración.

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 'Carmenère' 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 'Carmenère', 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 viñedos monovarietales presentan mezclas de otros cultivares en proporciones menores. Algunos de estos cultivares son desconocidos y podrían representar una oportunidad para descubrir genotipos nuevos y potencialmente útiles en investigación y/o producción. En un viñedo cv. 'Carmenère', plantado en 1994 en la comuna de Palmilla (Valle de Colchagua, Chile), se determinó la presencia minoritaria de otros cultivares. El presente trabajo cubre por primera vez la identificación y caracterización de uno de estos cultivares, el cual presentó una muy pobre fructificación. A través de ampelografía clásica, no fue posible asociar el cultivar en estudio a ningún cultivar conocido en Chile. Sin embargo, a través de una comparación de marcadores moleculares microsatélites 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 había sido descubierto en Chile previamente durante la temporada 1950-1951. Este cultivar presenta una brotación más precoz que la del cv. 'Carmenère', posee flores morfológicamente completas y muestra un notorio desorden fisiológico en su fructificación, el cual se manifiesta a través de una necrosis de racimo parcial o completa, bajo las condiciones ambientales de Palmilla. Este cultivar contribuye a la riqueza genotípica presente en Chile y eventualmente podría llegar a ser una herramienta interesante para estudios fisiológicos y moleculares. Adicionalmente, podría volverse productiva bajo otras condiciones ambientales (i.e. condiciones ambientales que favorezcan una buena cuaja frutal) o por la aplicación de prácticas vitícolas adecuadas, como el anillamiento de cargadores durante la floración.

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

Clonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, coffee and grape. After several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation known as "clonal diversity". Clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation wines specifications. The most parsimonious hypothesis explaining clonal diversity is the accumulation of somatic mutations. Using the power of NGS, we provided the first broad description of polymorphism in different clones of a single grapevine cultivar (Pinot) and then compared the clonal polymorphism in 4 different cultivars: Pinot, Syrah, Grenache and Sultanine. Three types of polymorphism (SNPs, Indels, mobile elements) were observed. As expected, the polymorphism at cultivars level was much higher than at clonal level. The insertion polymorphism generated by mobile elements represented the highest mutational event with respect to clonal variation while SNP and indel polymorphisms were of higher importance for cultivar diversity. Among mobile element with a high polymorphism level, four were analyzed and polymorphisms were confirmed at different diversity levels: inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual. We confirm the high instability of these elements between clones and between tissues in single individuals. Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could have much potential for accurate identification.

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

Clonal variation is considered as an effective contribution to breeding programs of vegetatively propagated species with major agronomical interest such as banana, coffee and grape. After several propagation cycles, stable and heritable phenotypic variations appear giving rise to a phenotypic variation known as "clonal diversity". Clonal diversity is very important for wine-growers because it allows preserving cultivars identity in the strict respect of Appellation wines specifications. The most parsimonious hypothesis explaining clonal diversity is the accumulation of somatic mutations. Using the power of NGS, we provided the first broad description of polymorphism in different clones of a single grapevine cultivar (Pinot) and then compared the clonal polymorphism in 4 different cultivars: Pinot, Syrah, Grenache and Sultanine. Three types of polymorphism (SNPs, Indels, mobile elements) were observed. As expected, the polymorphism at cultivars level was much higher than at clonal level. The insertion polymorphism generated by mobile elements represented the highest mutational event with respect to clonal variation while SNP and indel polymorphisms were of higher importance for cultivar diversity. Among mobile element with a high polymorphism level, four were analyzed and polymorphisms were confirmed at different diversity levels: inter-species, inter-cultivars, inter-clones and between organs/tissues of a single individual. We confirm the high instability of these elements between clones and between tissues in single individuals. Clone identification through molecular methods would be of high significance for the wine industry. SNP or small indels mutations are less frequent but more stable than structural variation and could have much potential for accurate identification.

With NGS development, bioinformatics has become central in plant breeding laboratories, and researchers are in need of some autonomy in its use. The Southgreen platform (CIRAD, IRD, INRA) performs bioinformatics analyses for many plant breeding research teams in Montpellier (France), and offers many systems to users: for example GNPAnnot (automatic genomic sequence annotation), Greenphyl (phylogenetic orthology prediction), ESTtik (EST annotation) or the Bacchus analysis pipeline. Most of these systems have been translated into Galaxy workflows. As for the Bacchus pipeline, it has been created at INRA Montpellier (France) to investigate clonal diversity in grapevine genomes. For this task, many softwares have been wrapped in the Galaxy framework. Bacchus can be decomposed in three steps: i) Genome reconstruction, ii) test of reconstruction results, and iii) diversity analysis. This last step is done using SNP's and structural variations. To detect SNP's, the latest Freebayes version was used, while the IDfixe software was developped for structural variation detection. Some of the softwares developped for this pipeline are now used in the international project Grapereseq. Today, the Galaxy framework is widely used by Southgreen plateform users as an alternative to the command line system. In this context, dozens of users have already been trained in Galaxy-using bioinformatics. During weekly collective pair-programming sessions, platform engineers and interested scientists integrate new tools and functionalities.Thus, Galaxy is now a core component of the plant breeding community around the Southgreen platform, and the main access portal for non- bioinformatics specialists to our computing clusters.

With NGS development, bioinformatics has become central in plant breeding laboratories, and researchers are in need of some autonomy in its use. The Southgreen platform (CIRAD, IRD, INRA) performs bioinformatics analyses for many plant breeding research teams in Montpellier (France), and offers many systems to users: for example GNPAnnot (automatic genomic sequence annotation), Greenphyl (phylogenetic orthology prediction), ESTtik (EST annotation) or the Bacchus analysis pipeline. Most of these systems have been translated into Galaxy workflows. As for the Bacchus pipeline, it has been created at INRA Montpellier (France) to investigate clonal diversity in grapevine genomes. For this task, many softwares have been wrapped in the Galaxy framework. Bacchus can be decomposed in three steps: i) Genome reconstruction, ii) test of reconstruction results, and iii) diversity analysis. This last step is done using SNP's and structural variations. To detect SNP's, the latest Freebayes version was used, while the IDfixe software was developped for structural variation detection. Some of the softwares developped for this pipeline are now used in the international project Grapereseq. Today, the Galaxy framework is widely used by Southgreen plateform users as an alternative to the command line system. In this context, dozens of users have already been trained in Galaxy-using bioinformatics. During weekly collective pair-programming sessions, platform engineers and interested scientists integrate new tools and functionalities.Thus, Galaxy is now a core component of the plant breeding community around the Southgreen platform, and the main access portal for non- bioinformatics specialists to our computing clusters.