Development and characterization of new microsatellite markers for grape

Thirty five new grape microsatellite markers were developed under an international consortium involving AGROGENE. These loci were amplified in 41 Spanish cultivars of V. vinifera. Eleven of the markers were polymorphic and informative in V. vinifera. Twelve were monomorphic and of the remaining markers one was polymorphic but less useful because individuals amplified more than two bands and the rest had amplification problems. The number of alleles detected for the 11 informative markers ranged from 4 to 12, with heterozygosity values ranging from 0.6 to 0.8. Primer sequences are reported for these markers.

Malignant fibrous histiocytoma of the head and neck. Case report

Malignant fibrous histiocytoma (MFH) is a rare tumor included in the group of soft tissue sarcomas. Approximately 1-3% of these tumors affect the head and neck, with about 100 cases reported to date. A case affecting the retromolar trigone and involving the postero-lateral portion of the left hemi-tongue is reported. Etiological and pathological aspects are discussed. Diagnosis, treatment and prognosis of this neoplasm are reviewed.Le fibro-histiocytome malin est une tumeur rare faisant partie du groupe des sarcomes des tissus mous. Environ 1-3% de ce type de tumeur est localisé dans la région de la tête et cou, dont 100 cas ont été rapportés à ce jour. Le cas rapporté affecte le trigone rétromolaire envahissant la portion postéro-latérale de l’hémi-langue. Les aspects étiologiques et pathologiques sont discutés. Le diagnostic, le traitement et le pronostic sont passés en revue

High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a re-sequencing approach and SNPlex technology

Background: Single-nucleotide polymorphisms (SNPs) are the most abundant type of DNA sequence polymorphisms. Their higher availability and stability when compared to simple sequence repeats (SSRs) provide enhanced possibilities for genetic and breeding applications such as cultivar identification, construction of genetic maps, the assessment of genetic diversity, the detection of genotype/phenotype associations, or marker-assisted breeding. In addition, the efficiency of these activities can be improved thanks to the ease with which SNP genotyping can be automated. Expressed sequence tags (EST) sequencing projects in grapevine are allowing for the in silico detection of multiple putative sequence polymorphisms within and among a reduced number of cultivars. In parallel, the sequence of the grapevine cultivar Pinot Noir is also providing thousands of polymorphisms present in this highly heterozygous genome. Still the general application of those SNPs requires further validation since their use could be restricted to those specific genotypes. Results: In order to develop a large SNP set of wide application in grapevine we followed a systematic re-sequencing approach in a group of 11 grape genotypes corresponding to ancient unrelated cultivars as well as wild plants. Using this approach, we have sequenced 230 gene fragments, what represents the analysis of over 1 Mb of grape DNA sequence. This analysis has allowed the discovery of 1573 SNPs with an average of one SNP every 64 bp (one SNP every 47 bp in non-coding regions and every 69 bp in coding regions). Nucleotide diversity in grape ( = 0.0051) was found to be similar to values observed in highly polymorphic plant species such as maize. The average number of haplotypes per gene sequence was estimated as six, with three haplotypes representing over 83% of the analyzed sequences. Short-range linkage disequilibrium (LD) studies within the analyzed sequences indicate the existence of a rapid decay of LD within the selected grapevine genotypes. To validate the use of the detected polymorphisms in genetic mapping, cultivar identification and genetic diversity studies we have used the SNPlex genotyping technology in a sample of grapevine genotypes and segregating progenies. Conclusion: These results provide accurate values for nucleotide diversity in coding sequences and a first estimate of short-range LD in grapevine. Using SNPlex genotyping we have shown the application of a set of discovered SNPs as molecular markers for cultivar identification, linkage mapping and genetic diversity studies. Thus, the combination a highly efficient re-sequencing approach and the SNPlex high throughput genotyping technology provide a powerful tool for grapevine genetic analysis. © 2007 Lijavetzky et al; licensee BioMed Central Ltd

The LATERAL ORGAN BOUNDARIES Domain gene family in grapevine: Genome-wide characterization and expression analyses during developmental processes and stress responses

LATERAL ORGAN BOUNDARIES (LOB) DOMAIN (LBD) constitute a family of plant-specific transcription factors with key roles in the regulation of plant organ development, pollen development, plant regeneration, pathogen response, and anthocyanin and nitrogen metabolisms. However, the role of LBDs in fruit ripening and in grapevine (Vitis vinifera L.) development and stress responses is poorly documented. By performing a model curation of LBDs in the latest genome annotation 50 genes were identified. Phylogenetic analysis showed that LBD genes can be grouped into two classes mapping on 16 out of the 19 V. vinifera chromosomes. New gene subclasses were identified that have not been characterized in other species. Segmental and tandem duplications contributed significantly to the expansion and evolution of the LBD gene family in grapevine as noticed for other species. The analysis of cis-regulatory elements and transcription factor binding sites in the VviLBD promoter regions suggests the involvement of several hormones in the regulation of LBDs expression. Expression profiling suggest the involvement of LBD transcription factors in grapevine development, berry ripening and stress responses. Altogether this study provides valuable information and robust candidate genes for future functional analysis aiming to clarify mechanisms responsible for the onset of fruit ripening and fruit defense strategies. © 2017 The Author(s)

Pedigree analysis of the Spanish grapevine cultivar 'Hebén'

The use of Single Nucleotide Polymorphism (SNP) markers allows genetic identification and parentage analysis of grapevine cultivars. Ancient cultivars like 'Hebén' were widely cultivated in the Iberian Peninsula along its history and likely contributed to the origin of varieties which are still cultivated today. The goal of our study was to search for possible first-degree relationships between the female variety 'Hebén' and other Iberian and Mediterranean cultivars. For this purpose, we used a set of 261 SNP markers which allowed identifying 23 trios and 37 parent-offspring relationships supported by high overall likelihood ratios (LOD scores). The results shed light on the relationships among several cultivars from Spain and Portugal, and demonstrated that 'Hebén' is a major founder of current varieties in the Iberian Peninsula viticulture, and contributed to spread the chlorotype A in this region

Intra-varietal diversity for agronomic traits in 'Garnacha Blanca'

'Garnacha Blanca' is a somatic variant derived from 'Garnacha Tinta', an old variety with large genetic and phenotypic variability. In this work we have studied for two years the phenotypic variation existing in 'Garnacha Blanca' for yield and quality related traits in accessions from 14 sampling locations of ancient vineyards in the Ebro Valley, Spain. The results showed high variability among the accessions in many of the traits studied in 'Garnacha Blanca'. Different accessions could be distinguished both years using several traits, including two important traits in terms of quality and yield: bunch compactness and yield per plant. A large environment effect, intrinsic to the 'Garnacha' group, enhances phenotypic variation among years, what requires increasing the number of bunches and years for clonal characterization in this variety. The dimensions of the berry showed the least variability, while traits related to bunch architecture like bunch length were discriminant and also stable

Characterization of genetic variation within table grape varieties (Vitis vinifera L.) based on AFLP markers

AFLPs were used to characterize a collection of 35 table grape varieties. A single AFLP reaction with a single combination of selective primers yielded an average of 50 polymorphic and scorable amplified bands in this collection and was enough to unequivocally identify each analyzed variety, Genetic similarity between different varieties was estimated, based on the results obtained with two primer combinations, to be between 0.65 and 0.90, while sibling varieties derived from the same cross showed a genetic similarity higher than 0.80, The analysis of several samples belonging to the same varieties, yet from different origins, showed stability of the AFLP patterns as to unequivocally and reproducibly identify them. Furthermore, some specific primer combinations detected a low level of variation that could be due to somatic variation and would be useful in clonal identification

Molecular identification and genetic relationships of Algerian grapevine cultivars maintained at the germplasm collection of Skikda (Algeria)

We have used nuclear and chloroplast microsatellite markers to characterize a collection of 36 Algerian grapevine (Vitis vinifera L.) accessions maintained at the germplasm collection of Skikda (Algeria). The genetic diversity observed within the collection was comparable to what has been described for cultivated accessions of grapevine. Moreover, chlorotype C, associated to eastern accessions and highly frequent among table grape cultivars, was overrepresented in the collection. Genotype comparisons among the accessions and published cultivar genotypes identified a few synonyms within the collection as well as putative synonyms for Algerian accessions such as 'Aïn el Kelb', 'Ahmar Mechtras', 'Ahmar de Mascara' or 'Bouni' among cultivars grown in both Eastern and Western areas of the Mediterranean basin. Furthermore, the study of genetic relationships among the Algerian accessions suggests the existence of close relatedness within some groups of cultivars that could have been originated by spontaneous hybridization and seed propagation.

Varietal diversity within grapevine accessions of cv. Tempranillo

Intra-varietal diversity of 31 accessions named as Tempranillo or described as synonyms of this representative Spanish grapevine variety was assessed using 48 morphological descriptors and 95 AFLP markers obtained using 2 primer combinations. We could identify homonyms as well as accessions belonging to varieties which, depending on their regional origin, are incorrectly cited as Tempranillo synonyms. Genetic analysis revealed a high level of genetic similarity between Tempranillo accessions (SG >0.97), which could correspond to three highly related genotypes. This narrow genetic variation supports a monophyletic origin of Tempranillo, and could be the result of rapid multiplication and distribution of a very low number of clones.

Solar ultraviolet radiation is necessary to enhance grapevine fruit ripening transcriptional and phenolic responses

Background: Ultraviolet (UV) radiation modulates secondary metabolism in the skin of Vitis vinifera L. berries, which affects the final composition of both grapes and wines. The expression of several phenylpropanoid biosynthesis-related genes is regulated by UV radiation in grape berries. However, the complete portion of transcriptome and ripening processes influenced by solar UV radiation in grapes remains unknown.Results: Whole genome arrays were used to identify the berry skin transcriptome modulated by the UV radiation received naturally in a mid-altitude Tempranillo vineyard. UV radiation-blocking and transmitting filters were used to generate the experimental conditions. The expression of 121 genes was significantly altered by solar UV radiation. Functional enrichment analysis of altered transcripts mainly pointed out that secondary metabolism-related transcripts were induced by UV radiation including VvFLS1, VvGT5 and VvGT6 flavonol biosynthetic genes and monoterpenoid biosynthetic genes. Berry skin phenolic composition was also analysed to search for correlation with gene expression changes and UV-increased flavonols accumulation was the most evident impact. Among regulatory genes, novel UV radiation-responsive transcription factors including VvMYB24 and three bHLH, together with known grapevine UV-responsive genes such as VvMYBF1, were identified. A transcriptomic meta-analysis revealed that genes up-regulated by UV radiation in the berry skin were also enriched in homologs of Arabidopsis UVR8 UV-B photoreceptor-dependent UV-B -responsive genes. Indeed, a search of the grapevine reference genomic sequence identified UV-B signalling pathway homologs and among them, VvHY5-1, VvHY5-2 and VvRUP were up-regulated by UV radiation in the berry skin.Conclusions: Results suggest that the UV-B radiation-specific signalling pathway is activated in the skin of grapes grown at mid-altitudes. The biosynthesis and accumulation of secondary metabolites, which are appreciated in winemaking and potentially confer cross-tolerance, were almost specifically triggered. This draws attention to viticultural practices that increase solar UV radiation on vineyards as they may improve grape features. © 2014 Carbonell-Bejerano et al.; licensee BioMed Central Ltd