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      Unraveling the genetic origin of ‘Glera’, ‘Ribolla Gialla’ and other autochthonous grapevine varieties from Friuli Venezia Giulia (northeastern Italy)

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          Abstract

          ‘Glera’ and ‘Ribolla Gialla’ are the most economically relevant local grapevine cultivars of Friuli Venezia Giulia region (north-eastern Italy). ‘Glera’ is used to produce the world-renowned Prosecco wine. ‘Ribolla Gialla’ cultivation is constantly increasing due to the strong demand for sparkling wine and is the most important variety in Brda (Slovenia). Knowledge of local varieties history in terms of migration and pedigree relationships has scientific and marketing appeal. Following prospections, genotyping and ampelographic characterization of minor germplasm in Friuli Venezia Giulia, a further research was developed to understand the parentage relationships among the grapevine varieties grown in this region. An integrated strategy was followed combining the analysis of nuclear and chloroplast microsatellites with the Vitis 18k SNP chip. Two main recurrent parents were found, which can be regarded as “founders”: ‘Vulpea’, an Austrian variety parent-offspring related with at least ten Friuli Venezia Giulia cultivars, among them ‘Glera’, and ‘Refosco Nostrano’, first degree related with other six Friuli Venezia Giulia varieties. ‘Ribolla Gialla’ was shown to be another member of the impressively long list of offspring derived from the prolific ‘Heunisch Weiss’. Combining molecular markers and historical references was a high-performance strategy for retracing and adjusting the history of cultivars.

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          Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms.

          The domestication of the Eurasian grape (Vitis vinifera ssp. sativa) from its wild ancestor (Vitis vinifera ssp. sylvestris) has long been claimed to have occurred in Transcaucasia where its greatest genetic diversity is found and where very early archaeological evidence, including grape pips and artefacts of a 'wine culture', have been excavated. Whether from Transcaucasia or the nearby Taurus or Zagros Mountains, it is hypothesized that this wine culture spread southwards and eventually westwards around the Mediterranean basin, together with the transplantation of cultivated grape cuttings. However, the existence of morphological differentiation between cultivars from eastern and western ends of the modern distribution of the Eurasian grape suggests the existence of different genetic contribution from local sylvestris populations or multilocal selection and domestication of sylvestris genotypes. To tackle this issue, we analysed chlorotype variation and distribution in 1201 samples of sylvestris and sativa genotypes from the whole area of the species' distribution and studied their genetic relationships. The results suggest the existence of at least two important origins for the cultivated germplasm, one in the Near East and another in the western Mediterranean region, the latter of which gave rise to many of the current Western European cultivars. Indeed, over 70% of the Iberian Peninsula cultivars display chlorotypes that are only compatible with their having derived from western sylvestris populations.
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            ASSIsT: an automatic SNP scoring tool for in- and outbreeding species

            ASSIsT (Automatic SNP ScorIng Tool) is a user-friendly customized pipeline for efficient calling and filtering of SNPs from Illumina Infinium arrays, specifically devised for custom genotyping arrays. Illumina has developed an integrated software for SNP data visualization and inspection called GenomeStudio® (GS). ASSIsT builds on GS-derived data and identifies those markers that follow a bi-allelic genetic model and show reliable genotype calls. Moreover, ASSIsT re-edits SNP calls with null alleles or additional SNPs in the probe annealing site. ASSIsT can be employed in the analysis of different population types such as full-sib families and mating schemes used in the plant kingdom (backcross, F1, F2), and unrelated individuals. The final result can be directly exported in the format required by the most common software for genetic mapping and marker–trait association analysis. ASSIsT is developed in Python and runs in Windows and Linux. Availability and implementation: The software, example data sets and tutorials are freely available at http://compbiotoolbox.fmach.it/assist/. Contact: eric.vandeweg@wur.nl
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              An extensive study of the genetic diversity within seven French wine grape variety collections.

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

                Contributors
                manna.crespan@crea.gov.it
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                29 April 2020
                29 April 2020
                2020
                : 10
                : 7206
                Affiliations
                [1 ]CREA Research Centre of Viticulture and Enology, Conegliano, Treviso Italy
                [2 ]ISNI 0000 0004 1755 6224, GRID grid.424414.3, Unit of Computational Biology, Research and Innovation Centre, Fondazione Edmund Mach, San Michele all’Adige, ; Trento, Italy
                [3 ]Viticulturist, Cividale del Friuli, Udine, Italy
                [4 ]ERSA, Agenzia Regionale per lo Sviluppo Rurale, Pozzuolo del Friuli, Udine, Italy
                [5 ]ISNI 0000 0001 0721 6013, GRID grid.8954.0, Department of Agronomy, Biotechnical Faculty, University of Ljubljana, ; Ljubljana, Slovenia
                [6 ]ISNI 0000 0001 2113 062X, GRID grid.5390.f, Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, ; Udine, Italy
                [7 ]JKI - Institute for Grapevine Breeding Geilweilerhof, Siebeldingen, Germany
                Author information
                http://orcid.org/0000-0001-6328-9591
                http://orcid.org/0000-0001-8366-4942
                http://orcid.org/0000-0002-5365-3342
                http://orcid.org/0000-0002-8516-9010
                http://orcid.org/0000-0002-1552-4443
                http://orcid.org/0000-0003-1405-6358
                http://orcid.org/0000-0002-8760-5031
                http://orcid.org/0000-0002-3467-7672
                Article
                64061
                10.1038/s41598-020-64061-w
                7190720
                32350312
                5718d80c-da8b-48ef-b9aa-094dc6693033
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 27 October 2019
                : 1 April 2020
                Funding
                Funded by: ERSA
                Categories
                Article
                Custom metadata
                © The Author(s) 2020

                Uncategorized
                genotype,plant genetics
                Uncategorized
                genotype, plant genetics

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