Large-scale parentage analysis in an extended set of grapevine cultivars (Vitis vinifera L.)

Inheritance of nuclear microsatellite markers (nSSR) has been proved to be a powerful tool to verify or uncover the parentage of grapevine cultivars. The aim of the present study was to undertake an extended parentage analysis using a large sample of Vitis vinifera cultivars held in the INRA “Domaine de Vassal” Grape Germplasm Repository (France). A dataset of 2,344 unique genotypes (i.e. cultivars without synonyms, clones or mutants) identified using 20 nSSR was analysed with FAMOZ software. Parentages showing a logarithm of odds score higher than 18 were validated in relation to the historical data available. The analysis first revealed the full parentage of 828 cultivars resulting in: (1) 315 original full parentages uncovered for traditional cultivars, (2) 100 full parentages confirming results established with molecular markers in prior papers and 32 full parentages that invalidated prior results, (3) 255 full parentages confirming pedigrees as disclosed by the breeders and (4) 126 full parentages that invalidated breeders’ data. Second, incomplete parentages were determined in 1,087 cultivars due to the absence of complementary parents in our cultivar sample. Last, a group of 276 genotypes showed no direct relationship with any other cultivar in the collection. Compiling these results from the largest set of parentage data published so far both enlarges and clarifies our knowledge of the genetic constitution of cultivated V. vinifera germplasm. It also allows the identification of the main genitors involved in varietal assortment evolution and grapevine breeding.

[1]  Amanda B. Hepler,et al.  Genetic relatedness analysis: modern data and new challenges , 2006, Nature Reviews Genetics.

[2]  Edward S. Buckler,et al.  Genetic structure and domestication history of the grape , 2011, Proceedings of the National Academy of Sciences.

[3]  M. Morgante,et al.  The SSR-based molecular profile of 1005 grapevine (Vitis vinifera L.) accessions uncovers new synonymy and parentages, and reveals a large admixture amongst varieties of different geographic origin , 2010, Theoretical and Applied Genetics.

[4]  A. Bouquet,et al.  Application des méthodes de sélection récurrente à l'amélioration génétique de la Vigne , 1981 .

[5]  T. Lacombe,et al.  Historical origins and genetic diversity of wine grapes. , 2006, Trends in genetics : TIG.

[6]  T. Lacombe,et al.  Relationships and Genetic Diversity within the Accessions Related to Malvasia Held in the Domaine de Vassal Grape Germplasm Repository , 2007, American Journal of Enology and Viticulture.

[7]  T. Lacombe,et al.  Zinfandel, Dobricic, and Plavac mali: The Genetic Relationship among Three Cultivars of the Dalmatian Coast of Croatia , 2004 .

[8]  H. Olmo The Origin and Domestication of the Vinifera Grape , 2003 .

[9]  T. Lacombe,et al.  Evolution of the VvMybA gene family, the major determinant of berry colour in cultivated grapevine (Vitis vinifera L.) , 2010, Heredity.

[10]  L. Levadoux LES POPULATIONS SAUVAGES ET CULTIVÉES DE VITIS VINIFERA L. , 1956 .

[11]  T. Lacombe,et al.  High throughput analysis of grape genetic diversity as a tool for germplasm collection management , 2011, Theoretical and Applied Genetics.

[12]  M. Thomas,et al.  DNA typing of grapevines: A universal methodology and database for describing cultivars and evaluating genetic relatedness , 1994, Plant Molecular Biology.

[13]  C. Meredith,et al.  Identity and Parentage of Torrontés Cultivars in Argentina , 2003, American Journal of Enology and Viticulture.

[14]  C. Meredith,et al.  Microsatellite analysis of ancient alpine grape cultivars: pedigree reconstruction of Vitis vinifera L. 'Cornalin du Valais' , 2003, Theoretical and Applied Genetics.

[15]  M. Ashley Plant Parentage, Pollination, and Dispersal: How DNA Microsatellites Have Altered the Landscape , 2010 .

[16]  Grape varieties (Vitis vinifera L.) from the Balearic Islands: genetic characterization and relationship with Iberian Peninsula and Mediterranean Basin , 2012, Genetic Resources and Crop Evolution.

[17]  M. Morgante,et al.  Selective sweep at the Rpv3 locus during grapevine breeding for downy mildew resistance , 2011, Theoretical and Applied Genetics.

[18]  R. Jansen,et al.  Using complex plant pedigrees to map valuable genes. , 2001, Trends in plant science.

[19]  J. Ibáñez,et al.  Genetic Relationships among Table-Grape Varieties , 2009, American Journal of Enology and Viticulture.

[20]  J. Boursiquot,et al.  Genetic structure and differentiation in cultivated grape, Vitis vinifera L. , 2003, Genetical research.

[21]  P. Smouse,et al.  genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .

[22]  K. Roubelakis-Angelakis Grapevine molecular physiology & biotechnology , 2009 .

[23]  F. Regner,et al.  Considerations about the evolution of grapevine and the role of Traminer. , 2000 .

[24]  F. Cabello,et al.  Garnacha and Garnacha Tintorera: Genetic Relationships and the Origin of Teinturier Varieties Cultivated in Spain , 2003, American Journal of Enology and Viticulture.

[25]  J. Possingham,et al.  Progress in grapevine breeding , 1988, Theoretical and Applied Genetics.

[26]  H. Steinkellner,et al.  The use of microsatellites for germplasm management in a Portuguese grapevine collection , 1999, Theoretical and Applied Genetics.

[27]  Bowers,et al.  Historical Genetics: The Parentage of Chardonnay, Gamay, and Other Wine Grapes of Northeastern France. , 1999, Science.

[28]  T. Lacombe,et al.  Parentage of Merlot and related winegrape cultivars of southwestern France: discovery of the missing link , 2009 .

[29]  I. Pejić,et al.  Microsatellite Markers for Grapevine: Tools for Cultivar Identification & Pedigree Reconstruction , 2009 .

[30]  K. A. Paczolt,et al.  A practical guide to methods of parentage analysis , 2010, Molecular ecology resources.

[31]  T. Lacombe,et al.  Determining the Spanish Origin of Representative Ancient American Grapevine Varieties , 2007, American Journal of Enology and Viticulture.

[32]  Javier Ibáñez,et al.  A 48 SNP set for grapevine cultivar identification , 2011, BMC Plant Biology.

[33]  F. Regner,et al.  Reconstruction of a grapevine pedigree by microsatellite analysis , 1998, Theoretical and Applied Genetics.

[34]  T. Lacombe,et al.  Genetic diversity of Moroccan grape accessions conserved ex situ compared to Maghreb and European gene pools , 2011, Tree Genetics & Genomes.

[35]  Michael S. Blouin,et al.  DNA-based methods for pedigree reconstruction and kinship analysis in natural populations , 2003 .

[36]  G. Tamura,et al.  [Microsatellite analysis]. , 1996, Nihon rinsho. Japanese journal of clinical medicine.

[37]  T. Lacombe,et al.  Linkage disequilibrium in wild French grapevine, Vitis vinifera L. subsp. silvestris , 2010, Heredity.

[38]  M. S. Grando,et al.  Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. sativa) based on chloroplast DNA polymorphisms , 2006, Molecular ecology.

[39]  P. Chabrier,et al.  famoz: a software for parentage analysis using dominant, codominant and uniparentally inherited markers , 2003 .

[40]  S. J. Fleming,et al.  Origins and ancient history of wine , 1995 .

[41]  T. Lacombe,et al.  Genetic Structuring and Parentage Analysis for Evolutionary Studies in Grapevine: Kin Group and Origin of the Cultivar Sangiovese Revealed , 2007 .