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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

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Abstract

A collection of 1005 grapevine accessions was genotyped at 34 microsatellite loci (SSR) with the aim of analysing genetic diversity and exploring parentages. The comparison of molecular profiles revealed 200 groups of synonymy. The removal of perfect synonyms reduced the database to 745 unique genotypes, on which population genetic parameters were calculated. The analysis of kinship uncovered 74 complete pedigrees, with both parents identified. Many of these parentages were not previously known and are of considerable historical interest, e.g. Chenin blanc (Sauvignon × Traminer rot), Covè (Harslevelu selfed), Incrocio Manzoni 2–14 and 2–15 (Cabernet franc × Prosecco), Lagrein (Schiava gentile × Teroldego), Malvasia nera of Bolzano (Perera × Schiava gentile), Manzoni moscato (Raboso veronese × Moscato d’Amburgo), Moscato violetto (Moscato bianco × Duraguzza), Muscat of Alexandria (Muscat blanc à petit grain × Axina de tres bias) and others. Statistical robustness of unexpected pedigrees was reinforced with the analysis of an additional 7–30 SSRs. Grouping the accessions by profile resulted in a weak correlation with their geographical origin and/or current area of cultivation, revealing a large admixture of local varieties with those most widely cultivated, as a result of ancient commerce and population flow. The SSRs with tri- to penta-nucleotide repeats adopted for the present study showed a great capacity for discriminating amongst accessions, with probabilities of identity by chance as low as 1.45 × 10−27 and 9.35 × 10−12 for unrelated and full sib individuals, respectively. A database of allele frequencies and SSR profiles of 32 reference cultivars are provided.

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Acknowledgments

This research was financially supported by the Ministry of Agriculture and Forestry, project VIGNA, and by the Istituto di Genomica Applicata (IGA), Parco Scientifico e Tecnologico di Udine. The authors thank Alberto Stefan at IGA, who wrote several scripts for the management of input/output data, and Courtney Coleman at the University of Missouri State University for the critical review of the manuscript. Authors thank also Mirella Giust for field collection of samples, and Massimo Gardiman and Roberto Carraro for the visual inspection of genotypes of dubious identity.

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Authors and Affiliations

  1. Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100, Udine, Italy

    Guido Cipriani, Gabriele Di Gaspero, Michele Morgante & Raffaele Testolin

  2. Istituto di Genomica Applicata, Parco Scientifico e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100, Udine, Italy

    Alessandro Spadotto, Irena Jurman, Gabriele Di Gaspero, Michele Morgante, Alberto Policriti & Raffaele Testolin

  3. CRA-VIT, Centro di Ricerca per la Viticoltura, Viale XXVIII Aprile 26, 31015, Conegliano (TV), Italy

    Manna Crespan, Stefano Meneghetti & Enrica Frare

  4. Dipartimento di Scienze Ambientali, University of Siena, via P.A. Mattioli 4, 53100, Siena, Italy

    Rita Vignani & Mauro Cresti

  5. Dipartimento di Biotecnologie, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy

    Mario Pezzotti

  6. Scuola Superiore S. Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy

    Enrico Pe

  7. Dipartimento di Matematica e Informatica (DIMI), University of Udine, via delle Scienze 208, 33100, Udine, Italy

    Alberto Policriti

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  1. Guido Cipriani
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  2. Alessandro Spadotto
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  3. Irena Jurman
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  4. Gabriele Di Gaspero
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  5. Manna Crespan
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  8. Rita Vignani
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  13. Alberto Policriti
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  14. Raffaele Testolin
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Correspondence to Raffaele Testolin.

Additional information

Communicated by M. Frisch.

Electronic supplementary material

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S1 -

List of accessions analysed in the present study (XLS 79 kb)

S2 -

Groups of synonymy found amongst 1005 grapevine accessions. Up to two mismatches were allowed for comparison of each pair (XLS 38 kb)

S3 -

Evolutionary relationships of 795 taxa. The evolutionary history was inferred using the UPGMA method. The optimal tree with the sum of branch length = 10,160 is shown. The tree is drawn to scale with branch lengths proportional to Nei’s genetic distances. Analyses were conducted using the MEGA4 software. Accessions were categorised according to either their putative geographic origin or the most relevant growing area. Accessions are labelled with different colours according to their geographical origin as in Fig. 2 (TIFF 1844 kb)

S4 -

List of complete pedigrees (both parents identified) found using the CERVUS software. Legend: VIVC, Vitis International Variety Catalogue at the URL http://www.vivc.bafz.de/index.php; EVDB, European Vitis Data Base at the URL http://www.eu-vitis.de/index.php; Trio LOD, the Log-likelihood ratio for the parent–offspring relationship for the most likely candidate parent pair (XLS 22 kb)

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Cipriani, G., Spadotto, A., Jurman, I. 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. Theor Appl Genet 121, 1569–1585 (2010). https://doi.org/10.1007/s00122-010-1411-9

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