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.
Similar content being viewed by others
References
Akkak A, Boccacci P, Botta R (2007) ‘Cardinal’ grape parentage: a case of a breeding mistake. Genome 50:325–328
Alleweldt G, Spiegel-Roy P, Reisch (1990) Grapes (Vitis). In: Moore JN, Ballington JR Jr (eds) Genetic resources of temperate fruit and nut crops, vol I. ISHS, Leuven, pp 291–327
Amos W, Hoffman JI, Frodsham A, Zhang L, Best S, Hill AVS (2007) Automated binning of microsatellite alleles: problems and solutions. Mol Ecol Notes 7:10–14
Arroyo-García R, Ruiz-García L, Bolling L, Ocete R, López MA, Arnold C, Ergul A, Söylemezoğlu G, Uzun HI, Cabello F, Ibáñez J, Aradhya MK, Atanassov A, Atanassov I, Balint S, Cenis JL, Costantini L, Gorislavets S, Grando MS, Klein BY, McGovern PE, Merdinoglu D, Pejic I, Pelsy F, Primikirios N, Risovannaya V, Roubelakis-Angelakis KA, Snoussi H, Sotiri P, Tamhankar S, This P, Troshin L, Malpica JM, Lefort F, Martinez-Zapater JM (2006) Multiple origins of cultivated grapevine (Vitis vinifera L, ssp sativa) based on chloroplast DNA polymorphisms. Mol Ecol 15(12):3707–3714
Bautista J, Dangl GS, Yang J, Reisch B, Stover E (2008) Use of genetic markers to assess pedigrees of grape cultivars and breeding program selections. Am J Enol Vitic 59(3):248–254
Botstein D, White RL, Skolnick M, Davis RW (1980) Construction of a genetic linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 32:314–331
Boursiquot JM, Lacombe T, Bowers J, Meredith C (2004) Le Gouais, un cépage clé du patrimoine viticole européen [Gouais, a key vine of the European wine heritage]. Bull l’OIV 77(875–876):5–19
Bowers JE, Meredith CP (1997) The parentage of classic wine grape: Cabernet Sauvignon. Nat Genet 16:84–87
Bowers J, Boursiquot JM, This P, Chu K, Johansson M, Meredith C (1999) Historical genetics: the parentage of Chardonnay, Gamay and other wine grapes of Northeastern France. Science 285:1562–1565
Butler JM (2006) Genetics and genomics of core short tandem repeats loci used in human identity testing. J Forensic Sci 51(2):253–265
Calò A, Scienza A, Costacurta A (2001) Vitigni d’Italia. Calderini Edagricole, Bologna, Italy
Cancellier S, Roncador I (1997) Gli incroci Manzoni. La Tipografica 2000. Treviso, Italy
Cipriani G, Marrazzo MT, Di Gaspero G, Pfeiffer A, Morgante M, Testolin R (2008) A set of microsatellite markers with long core repeat optimized for grape (Vitis spp.) genotyping. BMC Plant Biol 8:127
Cipriani G, Di Gaspero G, Canaguier A, Jusseaumes J, Tassin J, Lemainque A, Adam-Blondon AF, Testolin R (2009) Molecular linkage maps: Strategies, resources and achievements. In: Zapater MM, Adam-Blondon AF (eds) Grapes. Series on “Genomics of fruits and vegetables crops”, Series Editor: Chittaranjan Kole. Sciences Publishers, Enfield (in press)
Costantini L, Monaco A, Vouillamoz J, Forlani M, Grando MS (2005) Genetic relationships among local Vitis vinifera cultivars from Campania (Italy). Vitis 44(1):25–34
Crespan M (2003) The parentage of Muscat of Hamburg. Vitis 42:193–197
Crespan M (2004) Evidence on the evolution of polymorphism of microsatellite markers in varieties of Vitis vinifera L. Theor Appl Genet 108:231–237
Crespan M, Milani N (2001) The Muscats: a molecular analysis of synonyms, homonyms and genetic relationships within a large family of grapevine cultivars. Vitis 40(1):23–30
Crespan M, Crespan G, Giannetto S, Meneghetti S, Costacurta A (2007) Vitouska’ is the progeny of ‘Prosecco tondo’ and ‘Malvasia bianca lunga. Vitis 46(4):192–194
Crespan M, Calò A, Giannetto S, Sparacio A, Storchi P, Costacurta A (2008a) ‘Sangiovese’ and ‘Garganega’ are two key varieties of the Italian grapevine assortment evolution. Vitis 47(2):97–104
Crespan M, Coletta A, Crupi P, Giannetto S, Antonacci D (2008b) Malvasia nera di Brindisi/Lecce’ grapevine cultivar (Vitis vinifera L.) originated from ‘Negroamaro’ and ‘Malvasia bianca lunga’. Vitis 47(4):205–212
Di Vecchi Staraz M, Bandinelli R, Borselli M, This P, Boursiquot JM, Laucou V, Lacombe T (2007) Genetic structuring and parentage analysis for evolutionary studies in grapevine: kin group and origin of the cultivar Sangiovese revealed. J Amer Soc Hort Sci 132(4):514–524
Ewen KR, Bahlo M, Treloar SA, Levinso DF, Mowry B, Barlow JW, Foote SJ (2000) Identification and analysis of error types in high-throughput genotyping. Am J Hum Genet 67:727–736
Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587
Galet P (2000) Dictionnaire encyclopedique des cépages. Hachette Pratique, Paris, France
Gouesnard B, Bataillon TM, Decoux G, Rozale C, Schoen DJ, David JL (2001) MSTRAT: an algorithm for building germplasm core collections by maximizing allelic or phenotypic richness. J Heredity 92:93–94
Ibáñez J, Vargas AM, Palancar M, Borrego J, de Andrés MT (2009) Genetic relationships among table-grape varieties. Am J Enol Vitic 60(1):35–42
Idury RM, Cardon LR (1997) A simple method for automated allele binning in microsatellite markers. Genome Res 7:1104–1109
Jaillon O, Aury J-M, Noel B, Policriti A, Clepet C, Casagrande A, Choisne N, Aubourg S, Vitulo N, Jubin C, Vezzi A, Legeai F, Hugueney P, Dasilva C, Horner D, Mica E, Jublot D, Poulain J, Bruyere C, Billault A, Segurens B, Gouyvenoux M, Ugarte E, Cattonaro F, Anthouard V, Vico V, Del Fabbro C, Alaux M, Di Gaspero G, Dumas V, Felice N, Paillard S, Juman I, Moroldo M, Scalabrin S, Canaguier A, Le Clainche I, Malacrida G, Durand E, Pesole G, Laucou V, Chatelet P, Merdinoglu D, Delledonne M, Pezzotti M, Lecharny A, Scarpelli C, Artiguenave F, Pé E, Valle G, Morgante M, Caboche M, Adam-Blondon A-F, Weissenbach J, Quétier F, Wincker P (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449:463–468
Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106
Kloosterman AD, Budowle B, Daselaar P (1993) PCR-amplification and detection of the human DIS80 VNTR locus. Amplification conditions, population genetics and application in forensic analysis. Int J Leg Med 105:257–264
Konovalov DA, Manning C, Henshaw MT (2004) KINGROUP: a computer program for pedigree relationship reconstruction and kin group assignments using genetic markers. Mol Ecol Notes 4:779–782
Lacombe T, Boursiquot JM, Dechesne F, Varès D, This P (2007) Relationships and genetic diversity within the accessions related to Malvasia Held in the Domaine de Vassal Grape Germplasm Repository. Am J Enol Vitic 58(1):124–131
Le Cunff L, Fournier-Level A, Laucou V, Vezzulli S, Lacombe T, Adam-Blondon AF, Boursiquot JM, This P (2008) Construction of nested genetic core collections to optimize the exploitation of natural diversity in Vitis vinifera L. subsp sativa. BMC Plant Biol 8:31
Marshall TC, Slate J, Kruuk LEB, Pemberton JM (1998) Statistical confidence for likelihood-based paternity inference in natural populations. Mol Ecol 7:639–655
Matsuoka Y, Vigouroux Y, Goodman MM, Jesus Sanchez G, Buckler E, Doebley J (2002) A single domestication for maize shown by multilocus microsatellite genotyping. Proc Natl Acad Sci USA 99:6080–6084
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci USA 70:3321–3323
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Olmo HP (1995) Grapes. In: Smartt J, Simmonds NW (eds) Evolution of crop plants, 2nd edn. Longman, London, pp 485–490
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295
Pemberton JM, Slate J, Bancroft DR, Barrett JA (1995) Non-amplifying alleles at microsatellite loci: a caution for parentage and population studies. Mol Ecol 4:249–252
Pritchard JK, Wen W (2004) Documentation for structure software, Version 2. Department of Human Genetics, University of Chicago, Chicago, USA
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure from multi-locus genotype data. Genetics 155:945–959
Reynolds J, Wier BS, Cockerham CC (1983) Estimation of the coancestry coefficient: basis for a short-term genetic distance. Genetics 105:767–779
Roncador I, Malossini U, Grando MS, Mattivi F, Nicolini G, Versini G (2002) Caratteristiche viti-enologiche dei nuovi vini Goldtraminer, Sennen e Gosen. Terra Trentina 48:28–36
Schlötterer C (2004) The evolution of molecular markers—just a matter of fashion? Nat Rev Genet 5:63–69
Schoen DJ, Brown AHD (1993) Conservation of allelic richness in wild crop relatives is aided by assessment of genetic markers. Proc Natl Acad Sci USA 90:10623–10627
Sefc KM, Steinkellner H, Glőssl J, Kampfer S, Regner F (1998) Reconstruction of a grapevine pedigree by microsatellite analysis. Theor Appl Genet 97:227–231
Sefc KM, Lopes MS, Lefort F, Botta R, Boubelakis-Angelakis KA, Ibañez J, Pejić I, Wagner HW, Glőssl J, Steinkellner H (2000) Microsatellite variability in grapevine cultivars from different European regions and evaluation of assignment testing to assess the geographic origin of cultivars. Theor Appl Genet 100:498–505
Summers K, Amos W (1997) Behavioral, ecological and molecular genetic analyses of reproductive strategies in the Amazonian dart-poison frog, Dendrobates ventrimaculatus. Behav Ecol 8:260–267
Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599
This P, Jung A, Boccacci P, Borrego J, Botta R, Costantini L, Crespan M, Dangl GS, Eisenheld C, Ferreira-Monteiro F, Grando S, Ibáñez J, Lacombe T, Laucou V, Magalhães R, Meredith CP, Milani N, Peterlunger E, Regner F, Zulini L, Maul E (2004) Development of a standard set of microsatellite reference alleles for identification of grape cultivars. Theor Appl Genet 109:1448–1458
This P, Lacombe T, Thomas MR (2006) Historical origins and genetic diversity of wine grapes. Trends Genet 22(9):511–519
Vouillamoz JF, Grando MS (2006) Genealogy of wine grape cultivars: ‘Pinot’ is related to ‘Syrah’. Heredity 97:102–110
Vouillamoz JF, Monaco A, Costantini L, Stefanini M, Scienza A, Grando MS (2007) The parentage of ‘Sangiovese’, the most important Italian wine grape. Vitis 46(1):19–22
Waits LP, Luikart G, Taberlet P (2001) Estimating the probability of identity among genotypes in natural populations: cautions and guidelines. Mol Ecol Notes 10:249–256
Wright S (1951) The genetical structure of populations. Ann Eugen 15:323–354
Zohary D, Hopf M (2000) Domestication of plants in the old world, 3rd edn. Oxford University Press, Oxford
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.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by M. Frisch.
Electronic supplementary material
Below is the link to the electronic supplementary material.
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)
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00122-010-1411-9