Genet. Res., Camb. (2003), 81, pp. 179–192. With 4 figures. f 2003 Cambridge University Press 179 DOI: 10.1017/S0016672303006177 Printed in the United Kingdom Genetic structure and differentiation in cultivated grape, Vitis vinifera L. MALLIKARJUNA K. ARADHYA1,GERALDS.DANGL2,BERNARDH.PRINS1, JEAN-MICHEL BOURSIQUOT3,M.ANDREWWALKER2,CAROLEP.MEREDITH2 AND CHARLES J. SIMON1* 1 National Clonal Germplasm Repository, US Department of Agriculture, One Shields Avenue, University of California, Davis, CA 95616, USA 2 Department of Viticulture and Enology, University of California, Davis, CA 95616, USA 3 UMR, 1097, Equipe Vigne, ENSA.M-INRA, Montpellier, France (Received 11 July 2002 and in revised form 30 December 2002) Summary 222 cultivated (Vitis vinifera) and 22 wild (V. vinifera ssp. sylvestris) grape accessions were analysed for genetic diversity and differentiation at eight microsatellite loci. A total of 94 alleles were detected, with extensive polymorphism among the accessions. Multivariate relationships among accessions revealed 16 genetic groups structured into three clusters, supporting the classical eco-geographic grouping of grape cultivars: occidentalis, pontica and orientalis. French cultivars appeared to be distinct and showed close affinity to the wild progenitor, ssp. sylvestris from south-western France (Pyrenees) and Tunisia, probably reflecting the origin and domestication history of many of the old wine cultivars from France. There was appreciable level of differentiation between table and wine grape cultivars, and the Muscat types were somewhat distinct within the wine grapes. Contingency x2 analysis indicated significant heterogeneity in allele frequencies among groups at all loci. The observed heterozygosities for different groups ranged from 0.625 to 0.9 with an overall average of 0.771. Genetic relationships among groups suggested hierarchical differentiation within cultivated grape. The gene diversity analysis indicated narrow divergence among groups and that most variation was found within groups (y85%). Partitioning of diversity suggested that the remaining variation is somewhat structured hierarchically at different levels of differentiation. The overall organization of genetic diversity suggests that the germplasm of cultivated grape represents a single complex gene pool and that its structure is determined by strong artificial selection and a vegetative mode of reproduction. 1. Introduction on a recent archaeological finding in the Zagros mountains of Iran, McGovern et al. (1996) suggested Cultivated grape, Vitis vinifera L., is the sole European 5400–5000 BC as the probable period of domestication representative of the genus Vitis L., a large member of of the grape. Vitaceae with y60 species (Galet, 1988). Two-thirds Currently, most botanists regard the wild ancestral of these species are native to North America and one- grape V. sylvestris as the primitive form of the culti- third is distributed over central and east Asia. The vated grape because of the close morphological resem- cultivated grape is believed to have been domesticated blance and free gene flow between them (Heywood & around 4000 BC from a perennial wild grape originally Zohary, 1991) and consequently have reduced its taxo- classified as V. sylvestris C.C. Gmelin occurring from nomic status to subspecies level within the V. vinifera north-eastern Afghanistan to the southern borders of crop complex (Levadoux, 1956). The wild grapes are the Black Sea and the Caspian Sea (Zohary & Spiegel- predominantly forest climbers and occur in disjunct Roy, 1975; Ketsa & Verheij, 1992). However, based populations from the Atlantic coast to Tadzhikistan * Corresponding author. Tel: +1 530 752 6504. Fax: +1 530 and the western Himalayas (Zohary & Hopf, 1993). 752 5974. e-mail: [email protected] They occasionally come into contact with cultivated M. K. Aradhya et al. 180 Table 1. Grape germplasm accessions included in the study (organized into 16 groups as illustrated in Fig. 1). Parentheses list first the grape type (T, table; W, wine; TW, table/wine dual; S, sylvestris), then the country (abbreviated according to the ISO3166 code; ? represents unknown origin) and finally the number of samples assayed Group 1 17 Vitis vinifera ssp. sylvestris NT1 (S/TUN/1) 1 Ab jusht (T/AFG/2) 18 Treixadura Blanca (W/ESP/1) 2 Askari (T/IRN/1) 19 Vilana (W/GRC/2) 3 Assirtico (W/GRC/5) 20 Vidiano (W/GRC/1) 4 Azzazy (T/MAR/1) 21 Volitsa B (W/GRC/1) 5 Bez el Anza (W/EGY/1) Group 4 6 Black Kishmish (T/SUN/3) 1 Affenthaler (W/DEU/1) 7 DVIT715 (T/?/1) 2 Black Damascus (T/?/1) 8 Fahri (T/AFG/1) 3 Cornichon (T/?/1) 9 Hassaine (T/TUR/1) 4 Malvasia (W/ITA/1) 10 Husseine (T/AFG/2) 5 Robola Kokkini (W/GRC/1) 11 Kandahar (T/AFG/1) 6 Sultana (T/TUR/1) 12 Kandahari (T/AFG/1) 7 Sultana Moschata (T/ITA/3) 13 Khalili (T/AFG/1) 8 Tavriz (TW/AZB/1) 14 Kishmish of Vir (T/SUN/1) 9 Tokay (T/ALG/1) 15 Kishmish Sorkh (T/AFG/2) 16 Kishmishi (T/AFG/1) Group 5 17 Mavroudi School of Patras (TW/GRC/1) 1 Asprouda Mikinon (W/GRC/1) 18 Monukka (T/AFG/2) 2 Aspruda Halkidos (W/GRC/2) 19 Takhani (T/AFG/1) 3 Aspruda Zakinthou (W/GRC/1) 20 Thompson Seedless (T/TUR/7) 4 Divromos (W/GRC/1) 5 DVIT881 (TW/?/1) Group 2 6 Karvouniariz (W/GRC/1) 1 Black Corinth (T/GRC/2) 7 Lagorthi B (TW/GRC/1) 2 Chaouch (T/GRC/3) 8 Maloukato (W/GRC/2) 3 Dabouki (T/ISR/1) 9 Mammolo Toscano (TW/ITA/1) 4 Daphne (TW/GRC/3) 10 Mavrodaphne (W/GRC/5) 5 Dolcetto (W/ITA/1) 11 Migdali (W/GRC/1) 6 Fraoula Kokkini (T/GRC/1) 12 Prune de Cazouls (T/?/1) 7 Hakiki (T/GRC/2) 13 Skiadopoulo (W/GRC/2) 8 Kislev (T/ISR/1) 14 Tsoupi (TW/GRC/1) 9 Kurutaktas (T/GRC/1) 15 Vertzami (W/GRC/2) 10 Ladikinah (W/GRC/3) 16 Zakinthino (W/GRC/2) 11 Leanoy (W/SUN/1) 12 Medaur (T/ISR/1) Group 6 13 Migdali (W/GRC/1) 1 Sciacarello (W/FRA/1) 14 Nava (T/ISR/1) 2 V. vinifera ssp. sylvestris NT6 (S/TUN/1) 15 Nemea (W/GRC/2) 3 V. vinifera ssp. sylvestris NT10 (S/TUN/1) 16 Petinos (T/GRC/1) 4 V. vinifera ssp. sylvestris NT12 (S/TUN/1) 17 Red Malaga (T/ESP/1) Group 7 18 Rhasaki Anatolico (T/GRC/1) 1 Bequignol (W/FRA/1) 19 Rodiares (TW/GRC/1) 2 Cabernet Sauvignon (W/FRA/1) 20 Romeiko (W/GRC/3) 3 Gewurztraminer (W/FRA/3) 21 Shami (T/GRC/1) 4 Mueller-thurgau (W/DEU/1) 22 Sidezitis (T/GRC/1) 5 Perle (W/DEU/1) 23 Thrapsathiri B (W/GRC/1) 6 Petite Manseng (W/FRA/1) 24 Trapanlarin Kara (TW/SUN/1) 7 Sauvignon Gris (W/FRA/1) 25 Ughetta (W/ITA/1) 8 V. vinifera ssp. sylvestris NT1 (S/TUN/1) 26 White Corinth (T/GRC/1) 9 V. vinifera ssp. sylvestris NT4 (S/TUN/1) Group 3 10 V. vinifera ssp. sylvestris NT7 (S/TUN/1) 1 A’asemi (T/YEM/1) 11 V. vinifera ssp. sylvestris NT9 (S/TUN/1) 2 Aglianico (W/ITA/1) 13 Touriga Nacional (W/PRT/1) 3 Boal Dulce (TW/DZA/1) Group 8 4 Daphnata (TW/GRC/1) 1 Cabernet Franc (W/FRA/2) 5 DVIT652 (TW/?/1) 2 Merlot (W/FRA/1) 6 DVIT789 (TW/?/1) 3 Mondeuse noire (W/FRA/1) 7 Goustolidi (W/GRC/3) 4 Petite Verdot (W/FRA/1) 8 Kotsifali (W/GRC/3) 5 V. vinifera ssp. sylvestris F1 (S/FRA/1) 9 Lagorthi A (W/GRC/2) 6 V. vinifera ssp. sylvestris F2 (S/FRA/1) 10 Lianoroi (T/GRC/2) 7 V. vinifera ssp. sylvestris F3 (S/FRA/1) 11 Mandilaria (W/GRC/4) 8 V. vinifera ssp. sylvestris F4 (S/FRA/1) 12 Mausac Blanc (W/FRA/1) 9 V. vinifera ssp. sylvestris F5 (S/FRA/1) 13 Monica (W/ITA/3) 10 V. vinifera ssp. sylvestris F6 (S/FRA/2) 14 Pedro Ximenez (W/ESP/1) 11 V. vinifera ssp. sylvestris F7 (S/FRA/1) 15 Plavac Mali (W/HRV/1) 12 V. vinifera ssp. sylvestris F8 (S/FRA/1) 16 Plito (W/GRC/1) 13 V. vinifera ssp. sylvestris F9 (S/FRA/1) Genetic diversity in Vitis vinifera 181 Table 1. (cont.). 14 V. vinifera ssp. sylvestris F10 (S/FRA/1) 8 Dan ben Chana (T/ISR/1) 15 V. vinifera ssp. sylvestris F11 (S/FRA/1) 9 Dermatas (TW/GRC/2) 16 V. vinifera ssp. sylvestris F12 (S/FRA/1) 10 Doradillo (W/ESP/1) 17 V. vinifera ssp. sylvestris NT3 (S/TUN/1) 11 Emperor (T/USA/2) 18 V. vinifera ssp. sylvestris NT5 (S/TUN/1) 12 Folle Blanche (W/FRA/3) 13 Grec Rouge (TW/FRA/1) Group 9 14 Ithani Lefko (W/GRC/2) 1 Aligote (W/FRA/1) 15 Ithani Mavro (W/GRC/3) 2 Chardonnay (W/FRA/2) 16 Kratosija (W/YUG/1) 3 Chasselas Ciotat (TW/FRA/2) 17 Malaga (T/FRA/1) 4 Lagrain (W/ITA/2) 18 Mavroudi (W/GRC/1) 5 Madam Matijas (T/HUN/1) 19 Montils (W/FRA/1) 6 Melon (W/FRA/1) 20 Muscat Oliver (TW/HUN/1) 7 Muscat Ottonel (W/FRA/1) 21 Periquita (W/PRT/1) 8 Perla di Csaba (TW/ITA/1) 22 Perle de Csaba (T/HUN/1) 9 Pinot Nior (W/FRA/7) 23 Rondinella (W/ITA/1) Group 10 24 Ruby Cabernet (W/USA/1) 1 Durif (W/FRA/1) 25 Sereksiya Rosavi (W/SUN/1) 2 Juracon Noir (W/FRA/1) 26 Terret blanc (W/FRA/1) 3 Malbec (W/FRA/1) 27 Voivoginiova (TW/CHN/1) 4 Marsanne (W/FRA/1) 28 Vranac (W/YUG/2) 5 Negrette (W/FRA/2) 29 Vuthomato (T/GRC/1) 6 Peloursin (W/FRA/1) 30 Xynomavro (W/GRC/3) Group 11 31 Zeni (T/LBN/1) 1 Alicante Bouschet (W/FRA/2) 32 Zimsko Belo (T/YUG/1) 2 Angulata (T/GRC/1) 33 Zinfandel (W/YUG/1) 3 Araklinos (W/GRC/3) Group 14 4 Aramon (W/FRA/1) 1 Aleatico (W/ITA/1) 5 Asprouda Patron (W/GRC/1) 2 Carolina Blackrose (T/USA/1) 6 Aspruda Ariloghi (W/GRC/2) 3 Criolla Mesa (T/ARG/1) 7 Aspruda Mikinon (W/GRC/1) 4 Kontehgalo (T/GRC/1) 8 Chisostaphylo (W/GRC/1) 5 Malagouzia (W/GRC/3) 9 Fileri (W/GRC/4) 6 Malvasia Bianca (W/ITA/1) 10 French Colombard (W/FRA/1) 7 Moschato Mavro (W/GRC/1) 11 Ghlicopati (W/GRC/1) 8 Moschato Samou (W/GRC/4) 12 Grand Noir (W/FRA/1) 9 Moschardina (W/GRC/1) 13 Hunisa (T/TUR/1) 10 Muscat of Alexandria (TW/ITA/2) 14 Jurancon Blanc (W/FRA/1) 11 Ohanes (T/ESP/1) 15 Kontocladi (T/GRC/1) 12 Opale (T/ITA/1) 16 Kritiko (W/GRC/1) 13 Volitsa A (W/GRC/1) 17 Liatiko (W/GRC/3) Group 15 18 Limberger (W/HUN/3) 1 Barbera (W/ITA/2) 19 Petite Bouschet (W/FRA/1) 2 Corbeau