Theor Appl Genet (1998) 97 : 51 — 59  Springer-Verlag 1998 M.-T. Cervera · J. A. Cabezas · J. C. Sancha F. Martı ´ nez de Toda · J. M. Martı ´ nez-Zapater Application of AFLPs to the characterization of grapevine Vitis vinifera L. genetic resources. A case study with accessions from Rioja (Spain) Received: 1 February 1998/Accepted: 25 February 1998 Abstract AFLPs were used to characterize 67 different grapevine accessions from a collection of D.O.Ca. Rioja in Spain. A correct selection of primers and selective nucleotides allowed us to maximize the num- ber of amplified fragments analyzed per reaction yield- ing an average of 100 per reaction, 49% of which were polymorphic. Based on the presence or absence of amplified fragments for each genotype resulting from a reaction with two primer combinations, we have established the genetic similarity between the different accessions in the collection. These results allowed us to resolve different genotypes maintained under the same name (homonyms) and to identify the same genotype under different names (synonyms) thus permitting the elimination of redundant germplasm. Furthermore, by providing information on more than 50 polymorphic loci per reaction, a few reactions were sufficient to identify distinct AFLP patterns characteristic of speci- fic clones, with different agronomic and organoleptic features, belonging to the same cultivar. The possibility for clonal identification, shown here for grapevines, can have important implications in the protection and management of clonal selections. Key words » itis vinifera · AFLPs · Cultivar identification · Clone identification Communicated by P. M. A. Tigerstedt M.-T. Cervera · J. A. Cabezas · J. M. Martı´nez-Zapater ( ) Departamento de Mejora Gene´tica y Biotecnologi´a, Subdireccio´n General de Investigacio´n y Tecnologi´a, I.N.I.A., Carretera de La Corun  a Km 7, 28040 Madrid, Spain Fax: # 34-1-3573107, e-mail: zapater@inia.es J. C. Sancha · F. Martı´nez de Toda Departamento de Agricultura y Alimentacio´n, Universidad de La Rioja, Avda. de la Paz, 105. 26004 Logron  o, La Rioja, Spain Introduction Many morphological and molecular markers have been used for the characterization of grapevine » itis vinifera (L.) germplasm. Among them, ampelographic characterization according to morphological features (Galet 1979) has been useful in the identification of well-known grape varieties and has facilitated the clari- fication of ambigous denominations or the establish- ment of phenological relationships. Unfortunately, morphological characterization is a time-consuming process, is based on characters which can be affected by the environment (Levadoux 1956), and does not gener- ally help to distinguish very close genotypes, such as clonal selections derived from a variety, or to predict genetic identity with a high probability. Other methods, based on the use of genetic variability at the level of proteins or nucleic acids, have frequently been used for these purposes with more or less success de- pending on the genetic relationships among the mater- ials analyzed and the number of markers employed. From these studies, it is possible to conclude that the high genetic variability present in vegetatively repro- duced grapevine cultivars allows their distinction with almost any molecular marker used, isozymes (Wolfe 1976; Schwennesen et al. 1982; Loukas et al. 1983; Stavrakakis and Loukas 1983; Bachmann and Blaisch 1988; Calo´ et al. 1989; Chaparro et al. 1989; Altube et al. 1991; Bachmann 1994; Cabello and Ortı´z 1995), RFLPs (Striem et al. 1990; Bourquin et al. 1993; Bowers et al. 1993; Gogorcena et al. 1993), SSRPs (Thomas and Scott 1993; Bowers and Meredith 1994), RAPDs (Collins and Symons 1993; Jean-Jaques et al. 1993; Tschammer and Zyprian 1994; Grando et al. 1995, 1996; Lodhi et al. 1997), or, more recently, ISTRs and AFLPs (Sensi et al. 1996) as well as the 5 untran- slated regions of specific genes (Geuna et al. 1997). However, in many cases these methods do not have sufficient resolution to identify with enough certainty a specific cultivar as belonging to a given variety or to