Abstract Citrus phylogeny was investigated using RAPD, SCAR and cpDNA markers. The genotypes ana- lyzed included 36 accessions belonging to Citrus to- gether with 1 accession from each of the related genera Poncirus, Fortunella, Microcitrus and Eremocitrus. Phylogenetic analysis with 262 RAPDs and 14 SCARs indicated that Fortunella is phylogenetically close to Citrus while the other three related genera are distant from Citrus and from each other. Within Citrus, the sep- aration into two subgenera, Citrus and Papeda, desig- nated by Swingle, was clearly observed except for C. celebica and C. indica. Almost all the accessions be- longing to subgenus Citrus fell into three clusters, each including 1 genotype that was considered to be a true species. Different phylogenetic relationships were re- vealed with cpDNA data. Citrus genotypes were sepa- rated into subgenera Archicitrus and Metacitrus, as pro- posed by Tanaka, while the division of subgenera Citrus and Papeda disappeared. C. medica and C. indica were quite distant from other citrus as well from related gen- era. C. ichangensis appeared to be the ancestor of the mandarin cluster, including C. tachibana. Lemon and Palestine sweet lime were clustered into the Pummelo cluster led by C. latipes. C. aurantifolia was located in the Micrantha cluster. Furthermore, genetic origin was studied on 17 cultivated citrus genotypes by the same molecular markers, and a hybrid origin was hypothe- sized for all the tested genotypes. The assumptions are discussed with respect to previous studies; similar re- sults were obtained for the origin of orange and grape- fruit. Hybrids of citron and sour orange were assumed for lemon, Palestine sweet lime, bergamot and Volkamer lemon, while a citron × mandarin hybrid was assumed for Rangpur lime and Rough lemon. For Mexican lime our molecular data indicated C. micrantha to be the fe- male parent and C. medica as the male one. Key words Citrus · RAPD · SCAR · cpDNA · Phylogeny · Origin Introduction Different hypotheses have been formulated on the origin of Citrus. In general, Citrus is believed to have originat- ed in the tropical and subtropical regions of Southeast Asia and then spread to other continents (Webber 1967; Calabrese 1992). Citrus taxonomy and phylogeny, how- ever, are very complicated, controversial and confusing, mainly due to sexual compatibility between Citrus and related genera, the high frequency of bud mutations and the long history of cultivation and wide dispersion. In the past, studies on relationships between genera and species were carried out based mainly on morpho- logical characteristics. Numerous classification systems have been formulated, among which those of Swingle (1943) and Tanaka (1977) have been the most widely ac- cepted. Even these two researchers, however, have quite different concepts with respect to species classification, as Swingle included only 16 species in Citrus while Tanaka described 162. Later phylogenetic analysis by Scora (1975) and Barrett and Rhodes (1976) suggested that there were only 3 true species within the cultivated Citrus, i.e. citron (Citrus medica L.), mandarin (C. reti- culata Blanco) and pummelo [C. grandis (L.) Osb.] (in 1988 Scora added another true species: C. halimii Stone). The other genotypes were derived from hybrid- ization between these true species. More recently, this concept has gained further support from various studies using biochemical and molecular markers, including iso- zymes (Torres et al. 1978; Fang et al. 1993; Herrero et al. 1996), organeller genome analysis (Green et al. 1986; Yamamoto et al. 1993) and microsatellites (Fang and Roose 1997; Fang et al. 1998). Communicated by P.M.A. Tigerstedt E. Nicolosi ( ✉ ) · Z.N. Deng · A. Gentile · S. La Malfa G. Continella · E. Tribulato Istituto di Coltivazioni arboree, University of Catania, Via Valdisavoia, 5, 95123 Catania, Italy Fax: +39-095-356322 e-mail: nicoeli@mbox.fagr.unict.it Theor Appl Genet (2000) 100:1155–1166 © Springer-Verlag 2000 ORIGINAL PAPER E. Nicolosi · Z.N. Deng · A. Gentile · S. La Malfa G. Continella · E. Tribulato Citrus phylogeny and genetic origin of important species as investigated by molecular markers Received: 5 October 1999 / Accepted: 3 November 1999