Theor Appl Genet (1995) 91:987 993 9 Springer-Verlag 1995 C. Lanaud - A. M. Risterueei 9 A. K. J. N'Goran D. Clement 9 M. H. Flament 9 V. Laurent 9 M. Falque A genetic linkage map of Theobroma cacao L. Received: 3 January 1995 / Accepted: 12 May 1995 Abstract A linkage map of the cocoa genome compri- sing 193 loci has been constructed. These loci consist of 5 isozymes, 101 cDNA/RFLPs, 4 loci from genes of known function, 55 genomic DNA/RFLPs and 28 RAPDs. A population of 100 individuals derived from a cross between two heterozygous genotypes was used. Segregation analyses were performed with the JoinMap program. Ten linkage groups, which putatively corre- spond to the ten gametic chromosomes of cocoa, were identified. The map covers a total length of 759 cM with a 3.9 cM average distance between 2 markers. A small fraction (9 %) of the markers deviated significantly from the expected Mendelian ratios. Key words Theobroma cacao 9 Isozyme 9 RFLP RAPD 9 Linkage map Introduction Theobroma cacao L. (2n = 2x = 20) (Carletto 1946) is native to Central and South America. Its genome is small (0.4pg/1C) (Lanaud etal. 1992; Figueira etal. 1992), and three main genetic groups may be distin- guished, Criollo, Forastero and their hybrid form, Trinitario. Present-day breeding schemes are based on crosses between parents belonging to these different groups, but in tree crops such as cocoa, with a long generation time, breeding and classical genetic studies do not lead to rapid progress. Genetic markers may be particularly helpful when used to improve breeding Communicated by J. S. Beckmann C. Lanaud ([]) 9 A. M. Risterucci 9 A. K. J. N'Goran 9 M. H. Fla- ment 9 V. Laurent C1RAD-Biotrop, BP 5035, F-34032, Montpellier Cedex, France D. Clement 9 M. Falque IDEFOR/DCC and CIRAD-CP, 01 BP, 1827 Abidjan 01, Ivory Coast strategies and increase our knowledge of the genetics of important agronomic and quality traits. Restriction fragment length polymorphism (RFLP) markers, first proposed by Botstein et al. (1980) have been extensively used to construct genetic maps in many species, such as tomato (Tanksley et al. 1992), potato (Bonierbale et al. 1988; Gebhart et al. 1989, 1991) and Brassica (Landry et al. 1991; Chyi et al. 1992). Random amplified poly- morphic DNA (RAPD) markers (Williams et al. 1990) have been more recently used and have also helped in the construction or completion of several linkage maps in species such as Arabidopsis thaliana (Reiter et al. 1992), slashpine (Nelson et al. 1993) or Sorghum (Chit- tenden et al. 1994). This paper presents the first linkage map of the cocoa genome containing 193 RFLP, RAPD and isozyme markers. Materials and methods Plant material Parental accessions The two parents of the mapping population were: UPA402: This is an upper Amazon Forastero clone obtained from a sib-mating involving IMC60 and Na 34, two Forastero genotypes collected in Ecuador. Forastero clones are generally vigorous, con- tain many interesting agronomic and disease resistance traits but generally give a chocolate of only a medium quality. UF676: This is a Trinitario selection (hybrid between Forastero and Criollo) made by the United Company in Costa Rica. Criollo clones, which originated from Central America, have unfavorable agronomic traits but give a fine chocolate. Both parental clones are more or less heterozygous, and pedigree and previous isozyme analyses (Lanaud 1987) indicated that UF676 has a higher level of heterozygosity than UPA402. Thus, a specific analytical approach and software for mapping were required. Mapping population A segregating population of 100 individuals from a cross between UPA402 (~) and UF676 (d') was used for the genetic linkage analyses. This progeny is still standing in the Ivory coast (IDEFOR/DCC).