Euphytica 124: 265–271, 2002. © 2002 Kluwer Academic Publishers. Printed in the Netherlands. 265 AFLP analysis of introgression in coffee cultivars (Coffea arabica L.) derived from a natural interspecific hybrid Nayani Surya Prakash 1 , Marie-Christine Combes 2 , Naveen Somanna 3 & Philippe Lashermes 2,∗ 1 Regional Coffee Research Station, Coffee Board, R.V. Nagar, 531133, Andhra Pradesh, India; 2 IRD, GeneTrop, BP 5045, F-34032, Montpellier, France; 3 Biotechnology centre, Coffee Board, Manasagangotri, Mysore-570 006, Karnataka, India; ( ∗ author for correspondence, e-mail: Philippe.Lashermes@mpl.ird.fr) Received 4 August 2000; accepted 16 March 2001 Key words: alien gene transfer, Coffea liberica, genetic diversity, polyploid Summary S.288 an offspring of a putative spontaneous interspecific hybrid between tetraploid Coffea arabica (2n = 4x = 44) and diploid C. liberica (2n = 2x = 22) and 17 arabica coffee introgression lines (representing F 2 and F 4 ) derived from the cross S.288 x Kent arabica were evaluated for introgression of C. liberica genetic material. In all, 36 AFLP primer combinations were used in the analysis. The AFLP profiles of introgressed lines were compared to five accessions each of C. arabica and C. liberica. A total of 137 polymorphic bands were scored among the 29 accessions analysed. The introgressed genotypes exhibited 102 marker bands consisting of 65 additional bands and 37 missing bands associated with introgression of C. liberica genetic material. C. liberica accessions of EA group (C. liberica var liberica of Guinean origin) seemed to be the likely progenitor in the origin of natural hybrid. Analysis of genetic relationships in the introgressed lines suggested that introgression was limited to few fragments. Segregation and wide variation in number of marker fragments in the F 2 and F 4 progenies were attributed to chromosome recombinations. The differences in the level of introgression between introgressed parent, F 2 and F 4 groups was not pronounced. Therefore the alien genetic material appeared to be fixed and there was no elimination or counter-selection over generations, from introgressed parent to F 4 . In C. arabica accessions, only 35 polymorphic bands were seen confirming the low genetic diversity. On the contrary, although representing a small amount of alien genome introgression, the Liberica-introgressed genotypes provided notable genetic diversity. Considering the fact that the diploid species of Coffea constitute a valuable source of genetic diversity, the potential implications of variability generated by Liberica-introgressed genotypes in C. arabica breeding are discussed. Introduction Coffee is the second important commodity in global trade rated after petroleum products. It is grown in over 80 countries in the tropical and sub-tropical re- gions of the world contributing substantially to their national economies. Although the genus Coffea is reported to comprise over 80 species (Bridson & Ver- dcourt, 1988), only two species Coffea arabica L. popularly called as arabica and C. canephora Pierre, known as robusta are under commercial cultivation. Arabica, the high land coffee accounts for nearly 70 per cent of global production while robusta coffee is more adaptable for low lands and contributes remain- ing 30 per cent. Another species Coffea liberica (liber- ica coffee) stands third with a share of less than one per cent of world coffee production. Interestingly, Coffea arabica L. is the only self-fertile, allotetraploid spe- cies (2n = 4x = 44) in the genus while others, including C. canephora are diploids (2n = 22) and generally self-incompatible (Charrier & Berthaud, 1985). Re- cent molecular–cytogenetic analysis established that C. arabica is an amphidiploid formed by natural hy- bridization between C. eugenioides and C. canephora or ecotypes related to these diploid species (Lasher- mes et al., 1999). C. arabica is characterised by low genetic diversity (Lashermes et al., 1996) which has been attributed to the allotetraploid origin, reproduct-