Genetic Resources and Crop Evolution 50: 649–661, 2003. 649  2003 Kluwer Academic Publishers. Printed in the Netherlands. Genetic diversity and differentiation in Ethiopian populations of Phytolacca dodecandra as revealed by AFLP and RAPD analyses 1, 2 3 * Kassa Seman , Asmund Bjornstad and Brita Stedje 1 2 Ethio-Coffee and Tea Plantation and Marketing, P. O. Box 1006, Addis Ababa, Ethiopia; Department of ˚ Horticulture and Crop Sciences, Agricultural University of Norway, P. O. Box 5022, N-1432 As, Norway; 3 * Botanical Garden and Museum, University of Oslo, Trondheimsveien 23B, N-0562 Oslo; Author for correspondence (e-mail: semagnk@yahoo.com; fax: 1 251 1 615577) Received 28 August 2001; accepted in revised form 2 April 2002 Key words: AFLP, Altitude, Endod, Genetic diversity, Phytolacca dodecandra, RAPD Abstract Amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) analyses were performed on six populations (a total of 89 individuals) of Phytolacca dodecandra (endod) collected in Ethiopia. The populations were selected based on our previous investigation to represent two altitude groups: lowland / central-highland (1600–2500 m) and highland (2501–3000 m). A total of 197 AFLP and 68 RAPD markers were scored from 5 primer pairs and 12 random primers, respectively. The overall patterns obtained for AFLPs and RAPDs from diversity, cluster and principal component analyses were very comparable. However, the moderate correlation (r 5 0.56) between AFLP and RAPD similarity matrices as well as the discrepancies in diversity estimates between the two techniques in some populations and in the lowland / central-highland plants could be due to differences in sensitivity of reaction conditions, bias in scoring of bands, number of markers used for analyses, and / or parts of the genome surveyed. For both AFLP and RAPD, the lowland / central-highland populations showed higher polymorphism and Shannon information measure (H) than the highlands. Cluster and principal component analyses performed for both marker types have also clearly demonstrated the differentiation of all the lowland / central highland plants from those of the highlands, in agreement with our previous conclusion. Markers scored from any of the five AFLP primer pairs were sufficient to clearly distinguish the two altitude groups; with RAPD, selection of about 8 informative markers produced by seven random primers was needed for the same purpose. Introduction lar markers useful for assessing plant genetic diversity (e.g. Rafalski and Tingey 1993, Staub et al. 1996). Genetic diversity of natural populations results from Numerous crops and crop relatives have been char- the interaction of drift, migration, mutation, and selec- acterized using molecular markers, at first using re- tion (Wright 1978). The interactions between these striction fragment length polymorphisms (RFLPs), factors can lead to complex genetic structures within and more commonly now with various PCR-based populations, which are often difficult to resolve. The markers: simple sequence repeats (SSRs), random use of biochemical and molecular markers can en- amplified polymorphic DNA (RAPDs), and amplified hance the understanding of such complexities (Daw- fragment length polymorphisms (AFLPs). The RFLP son et al. 1993). The assumption that forms the basis technique is, however, laborious, expensive, and few for such analysis is that genetic structure as measured loci are detected per assay. Microsatellites, also by neutral and selective genes reflects both deter- known as simple sequence repeats (SSR), are repeated ministic and stochastic evolutionary processes. Sever- short DNA motifs that offer codominant markers, al reviews have described a detailed range of molecu- often highly polymorphic (e.g. Tautz and Renz 1984)