-1 The use of morphological and AFLP markers in diversity analysis of linseed W. ADUGNA, M.T. LABUSCHAGNE* and C.D. VILJOEN Department of Plant Sciences, UFS, P.O. Box 339, Bloemfontein 9300, South Africa *Author for correspondence (e-mail: labuscm.sci@mail.uovs.ac.za; phone: +27514012715; fax: +27514305692) Received 27 April 2004; accepted in revised form 25 April 2005 Key words: AFLP, Genetic diversity, Linseed, Morphology Abstract. Different methods of genetic diversity measures could give better judgment of differen- tiating important accessions for growers, germplasm curators and plant breeders. Data of 60 accessions of linseed, mainly from Ethiopia, were used to assess their genetic diversity, employing morphological and amplified fragment length polymorphism (AFLP) methods. Analyses of genetic distance, principal components and clusters showed the presence of a wide range of diversity among the studied accessions. The mean for genetic distance estimates of the entire 1770 pairwise acces- sions was 0.6684 for morphology, while that of AFLP was 0.5734. These genetic distances varied from zero to one for morphology in contrast to 0.29 to 0.71 of the AFLP. Morphological and AFLP based clusters and their accompanying analyses showed different hierarchical patterns of genetic diversity among the accessions. Despite their disparity, the two diversity measures were found independently useful for assessing the degree of relatedness and the overall patterns of genetic variation among the analysed linseed accessions. Introduction Diversity analysis of linseed (Linum usitatissimum L.) is an important com- ponent for efficient management and utilisation of its genetic resources, and for proper handling of the seed certification programs (Frankel 1989; Blakeney 2002). Accurate identification of genotypes or varieties is very useful during all the steps of breeding from initial parent selection to the final utilisation of cultivars in production schemes (UPOV 1991). Diversity analysis is an essential process for clear and sound identification of the genetic relatedness of the available genetic resources. It is also required for effective choice of parents for subsequent crossing and selection of the progenies. That is why breeders look for suitable descriptors or genetic markers. Morphological or phenotypic descriptors have traditionally been used to distinguish one accession from the other. Although this type of agronomical characterisation provides useful information, they are subjected to environ- mental influences, time-consuming and they must be assessed during a fixed vegetative phase of the crop (Swanepoel 1999). Conversely, the biochemical Biodiversity and Conservation (2006) 15:3193–3205 Ó Springer 2006 DOI 10.1007/s10531-005-6970-8