Molecular Breeding 3: 359–369, 1997. 359 c 1997 Kluwer Academic Publishers. Printed in Belgium. The use of AFLPs to examine genetic relatedness in barley Roger P. Ellis 1 , James W. McNicol 2 , Eileen Baird 1 , Allan Booth 1 , Pat Lawrence 1 , Bill Thomas 1 & Wayne Powell 1 1 Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK ( author for correspondence; e-mail rellis @scri.sari.ac.uk) 2 Biomathematics and Statistics Scotland, Scottish Crop Research Institute, Invergowrie, Dundee DD2 5DA, UK Received 12 February 1997; accepted in revised form 23 May 1997 Key words: AFLPs, barley, genetic diversity, kinship Abstract The generation of AFLPs in spring barley cultivars provided genetic information relating to the development of the crop in the UK since 1953. Principal co-ordinate (PCO) analysis of genetic similarities (gs) confirmed the marked contrast in the cultivars used in the 1970s and 1980s. The earliest cultivars, many derived from Proctor, were succeeded by tall-strawed, disease-resistant types with high yield but poor malting potential. In the 1980s they were in turn replaced by short-strawed cultivars with excellent yield and good malting quality, which originated from Triumph. A PCO plot of gs provided insight into the effects of selection for disease resistance and the antagonism between malting quality and particular resistance genes. The analysis of gs was more useful than pedigrees and estimates of kinship in revealing the genetic relationship between cultivars. Theoretical considerations for maximising the efficiency of an AFLP genotyping programme are discussed in the context of the number of primer pairs required to distinguish genotypes at varying levels of similarity. Introduction For the effective management of germplasm resources and biodiversity in breeding programmes it is neces- sary to characterise material at both the agronomic (phenotype) and genetic levels. Plant breeders focus on agronomic and morphological traits to generate new cultivars and to meet the legal requirements for cultivar registration, i.e. distinctness, uniformity and stability. The recent development of a range of DNA- based profiling methods (see [17] for a review) offers new opportunities for genotype assessment. Restric- tion fragment length polymorphisms (RFLPs) have been used extensively to characterise plant germplasm [3, 5, 11] but often require large numbers of probe by restriction enzyme combinations to achieve gen- otype discrimination and adequate genome coverage. Methods deployed for DNA fingerprinting are there- fore often characterised by high multiplex ratios, which refers to the number of different genetic loci that may be simultaneously analysed per experiment [14, 15]. Amplified fragment length polymorphism (AFLP), first developed by Zabeau and Vos [28], is a repro- ducible, highly multiplex assay with the ability to gen- erate large numbers of polymorphic genetic loci. This technology has been used to analyse diversity in rice [8], soybean [10], tea [13] and an endangered plant species (Astragalus cremnophylax) [26]. The generation of molecular marker profiles based on AFLPs allows a retrospective analysis of the con- sequences of breeding and selection on the production of new cultivars. In addition, it can facilitate the stra- tegic planning of new breeding approaches based on combining and selecting new combinations of geno- types to maximise the rate of cultivar improvement. In order to evaluate the role of AFLPs in the character- isation of plant breeding germplasm we have focused on barley since there are well documented improve- ments of grain yield and quality associated with the introduction of new cultivars [6, 18, 20]. Our specific objectives were as follows: (1) to establish how useful AFLPs are in determining unique-