Estimation of genetic variation and relationship in potato (Solanum tuberosum L.) cultivars using AFLP markers

Amplified fragment length polymorphism (AFLP) markers were used to distinguish commercial cultivars and to assess the level of polymorphism in potato. AFLP analysis templates were made using Eco RI and Mse I as described in the Gibco BRL AFLP kit protocol. Seven primer combinations with three selective nucleotides on both primers were screened individually with 12 potato cultivars. Multiple polymorphisms could be detected in a single reaction to the extent that all 12 commercial potatoes tested could be distinguished using any one primer combination. Up to 84 polymorphic bands were detected with a single primer combination among 12 accessions. The seven primer combinations generated a total of 466 bands, of which 409 (88%) were clearly polymorphic among the cultivars. The presence or absence of each AFLP markers was scored and then phylogenetic and genetic distance analyses were used to generate dendrograms showing genetic relationships among the cultivars evaluated. The analyses based on amplified DNA fragments did not always reflect the known genetic relationships among the cultivars. These results demonstrate that AFLP DNA markers can be of great value in identification and measurement of variation, but should be treated with caution for purposes of estimating true measures of genetic similarity in potato.