RAPD IDENTIFICATION OF MICROSATELLITES IN DAPHNIA

Simple sequence repeats (SSRs, or microsatellites) have been constantl y gaining importance as single-locus DNA markers in population genetic s and behavioural ecology. We tested a PCR-based strategy for finding microsatellite loci in anonymous genomes, which avoids genomic library construction and screening, and the need for larger amounts of DNA. I n the first step, parts of a genome are randomly amplified with arbitr ary 10mer primers using RAPD fingerprinting. Labelled SSR-oligonucleot ides serve as probes to detect complementary sequences in RAPD product s by means of Southern analyses. Subsequently, positive RAPD fragments of suitable size are cloned and sequenced. Using GA and GT probes, we applied this approach to waterfleas (Daphnia) and revealed 37 hybridi zation signals in 20 RAPD profiles. Thirteen positive RAPD fragments f rom three Daphnia species and two hybrid 'species' were cloned and seq uenced. In all cases simple sequence repeats were detected. We charact erized seven perfect repeat loci, which were found to be polymorphic w ithin and between species.