CHARACTERIZATION OF RABBIT DNA MICROSATELLITES EXTRACTED FROM THE EMBL NUCLEOTIDE-SEQUENCE DATABASE

Microsatellite polymorphisms are invaluable for mapping vertebrate gen omes. In order to estimate the occurrence of microsatellites in the ra bbit genome and to assess their feasibility as markers in rabbit genet ics, a survey on the presence of all types of mononucleotide, dinucleo tide, trinucleotide and tetranucleotide repeats, with a length of abou t 20 bp or more, was conducted by searching the published rabbit DNA s equences in the EMBL nucleotide database (version 32). A total of 181 rabbit microsatellites could be extracted from the present database. T he estimated frequency of microsatellites in the rabbit genome was one microsatellite for every 2-3 kb of DNA. Dinucleotide repeats constitu ted the prevailing class of microsatellites, followed by trinucleotide , mononucleotide and tetranucleotide repeats, respectively. The averag e length of the microsatellites, as found in the database, was 26, 23, 23 and 22 bp for mono-, di-, tri- and tetranucleotide repeats, respec tively. The most common repeat motif was AC, followed by A, AC, AGG an d CCG. This group comprised about 70% of all extracted rabbit microsat ellites. About 61% of the microsatellites were found in non-coding reg ions of genes, whereas 15% resided in (protein) coding regions. A sign ificant fraction of rabbit microsatellites (about 22%) was found withi n interspersed repetitive DNA sequences.