Isolation, characterization and amplification of simple sequence repeat loci in coffee

Simple sequence repeat (microsatellite) loci in coffee were identified in clones isolated from enriched andrandom genomic libraries. It was shown that coffee is a plant species with low microsatellite frequency. However, the averagedistance between two loci, estimated at 127kb for poly (AG), is one of the shortest of all plant genomes. In contrast, thedistance between two poly (AC) loci, estimated at 769kb, is one of the largest in plant genomes. Coffee (AC)n microsatellites arefrequently associated with other microsatellites, mainly (AT)n motifs, while (AG)n microsatellites are not normally associatedwith other microsatellites and have a higher number of perfect motifs. Dinucleotide repeats (AG) and (AC) were found in ATrichregions in coffee. Sequence analysis of (AC)n microsatellites identified in coffee revealed the possible association of theserepeated elements with miniature inverted-repeat transposable elements (MITEs). In addition, some of the evaluated SSRmarkers produced transposon-like amplification patterns in tetraploid genotypes. Of 12 SSR markers developed, nine werepolymorphic in diploid genotypes while 5 were polymorphic in tetraploid genotypes, confirming a greater genetic diversity indiploid species.