EST-derived microsatellites as a rich source of molecular markers for oats

Polymerase chain reaction-based microsatellite markers are valuable tools for molecular breeding because of their co-dominant inheritance and their applicability for high-throughput analysis. Being still very limited for oats, their number has to be increased significantly to cover the entire genome. For these purposes, a set of 7031 recently published expressed sequence tags (ESTs) was screened for microsatellites with dinucleotide, trinucleotide and tetranucleotide repeat motifs. Subsequent in silico analysis resulted in the development of 216 primer pairs for Avena EST-derived microsatellite loci (AME). Using a sample set of 12 oat lines, 107 of 195 functional primers could be assayed as polymorphic. The marker variability averaged out at three alleles per locus and a polymorphic information content (PIC) value of 0.42. This variability documents their suitability for molecular oat-breeding purposes. Finally, 51 of the AME loci could be placed within the known reference map of 'Kanota' x 'Ogle' that previously contained only 12 microsatellite loci. Thus, a remarkable enhancing of the number of mapped oat microsatellite loci could be achieved.