Detection and characterization of genome-specific microsatellite markers in the allotetraploid Prunus serotina

The utility of microsatellite markers to characterize the genetic diversity of a polyploid species with disomic inheritance is often hampered by the impossibility of determining allele frequencies and the complexity of inheritance patterns. The objective of this study was to solve these problems in the allotetraploid Prunus serotina Ehrh. by finding genome-specific primers (i.e., primers that are specific to one of the two genomes that initially formed the species). Sixty-seven microsatellite primers described in cultivated Prunus L. species were tested for cross-amplification in P. serotina, and evidence that conserved markers were genome-specific was found by demonstrating their typical Mendelian diploid inheritance in embryos resulting from controlled crosses. Among the 67 microsatellite markers tested, 26 produced successful amplification and five were genome-specific. No linkage disequilibrium was detected for these loci, but evidence was found for the presence of a null allele at one locus. We found both a high number of alleles per locus (three to 12) and a high mean expected heterozygosity (0.71), which were nonsignificantly different from the number of alleles and estimates of expected heterozygosity calculated for three non-genome-specific markers in the same population. The potential use of these genome-specific markers in population genetic studies is discussed.