Development of polymorphic nuclear microsatellite markers in sugar maple (Acer saccharum Marsh.) using cross-species transfer and SSR-enriched shotgun pyrosequencing

A set of 23 polymorphic microsatellites was successfully tested for Acer saccharum. Eighteen of these new polymorphic markers were developed using next-generation sequencing and five were transferred from other Acer species. A total of 68 individuals from two populations were genotyped at all markers using a multiplex approach. Mean allelic diversity was 7.7, polymorphism ranged from 2 to 16 alleles per locus. Overall heterozygosity was high, with an average observed heterozygosity of 0.644. Two loci that were obtained from cross-species transfer and one from shotgun pyrosequencing showed heterozygote deficiencies, deviations from Hardy–Weinberg equilibrium, and high frequencies of null alleles for one or both populations. No evidence for linkage disequilibrium was detected. Finally, 20 of the 90 markers could be used in future population genetics studies of A. saccharum.