Development of microsatellites using next-generation sequencing for Acacia crassicarpa

Acacia crassicarpa is a tropical forestry species that is increasingly being planted in South-East Asia. Using next- generation sequencing, we developed 12 nuclear microsatellite markers for A. crassicarpa and optimised them for assay in three multiplex sets. We tested the 12 loci on 34 A. crassicarpa samples and found that polymorphism ranged from 4 to 8 alleles per locus (average = 5.8). The loci were easy to score in terms of binning and their reproducibility and polymerase chain reaction success rate were high. Given their usability and polymorphism we believe that these 12 loci will be useful for DNA profiling and mating system analysis with direct application in breeding programmes and the conservation of wild populations. Six of the markers also amplified products in related A. mangium and A. auriculiformis, with four being polymorphic in three samples of each species. Therefore, these markers added more broadly to the genomic resources available in Acacia.