A multiplexed set of microsatellite markers for discriminating Acacia mangium, A. auriculiformis, and their hybrid

In order to assist breeding and gene pool conservation in tropical Acacias, we aimed to develop a set of multipurpose SSR markers for use in both Acacia mangium and A. auriculiformis. A total of 51 SSR markers (developed in A. mangium and natural A. mangium x A. auriculiformis hybrid) were tested. A final set of 16 well-performing SSR markers were identified, six of which were species diagnostic. The markers were optimized for assay in four multiplex mixes and used to genotype range-wide samples of A. mangium, A. auriculiformis, and putative F1 hybrids. Simulation analysis was used to investigate the power of the markers for identifying the pure species and their F1, F2, and backcross hybrids. The six species diagnostic markers were particularly powerful for detecting F1 hybrids from pure species but could also discriminate the pure species from F2 and backcross progenies in most cases (97 %). STRUCTURE analysis using all 16 markers was likewise able to distinguish these cross types and pure species sets. Both sets of markers had difficulties in distinguishing F2 and backcross progenies. However, identifying F1 from pure species is the current primary concern in countries where these species are planted. The SSR marker set also has direct application in DNA profiling (probability of identity = 4.1 × 10−13), breeding system analysis, and population genetics.