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 F-1 hybrids. Simulation analysis was used to investigate the power of the markers for identifying the pure species and their F-1, F-2, and backcross hybrids. The six species diagnostic markers were particularly powerful for detecting F-1 hybrids from pure species but could also discriminate the pure species from F-2 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 F-2 and backcross progenies. However, identifying F-1 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 x 10(-13)), breeding system analysis, and population genetics.