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 <em>Acacias</em>, we aimed to develop a set of multipurpose SSR markers for use in both <em>Acacia mangium</em> and <em>A. auriculiformis</em>. A total of 51 SSR markers (developed in <em>A. mangium</em> and natural <em>A. mangium</em> x <em>A. auriculiformis</em> 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 <em>A. mangium</em>, <em>A. auriculiformis</em>, 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.