Using SSR markers for hybrid identification and resource management in Vietnamese Acacia breeding programs

We used a set of 16 SSR markers to check the identity of pure-species and hybrid clones in Vietnam’s <em>Acacia auriculiformis</em>, <em>Acacia mangium</em>, and acacia hybrid (<em>A. mangium</em> × <em>A. auriculiformis</em>) breeding programs. The statistics package HIest, applied to a large synthesized population, enabled accurate allocation of genotypes to the two pure species, F₁ and F₂ inter-specific hybrids and backcrosses, based on estimates of hybridity and heterozygosity. The hybridity status of putatively pure <em>A. mangium</em> and <em>A. auriculiformis</em> clones in adjacent clonal seed orchards was checked. Four out of 100 clones selected as <em>A. mangium</em> were found to be backcrosses (<em>A. mangium</em> × F₁ inter-specific hybrid) while out of 96 clones selected as <em>A. auriculiformis</em>, two were F₁ hybrids and two were backcrosses (<em>A. auriculiformis</em> × F₁ hybrid). The markers were then applied to check the hybridity status of 160 putative acacia F₁ hybrid genotypes that had been selected on morphological criteria from open-pollinated progenies collected from <em>A. auriculiformis</em> and <em>A. mangium</em> parents. Many selections based on morphology were found to be mistaken. Only thirteen of 63 clones originating from <em>A. auriculiformis</em> mothers were F₁ hybrids, four were backcrosses, and the remaining 46 were pure <em>A. auriculiformis</em>. Fewer mistakes were evident for clones selected from <em>A. mangium</em> mothers, with 82 out of 89 clones confirmed as F₁ hybrids, three as backcrosses, and four as pure <em>A. mangium</em>. The occurrence of F₁ hybrids and backcrosses in pure-species seed orchards and their progeny shows that inter-species contamination is an issue requiring management in both pure-species and in hybrid breeding of these species in Vietnam. Examination of genetic distances among verified clones showed patterns of relatedness that were consistent with pedigree records. Implications for resource management as well as for breeding and clonal selection strategies are considered.