Verification of interspecific pine hybrids using paternally inherited chloroplast microsatellites

Pollen contamination continues to be a problem for many operational controlled-pollination programs for hybrid trees. In the case of the Slash x Caribbean pine hybrid in Queensland, productivity losses may occur if pure Slash is deployed on sites optimal for hybrids. We report a DNA marker assay that distinguishes between representatives of Slash and Caribbean pine breeding populations. Furthermore, interspecific hybrid F1s were distinguishable from individuals believed to be derived from self fertilisation or outcrossing to other Slash pine. Unlike earlier reported DNA assays for verification of hybrid pines, this assay was definitive for the reference population. The multi-locus assay was optimised for a single-tube PCR reaction, offering estimated 75% savings in the turnaround time and costs compared with individual PCR amplification of the six loci. The PEE displayed more variation at these loci than PCH despite the PCH having been sampled over a more extensive geographical range than the PEE.