Microsatellite maps for Pinus elliottii and P. caribaea: lessons from transpecific microsatellites in pines

Transfer of microsatellites amongst pines makes sense because it avoids the considerable up-front development costs of microsatellites for new species and facilitates comparative mapping. We have evaluated some 260 microsatellite loci for use the Pinus elliottii var. elliottii and P. caribaea var. hondurensis taxa and their hybrids from a range of pines but mainly other hard pines. We have generated genetic maps for a male and female parent from 99 loci which transfer and segregate in our mapping cross. These maps differ from earlier maps for these individuals based on AFLP in that they lack prominent differences apparently due to sex related recombination rates. They shared in common with the earlier maps a high level of marker distortion, however, typically of mapping experiments in interspecific hybrids. Transferred microsatellite markers were characterised by a high level of null alleles, the level of which corresponded with taxonomic distances of the transfer. Transferred microsatellite loci were also characterised by amplification of multiple loci. To some extent non-specific amplification was addressed through modified PCR conditions but multiple loci amplification was a hindrance to post-PCR multiplexing. The use of haploid megagametophyte populations was mandatory in many cases to determine alleles and parental genotypes. Using ABI 5 dye fluorescence chemistry typically mutiplex ratios of 9x were readily achieved. The advantage of 5 dye chemistry, however, was offset somewhat by a need to repeat markers labelled with dyes of weaker fluorescence, predominantly PET labelled, at lower multiplex ratios, as signals strengths were too low.