A set of microsatellite markers for fingerprinting and breeding applications in Pinus radiata.

Fifty microsatellite markers were developed and characterized in Pinus radiata, and from among these, a subset of 10 easily scored and highly polymorphic markers was selected for use in fingerprinting, quality control, and breeding applications. The markers were characterized based on reliable and reproducible amplification, observed and expected heterozygosities, number of alleles, a low frequency of null alleles, and a lack of close linkage with other selected markers. Allele numbers and frequencies were estimated using 24 first-generation breeding clones from Australia and New Zealand. Observed heterozygosities for the selected markers were all greater than 0.67, and there was an average of 10.5 alleles/locus. The occurrence of null alleles was checked with megagametophytes from mother trees for loci that appeared to be homozygous. The 10 markers are not closely linked (r < 0.20 and LOD > 3) to each other. The selected microsatellites fall into three discrete size classes, and with appropriate selection of fluorescent dyes for 5' end labeling, can be multiplexed with up to 6 markers/sample on an ABI PRISM 310 or similar instrument.