Testing for unequal paternal contributions using nuclear and chloroplast SSR markers in polycross families of radiata pine

The lack of male pedigree control is the major limitation of an otherwise very useful and cost effective mating design, namely, the polycross. This study was conducted to investigate the relative contribution of different pollen parents to the sound-seeds stage, and also in a field progeny trial. Pollen from 15 radiata pine (Pinus radiata D. Don) parents was mixed in equal volume and applied to the same 15 parents, potentially allowing selfing. Samples of 8-year-old offspring were genotyped from five polycross families, and available seed from three of these five families was tested for unequal paternal contributions. The total paternal exclusion probability of five chloroplast markers and four microsatellite markers in our study was 99.1%. Overall, 81% of the offspring (both seeds and 8-year-old offspring) were assigned to 1 out of the 15 potential male parents, but a surprisingly high proportion (about 13%) was evidently fathered by pollen not included in the pollen-mix. Inconclusive evidence of unequal paternal contribution was observed in some families, but it did not influence the general combining ability (GCA) estimates appreciably, as evident from a high degree of correspondence between GCA estimates obtained from polycross and female-tester mating designs. A non-significant negative correlation was observed between the relative reproductive success (across polycross families) and predicted breeding values for diameter growth.