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The reproductive success of pollen derived from selected and non-selected sources and its impact on the performance of orchard crops were evaluated, using five pairs of microsatellite markers, in a Japanese black pine (Pinus thunbergii Parl.) clonal seed orchard consisting of 16 nematode-resistant clones. The paternity of each open-pollinated seed was determined by comparing the genotypes of seeds from six clones (24 trees) with genotypes of the 16 orchard clones and two trees (N1, N2) representing other genotypes that had been inadvertently included in the orchard. Out of 384 seeds examined, the paternity of 316 seeds (82.3%) was assigned to the clones within the seed orchard. On average, the male reproductive success of orchard clones varied from 0.0% to 10.5%, and was significantly related to the male-flowering fecundity of each clone. It was not related to the synchrony of flowering phenology between mates. The expected proportions of seeds produced by clonal trees as a result of pollination by orchard clones, and by contaminating pollen originating from internal and external sources were estimated at 86.8%, 3.3% and 9.9%, respectively. Nematode-resistant seedlings of Japanese black pine were produced from surviving 2-yr seedlings that had previously been inoculated with pinewood nematode (Bursaphelenchus xylophilus). Without pollen contamination, the survival rate of seedlings produced by mating between resistant clones is expected to be 62.4%. However, in this orchard the figure was reduced to 57.5%, due to pollen contamination from both internal and external sources.

Overall male reproductive success was investigated in a Japanese black pine (Pinus thunbergii Parl.) clonal seed orchard consisting of 16 nematode-resistant clones, using random amplified polymorphic DNA (RAPD) markers. We genotyped all 16 of the orchard clones at selected RAPD loci by analyzing diploid needles and 10 haploid megagametophytes from each of them. In addition, the male parent of open-pollinated seedlings was identified by comparing their phenotypes with the genotypes of the orchard clones. In this way the male parents of 559 seedlings of 648 seedlings of progenies from 14 parental (orchard) clones were determined. The level of external pollen contamination in the seed orchard was estimated to be 2.2% for the total population. The effective mean selfing rate observed was 1.5%. Male reproductive success among clones varied widely, from 0.8 to 24.4%, for the total population. Our data suggest that the significant deviation in male reproductive success of individual clones from panmictic ratios may be a problem for the genetic quality in seed orchard crops. To improve the parental balance of seed orchard crops, the use of artificial management techniques such as gibberellin A4/7 treatment, supplemental mass pollination, and rearrangement of clonal ramets is recommended in seed orchards.