We investigated gene flow in five Cryptomeria japonica D. Don seed orchards of two different types (common and miniature) at widely spaced locations using microsatellite markers. The quality of a seed crop is determined by many factors, including pollen contamination from outside sources, self-fertilization, and the proportion of contributions from constituent clones. Contamination rates were found to vary among ramets both within seed orchards (10.0-76.7% in the most variable seed orchard) and among seed orchards (35.0-65.8% on average). Among ramets, there were significant negative correlations between pollen contamination rate and their distance from the orchard edge; among seed orchards, there were significant positive correlations between the pollen contamination rate and the C. japonica forest area nearby. Some proportion of the pollen (10.7% of total contamination) also migrated from parts of the orchards that had not been treated with gibberellin to induce flowering. Self-fertilization rates varied among seed orchards (1.4-4.4% on average), and there were significant positive correlations between self-fertilization rate and the number of ramets per clone in both types of seed orchard. Contributions as pollen donors differed significantly among clones in all seed orchards. The distance between planted ramets, flowering phenology, and relative pollen fecundity may also have contributed to observed differences in paternal contribution. The influence of these factors on genetic potential did not differ greatly between the two types of orchards.

We investigated the influence of male flower production, floral synchrony and inter-tree distances on male reproductive success in a miniature seed orchard of Cryptomeria japonica. We used six microsatellite markers to determine the paternity of each seed. In the seed orchard, the average pollen contamination and clonal self-fertilization rates were 38.7 % and 1.7 %, respectively. The level of male reproductive success of constituent clones varied from 0.0 to 15.7 %. Five clones showing the highest male reproductive success contributed ca. 30 % of all analyzed seeds as a pollen donor after excluding contamination by external sources of pollen. The statistical analyses showed that male reproductive success was strongly influenced by male flower production of each clone and, possibly, by their distance to the mother trees. The linear regression which included male flower production and floral synchrony as independent variables, however, accounted for only 14.7 % of variation of male reproductive success, suggesting that other factors such as pollen competition might also influence male reproductive success. Since we found no significant correlation between male reproductive and female reproductive successes, it may be better to equalize male and female reproductive successes independently.

Polycrossing is a very useful and cost-effective approach when designing mating trials. However, since the maternal general combining ability (GCA) in polycross designs is estimated on the assumption of equal contributions from paternal parents; any unequal paternal contribution leads to biased GCA estimates. Progeny from polycrossing Cryptomeria japonica, in which three mixtures from three paternal donors were crossed with each of three maternal parents, were analyzed using microsatellite markers to detect departures from equal paternal contribution. The deviations from equal paternal contribution were evaluated using a χ2 goodness of fit test. In this test, we examined the null hypothesis of equal paternal contribution for each mother tree. Two different methods were used to calculate paternal contribution: first, simply the number of seeds produced by each male parent, and second, the number of seeds produced by each male parent weighted according to the proportion of full seeds in single cross. The results of the χ2 test showed that the contribution to seed production by each paternal clone differed significantly in all polycrosses. The average pollen germination rate was significantly different between paternal clones. The contribution of each pollen donor in a polycross was related to their pollen germination rate.

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