Reproductive synchronicity between parents influences the seed production and quality in seed orchards. Our objective was to determine clonal variation in fertility and phenological synchronization, as well as their effect on seed production, in a Chinese fir (Cunninghamia lanceolata) open-pollinated seed orchard. Significant variation of female fertility and male phenological synchronization occurred in the clones. The flowering of the male was 2 days earlier than the female. The gamete contribution of female and male were unbalanced between clones (the phenological synchronization indexes (POij) were 0.000–0.585 (as female) vs. 0.000–0.385 (as male)). In general, the average POij value of as a male was lower than as a female, but the number of male flowers were significantly higher than female, indicating that the management of female flowers should be enhanced. The average POij of self-pollination was 0.298, higher than cross-pollination (0.236), indicating that there was a larger probability to selfing in the orchard. The middle phenological type possessed higher phenological synchronization indexes than early and late phenological type. Genetic control was stronger for number of female flowers (H2 = 0.277) than for male and female initial stages and flower duration (H2 = 0.193–0.239). We found a positive correlation between POij and TSW (r = 0.756), SOsc (r = 0.612), and Cp (r = 0.337), suggesting the phenological synchronization determined the seed quality and yield. Comprehensively, this study provided fertility and phenology information for management of a Chinese fir seed orchard, as well as a reference for the establishment of advanced seed orchards of conifer trees.
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