Shortening the growth cycle and maintaining high yields are the goals pursued by all breeders. Under the distinct ecological conditions of tropical and rainy and dry seasons, many plants experience the phenomenon of early flowering and fruiting under adverse conditions. However, there is still no clear conclusion as to whether early flowering and fruiting will affect the vegetative growth of plants. In this study, the vegetative and reproductive growth traits of 270 families of Pinus yunnanensis of 6 years old in common garden were analyzed. There were significant differences in phenotypic traits of different populations, indicating that the trait differences were genetically stable. The variation of vegetative growth traits mainly comes from within populations, and the variation of reproductive growth traits mainly comes among populations. The average coefficient of variation of reproductive growth traits was significantly higher than that of vegetative growth traits. There was a positive correlation between vegetative growth traits and precocity of fruiting. Ecological environment factors have impact on phenotypic variation, among which the temperature of the wettest season has the greatest impact. According to cluster analysis, the nine populations could be divided into three categories. These cluster results were not due to geographic distances, indicating the discontinuity of phenotypic variation. By association analysis, 9 and 3 SSR loci were found to be significantly associated with the trait of precocity of fruiting, respectively. Among them, PK840 locus had the highest interpretation rate for the trait of precocity of fruiting. There were 10 and 7 unique haplotypes in precocity and non-precocity of fruiting individuals, with 179 bp and 183 bp bands, respectively. According to the breeding goal of high productivity and precocity of fruiting, 54 superior families and 200 superior individuals were selected. This study explored the adaptation strategies of tree growth traits to environmental changes.
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