To analyze the genetic diversity and genetic structure of different generations of Chinese fir breeding populations, reconstruct the genetic pedigree of breeding parents from each generation to guide the selection and mating of breeding parents, and establish a core germplasm of Chinese fir.

A total of 388 Chinese fir breeding clonal parents from different generations (74 from the initial generation, 70 from the first generation, 107 from the second generation, and 137 from the third generation) were used as materials. Genetic data were analyzed based on EST-SSR, and the overall level of breeding populations was reflected by the polymorphism and genetic differentiation parameters of 16 loci. Genetic diversity parameters, genetic variation, and genetic differentiation coefficients were used to analyze the genetic diversity levels of Chinese fir breeding populations across different generations. Clustering analysis and population structure analysis were conducted to determine population groupings and genetic pedigrees of breeding populations. Core germplasm was selected based on the principle of maximizing alleles.

1) A total of 640 polymorphic loci were amplified with 16 primer pairs, with an average of 40 alleles per locus. The mean effective number of alleles was 16.25, the Shannon index was 2.942, the mean polymorphism information content (PIC) was 0.942, and the mean fixation index was 0.97, indicating high polymorphism among populations. The overall genetic diversity of the Chinese fir breeding populations was higher than that of the initial generation, with the second and third generations exhibiting higher diversity than the overall level; 2) The four breeding populations were divided into three different groups, with individuals grouped according to material characteristics and genetic relationships; 3) A total of 127 core germplasms were selected, and the constructed core germplasm bank retained 100% of the alleles. The effectiveness of the core germplasm bank was verified through a genetic parameter T-test.

The different generations of Chinese fir breeding populations exhibited high genetic diversity and low genetic differentiation, indicating that advanced-generation breeding effectively maintains genetic variation within populations. The reconstructed pedigree map of breeding parents provides a scientific basis for the rational selection and crossbreeding of elite parents. Moreover, the identified core collection retains 100% of the allelic diversity of the original germplasm and shows strong representativeness, laying a solid genetic foundation for the future selection of superior varieties, efficient utilization of germplasm resources, and sustainable development of breeding populations.