Effects of generation improvement of Cunninghamia lanceolata (Lamb.) Hook on genetic diversity and genetic structure in seed orchards

Maintaining genetic diversity among generations in seed orchards is an important management goal because it lays a foundation for the generation process of seed orchards and the formulation of breeding plans. Meanwhile, clonal seed orchards play a pivotal role in supplying genetically improved seeds for afforestation, but the dynamics of genetic diversity and structure across multiple generations and geographic regions remain poorly understood. This study aimed to investigate genetic variation patterns across generations and geographic genetic differences in Chinese fir seed orchards using microsatellite markers. We analyzed genetic diversity, population structure, and co-ancestry of nine Chinese fir seed orchards, with three generations each in Hunan, Fujian, and Zhejiang provinces (representing central and marginal production regions, respectively). Results showed genetic diversity of the seed orchards remained relatively high (mean Ho = 0.553, He = 0.657) and exhibited distinct geographic variations with generational advancement, reflecting differences in parental selection strategies. Genetic diversity in Hunan (HN) first increased (HN2 > HN1) then slightly decreased (HN3 < HN2), while Fujian (FJ) showed a trend of initial decline followed by recovery (FJ1 > FJ3 > FJ2), and Zhejiang (ZJ) exhibited a gradual decrease (ZJ1 > ZJ2 > ZJ3). Geographic differences were evident, with diversity levels ordered ZJ > FJ > HN. Genetic differentiation among populations was low (Fst = 0.007 – 0.043), with 97.81 % of variance attributed to within-population variation. The population structure of the Hunan seed orchard was different from those of the Fujian and Zhejiang orchards, the population structure of Zhejiang’s advanced-generation seed orchards risked genetic convergence. All seed orchard populations had mixed branches, which shows the complex relationships among the population genotypes. There was a moderate degree of genetic homology (56 %) among the seed orchard resources, and the genetic relationship between generations in seed orchards in the same region became closer as generations improved. Population genetic analysis will greatly promote the molecular breeding of Chinese fir. • First comprehensive large-scale genetic analysis of Chinese fir seed orchards, evaluates generational/regional dynamics. • Seed orchards maintain high genetic diversity, with geographic generational variations reflecting selection strategies. • Moderate genetic homology and increasing regional/generational proximity guide breeding strategies.