Genetic diversity and population structure of Fraxinus mandshurica: Precipitation of the driest month is associated with genetic diversity and guides a dual core collection strategy

Rapid climate change is altering tree evolution, but how geography and climate shape genetic variation in temperate species remains unclear. This study integrated phenotypic, molecular marker, and climatic data from Fraxinus mandshurica populations in northeastern China to characterize phenotypic variation and population genetic structure, examine their associations with provenance geography and climate, and support germplasm conservation and climate-adaptive breeding. Phenotypic assessment of 209 half-sib families in a common garden experiment detected substantial variation across 17 seed and seedling phenotypic traits. The between-year difference in family mean basal diameter exhibited the highest phenotypic coefficient of variation (49.77%). Seven simple sequence repeat (SSR) primer pairs generated 56 polymorphic SSR bands. Pairwise genetic differentiation among populations was not significantly associated with geographic or multivariate climatic distances; however, population-level genetic diversity indices were significantly positively correlated with precipitation of the driest month (BIO14). Using the multitrait index based on factor analysis and ideotype-design (FAI-BLUP), 42 superior families were identified, representing the top 20% of the 209 families evaluated. Two independent core germplasm collections were established, designated as the phenotypic core C1 derived from BLUP data and the molecular core C2 based on SSR markers, with only 10.0% overlap. Families retained in the C1 core exhibited enhanced growth performance and drought tolerance, whereas the C2 core maximized the retention of population-level genetic diversity. This dual-strategy framework provides a data-driven foundation for balancing genetic conservation and short-term breeding gains in temperate forest trees under climate change.