Liquidambar formosana is a multipurpose tree species native to China. There has been increasing interest in L. formosana due to its leaves being rich in shikimic acid, which plays a key role in the synthesis of the antiviral drug oseltamivir phosphate. Here, shikimic acid content (SAC) and other breeding traits, including tree height (HT), diameter at breast height (DBH), height to crown base (HCB), individual tree volume (VOL), leaf color (LC) and stem straightness degree (SSD), for 387 families of 19 provenances were evaluated in a provenance–family trial of L. formosana to estimate genetic parameters and reveal geographical variation patterns and, ultimately, screen out superior provenances and families. Differences among provenances and families were significant for all tested traits, indicating a high potential for selective breeding. Broad-sense heritabilities of provenance ($h_p^2$ = 0.19–0.57) and family ($h_f^2$ = 0.16–0.31) were moderate for most traits. Moderate to strong genetic correlations were found among HT, DBH, VOL, HCB and LC (r_A = 0.339–0.982), while adverse correlations (r_A = −0.494 to −0.816) were observed between SAC and growth traits. All target traits, excluding SSD, exhibited clinal variation in response to latitudinal gradients, and a clustering heatmap divided the 19 provenances into three groups. For single-trait selection, SAC persistently had the highest genetic gains (85.14%–163.57%). A weighted index based on breeding values was used to concomitantly improve SAC, HT and DBH. At a selection rate of 25%, the genetic gains at the provenance and family levels for SAC were 36.42% and 73.52%, and those for core growth traits ranged from −2.29% to 3.49% and 4.05% to 4.47%, respectively. As far as we know, this is the first study in L. formosana to explore the inheritance of SAC and its correlations with other traditional breeding traits. The genetic parameter estimations contribute to a better understanding of the genetic basis of SAC, and the superior provenances and families obtained lay a material foundation for the development of new varieties rich in shikimic acid, thereby promoting the in-depth exploitation and utilization of germplasm resources of L. formosana.

Liquidambar formosana, endemic to China, is a multifunctional tree species valued for its wood production, urban landscaping, and medicinal applications. Here, 111 superior L. formosana accessions were genotyped using 24 novel expressed sequence tag-simple sequence repeat (EST-SSR) markers to assess genetic diversity and structure, establish DNA fingerprints, and construct a core collection. A high degree of genetic diversity was detected in the tested accessions, with mean values for the number of observed alleles (Na), polymorphism information content (PIC), and Shannon’s information index (I) recorded at 8.458, 0.579, and 1.336 per locus, respectively. Cluster analysis, principal coordinate analysis (PCoA), and population structure analysis collectively categorized these accessions into two major groups. Specifically, those from the SangZ provenance formed a distinct group, whereas accessions from other provenances exhibiting extensive gene exchange were assigned to the second group. The combined values of the probability of identity (PI) and the probability of identity among siblings (PIsibs) across 24 SSR loci were 1.475 × 10⁻¹⁹ and 2.561 × 10⁻⁸, respectively, indicating a strong ability for fingerprint identification. Unique fingerprints for the 111 accessions were established using four selected core markers. A final core collection consisting of 34 accessions was constructed using the allele maximization (M) strategy, accounting for 30.63% of the analyzed accessions. No significant differences in genetic diversity indicators, allele frequency distributions, and accession dispersion patterns were observed between the core and original collections, suggesting that the core collection could effectively represent the entire collection. This work will promote the identification, management, and conservation of L. formosana germplasm resources while providing valuable materials for the subsequent selection and breeding of this tree species.