Objective This study employed SSR (Simple Sequence Repeat) molecular markers to assess the genetic diversity among major Aquilaria sinensis cultivars in China and to establish a molecular identification system, thereby providing a theoretical basis for the conservation and authentication of A. sinensis germplasm.

Method Based on a total of 68 primary domestic varieties of A. sinensis, genomic DNA was extracted from leaf samples, and SSR markers were used to analyze polymorphic loci. Following the principle of maximizing the discrimination of the greatest number of varieties with the fewest primers, core SSR primers were selected to construct fingerprint profiles and molecular IDs for A. sinensis varieties.

Result (1) A total of 179 alleles (N_a) were detected across the 68 accessions using 36 SSR primer pairs, with an average of 4.972 alleles and 2.586 effective alleles (N_e) per locus. The mean values for Shannon’s information index (I), expected heterozygosity (H_e), observed heterozygosity (H_o), and polymorphism information content (PIC) were 1.079, 0.579, 0.512, and 0.523, respectively. (2) Genetic structure analysis indicated that the 68 accessions could be divided into two populations (K = 2). (3) Based on polymorphism parameters, stepwise primer reduction identified four primer pairs (DRYBMX089, AquSSR29, AquSSR42, and AquSSR59) sufficient to distinguish all accessions. Accordingly, SSR molecular fingerprints and QR code-based molecular identity cards were established for each variety.

Conclusion The 36 primer pairs successfully discriminated all 68 A. sinensis varieties. A molecular ID system was established using a core set of four primers, offering both a theoretical foundation and practical support for the molecular authentication of A. sinensis.