SSR-Based Genotyping of Korean Native Pear Germplasm for Accession Identity Assessment and Germplasm Management

Korean native pear germplasm is valuable for conservation and breeding, but long-term ex situ maintenance may result in accession redundancy and identity uncertainty. This study established simple sequence repeat (SSR) fingerprints, identified putative duplicate accessions, assessed phenotypic consistency within duplicate groups, and characterized genetic relationships and regional differentiation in the collection. A total of 644 accessions, including 626 Korean native pear accessions and 18 additional Pyrus accessions, were genotyped using 18 SSR markers from the European Cooperative Programme for Plant Genetic Resources and U.S. Pyrus Genetic Resources sets. The markers produced 4–13 alleles per locus, with mean gene diversity, observed heterozygosity, and polymorphic information content values of 0.669, 0.448, and 0.628, respectively. Forty-three putative duplicate groups comprising 142 accessions were identified, with no discrepancies observed in the available flower and young leaf traits. A non-redundant set of 545 accessions was established and used for subsequent genetic analyses. Genetic relationship and population structure analyses revealed diverse genetic backgrounds and broad sharing of genetic components across regions. Regional differentiation was weak but significant, with 92.72% of variation occurring within regions and 7.28% among regions; Ulleungdo accessions showed the most distinctive regional pattern. This study demonstrates the utility of SSR fingerprinting for accession verification, redundancy management, and germplasm curation and provides a non-redundant resource set for subsequent phenotypic evaluation and potential use in pear breeding.