The Development of a Core SSR Marker Set for DNA Fingerprinting and Accession Discrimination in Durian (Durio zibethinus)

Durian (Durio zibethinus) germplasm may be incorrectly named, mislabeled, or genetically misidentified during introduction, exchange, and nursery stock distribution. Morphological identification is also affected by environmental conditions and plant developmental stages. A core simple sequence repeat (SSR) marker set was developed for the identification of durian germplasm. Genome-wide mining identified 106,776 SSR loci in the durian reference genome, and 18 stable and polymorphic markers were selected from 160 candidate primer pairs through agarose gel screening and M13-tailed fluorescent capillary electrophoresis. A total of 142 alleles were detected at the 18 SSR loci across the 58 durian accessions, with 3–15 alleles per locus and PIC values ranging from 0.422 to 0.849. Exhaustive evaluation of all marker combinations identified a minimum six-locus core SSR marker set comprising Y6, Y12, Y15, Y75, Y91, and Y108, which generated unique multilocus genotypes for all 58 accessions in the current validation panel, with a cumulative probability of identity (PID) of 7.99 × 10−8. STRUCTURE analysis, with K representing the number of inferred genetic clusters, supported K = 8 and revealed admixture in several accessions. The core SSR marker set developed in this study can distinguish the 58 durian accessions and be used to construct their DNA fingerprints. Validation in larger and more genetically diverse germplasm collections is required before routine commercial deployment.