Abstract Sequence-specific amplification polymorphism (SSAP) retrotransposon-based molecular marker for germplasm identification and genetic relationship analysis in the genus Diospyros were investigated, and the performance of each SSAP primer pair when individually used for aforementioned studies was also studied in detail. Twenty five SSAP primer pairs generated a total of 1 300 robust fragments among inter- and intra-species genotypes examined, of which 1 214 (93.38%) were polymorphic with an average of 48 polymorphic bands per primer pair, indicating that SSAP is a high multiplex ratio and high polymorphic marker system. The analysis of genetic relationships of 28 genotypes based on the molecular data from SSAPs revealed that the Chinese genotypes, Japanese genotypes and related species were distinctly separated and some genotypes known genetic relationships were clustered together, which was consistent with previous studies, suggesting that SSAP was feasible and reliable for the future genetic analysis in the genus of Diospyros. Additionally, three SSAP primer pairs were found to be the most informative. Our results suggest that SSAP can be as a potentially powerful tool for characterization of Diospyros germplasm in the future.
