Pomegranate (Punica granatum L.) germplasm collections are increasingly appreciated as a repository for the genetic improvement of species, and their genetic analysis is an essential prerequisite for their utilization in pomegranate breeding. Sufficient markers are a prerequisite for genetic analysis. In this study, we identified 36,792 simple sequence repeat (SSR) markers in the pomegranate genome. Dinucleotide repeats are the most abundant SSRs, and of the mono-, di-, tri-, and tetranucleotide repeats, A/T, AT/AT, AAT/ATT, and AAAT/ATTT were the most dominant motif type. There were only 1.80% SSR motifs located in the coding regions, while most (98.20%) SSR motifs were located in noncoding regions. We confirmed the reliability of 50 SSR markers by PCR amplification, from which 11 highly polymorphic SSR markers were selected to study the genetic diversity of 218 pomegranate accessions. A total of 63 alleles was detected for the 11 SSR primers, ranging from 2 (PG152) to 9 (PG093, PG080) across the pomegranate accessions. The polymorphism information content values of each SSR primer pair ranged from 0.22 to 0.70, with a mean value of 0.45. Based on population structure analysis, these accessions were clustered into three main populations and 42 accessions were chosen as the core set. The availability of these SSR markers and the clustering result for the pomegranate germplasm provide new important information for pomegranate genetics and breeding programs.

石榴（Punica granatum L.）种质收藏作为物种遗传改良的存储库越来越受到赞赏，其遗传分析是将其用于石榴育种的必要先决条件。足够的标记是进行遗传分析的前提。在这项研究中，我们在石榴基因组中鉴定了36,792个简单序列重复（SSR）标记。二核苷酸重复序列是最丰富的SSR，在单核苷酸，二核苷酸，三核苷酸和四核苷酸重复序列中，A / T，AT / AT，AAT / ATT和AAAT / ATTT是最主要的基序类型。只有1.80％的SSR图案位于编码区，而大多数（98.20％）的SSR图案位于非编码区。我们通过PCR扩增确认了50个SSR标记的可靠性，从中选择了11个高度多态的SSR标记来研究218个石榴种质的遗传多样性。共有11种SSR引物检测到63个等位基因，范围从2个（PG152）到9个（PG093，PG080），全部来自石榴。每个SSR引物对的多态信息含量值范围为0.22至0.70，平均值为0.45。根据人口结构分析，这些种质被分为三个主要种群，并选择了42种种质作为核心集。这些SSR标记的可用性以及石榴种质的聚类结果为石榴遗传学和育种计划提供了新的重要信息。