Genetic diversity and population structure of Chinese mountain cultivated Panax ginseng accessions using SSR and KASP markers

Ginseng ( Panax ginseng Meyer) possesses numerous pharmacological effects. The economic and medicinal value of mountain-cultivated P. ginseng (MCPG) exceeds that of garden P. ginseng . However, the genetic diversity of MCPG populations remains poorly understood. Therefore, this study aims to explore the genetic diversity of MCPG in three locations in China and provide guidance for resource conservation and utilization. We conducted an analysis of the genetic diversity and population structure of 108 MCPG germplasms using 10 simple sequence repeat (SSR) markers and 10 Kompetitive allele-specific PCR (KASP) markers. These germplasms were collected from various locations, including Huinan County (HN) of Tonghua City, Jilin Province, Kuandian Manchu Autonomous County (KD) of Dandong City, Liaoning Province, and Yanji City (YJ) of Yanbian Korean Autonomous Prefecture, Jilin Province. The research findings indicate that most of the 10 SSR markers exhibited multiple-band patterns. The markers used in the study revealed a range of 2 to 20 alleles at each single locus. The polymorphism information content (PIC) of the markers varied from 0.2603 to 0.8325, with an average of 0.5291. As expected, all the KASP loci displayed two alleles, and the PIC of these markers ranged from 0.2562 to 0.3701, with an average of 0.3242. Our results highlight that both sets of markers indicated a relatively high genetic diversity in MCPG. Additionally, there was no significant difference in genetic diversity among the three populations, and their phylogenetic relationship displayed intermingled positioning. The total genetic differences mainly originated from individual variations rather than different groups.