Quality control remains a challenge in traditional Chinese medicine (TCM). This study introduced a novel genetic-based quality control method for TCM. Genetic variations in ginseng were evaluated across whole-genome, chloroplast genome, and ITS2 DNA barcode dimensions. Significant genetic variations were found in whole-genome comparison, leading to the use of inter-simple sequence repeat markers to assess the genetic diversity of ginseng decoction pieces (PG), garden ginseng (GG), and ginseng under forest (FG). Fingerprints of ginseng samples revealed instability within some batches. These evaluations were transformed into information entropy to calculate the size of Hardy–Weinberg equilibrium population (HWEP). FG had significantly higher genetic and chemical minimum HWEP than GG (p < 0.05). Notably, a significant positive correlation was observed between the minimum HWEP for genetics and for chemistry (r = 0.857, p = 0.014). Genetic polymorphism analysis of ginseng has the potential to evaluate chemical quality consistency, offering a new method to ensure quality consistency in TCM.

This study aims to further analyze the chemical characteristics of mountainous forest cultivated ginseng (MFCG) and garden ginseng (GG), concerning their calcium oxalate crystals, organic acids, and ginsenosides. The results demonstrate that MFCG had higher levels of non-free oxalate, calcium oxalate crystals, and most ginsenosides, while GG had higher fumaric acid/total organic acids. The content of non-free oxalate and calcium oxalate crystals in rhizome was the highest, showing a positive correlation with the growth years (5–20 years). In most cases, in MFCG, non-free oxalic acid ≥ 0.8%, calcium oxalate ≥ 160/mg, fumaric acid/total organic acids < 9%, Rb1 ≥ 6 mg/g, PPD/PPT was close to 2, and Rb1/Ro ≥ 2.5, while in GG, non-free oxalic acid < 0.8%, calcium oxalate ≤ 60/mg, fumaric acid/total organic acids ≥ 9%, Rb1 < 6 mg/g, PPD/PPT was close to 1, and Rb1/Ro < 2.5. These results can be used as the basis for distinguishing between GG and MFCG. Chemometric analysis of non-free oxalate, calcium oxalate crystals, and ginsenosides could distinguish MFCG from GG. Chemometric analysis of succinate, citrate, and malonic acids could mostly differentiate MFCG of over 15 years from that of less than 12 years. As far as we know, the present study is the first to determine the difference in the ratio of ginsenosides (Rb1/Ro, PPD/PPT) and the ratio of organic acids, which provides an innovative method for the distinction between the two and a scientific basis for effective quality control of MFCG.

Panax ginseng C. A. Mey., a precious traditional medicinal herb, demonstrates diverse pharmacological activities, including immunomodulation and anti-fatigue effects. However, prolonged cultivation has led to germplasm admixture and cultivar degeneration, resulting in inconsistent quality that severely compromises its medicinal value and industrial standardization. Therefore, establishing accurate and efficient germplasm evaluation tools is critical for ensuring the quality of P. ginseng medicinal materials. To integrate whole-genome sequencing and chemical fingerprinting for ginseng germplasm identification and quality consistency assessment. Chromosome-level genomes of ginseng from Jilin (JA) and Liaoning (FC) were assembled using PacBio HiFi, Illumina, and Hi-C technologies. Gene family identification and phylogenetic analysis were performed across 13 representative species. Using the JA genome as the reference, we constructed a pan-genome incorporating 7 ginseng genomes to dissect gene repertoire composition and structural variation distribution across ginseng populations. Population structure analysis with 76 individual ginseng samples revealed genetic diversity, and its integration with HPLC chemical fingerprints provided a joint assessment of quality consistency. We assembled two chromosome-level genomes and, through comparative genomics, revealed significant expansion of ginsenoside biosynthesis-related gene families and subgenome divergence. The core gene set accounted for 54.1% of the pan-genome, indicating high genetic conservation. SNP distribution patterns from population resequencing enabled the development of germplasm-specific molecular markers and a genetic-chemical integrated evaluation model. The molecular marker system and genetic-chemical joint assessment developed here provide reliable novel tools for germplasm identification and quality control, advancing standardization in the ginseng industry.