High-resolution genetic tools pave way for future ginseng cultivars
image: Case study for application of SNP chip across inbreeding population which bred and maintained by pureline selection. Five accessions (A–E) were inspected and two individuals from each accession were randomly selected and genotyped by SNP chip. Homozygous genotypes were represented as A, T, G, or C and heterozygous genotypes were represented as H. Individuals showed different genotypes were denoted as *. Homozygosity was revealed for each individual and homogeneity was revealed for each accession by comparing genotypes of two individuals.
Credit: Horticulture Research
Ginseng (Panax ginseng), long valued as the “king of medicinal plants,” faces breeding challenges due to its slow growth, limited seed production, and complex tetraploid genome. To overcome these barriers, researchers developed the first high-resolution genetic map and a breeder-friendly single nucleotide polymorphism (SNP) chip tailored for ginseng. These tools allow precise assessment of genetic diversity, seed purity, cultivar authentication, and identification of promising breeding lines. By genotyping more than 900 ginseng accessions, the team demonstrated the utility of these resources for building homozygous inbred lines and preserving cultivar integrity. Together, they provide a crucial foundation for molecular breeding and the future development of elite ginseng cultivars.
Ginseng has long been recognized for its pharmacological properties and economic importance, but conventional breeding has faced substantial barriers. The crop requires at least four years to complete a reproductive cycle and produces limited seeds, making genetic improvement slow and resource-intensive. Environmental sensitivity and problems associated with continuous cropping further complicate cultivation. Moreover, its complex tetraploid genome poses difficulties for marker development, with many existing tools suffering from low reliability due to paralogous sequences. As a result, cultivar development has depended heavily on labor-intensive pure line selection. Because of these challenges, there is a pressing need to conduct in-depth research on molecular breeding systems for ginseng.
A research team from Seoul National University, Chungbuk National University, and collaborating institutions has published (DOI: 10.1093/hr/uhae257) a new study in Horticulture Research on September 9, 2024 . The study reports the construction of a high-density genetic map and the development of a single nucleotide polymorphism (SNP) chip specifically designed for Panax ginseng. By integrating genotyping-by-sequencing and advanced SNP assays, the researchers provide the first comprehensive genomic resource to accelerate molecular breeding in this medicinal crop.
To address the genetic complexity of ginseng, the team first constructed a genetic map using over 10,000 filtered SNPs derived from an F2 population between two Korean cultivars, Chunpoong and Yunpoong. The final high-resolution map, composed of 1,216 nonredundant SNPs across 24 linkage groups, aligned closely with the chromosome-scale genome assembly, confirming its accuracy. Next, the researchers analyzed more than 431,000 variants from 119 ginseng collections and distilled them into 192 highly informative markers distributed across the genome. These formed the basis of a practical SNP chip.
The chip was validated by genotyping 919 ginseng accessions, including cultivars, breeding lines, and wild ginseng from Korea, China, and Russia. Results revealed high homozygosity levels in many accessions, making them promising candidates for inbred line development. The chip also enabled clear differentiation among cultivars, population structure analysis, and detection of hybridization events. Importantly, the team demonstrated how the chip can monitor cultivar purity and ensure homogeneity, both critical for commercial breeding and intellectual property protection. By combining a robust genetic map with a versatile SNP chip, the study delivers essential resources for precision breeding and conservation of this iconic medicinal crop.
“This research provides the first truly reliable molecular toolkit for ginseng breeding,” said Professor Tae-Jin Yang, senior author of the study. “Traditional ginseng improvement has been a slow and uncertain process due to its long generation time and complex genome. Our SNP chip and genetic map overcome these barriers, enabling breeders to rapidly identify, authenticate, and stabilize elite lines. These tools not only safeguard cultivar integrity but also open the door to marker-assisted selection for desirable traits such as yield, disease resistance, and medicinal compound quality.”
The new genetic map and SNP chip represent a breakthrough for the modernization of ginseng breeding. By offering rapid, accurate genotyping, these tools will shorten breeding cycles, improve cultivar purity, and accelerate the release of high-quality varieties with consistent medicinal value. Beyond breeding, the chip supports seed purity testing, product authentication, and cross-species analysis within the Panax genus. It also enhances genomic research by providing a framework for pan-genome studies and trait mapping. Ultimately, these innovations will strengthen global ginseng cultivation, ensuring reliable supply for traditional medicine, nutraceuticals, and pharmaceutical industries while preserving genetic diversity for future crop improvement.
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References
DOI
Original Source URL
https://doi.org/10.1093/hr/uhae257
Funding information
This work was also supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. 2020R1A2C3007885, No. 2021R1A4A1032888) and the National Key R&D Program of China (2023YFC3504000).
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.