Mapping the future of ginseng: New SNP chip speeds up breeding

A team of researchers has developed the first high-resolution genetic map and a versatile SNP chip for Panax ginseng, a tetraploid medicinal plant with complex genomic architecture. These tools are designed to overcome the traditional bottlenecks in ginseng breeding—long generation times, low seed yields, and genetic complexity. The SNP chip, validated across 919 genotypes, enables precise genotyping and the identification of homozygosity and genetic purity, facilitating inbred line development. This innovation lays the groundwork for a robust molecular breeding platform, offering new opportunities for improving cultivar traits, enhancing product authenticity, and accelerating breeding cycles in the ginseng industry.

Panax ginseng is globally valued for its pharmacological benefits, but its breeding process is hindered by biological and genomic challenges. The plant requires at least four years to produce seeds and yields limited progeny, making traditional breeding slow and inefficient. Furthermore, ginseng's allotetraploid genome, shaped by two whole genome duplications, contains abundant repetitive and paralogous regions, which complicate marker development and genetic analysis. Existing molecular tools are insufficient to reliably dissect its genome or track key traits in breeding programs. Due to these complexities, there is an urgent need to establish a high-throughput, accurate genotyping system and a reliable genetic framework to advance molecular breeding in ginseng.

On September 9, 2024, researchers from Seoul National University and collaborating institutions published a study (DOI: 10.1093/hr/uhae257) in Horticulture Research unveiling a high-resolution genetic map and an advanced SNP chip tailored for Panax ginseng. Utilizing genotyping-by-sequencing and next-generation SNP assays, the team developed a 24-chromosome genetic map and a validated 192-marker SNP chip. This chip was applied to over 900 ginseng genotypes, enabling precision in trait selection and germplasm authentication, marking a major step toward modern molecular breeding in this traditional medicinal crop.

To tackle ginseng's complex breeding challenges, the researchers employed genotyping-by-sequencing (GBS) to generate over 600,000 SNPs, from which 1216 non-redundant SNPs were used to construct a detailed linkage map spanning 24 chromosomes. They then screened 119 diverse ginseng accessions to identify subgenome-specific SNPs and designed a 192-assay SNP chip incorporating nuclear and plastid markers. The chip's performance was validated using 919 genotypes, revealing consistent homozygosity levels and identifying genetic outliers and cross-pollinated individuals.

Population structure analysis using these SNPs revealed four genetically distinct clusters, suggesting deep genomic diversity beyond geographical origin. Additionally, case studies demonstrated how the SNP chip could distinguish between breeding lines with complete homozygosity and those with hidden heterogeneity—crucial for selecting stable lines for cultivar registration.

The SNP chip also showed cross-species potential: it successfully differentiated P. quinquefolius and P. vietnamensis from P. ginseng, with null allele patterns correlating with evolutionary divergence. A dedicated SNP chip database was launched to store over 1200 genotyping results, supporting genomic-assisted selection and cultivar protection. Overall, this integrated platform provides breeders with a powerful tool to accelerate selection, ensure purity, and explore genetic diversity more efficiently.

“This work represents a critical leap forward for ginseng genomics,” said Dr. Tae-Jin Yang, senior author of the study. “For a plant that takes years to breed and suffers from complex genetics, our SNP chip offers a fast, cost-effective solution to assess genetic purity, identify elite lines, and enable informed breeding decisions. It not only supports commercial breeding but also aids in conserving genetic diversity and protecting cultivar rights. This is a foundation for a truly modern breeding program in Panax ginseng.”

The SNP chip and genetic map developed in this study provide a transformative platform for ginseng breeding and conservation. By enabling accurate genotyping of large populations, the tools support the rapid identification of elite cultivars, assist in maintaining cultivar purity, and offer legal protection through molecular fingerprinting. Additionally, breeders can use the SNP chip to shorten breeding cycles, monitor homozygosity in inbred lines, and explore genetic variation across germplasm collections. Its cross-species utility also opens the door to comparative genomics within the Panax genus. These innovations are poised to modernize ginseng breeding and ensure sustainable development of the ginseng industry in the era of precision agriculture.

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References

DOI

10.1093/hr/uhae257

Original Source URL

https://doi.org/10.1093/hr/uhae257

Funding information

This work was carried out with the support of "Cooperative Research Program for Agriculture Science and Technology Development (Project No. PJ015903)" Rural Development Administration, Republic of Korea. 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.