High-resolution genetic map and SNP chip for molecular breeding in Panax ginseng, a tetraploid medicinal plant

Abstract

Ginseng (Panax ginseng ) renowned as the king of medicinal plants. Ginseng grows slowly under shade conditions, requiring at least 4 years to produce a limited number of seeds. Molecular breeding of ginseng faces challenges due to its the tetraploid genome and the absence of an efficient molecular marker system. To overcome these obstacles, we adopted genotyping-by-sequencing to delve into genetic mapping and survey genetic diversity. We constructed a comprehensive genetic map comprising 24 linkage groups, each corresponding to one of the 24 chromosomes in the ginseng genome, based on 1216 nonredundant SNPs obtained from an F2 mapping population. Additionally, 431 103 SNPs were identified from 119 diverse ginseng genotypes. From these, 192 informative subgenome-specific single copy SNPs were selected to develop a SNP chip. The SNP chip was used to genotype a large ginseng collection, encompassing registered cultivars, breeding lines, wild-simulated ginseng, and wild ginseng from various countries and regions. We evaluated the utility of the assay for molecular breeding with 919 ginseng genotypes. This breeder-friendly SNP chip promises versatility, enabling purity assessments of seeds and products, the authentication of species and cultivars, and the determination of homozygosity and homogeneity rates for breeding lines. Genotype data for 1200 ginseng genotypes are now stored in our database. This SNP chip lays the foundation for a molecular breeding in ginseng and will facilitate the breeding process in this medicinal crop.

Acknowledgements

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).

Author Contributions

W.C., W.J., and T.-J.Y. designed the research. Y.C.K., J.-W.L., I.-H.J., M.L., J.G., X.L., and J.X. provided the ginseng samples. W.J. and H.S. constructed ginseng genetic map. W.J. and W.C. designed SNP chip primers. W.C. and Y.O. performed SNP chip experiment. W.C. analyzed SNP chip result. J.K. constructed SNP chip database. W.C., W.J. and T.-J.Y. wrote the manuscript, and J.Y.P., M.M., M.J., D.D., Y.L. and T.-J.Y. revised the manuscript.

Data availability statement

All the data generated or analyzed in this study are included in this published article and its supplementary information files. All the sequence data of the present study have been deposited in the NCBI Sequence Read Archive (SRA) database under BioProject PRJNA1062125 and PRJNA1026738.

Conflict of interests

The authors declare no competing interests.

Supplementary information

Supplementary data is available at Horticulture Research online.

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