biologia plantarum

International journal on Plant Life established by Bohumil Nìmec in 1959

Biologia plantarum 67:175-183, 2023 | DOI: 10.32615/bp.2023.020

Genetic diversity and population structure of two threatened ginseng species in Vietnam

D.D. Vu1, *, M.P. Pham1, H.P.L. Nguyen2, M.D. Nguyen3, T.T.X. Bui2, M.T. Nguyen4, D.G. Vu5, T.H. Nguyen6, T.P.T. Nguyen2, *
1 Join Vietnam-Russia Tropical Science and Technology Research Center, Cau Giay, Hanoi 100000, Vietnam
2 Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology (VAST), Cau Giay, Hanoi 100000, Vietnam
3 Institute of Genome Research, VAST, Cau Giay, Hanoi 100000, Vietnam
4 Vietnam National Museum of Nature, VAST, Cau Giay, Hanoi 100000, Vietnam
5 HaUI Institute of Technology, Hanoi University of Industry (HaUI), Bac Tu Liem, Hanoi 100000, Vietnam
6 Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam

Two ginseng species Panax vietnamensis and Panax stipuleanatus are precious medicinal plants restricted in several Vietnam provinces. They are very limited and endangered due to degraded habitats and over-harvesting. To preserve these two species, we used eight nuclear microsatellite markers to investigate genetic variability from the nine populations with 246 individuals for these two ginseng species. Our findings showed a moderate genetic heterozygosity in two species, P. vietnamensis (HE = 0.386) and P. stipuleanatus (HE = 0.342). Deficiency of heterozygosity was observed in all the studied populations of P. vietnamensis and three populations of P. stipuleanatus. Some populations had high allelic richness for both species. Private alleles were determined in all the studied populations of P. vietnamensis and two P. stipuleanatus populations. Genetic differentiation was low in two ginseng species. However, habitat loss, over-utilization and over-harvesting can be the main causes of reduced genetic heterozygosity. Neighbor-joining tree and discriminant analysis of principal components detected three major genetic groups. Finally, based on our findings, we propose in situ conservation of populations with high expected heterozygosity, allelic richness, and private alleles. Seed collection should be performed for ex-situ conservation as genetic pools in the future.

Keywords: degraded habitats, gene exchange, ginseng, medicinal plants, overharvesting, species conservation.

Received: March 11, 2023; Revised: May 11, 2023; Accepted: May 11, 2023; Published online: July 18, 2023  Show citation

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Vu, D.D., Pham, M.P., Nguyen, H.P.L., Nguyen, M.D., Bui, T.T.X., Nguyen, M.T., ... Nguyen, T.P.T. (2023). Genetic diversity and population structure of two threatened ginseng species in Vietnam. Biologia plantarum, 67, Article 175-183. https://doi.org/10.32615/bp.2023.020
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    References

    1. Ahn C.-H., Kim B.-B., Yoon E.-S., Choi Y.-E.: Development of microsatellite markers to distinguish south Korean and Chinese ginseng. - J. Korean For. Soc. 98: 568-575, 2009.
    2. Bijlsma R., Bundgaard J., Boerema A.C., Van Putten W.F.: Genetics and environmental stress, and the persistence of populations. - In: Bijlsma R., Loeschcke V. (ed.): Environmental Stress, Adaptation and Evolution. Pp. 193-207. Birkhäuser Verlag, Basel 1997. Go to original source...
    3. Bruford M.W., Davies N., Dulloo M.E. et al.: Monitoring changes in genetic diversity. - In: Walter M., Scholes R.J. (ed.): The GEO Handbook on Biodiversity Observation Networks. Pp. 107-128. Springer, Cham 2017. Go to original source...
    4. Brütting C., Wesche K., Mayer S., Hensen I.: Genetic diversity of six arable plants in relation to their Red List status. - Biodivers. Conserv. 21: 745-761, 2012. Go to original source...
    5. Chybicki I.J., Burczyk J.: Simultaneous estimation of null alleles and inbreeding coefficient. - J. Hered. 100: 106-113, 2009. Go to original source...
    6. Doyle J.J., Doyle L.J.: Isolation of plant DNA from fresh tissue. - Focus 12: 13-15, 1990. Go to original source...
    7. Excoffier L., Laval G., Schneider S.: Arlequin (version 3.0.): an integrated software package for population genetics data analysis. - Evol. Bioinform. Online 1: 47-50, 2005. Go to original source...
    8. Falk D.A., Holsinger K.E.: Genetic and Conservation of Rare Plants. Pp. 283. Oxford University Press, New York 1991. Go to original source...
    9. Flower C.E., Fant J.B., Hoban S. et al.: Optimizing conservation strategies for a threatened tree species: in situ conservation of white ash (Fraxinus americana L.) genetic diversity through insecticide treatment. - Forests 9: 202, 2018. Go to original source...
    10. Frankham R., Ballou J.D., Briscoe D.A.: Introduction to Conservation Genetics. Pp. 385-386. Cambridge University Press, Cambridge 2002. Go to original source...
    11. Gijbels P., De Hert K., Jacquemyn H., Honnay O.: Reduced fecundity and genetic diversity in small populations of rewarding versus deceptive orchid species: a meta-analysis. - Plant Ecol. Evol. 148: 153-159, 2015. Go to original source...
    12. Goudet J.: FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3.2), 2002. Available at: https://www2.unil.ch/popgen/softwares/fstat.htm.
    13. Hammer K., Khoshbakht K.: Towards a 'red list' for crop plant species. - Genet. Resour. Crop Evol. 52: 249-265, 2005. Go to original source...
    14. Hamrick J.L., Godt M.J.W.: Allozyme diversity in plant species. - In: Brown A.H.D., Clegg M.T., Kahler A.L., Weir B.S. (ed.): Plant Population Genetics, Breeding and Genetic Resources. Pp. 43-63. Sinauer Associates, Sunderland 1990.
    15. Hamrick J.L., Godt M.J.W.: Conservation genetics of endemic plant species. - In: Avise J.S., Hamrick J.L. (ed.): Conservation Genetics: Case Histories from Nature. Pp. 281-304. Chapman & Hall, New York 1996. Go to original source...
    16. Hamrick J.L, Godt M.J.W., Sherman-Broyles S.L.: Factors influencing levels of genetic diversity in woody plant species. - New Forest. 6: 95-124, 1992. Go to original source...
    17. Hedrick P.W.: A standardized genetic differentiation measure. - Evolution 59: 1633-1638, 2005. Go to original source...
    18. Ho P.H.: [An Illustrated Flora of Vietnam.] Tome II. Fascicle 2. Pp. 640-641. Tre Publishing House, Ho Chi Minh City 2002. [In Vietnamese]
    19. Honnay O., Jacquemyn H.: Susceptibility of common and rare plant species to the genetic consequence of habitat fragmentation. - Conserv. Biol. 21: 823-831, 2007. Go to original source...
    20. Hostettmann K., Marston A.: Saponins: Chemistry and Pharmacology of Natural Products. Pp. 548. Cambridge University Press, Cambridge 1995.
    21. Jo B.H., Suh D.S., Cho E.M. et al.: Characterization of polymorphic microsatellite loci in cultivated and wild Panax ginseng. - Genes Genom. 31: 119-127, 2009. Go to original source...
    22. Jombart T., Devillard S., Balloux F.: Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. - BMC Genet. 11: 94, 2010. Go to original source...
    23. Kalia R.K., Rai M.K., Kalia S. et al.: Microsatellite markers: an overview of the recent progress in plants. - Euphytica 177: 309-334, 2011. Go to original source...
    24. Kalinowski S.T., Taper M.L., Marshall T.C.: Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. - Mol. Ecol. 16: 1099-1106, 2007. Go to original source...
    25. Kim J., Jo B.H., Lee K.L. et al.: Identification of new microsatellite markers in Panax ginseng. - Mol. Cells 24: 60-68, 2007. Go to original source...
    26. Konoshima T., Takasaki M., Tokuda H. et al.: Anti-tumor-promoting activity of majonoside-R2 from Vietnamese ginseng, Panax vietnamensis Ha et Grushv. - Biol. Pharm. Bull. 21: 834-838, 1998. Go to original source...
    27. Laurance W.F.: Forest-climate interactions in fragmented tropical landscapes. - Philos. T. Roy. Soc. B 359: 245-252, 2004. Go to original source...
    28. Liu H., Xia T, Zuo Y.-J. et al.: Development and characterization of microsatellite markers for Panax notoginseng (Araliaceae), a Chinese traditional herb. - Am. J. Bot. 98: e218-e220, 2011. Go to original source...
    29. Ma K.-H., Dixit A., Kim Y.-C. et al.: Development and characterization of new microsatellite markers for ginseng (Panax ginseng C.A. Meyer). - Conserv. Genet. 8: 1507-1509, 2007. Go to original source...
    30. Nybom H.: Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants. - Mol. Ecol. 13: 1143-1155, 2004. Go to original source...
    31. Park S.W., Hyun Y.S., Chung K.W.: [Genetic polymorphism of microsatellite markers in Panax ginseng C.A. Meyer.] - J. Ginseng Res. 33: 199-205, 2009. [In Korean] Go to original source...
    32. Peakall R., Smouse P.E.: GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research - an update. - Bioinformatics 28: 2537-2539, 2012. Go to original source...
    33. Petit R.J., Mousadik E.I., Pons O.: Identifying populations for conservation on the basis of genetic markers. - Conserv. Biol. 12: 844-855, 1998. Go to original source...
    34. Piry S., Luikart G., Cornnet J.-M.: Bottleneck: a computer program for detecting recent reductions in the effective population size frequency data. - J. Hered. 90: 502-503, 1999. Go to original source...
    35. Reunova G.D., Kats I.L., Muzarok T.I. et al.: Diversity of microsatellite loci in the Panax vietnamensis Ha et Grushv. (Araliaceae) population. - Dokl. Biol. Sci. 441: 408-411, 2011. Go to original source...
    36. Reunova G.D., Kats I.L., Muzarok T.I., Zhuravlev Yu.N.: Polymorphism of RAPD, ISSR and AFLP markers of the Panax ginseng C.A. Meyer (Araliaceae) genome. - Russ. J. Genet. 46: 938-947, 2010. Go to original source...
    37. Reunova G.D., Koren O.G., Muzarok T.I., Zhuravlev Yu.N.: Microsatellite analysis of Panax ginseng natural population in Russia. - Chin. Med. 5: 231-243, 2014. Go to original source...
    38. Sebbenn A.M., Licona J.C., Mostacedo B., Degen B.: Gene flow in an overexploited population of Swietenia macrophylla King (Meliaceae) in the Bolivian Amazon. - Silvae Genet. 61: 212-220, 2017. Go to original source...
    39. Takezaki N., Nei M., Tamura K.: POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. - Mol. Biol. Evol. 27: 747-752, 2010. Go to original source...
    40. Tap N.: [The species of Panax L. in Vietnam.] - J. Med. Mater. 10: 71-76, 2005. [In Vietnamese]
    41. Trieu L.N., Mien N.T., Tien T.V. et al.: Genetic diversity of Panax stipuleanatus Tsai in North Vietnam detected by inter simple sequence repeat (ISSR) markers. - Biotechnol. Biotechnol. Equip. 30: 506-511, 2016. Go to original source...
    42. Van Dan N., Ramchiary N., Choi S.R. et al.: Development and characterization of new microsatellite markers in Panax ginseng (C.A. Meyer) from BAC end sequences. - Conserv. Genet. 11: 1223-1225, 2010. Go to original source...
    43. van Oosterhout C., Hutchinson W.F., Wills D.P.M., Shipley P.: Micro-Checker: software for identifying and correcting genotyping errors in microsatellite data. - Mol. Ecol. Notes 4: 535-538, 2004. Go to original source...
    44. Vietnam Red Data Book. Part II. Plants. Ministry of Science and Technology of Vietnam, Vietnamese Academy of Science and Technology, Science and Technics Publishing House, Hanoi 2007. [In Vietnamese]
    45. Vu D.D., Nguyen T.M., Nguyen D.M. et al.: Genetic population structure of the Vietnamese ginseng (Panax vietnamensis Ha et Grushv.) detected by microsatellite analysis. - Braz. J. Biol. 84: e264369, 2022. Go to original source...
    46. Vu D.D., Shah S.N.M., Pham M.P. et al.: De novo assembly and transcriptome characterization of an endemic species of Vietnam, Panax vietnamensis Ha et Grushv., including the development of EST-SSR markers for population genetics. - BMC Plant Biol. 20: 358, 2020. Go to original source...
    47. Weir B.S., Cockerham C.C.: Estimating F-statistics for the analysis of population structure. - Evolution 38: 1358-1370, 1984. Go to original source...
    48. Xiang Q.B., Lowry P.P.: Araliaceae. - In: Wu C.Y., Raven P.H., Hong D.Y. (ed.): Flora of China. Vol. 13. Pp. 435-491. Science Press, Beijing 2007.
    49. Zhuravlev Yu.N., Koren O.G., Reunova G.D. et al.: Ginseng conservation program in Russian Primorye: genetic structure of wild and cultivated populations. - J. Ginseng Res. 28: 60-66, 2004. Go to original source...
    50. Zhuravlev Yu.N., Koren O.G., Reunova G.D. et al.: Panax ginseng natural populations: their past, current state and perspectives. - Acta. Pharmacol. Sin. 29: 1127-1136, 2008. Go to original source...

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