Korean Journal of Plant Taxonomy (식물분류학회지)

The Korean Society of Plant Taxonomists (한국식물분류학회)
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A survey of the genome-wide genetic variation of Hibiscus hamabo (Malvaceae)

  • Geonha HWANG (Department of Medical & Biological Sciences, The Catholic University of Korea) ;
  • Ui-Chan JUNG (Department of Medical & Biological Sciences, The Catholic University of Korea) ;
  • Sang-Tae KIM (Department of Medical & Biological Sciences, The Catholic University of Korea)
  • Received : 2023.04.25
  • Accepted : 2023.06.19
  • Published : 2023.06.30
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Abstract

Hibiscus hamabo (Malvaceae) is a deciduous shrub mainly found in northeast Asia, including China, Japan, and Korea. Due to its limited distribution on Jejudo Island and at several sites in Jeollanam-do in Korea, H. hamabo has been designated as an endangered species by the Ministry of the Environment and has been the subject of several restoration programs. In this study, we quantified genetic variations using double-digestion restriction-associated DNA sequencing technology in 96 individuals of H. hamabo from 13 distinct populations in Korea. We determined 3,352 genome-wide single nucleotide polymorphism loci after stringent filtering processes and analyzed the level of genetic variation within and among populations as well as the population differentiation and genetic ancestry with various assumptions pertaining to the population origin. Our results indicated weak differentiations among populations surveyed in this study but clearly suggested that most of the H. hamabo populations maintain a relatively high level of genetic diversity as evidence of frequent genetic exchanges among populations via outcrossing or sequential gene flows. For a more detailed analysis of the origin of Korean H. hamabo and its demographic history, it will be necessary to expand sampling in China and Japan.

Keywords

Acknowledgement

This work is supported by NIBR202104201 National Institute of Biological Resources "A study on plant resources based on DNA sequences utilizing Next Generation technique (4th year)".

References

  1. Ahn, Y. H. 2003. Distribution of native Hibiscus hamabo and ecological characteristics of naturally inhabited areas in Jeju Island. Korean Journal of Horticultural Science and Technology 21: 440-446.
  2. Ahn, Y.-H., K. H. Chung and H.-S. Park. 2003. Vegetation and flora of Hibiscus hamabo inhabited naturally in Soan Island. Journal of Environmental Science International 12: 1181-1187. https://doi.org/10.5322/JES.2003.12.11.1181
  3. Catchen, J., P. A. Hohenlohe, S. Bassham, A. Amores and W. A. Cresko. 2013. Stacks: An analysis tool set for population genomics. Molecular Ecology 22: 3124-3140. https://doi.org/10.1111/mec.12354
  4. Chang, C.-S., H. S. Lee, T. Y. Park and H. Kim. 2005. Reconsideration of rare and endangered plant species in Korea based on the IUCN Red List Categories. The Korean Journal of Ecology 28: 305-320. https://doi.org/10.5141/JEFB.2005.28.5.305
  5. Chung, M. Y., J. Merila, J. Li, K. Mao, J. Lopez-Pujol, Y. Tsumura and M. G. Chung. 2023. Neutral and adaptive genetic diversity in plants: An overview. Frontiers in Ecology and Evolution 11:1116814.
  6. Danecek, P., A. Auton, G. Abecasis, C. A. Albers, E. Banks, M. A. DePristo, R. E. Handsaker, G. Lunter, G. T. Marth, S. T. Sherry, G. McVean, R. Durbin and 1000 Genomes Project Analysis Group. 2011. The variant call format and VCFtools. Bioinformatics 27: 2156-2158. https://doi.org/10.1093/bioinformatics/btr330
  7. Di Santo, L. N., S. Hoban, T. L. Parchman, J. W. Wright and J. A. Hamilton. 2022. Reduced representation sequencing to understand the evolutionary history of Torrey pine (Pinus torreyana parry) with implications for rare species conservation. Molecular Ecology 31: 4622-4639. https://doi.org/10.1111/mec.16615
  8. Earl, D. A. and B. M. vonHoldt. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetic Resources 4: 359-361. https://doi.org/10.1007/s12686-011-9548-7
  9. Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study. Molecular Ecology 14: 2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  10. Excoffier, L. and H. E. L. Lischer. 2010. Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources 10: 564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
  11. Frankham, R., J. D. Ballou and D. A. Briscoe. 2010. Introduction to Conservation Genetics. 2nd ed. Cambridge University Press, Cambridge, UK. Pp. 2, 5.
  12. Frankham, R., C. J. A. Bradshaw and B. W. Brook. 2014. Genetics in conservation management: Revised recommendations for the 50/500 rules, Red List criteria and population viability analyses. Biological Conservation 170: 56-63. https://doi.org/10.1016/j.biocon.2013.12.036
  13. Kim, C. S. 2006. Studies on the distribution and vegetation of the endangered wild plants in Jeju Island. PhD dissertation, Jeju National University Graduate School, Jeju, Korea, 139 pp.
  14. Kim, C. S., J. G. Koh, M. O. Moon, G. P. Song, S. Y. Kim, J. Kim, D. S. Kim, J. H. Tho and K. M. Song. 2008. Rare Plants of Jeju Island. Korea Forest Research Institute, Seoul. Pp. 278-279.
  15. Kim, Y.-D., K.-J. Kim, S.-H. Kim and H.-T. Kim. 2007. Genetic diversity in three populations of Hibiscus hamabo (Malvaceae) in Jeju Island, Korea. Korean Journal of Plant Taxonomy 37: 115-129. https://doi.org/10.11110/kjpt.2007.37.2.115
  16. Korea National Arboretum. 2021. The National Red List of Vascular Plants in Korea. Korea National Arboretum, Pocheon. Pp. 295.
  17. Li, Y.-L. and J.-X. Liu. 2018. StructureSelector: A web-based software to select and visualize the optimal number of clusters using multiple methods. Molecular Ecology Resources 18: 176-177. https://doi.org/10.1111/1755-0998.12719
  18. Lischer, H. E. L. and L. Excoffier. 2012. PGDSpider: An automated data conversion tool for connecting population genetics and genomics programs. Bioinformatics 28: 298-299. https://doi.org/10.1093/bioinformatics/btr642
  19. Nakai, T. 1914. Jeju Island Plant Survey Report. Government-General of Korea. P. 164.
  20. Nakanishi, H. 2001. Extincted localities of Hibiscus hamabo community in Nagasaki Prefecture. Transactions of Nagasaki Biological Society 53: 17-18.
  21. Nakanishi, H. 2010. History and present status of the conservation of a semi-mangrove plant, Hibiscus hamabo Siebold et Zucc. (Malvaceae). Japanese Journal of Conservation Ecology 15: 153-158. (in Japanese)
  22. Nakanishi, H., M. H. Kim and C. S. Kim. 2004. Distribution and ecology of Hibiscus hamabo and Paliurus ramosissimus in jeju Island, Korea. Bulletin of Faculty of Education, Nagasaki University: Natural Science 71: 1-10. (in Japanese)
  23. National Institute of Biological Resources. 2012. Red Data Book of Endangered Vascular Plants in Korea. National Institute of Biological Resources, Incheon, Korea. P. 254.
  24. National Institute of Biological Resources. 2021. Red Data Book of Endangered Vascular Plants in Korea. 2nd ed. National Institute of Biological Resources, Incheon. P. 468.
  25. Paris, J. R., J. R. Stevens and J. M. Catchen. 2017. Lost in parameter space: A road map for STACKS. Methods in Ecology and Evolution 8: 1360-1373. https://doi.org/10.1111/2041-210X.12775
  26. Peakall, R. and P. E. Smouse. 2012. GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research: An update. Bioinformatics 28: 2537-2539. https://doi.org/10.1093/bioinformatics/bts460
  27. Pritchard, J. K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959. https://doi.org/10.1093/genetics/155.2.945
  28. Rivera-Colon, A. G. and J. Catchen. 2022. Population genomics analysis with RAD, reprised: Stacks 2. Methods in Molecular Biology 2498: 99-149.
  29. Tamura, K., G. Stecher and S. Kumar. 2021. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Molecular Biology and Evolution 38: 3022-3027. https://doi.org/10.1093/molbev/msab120
  30. Weir, B. S. and Cockerham, C. C. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x
  31. Zheng, X., D. Levine, J. Shen, S. M. Gogarten, C. Laurie and B. S. Weir. 2012. A high-performance computing toolset for relatedness and principal component analysis of SNP data. Bioinformatics 28: 3326-3328. https://doi.org/10.1093/bioinformatics/bts606