Journal of Species Research

The National Institute of Biological Resources (국립생물자원관)
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Genetic diversity and population structure of endangered Neofinetia falcata (Orchidaceae) in South Korea based on microsatellite analysis

  • Han, Jeong Eun (Biological and Genetic Resources Utilization Division, National Institute of Biological Resources) ;
  • Choi, Byoung-Hee (Department of Biological Sciences, Inha University) ;
  • Kwak, Myounghai (Plant resources Division, National Institute of Biological Resources)
  • Received : 2018.05.18
  • Accepted : 2018.10.25
  • Published : 2018.11.30
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Abstract

Population genetic assessment is essential for the conservation and management of endangered and rare plants. Neofinetia falcata is endangered epiphyte orchid and protected by law in Korea. In Korea, this species is only found on islands in the South Sea of Korea (including Jeju-do) and the southern coast of the Korean Peninsula. We developed nine microsatellite makers to assess the genetic diversity and population genetic structure of three populations of N. falcata. The genetic diversity at the species level was low, which can be attributed to inbreeding or fragmentation into small, isolated populations. A recent bottleneck was detected in one population, likely due to overcollection. N. falcata exhibited moderated levels of differentiation among populations, with the three populations were divided into two clusters based on genetic structure. The genetic diversity and structure of N. falcata are affected by restricted gene flow by pollen or seeds due to isolation and geographic distance. Strategies for in situ and ex situ conservation of this species are been proposed based on the results of our study.

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References

  1. Barman, D. and R. Devadas. 2013. Climate change on orchid population and conservation strategies: A review. Journal of Crop and Weed 9(2):1-12.
  2. Chen, X. and J.W. Jeffrey. 2009. Neofinetia Hu. In: Z. Wu, H.R. Peter and D. Hong (eds), Flora of China Orchidaceae (volume 25). Science Press, Beijing and Missouri Botanical Garden Press, St. Louis. pp. 483-484.
  3. Chen, Y.-Y., Z.-X. Bao, Y. Qu, W. Li and Z.-Z. Li. 2014. Genetic diversity and population structure of the medicinal orchid Gastrodia elata revealed by microsatellite analysis. Biochemical Systematics and Ecology 54:182-189. https://doi.org/10.1016/j.bse.2014.01.007
  4. Chung, J.D. 1980. Seed culture of Neofinetia falcata in vitro II. Effect of hyponex medium added with various concentrations of peptone or tryptone on asymbiotic germination of seeds and growth of seedlings. Journal of Plant Biotechnology 7(1):13-21.
  5. Chung, J.D. 1981. Seed Culture of Neofinetia falcata in vitro III. Effect of auxin, kinetin, vitamin and apple juice on growth of seedlings after transplanting. Journal of Plant Biotechnology 8(1):1-10.
  6. Cornuet, J.M. and G. Luikart. 1996. Description and power analysis of two tests for detecting recent population bottlenecks from allele frequency data. Genetics 144:2001-2014.
  7. David, H.R. and F. Richard. 2003. Correlation between fitness and genetic diversity. Conservation Biology 17(1):230-237. https://doi.org/10.1046/j.1523-1739.2003.01236.x
  8. Dressler, R.L. 1993. Phylogeny and classification of the orchid family. Dioscorides Press, Portland, Oregon. pp. 205-207.
  9. Duttke, S., N. Zoulias and M. Kim. 2012. Mutant flower morphologies in the wind orchid, a novel orchid Model species. Plant Physiology 158(4):1542-1547. https://doi.org/10.1104/pp.111.191643
  10. Earl, D.A. and B.M. vonHoldt. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUC - TURE output and implementing the Evanno method. Conservation Genetics Resources 4:359-361. https://doi.org/10.1007/s12686-011-9548-7
  11. Ellstrand, N.C. and D.R. Elam. 1993. Population genetic consequences of small population size: Implications for plant conservation. Annual Review of Ecology and Systematics 24:217-242. https://doi.org/10.1146/annurev.es.24.110193.001245
  12. Escudero, A., J.M. Iriondo and M.E. Torres. 2003. Spatial analysis of genetic diversity as a tool for plant conservation. Biological Conservation 113:351-365. https://doi.org/10.1016/S0006-3207(03)00122-8
  13. 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
  14. 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(3):564-567. https://doi.org/10.1111/j.1755-0998.2010.02847.x
  15. Frankham, R. 1996. Relationship of genetic variation to population size in wildlife. Conservation Biology 10(6):1500-1508. https://doi.org/10.1046/j.1523-1739.1996.10061500.x
  16. Hahn, E.-J. and K.-Y. Paek. 2001. High photosynthetic photon flux and high $CO_2$ concentration under increased number of air exchanges promote growth and photosynthesis of four kinds of orchid plantlets in vitro. In Vitro Cellular & Development Biology-Plant 37(5):678-682. https://doi.org/10.1007/s11627-001-0118-7
  17. Han, K.-S., S.-C. Lee, Y.-K. Han, S. Kim and D. Kim. 2010. Sclerotium blight of Neofinetia falcata caused by Sclerotium rolfsii in Korea. Research in Plant Disease 16(3):320-322. https://doi.org/10.5423/RPD.2010.16.3.320
  18. Han, K.-S., S.-C. Lee, J.-S. Lee, J.-W. Soh and M.J. Park. 2013. Gray mold on Neofinetia falcata caused by Botrytis cinerea in Korea. The Korean Journal of Mycology 41(4):292-294. https://doi.org/10.4489/KJM.2013.41.4.292
  19. Hidayat, T., P.H. Weston, T. Yukawa, M. Ito and R. Rice. 2012. Phylogeny of subtribe Aeridinae (Orchidaceae) inferred from DNA sequences data: Advanced analyses including Australasian genera. Jurnal Teknologi (Sciences & Engineering) 59(1)suppl.:87-95.
  20. Honnay, O. and H. Jacquemyn. 2007. Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation. Conservation Biology 21(3):823-831. https://doi.org/10.1111/j.1523-1739.2006.00646.x
  21. Hou, B., M. Tian, J. Luo, Y. Ji, Q. Xue and X. Ding. 2012. Genetic diversity assessment and ex situ conservation strategy of the endangered Dendrobium officinale (Orchidaceae) using new trinucleotide microsatellite markers. Plant Systematics and Evolution 298(8):1483-1491. https://doi.org/10.1007/s00606-012-0651-3
  22. Hundera, K., R. Aerts, M.D. Beenhouwer, K.V. Overtveld, K. Helsen, B. Muys and O. Honnay. 2013. Both forest fragmentation and coffee cultivation negatively affect epiphytic orchid diversity in Ethiopian moist evergreen Afromontane forests. Biological Conservation 159:285-291. https://doi.org/10.1016/j.biocon.2012.10.029
  23. Ichihashi, S. and M.O. Islam. 1999. Effects of complex organic additives on callus growth in three orchid genera, Phalaenopsis, Doritaenopsis, and Neofinetia. Journal of the Japanese Society for Horticultural Science 68(2):269-274. https://doi.org/10.2503/jjshs.68.269
  24. Jakobsson, M and N.A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure, version 1.1. Bioinformatics 23:1801-1806. https://doi.org/10.1093/bioinformatics/btm233
  25. Johansen, B.B. and H.N. Rasmussen. 1992. Ex situ conservations of orchids. Opera Botanica 113:43-48.
  26. Kim, Y.-K., S.J. Jo and K.-J. Kim. 2014. Phylogenetic position of Neofinetia and Sedirea (Orchidaceae) and their species identification using the chloroplast matK and the nuclear ITS sequences. Korean Journal of Plant Taxonomy 44(1):39-50. https://doi.org/10.11110/kjpt.2014.44.1.39
  27. Kiyohara, S., H. Fukunaga and S. Sawa. 2012. Characteristics of the falling speed of Japanese orchid seeds. International Journal of Biology 4(3):10-12.
  28. Kwak, M., J.-K. Hong, J.H. Park, B.Y. Lee, M.H. Suh and C.S. Kim. 2017. Genetic assessment of Abies koreana (Pinaceae), the endangered Korean fir, and conservation implications. Conservation genetics 18(5):1165-1176. https://doi.org/10.1007/s10592-017-0968-0
  29. Lavor, P., C.V.D. Beag, C.M. Jacobi, F.F. Carmo and L.M. Versieux. 2014. Population genetics of the endemic and endangered Vriesea minarum (Bromeliaceae) in the Iron Quadrangle, Espinhaco range, Brazil. American Journal of Botany 101(7):1167-1175. https://doi.org/10.3732/ajb.1300388
  30. Lee, N.S. 2011. Illustrated Flora of Korean Orchids. Ewha Womans University Press, Seoul. pp. 326-329.
  31. Leimu, R., P. Mutikainen, J. Koricheva and M. Fischer. 2006. How general are positive relationships between plant population size, fitness and genetic variation?. Journal of Ecology 94(5):942-952. https://doi.org/10.1111/j.1365-2745.2006.01150.x
  32. Mallet, B., F. Martos, L. Blambert, T. Pailler and L. Humeau. 2014. Evidence for isolation-by-habitat among populations of an epiphytic orchid species on a small oceanic island. PLOS ONE 9(2):e87469. https://doi.org/10.1371/journal.pone.0087469
  33. Miao, Y.C., X.D. Lang, Z.Z. Zhang and J.R. Su. 2014. Phylogeography and genetic effects of habitat fragmentation on endangered Taxus yunnanensis in southwest China as revealed by microsatellite data. Plant Biology 16:365-374. https://doi.org/10.1111/plb.12059
  34. Miao, Y.-C., J.-R. Su, Z.-J. Zhang, X.-D. Lang, W.-D. Liu and S.-F. Li. 2015. Microsatellite markers indicate genetic differences between cultivated and natural population of endangered Taxus yunnanensis. Botanical Journal of the Linnean Society 177:450-461. https://doi.org/10.1111/boj.12249
  35. Michael, F.F. 2016. Orchid conservation: further links. Annals of Botany 118:89-91. https://doi.org/10.1093/aob/mcw147
  36. Mitsukuri, K., G. Mori, M. Johkan, K. Mishiba, T. Morikawa and M. Oda. 2009. Effects of explant source and dark-preconditioning on adventitious bud formation in Neofinetia falcata H. H. Hu in vitro. Journal of Japanese Society for Horticultural Science 78(2):252-256. https://doi.org/10.2503/jjshs1.78.252
  37. Murren, C.J. 2002. Effect of habitat fragmentation on pollination: pollinators, pollinia viability and reproductive success. Journal of Ecology 20:100-107.
  38. National Institute of Biological Resources. 2012. Red data book of endangered vascular plants in Korea. National Institute of Biological Resources, Incheon.
  39. 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
  40. Piry, S., G. Luikart and J. Cornuet. 1999. BOTTLENECK: a computer program for detecting recent reductions in the effective size using allele frequency data. The Journal of Heredity 90(4):502-503. https://doi.org/10.1093/jhered/90.4.502
  41. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  42. Rosenberg, N.A. 2004. DISTRUCT: a program for the graphical display of population structure, version 1.1. Molecular Ecology Notes 4:137-138.
  43. Rozen, S. and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. In: S. Misener and S.A. Krawetz (ed.), Bioinformatics Methods and Protocols: Methods in molecular biologyTM vol. 132. Humana Press, Totowa, New Jersey. pp. 365-386.
  44. Shanker, A., A. Bhargava, R. Bajpai, S. Singh, S. Srivastava and V. Shama. 2007. Bioinformatically mined simple sequence repeats in UniGene of Citrus sinensis. Scientia Horticulturae 113(4):353-361. https://doi.org/10.1016/j.scienta.2007.04.011
  45. Shimizu, N. 2012. Adaptation and evolution of seed shape on bleeding area in Japanese orchids. International journal of Biology 4(2):47-53.
  46. Shin, H., Y. Lim, J.-O. Hyun, K.W. Kang. 2009. A case of endangered plant restoration: Neofinetia falcata (Thunb.) Hu. In: H. Shin (ed.), Conservation biology of the Korea - the present situation and problem, Worldscience Press, Seoul. pp. 81-104.
  47. Segelbacher, G., J. Höglund and I. Storch. 2003. From connectivity to isolation: genetic consequences of population fragmentation in capercaillie across Europe. Molecular Ecology 12:1773-1780. https://doi.org/10.1046/j.1365-294X.2003.01873.x
  48. Spencer, C.C., J.E. Neigel and P.L. Leberg. 2000. Experimental evaluation of the usefulness of microsatellite DNA for detecting demographic bottlenecks. Molecular Ecology 9(10):1517-1528. https://doi.org/10.1046/j.1365-294x.2000.01031.x
  49. Su, Z., B.A. Richardson, L. Zhuo, X. Jiang, W. Li and X. Kang. 2017. Genetic diversity and structure of an endangered desert shrub and the implications for conservation. AoB Plants 9(3): plx016. [Available from: https://doi.org/10.1093/aobpla/plx016, accessed 17 April 2017].
  50. Suetsugu, K., K. Tanaka, Y. Okuyama and T. Yukawa. 2015. Potential pollinator of Vanda falcata (Orchidaceae): Theretra (Lepidoptera: Sphingidae) hawkmoths are visitors of long spurred orchid. European Journal of Entomology 112(2):393-397. https://doi.org/10.14411/eje.2015.031
  51. Sun, Y., X. Wen and H. Huang. 2011. Genetic diversity and differentiation of Michelia maudiae (Magnoliaceae) revealed by nuclear and chlorophlast microsatellite markers. Genetica 139:1439-1447. https://doi.org/10.1007/s10709-012-9642-0
  52. Szpiech, Z.A., M. Jakobsson and N.A. Rosenberg. 2008. ADZE: a rarefaction approach for counting alleles private to combinations of populations. Genetics and population analysis 24(21):2498-2504.
  53. Tian, H.Z., L.X. Han, J.L. Zhang, X.L. Li, T. Kawahara, T. Yukawa, J. López-Pujol, P. Kuamr, M.G. Chung and M.Y. Chung. 2018. Genetic diversity in the endangered terrestrial orchid Cypripedium japonicum in East Asia: Insights into population history and implications for conservation. Scienticific Reports 8:6467. https://doi.org/10.1038/s41598-018-24912-z
  54. Trapnell, D.W., R.R. Beasley, S.L. Lance, A.R. Field and K.L. Jones. 2015. Characterization of microsatellite loci for an australian epiphytic orchid, Dendrobium calamiforme, using illumina sequencing. Applications in Plant Sciences 3(6):1500016. https://doi.org/10.3732/apps.1500016
  55. Weremijewicz, J., J.I. Almonte, V.S. Hilaire, F.D. Lopez, S.H. Lu, S.M. Marrero, C.M. Martinez, E.A. Zarate, A.K. Lam, SA.N. Ferguson, N.Z. Petrakis, K.A. Peeples, E.D. Taylor, NM. Leon, C. Valdes, M. Hass, A.B. Reeve, D.T. Palow and J.L. Downing. 2016. Microsatellite primers for two threatened orchids in Florida: Encyclia tampensis and Cyrtopodium punctatum (Orchidaceae). Applications in Plant Sciences 4(4):1500095. https://doi.org/10.3732/apps.1500095
  56. Wone, B.W.M., J. Pathak and G. Davidowitz. 2018. Flight duration and flight muscle ultrastructure of unfed hawk moths. Arthropod Structure & Development (in Press).
  57. Xu, Y., R. Jia, Y. Zhou, H. Cheong, X. Zhao and H. Ge. 2018. Development and characterization of polymorphic ESTSSR markers for Paphiopedilum henryanum (Orchidaceae). Applications in Plant Sciences 6(5):e1152.
  58. Yoon, K.E and W.Y. Chung. 2011. Orchids of wold. Gimmyoung Press. Paju. 275 pp.
  59. Yun, Y.-E., J.-N. Yu, B.-Y. Lee and M. Kwak. 2011. An introduction to microsatellite development and analysis. Korean Journal of Plant Taxonomy 41(4):299-314. https://doi.org/10.11110/kjpt.2011.41.4.299
  60. Zhang, X., S. Shen, F. Wu and Y. Wang. 2017. Inferring genetic variation and demographic history of Michelia yunnanensis Franch. (Magnoliaceae) from chloroplast DNA sequences and microsatellite markers. Frontiers in Plant Science 8:583. https://doi.org/10.3389/fpls.2017.00583