Korean Journal of Plant Taxonomy (식물분류학회지)

The Korean Society of Plant Taxonomists (한국식물분류학회)
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Development and characterization of 21 microsatellite markers in Daphne kiusiana, an evergreen broad-leaved shrub endemic to Korea and Japan

  • Lee, Jung-Hyun (Department of Biology Education, Chonnam National University) ;
  • Cho, Won-Bum (Department of Biological Sciences, Inha University) ;
  • Yang, Sungyu (K-herb Research Center, Korea Institute of Oriental Medicine) ;
  • Han, Eun-Kyeong (Department of Biology Education, Chonnam National University) ;
  • Lyu, Eun-Seo (Department of Biology Education, Chonnam National University) ;
  • Kim, Wook Jin (K-herb Research Center, Korea Institute of Oriental Medicine) ;
  • Moon, Byeong Cheol (K-herb Research Center, Korea Institute of Oriental Medicine) ;
  • Choi, Goya (K-herb Research Center, Korea Institute of Oriental Medicine)
  • Received : 2017.01.31
  • Accepted : 2017.02.27
  • Published : 2017.03.31
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Abstract

Microsatellite markers were isolated for Daphne kiusiana var. kiusiana (Thymelaeaceae), an evergreen broad-leaved shrub endemic to Korea and Japan. Because its populations in Jeju Island are morphologically controversial, and consistently threatened by anthropogenic pressures, taxonomic delimitation and conservation effort are required at the genetic level. We developed 21 polymorphic microsatellite loci from Next Generation Sequencing data. The primer set included di-, tri-, and tetra-nucleotide repeats. Variability in the markers was tested for 80 individuals of D. kiusiana from three natural populations in Jeju Island and Japan. Among the 21 loci, three were unavailable for population JKJU of Japan. The Neighbor-Joining tree based on microsatellite markers described here classified the three populations into two groups according to geographical or morphological traits. These will be a powerful genetics tool for determining the taxonomic boundary and establishing suitable conservation strategies for D. kiusiana in Jeju Island.

Keywords

References

  1. Bolger, A. M., M. Lohse and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
  2. Dieringer, D. and C. Schlotterer. 2003. Microsatellite Analyser (MSA): A platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes 3: 167-169. https://doi.org/10.1046/j.1471-8286.2003.00351.x
  3. Felsenstein, J. 2004. PHYLIP: Phylogeny inference package. Department of Genome Sciences and Department of Biology, University of Washington, Seattle, WA.
  4. Frankham, R. 2005. Genetics and Extinction. Biological Conservation 126: 131-140. https://doi.org/10.1016/j.biocon.2005.05.002
  5. Korea National Arboretum. 2008. Rare Plants Data Book in Korea. Korea National Arboretum, Pocheon, 332 pp. (in Korean)
  6. Lee, J.-H. and B.-H. Choi. 2010. Distribution and northernmost limit on the Korean Peninsula of three evergreen trees. Korean Journal of Plant Taxonomy 40: 267-273. https://doi.org/10.11110/kjpt.2010.40.4.267
  7. Lee, J.-H., D.-H. Lee and B.-H. Choi. 2013. Phylogeography and genetic diversity of East Asian Neolitsea sericea (Lauraceae) based on variations in chloroplast DNA sequences. Journal of Plant Research 126: 193-202. https://doi.org/10.1007/s10265-012-0519-1
  8. Lee, J.-H., D.-H. Lee, I.-S. Choi and B.-H. Choi. 2014. Genetic diversity and historical migration patterns of an endemic evergreen oak, Quercus acuta, across Korea and Japan, inferred from nuclear microsatellites. Plant Systematics and Evolution 300: 1913-1923. https://doi.org/10.1007/s00606-014-1017-9
  9. Lee, J., K.-H. Lee, S. So, C. Choi and M. Kim. 2013. A new species of Daphne (Thymelaeaceae): D. jejudoensis M. Kim. Korean Journal of Plant Taxonomy 43: 94-98. https://doi.org/10.11110/kjpt.2013.43.2.94
  10. Miller, M. P., B. J. Knaus, T. D. Mullins and S. M. Haig. 2013. SSR pipeline: A bioinformatics infrastructure for identifying microsatellites from paired-end Illumina high-throughput DNA sequencing data. Journal of Heredity 104: 881-885. https://doi.org/10.1093/jhered/est056
  11. Ouborg, N. J., P. Vergeer and C. Mix. 2006. The rough edges of the conservation genetics paradigm for plants. Journal of Ecology 94: 1233-1248. https://doi.org/10.1111/j.1365-2745.2006.01167.x
  12. Peakall, R. and P. E. Smouse. 2006. GenAlEx 6: Genetic Analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6: 288-295. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  13. Rousset, F. 2008. GENEPOP’007: A complete reimplementation of the genepop software for Windows and Linux. Molecular Ecology Resources 8: 103-106. https://doi.org/10.1111/j.1471-8286.2007.01931.x
  14. Ro, N. Y., E. Y. Song, S. C. Kim, H. C. Ko and S. Y. Lee. 2010. Propagation of a rare variety Daphne kiusiana Miq. in Korea through softwood cuttings. Journal of Bio-Environment Control 19: 246-250. (in Korean)
  15. Satake, Y., H. Hara, S. Watari and T. Tominari. 1989. Wild Flowers of Japan: Woody Plants. Heibonsha, Tokyo, 300 pp.
  16. Willi, Y., J. Van Buskirk and A. A. Hoffmann. 2006. Limits to the adaptive potential of small populations. Annual Review of Ecology, Evolution, and Systematics 37: 433-458. https://doi.org/10.1146/annurev.ecolsys.37.091305.110145
  17. Yang, S. J. 2013. The distribution analysis for the flora of uninhabited islands in the Gyeongsangnamdo. MS thesis, Changwon National University, Changwon, Korea, 87 pp. (in Korean)

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  1. The complete chloroplast genome of Daphne kiusiana, an evergreen broad-leaved shrub on Jeju Island pp.1877-7260, 2017, https://doi.org/10.1007/s12686-017-0774-5