Horticultural Science & Technology (원예과학기술지)

Korean Society of Horticultural Science (한국원예학회)
권호 표지

Phylogenetic Relationship of Ligularia Species Based on RAPD and ITS Sequences Analyses

RAPD 및 ITS 염기서열 분석을 이용한 곰취 속(Ligularia) 식물의 유연관계 분석

  • Ahn, Soon-Young (Highland Agriculture Research Center, National Institute of Crop Science, Rural Development Administration) ;
  • Cho, Kwang-Soo (Highland Agriculture Research Center, National Institute of Crop Science, Rural Development Administration) ;
  • Yoo, Ki-Oug (Department of Biological Sciences, Kangwon National University) ;
  • Suh, Jong-Taek (Highland Agriculture Research Center, National Institute of Crop Science, Rural Development Administration)
  • 안순영 (농촌진흥청 국립식량과학원 고령지농업연구센터) ;
  • 조광수 (농촌진흥청 국립식량과학원 고령지농업연구센터) ;
  • 유기억 (강원대학교 생명과학과) ;
  • 서종택 (농촌진흥청 국립식량과학원 고령지농업연구센터)
  • Received : 2009.12.17
  • Accepted : 2010.04.08
  • Published : 2010.08.31
Download PDF
⟨ Previous Next ⟩

Abstract

The genetic relationships in 5 species of $Ligularia$ were investigated using RAPD (Randomly Amplified Polymorphic DNA) and ITS (Internal Transcribed Spacer) sequences analyses. In RAPD analysis, sixty three of 196 arbitrary primers showed polymorphism. The amplified fragments ranged from 0.2 to 1.6 kb in size. The dendrogram was constructed by the UPGMA clustering algorithm based on genetic similarity of RAPD markers. A total of 16 accessions were classified into 5 major groups corresponding each species at the similarity coefficient value of 0.77. In the ITS sequence analysis, the size of ITS 1 was varied from 248 to 256 bp, while ITS 2 was varied from 220 to 222 bp. The 5.8S coding region was 164 bp in lengths. Forty nine sites (10.2%) of the 478 nucleotides were variable, and the G+C content of ITS region ranged from 49.4 to 53.5%. In the ITS tree, five species of $Ligularia$ were monophyletic, and $L.$ $taquetii$ was the first branching within the clade. $Ligularia$ $intermedia$ formed a clade with $L.$ $fischeri$ var. $spiciformis$ (BS=79), and $L.$ $stenocephala$ and $L.$ $fischeri$ were also claded. Two data sets were congruent, except of the position of $L.$ $fischeri$ var. $spiciformis$.

RAPD와 ITS 염기서열 분석을 통하여 $Ligularia$ 속 식물 5종류의 유연관계를 밝혔다. RAPD 분석에서는 총 196개의 random primer를 사용하여 밴드수가 많고 선명한 63개의 primer를 선발하였다. 다형성을 나타낸 밴드는 141개(31.8%)이었으며, 증폭된 크기는 0.2-1.6kb로 다양하였다. 유집 분석 결과, 유사도 값은 0.54-0.95의 범위로 나타났고, 0.77을 기준으로 크게 5그룹으로 나누었다. ITS 영역의 염기서열 분석 결과, ITS 1과 ITS 2 지역은 각각 248-256bp와, 220-222bp로 구성되어 있으며, 5.8S 부분은 164bp로 나타났다. ITS 1과 ITS 2 지역의 총 478개의 염기 중 49(10.2%)군데에서 변이가 있었으며, 구아닌(G)과 시토신(C)의 비율은 ITS 1 지역에서 49.4%, ITS 2에서는 53.5%로 나타났다. 염기서열 분석결과 5종류는 단계통을 형성하였으며, 갯취는 군외군으로 부터 가장 먼저 분계조를 형성하였다. 한대리곰취와 어리곤달비는 79%의 지지율을 가지고 유집되었으며, 곰취와 곤달비도 함께 유집되었지만 지지도는 52%로 낮았다. 이상의 결과에서 두 데이터는 일치하는 결과를 보였지만 한 대리 곰취의 분류학적 위치는 RAPD와 ITS 분석결과가 일치하지 않았다.

Keywords

References

  1. Alvarez, I. and J.F. Wendel. 2003. Ribosomal ITS sequences and plant phylogenetic inference. Mol. Phylogenetics Evol. 29:417-434. https://doi.org/10.1016/S1055-7903(03)00208-2
  2. Baldwin, B.G., M.J. Sanderson, J.M. Porter, M.F. Wojciechowski, C.S. Campbell, and M.J. Donoghue. 1995. The ITS region of nuclear ribosomal DNA: A valuable source of evidence on angiosperm phylogeny. Ann. Missouri Botanical Garden 82:247-277. https://doi.org/10.2307/2399880
  3. Cho, Y.O. 2002, Antioxidative activity of the Korean wild leafy vegetables: Aster scaber and Ligularia fischeri. Nutraceuticals & Food. 7:146-150. https://doi.org/10.3746/jfn.2002.7.2.146
  4. Choi, E.M., Y. Ding, H.T. Nguyen, S.H. Park, and Y.H. Kim. 2007. Antioxidant activity of Gomchi (Ligularia fischeri) leaves. Food Sci. Biotechnol. 16:710-714.
  5. David, V.J. and L.B. Thien. 1997. A conserved motif in the 5.8S ribosomal RNA (rRNA) gene is a useful diagnostic marker for plant internal transcribed spacer (ITS) sequences. Plant Mol. Biol. Rep. 15:326-334 https://doi.org/10.1023/A:1007462330699
  6. Felsenstain, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:789-791.
  7. Fritsch, P., M.A. Hanson, C.D. Spore, and P.E. Pack. 1993. Constancy of RAPD primer amplification strength among distantly related taxa of flowering plants. Plant Mol. Biol. Rep. 11:10-20. https://doi.org/10.1007/BF02670555
  8. Ham, S.S., S.Y. Lee, D.H. Oh, S.W. Jung, S.H. Kim, C.K. Chung, and I.J. Kang. 1998. Antimutagenic and antigenotoxic effects of Ligularia fischeri extracts. J. Kor. Soc. Food Sci. Nutr. 27:745-750.
  9. In, J.G., B.S. Lee, E.J. Kim, K.S. Choi, S.H. Han, C.W. Shin, and D.C. Yang. 2006. Analysis of the ITS (Internal Transcribed Spacer) region of Opuntia ficus-indica. Kor. J. Plant Res. 19:161-168.
  10. Kapteyn, J., and J.E. Simon. 2002. The use of RAPDs for assessment of identity, diversity, and quality of Echinacea. p. 509-513. In: Trends in new crops and new uses. J. Janick, and A. Whipkey (eds.). ASHS Press, Alexandria, VA.
  11. Kim, K.J. 2007. Tribe Senecioneae, In The genera of vascular plants of Korea. C. W. Park (eds.), Academy Publ. Co., Seoul. P. 1033-1034.
  12. Kim, J.K. and R.K. Jansen. 1994. Comparisons of phylogenetic hypotheses among different data sets in dwarf dandelions (Krigia): Additional information from internal transcribed spacer sequences of nuclear ribosomal DNA. Pl. Syst. Evol. 190:157-185. https://doi.org/10.1007/BF00986191
  13. Kwon, Y.J., K.H. Kim, and H.K. Kim. 2002. Changes of total polyphenol content and activity of Ligularia fischeri extracts with different microwave-assisted extraction conditions. Kor. J. Food Preserv. 9:332-337.
  14. Lee, K.T., S.J. Koo, S.H. Jung, J. Cho, H.J. Jung, and H.J. Park. 2002. Structure of three new terpenoids, spiciformisins a and b, and monocyclosqualene, isolated from the herbs of Ligularia fischeri var. spiciformis and cytotoxicity. Arch. Pharm. Res. 25:820-823. https://doi.org/10.1007/BF02976998
  15. Lee, S.W. and J.H. Kim. 2003. Genetic relationship analysis of melons (Cucumis melo) germplasm by RAPD method. J. Kor. Soc. Hort. Sci. 44:307-313.
  16. Liu, J.Q., Y. Wangn, A. Wang, O. Hederik, and A. Richard. 2006. Radiation and diversification of Ligularia-Cremanthodium- Parasenecio triggered by uplifts of the Qinghai-Tibetan Plateau. Molec. Phylogenetics Evol. 38:31-49. https://doi.org/10.1016/j.ympev.2005.09.010
  17. Liu, J.Q. 2004. Uniformity of karyotypes of Ligularia (Asteraceae: Senecioneae), a highly diversified genus of the eastern Qinghai- Tibet Plateau highlands and adjacent areas. Botanical J. Linnean Soc. 144:329-342. https://doi.org/10.1111/j.1095-8339.2003.00225.x
  18. Murray, M.G., and W.F. Thompson. 1980. Rapid isolation of high molecular weight plant DNA. Nucl. Acids Res. 8:4321-4325. https://doi.org/10.1093/nar/8.19.4321
  19. Na, Y., J.H. Kim, K.S. Sim, B.C. Lee, and H.B. Pyo. 2006. Effects of antioxidation and inhibition of matrix metalloproteinase-1 from Ligularia fischeri. J. Soc. Cosmet. Scientists Kor. 32: 129-134.
  20. Nagano, H., Y. Iwazaki, X. Gong, Y. Shen, C. Kuroda, and R. Hanai. 2006. Chemical and genetic differentiation of Ligularia pleurocaulis in northwestern Yunnan and southwestern Sichuan provinces of China. Bull. Chem. Soc. Jpn. 79:300-304. https://doi.org/10.1246/bcsj.79.300
  21. Park, H.J. and M.Y. Choi. 2007. Antinocicepetive effects of 3,4-Dicaffeoyl Quinic acid of Ligularia fischeri var. spiciformis. Kor. J. Plant Res. 20:221-225.
  22. Russell, J.R., J.D. Fuller, M. Macaulay, B.G. Hatz, A. Jahoor, W. Powell, and R. Waugh. 1997. Direct comparison of levels of genetic variation among barley accessions detected by RFLPs, AFLPs, SSRs and RAPDs. Theor. Appl. Genet. 95:714-722. https://doi.org/10.1007/s001220050617
  23. Shin, S.K., J.S. Yun, T. Yun, and W.K. Sim. 2003. Taxonomic relationship of Lotus (Nelumbo nucifera) based on ITS sequences of nuclear ribosomal DNA. J. Kor. Soc. Hort. Sci. 44:451-457.
  24. Swofford, D.L. 1998. PAUP: Phylogenetic Analysis Using Parsimony and Other Methods. Version 4.02b Sinauer Asso. Inc., Massachusetts, USA.
  25. Tatineni, V., R.G. Cantrell, and D.D. Davis. 1996. Genetic diversity in elite cotton germplasm determined by morphological characteristics and RAPDs. Crop Sci. 36:186-192. https://doi.org/10.2135/cropsci1996.0011183X003600010033x
  26. Whang, S.S. 2006. Analysis of ITS DNA sequences of the Viola albida complex. Kor. J. Plant Res. 19:628-633.
  27. Williams, J.G.K., A.R.K. Kubelik, J.A. Rafalski, and S.V. Tingey. 1990. DNA polymorphisms amplified by arbitrary primers are useful as genetic markers. Nucl. Acids Res. 18: 6531-6535. https://doi.org/10.1093/nar/18.22.6531
  28. Williams, J.G.K., M.K. Hanafey, J.A. Rafalski, and S.V. Tingey. 1993. Genetic analysis using random amplified polymorphic DNA markers. Meth. Enzymol. 218:704-740. https://doi.org/10.1016/0076-6879(93)18053-F
  29. Yoo, K.O., S.D. Ahn, I.J. Chun, J.K. Hong, C.Y. Yoo, J.H. Kim, S.C. Kim, and H.T. Lim. 1996. Comparative studies of the five edible mountain vegetables by DNA marker fingerprinting. Kor. J. Plant Res. 9:305-310.