Korean Journal of Medicinal Crop Science (한국약용작물학회지)

The Korean Society of Medicinal Crop Science (한국약용작물학회)
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Phylogenic Relationship of Rubus Cultivated in Korea Revealed by Chloroplast DNA Spacers

Chloroplast DNA Spacers로 분석한 국내 Rubus 재배종의 계통학적 유연관계

  • Eu, Gee-Suck (Institute of Agricultural Science and Technology, Chonbuk National University) ;
  • Park, Myoung-Ryoul (Institute of Agricultural Science and Technology, Chonbuk National University) ;
  • Baek, So-Hyeon (National Institute of Crop Science, RDA) ;
  • Yun, Song-Joong (Department of Crop Science, Institute of Agricultural Science and Technology, Chonbuk National University)
  • 유기석 (전북대학교 농업생명과학대학 농업과학기술연구소) ;
  • 박명렬 (전북대학교 농업생명과학대학 농업과학기술연구소) ;
  • 백소현 (농촌진흥청 국립식량 과학원) ;
  • 윤성중 (전북대학교 농업생명과학대학 작물생명과학과)
  • Received : 2010.05.11
  • Accepted : 2010.08.19
  • Published : 2010.08.30
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Abstract

There is a considerable difference in morphological traits between Bokbunja cultivated in Korea (KCB) and Korea native Rubus coreanus, contrary to the conviction that the cultivated Bokbunja is the domestication of R. coreanus. To infer the phylogenetic relationship of KCB with other Rubus species, we compared the chloroplast DNA spacers of KCB with those of several Rubus species including black raspberry, R. occidentalis. The three chloroplast DNA spacers, atpB~rbcL, trnL~trnF, and trnT~trnL, were amplified using the specific primer pairs and converted to Single Strand Conformational Polymorphism (SSCP) markers. The SSCP makers of the chloroplast DNA spacers showed a considerable variation both within and among Rubus species. In the phylogenetic tree generated by the SSCP markers, KCB accessions were located in the same clade with R. occidentalis, but R. coreanus accessions in the different clade. Also, in the phylogenetic tree by the nucleotide sequences of the chloroplast DNA spacer trnL~trnF, KCB located in the same clade with R. occidentalis but not with R. coreanus. These results suggest that the three KCB accessions share higher similarity with R. occidentalis than with R. coreanus in the three chloroplast DNA spacers.

Keywords

References

  1. Altschul SF, Madden TL, Schaffer AA , Zhang J, Zang ZW, Miller W and Lipman DJ. (1997). Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acid Research. 25:3389-3402. https://doi.org/10.1093/nar/25.17.3389
  2. Brodsky LI, Ivanov VV, Kalaidzidis YL, Leontovich AM, Nikolaev VK, Feranchuk SI and Drachev VA. (1995). GeneBee-NET: Internet-based server for analyzing biopolymers structure. Biochemistry. 60:923-928.
  3. Chase MW, Soltis DE, Olmstead RG, Morgan D, Les HD, Mishler BD, Duvall MR, Price RA, Hills HG, Qiu YL, Kron KA, Rettig JH, Conti E, Palmer JD, Manhart JR, Sytsma KJ, Michaels HJ, Kress WJ, Karol KG, Clark WD, Hedren M, Gaut BS, Jansen RK, Kim KJ, Wimpee CF, Smith JF, Furnier GR, Strauss SH, Xiang QY, Plunkett GM, Soltis PS, Swensen SM, Williams SE, Gadek PA, Quinn CJ, Eguiarte LE, Golenberg E, Learn GH Jr., GrahamSW, Barrett SCH, Dayanandan S and Albert VA. (1993). Phylogenetics of seed plants: an analysis of nucleotide sequences from the plastid gene rbcL. Annals of the Missouri Botanical Garden. 80:526-580.
  4. Chang IM. (2003). Treatise on Asian Herbal Medicines. Natural Products Research Institute, Seoul National University. Seoul. Korea. p. 185.
  5. Gielly L and Taberlet P. (1994). The use of chloroplast DNA to resolve plant phylogenies: noncoding versus rbcL sequences. Molecular Biology and Evolution. 11:769-777.
  6. Gilbert DC. (1994). SeqApp 1.9. A biological sequence editor and analysis program for Macintosh computers. Available from ftp.bio.indiana.edu.
  7. Golenberg EM, Clegg MT, Durbin ML, Doebley J and DP MA. (1993). Evolution of a noncoding region of the chloroplast genome. Molecular Phylogenetics and Evolution. 2:52-64. https://doi.org/10.1006/mpev.1993.1006
  8. Eu GS, Chung BY, Rajib B, Yoo NH, Choi DG and Yun SJ. (2008). Phylogenic realtionships of Rubus species revealed by ramdomly amplified polymorphic DNA markers. Journal of Crop Science and Biotechnology. 11:39-44.
  9. Eu GS, Park MR and Yun SJ. (2009). Internal transcribed spacer (ITS) regions reveals phylogenic relationships of Rubus species cultivated in Korea. Korean Journal of Medicinal Crop Science. 17:161-164.
  10. Ham SS, Lee SY, Oh DH, Kim SH and Hong JG. (1997). Development of beverages drinks using mountain edible herbs. Journal of the Korean Society of Food Science and Nutrition. 26:92-97.
  11. Hodges SA and Arnold ML. (1994). Columbines: a geographically widespread species flock. Proceedings of the National Academy of Sciences. 91:5129-5132. https://doi.org/10.1073/pnas.91.11.5129
  12. Jennings DL. (1988). Raspberries and blackberries: their breeding, diseases and growth. Academic Press, London, England. p. 229.
  13. Jeong HS, Ha JH, Kim Y, Oh SH, Kim SS, Jeong MH and Lee HY. (2009). Effects of Rubus coreanus extracts on ultraviolet-A irradiated cultured human skin fibroblasts. Korean Journal of Medicinal Crop Science. 17:321-327.
  14. Jeong JS and Sin MK. (1996). Encyclopedia of oriental medical. Young Rim Publication Company Limited, Seoul. p. 461.
  15. Johnson LA and Soltis DE. (1994). matK DNA sequences and phylogenetic reconstruction in Saxifragaceae sensu strico. Systematic Botany. 19:143-156. https://doi.org/10.2307/2419718
  16. Jung J, Son MY, Jung S, Nam P, Sung JS, Lee SJ and Lee KG. (2009). Antioxidant properties of Korean black raspberry wines and their apoptotic effects on cancer cells. Journal of the Science of Food and Agriculture. 89:970-977. https://doi.org/10.1002/jsfa.3540
  17. Kee YW and Lim DY. (2007). Influence of polyphenolic compounds isolated from Rubus coreanum on catecholamine release in the rat adrenal medulla. Archives of Pharmacal Research. 30:1240-1251. https://doi.org/10.1007/BF02980265
  18. Kim KJ and Jansen RK. (1995). ndhF sequence evolution and the major clades in the sunflower family. Proceedings of National Academic Sciences. 92:10379-10383.
  19. Kong P, Hong CX, Richardson PA and Gallegly ME. (2003). Single- strand conformation-polymorphism of ribosomal DNA for rapid species differentiation in genus phytophthora. Fungal Genetics and Biology. 39:238-249. https://doi.org/10.1016/S1087-1845(03)00052-5
  20. Markowicz Y and Loiseaux-de Goer S. (1991). Plastid genomes of the rhodophyta and chromophyta constitute a distinct lineage which differs from that of the chlorophyta and have a composite phylogenetic origin, perhaps like that of the Euglenophyta. Current Genetics. 20:427-430. https://doi.org/10.1007/BF00317073
  21. Park JH, Lee HS, Mun HC, Kim DH, Seong NS, Jung HG, Bang JK and Lee HY. (2003). Effect of ultrasonification process on enhancement of immuno-stimulatory activity of Ephedra sinica Strapf and Rubus coreanus Miq. Korean Journal of Biotechnology and Bioprocess Engineering. 19:113-117
  22. Sneath HA and Sokal RR. (1973). Numerical Taxonomy. P. XV. W. H. Freeman, San Francisco.
  23. Steele KP and Vilgalys R. (1994). Phylogenetic analyses of polemoniaceae using nucleotide sequences of the plastid gene matK. Systematic Botany. 19:126-142. https://doi.org/10.2307/2419717
  24. Taberlet PL, Gielly G, Pautou and Bouvet J. (1991). Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology. 17:1105-1109. https://doi.org/10.1007/BF00037152
  25. Waugh R, Van de Ven, W. T. G., Phillips MS and Powell W. (1990). Chloroplast DNA diversity in the genus Rubus (Rosaceae) revealed by southern hybridization., plant systematics and evolution. Plant Systematics and Evolution. 172:65-75. https://doi.org/10.1007/BF00937798
  26. Wolf PG. (1997). Evaluation of atpB nucleotide sequences for phylogenetic studies of ferns and other pteridophytes. American Journal of Botany. 84:1429-1440. https://doi.org/10.2307/2446141