한국자원식물학회지 (Korean Journal of Plant Resources)

  • 제30권3호
  • /
  • Pages.323-330
  • /
  • 2017
  • /
  • 1226-3591(pISSN)
  • /
  • 2287-8203(eISSN)
한국자원식물학회 (The Plant Resources Society of Korea)
권호 표지
DOI QR코드

DOI QR Code

Development of Microsatellite Markers and their Use in Genetic Diversity and Population Analysis in Eleutherococcus senticosus

  • Lee, Kyung Jun (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • An, Yong-Jin (Ginseng & Medicinal Herb Experiment Station) ;
  • Ham, Jin-Kwan (Ginseng & Medicinal Herb Experiment Station) ;
  • Ma, Kyung-Ho (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Lee, Jung-Ro (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Cho, Yang-Hee (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA) ;
  • Lee, Gi-An (National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA)
  • 투고 : 2017.03.27
  • 심사 : 2017.05.04
  • 발행 : 2017.06.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

Eleutherococcus senticosus (Siberian ginseng) is an important medicinal tree found in northeast Asia. In this study, we analyzed the genome-wide distribution of microsatellites in E. senticosus. By sequencing 711 clones from an SSR-enriched genomic DNA library, we obtained 12 polymorphic SSR markers, which also revealed successful amplicons in E. senticosus accessions. Using the developed SSR markers, we estimated genetic diversity and population structure among 131 E. senticosus accessions in Korea and China. The number of alleles ranged from 2 to 11, with an average of 7.4 alleles. The mean values of observed heterozygosity ($H_O$) and expected heterozygosity ($H_E$) were 0.59 and 0.56, respectively. The average polymorphism information content (PIC) was 0.51 in all 131 E. senticosus accessions. E. senticosus accessions in Korea and China showed a close genetic similarity. Significantly low pairwise genetic divergence was observed between the two regions, suggesting a relatively narrow level of genetic basis among E. senticosus accessions. Our results not only provide molecular tools for genetic studies in E. senticosus but are also helpful for conservation and E. senticosus breeding programs.

키워드

참고문헌

  1. Ali, A., Y.-M. Choi, D.Y. Hyun, S. Lee, S. Oh, H.-J. Park, Y.-H. Cho and M.C. Lee. 2016. EST-SSR based genetic diversity and population structure among Korean landraces of foxtail millet (Setaria italica L.). Korean J. Plant Res. 29:322-330. https://doi.org/10.7732/kjpr.2016.29.3.322
  2. Butcher, P.A., S. Decroocq, Y. Gray and G.F. Moran. 2000. Development, inheritance and cross-species amplification of microsatellite markers from Acacia mangium. Theor. Appl. Genet. 101:1282-1290. https://doi.org/10.1007/s001220051608
  3. Cavagnaro, P.F., D.A. Senalik, L.M. Yang, P.W. Simon, T.T. Harkins, C.D. Kodira, S.W. Huang and Y.Q. Weng. 2010. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). BMC Genomics 11:569. https://doi.org/10.1186/1471-2164-11-569
  4. Cui H., K.T. Moe, J.W. Chung, Y.I. Cho, G.A. Lee and Y..J. Park. 2010. Genetic diversity and population structure of rice accessions from South Asia using SSR markers. Korean J. Breed. Sci. 42:11-22.
  5. Davydov, M. and A.D. Krikorian. 2000. Eleutherococcus senticosus (Rupr. & Maxim.) Maxim.(Araliaceae) as an adaptogen: a closer look. J. Ethnopharmacol. 72:345-393. https://doi.org/10.1016/S0378-8741(00)00181-1
  6. Evanno, G., S. Regnaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  7. Fang, J.N., A. Proksch and H. Wagner. 1985. Immunologically active polysaccharides of Acanthopanax senticosus. Phytochemistry 24:2619-2622. https://doi.org/10.1016/S0031-9422(00)80681-0
  8. Hong, K.N. and J. W. Lee. 2015. Fine-scale spatial genetic and clonal structure of Eleutherococcus senticosus populations in South Korea. Forest Sci. Technol. 11: 160-165. https://doi.org/10.1080/21580103.2014.975160
  9. Ishii, T., Y. Xu and S.R. McCouch. 2001. Nuclear-and chloroplastmicrosatellite variation in A-genome species of rice. Genome 44:658-666. https://doi.org/10.1139/g01-044
  10. Kim, J. and K.W. Chung. 2007. Isolation of new microsatellitecontaining sequences in Acanthopanax senticosus. J. Plant Biol. 50:557-561. https://doi.org/10.1007/BF03030709
  11. Kim, K.Y. 2004. Developing one step program (SSR Manager) for rapid identification of clones with SSRs and primer designing. Department of Plant Science, MS. Thesis, Seoul National Univ., Korea.
  12. Konishi, T., H. Iwata, K. Yashiro, Y. Tsumura, R. Ohsawa, Y. Yasui and O. Ohnishi. 2006. Development and characterization of microsatellite markers for common buckwheat. Breed. Sci. 56:277-285. https://doi.org/10.1270/jsbbs.56.277
  13. Lai, C.W.J., Q.Y. Yu, S.B. Hou, R.L. Skelton, M.R. Jones, K.L.T. Lewis, J. Murray, M. Eustice, P.Z. Guan, R. Agbayani, P.H. Moore, R. Ming and G.G. Presting. 2006. Analysis of papaya BAC end sequences reveals first insights into the organization of a fruit tree genome. Mol. Genet. Genomics 276:1-12. https://doi.org/10.1007/s00438-006-0122-z
  14. Lee, S., D. Son, J. Ryu, Y.S. Lee, S.H. Jung, J. Kang, S.Y. Lee, H.S. Kim and K.H. Shin. 2004. Anti-oxidant activities of Acanthopanax senticosus stems and their lignan components. Arch. Pharm. Res. 27:106-110. https://doi.org/10.1007/BF02980055
  15. Liu, K.J. and S.V. Muse. 2005. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128-2129. https://doi.org/10.1093/bioinformatics/bti282
  16. Ma, K.H., N.S. Kim, G.A. Lee, S.Y. Lee, J.K. Lee, J.Y. Yi, Y.J. Park, T.S. Kim, J.G. Gwag and S.J. Kwon. 2009. Development of SSR markers for studies of diversity in the genus Fagopyrum. Theor. Appl. Genet. 119:1247-1254. https://doi.org/10.1007/s00122-009-1129-8
  17. Nishibe, S., H. Kinoshita, H. Takeda and G. Okano. 1990. Phenolic compounds from stem bark of Acanthopanax senticosus and their pharmacological effect in chronic swimming stressed rats. Chem. Pharm. Bull. 38:1763. https://doi.org/10.1248/cpb.38.1763
  18. Ogutu, C., T. Fang, L. Yan, L. Wang, L.F. Huang, X.Y. Wang, B.Q. Ma, X.B. Deng, A. Owiti, A. Nyende and Y.P. Han. 2016. Characterization and utilization of microsatellites in the Coffea canephora genome to assess genetic association between wild species in Kenya and cultivated coffee. Tree Genet. Genomes. 12.
  19. 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
  20. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  21. Schuelke, M. 2000. An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnol. 18:233-234. https://doi.org/10.1038/72708
  22. Shultz, J.L., S. Kazi, R. Bashir, J.A. Afzal and D.A. Lightfoot. 2007. The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. Theor. Appl. Genet. 114:1081-1090. https://doi.org/10.1007/s00122-007-0501-9
  23. Stajner, N., J. Jakse, P. Kozjak and B. Javornik. 2005. The isolation and characterisation of microsatellites in hop (Humulus lupulus L.). Plant Sci. 168:213-221. https://doi.org/10.1016/j.plantsci.2004.07.031
  24. Tamanna, A. and A.U. Khan. 2005. Mapping and analysis of Simple Sequence Repeats in the Arabidopsis thaliana Genome. Bioinformation 1:64-68. https://doi.org/10.6026/97320630001064
  25. Tamura, K., J. Dudley, M. Nei and S. Kumar. 2007. MEGA4: Molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. 24:1596-1599. https://doi.org/10.1093/molbev/msm092
  26. Wang, S.H., L. Bao, T.M. Wang, H.F. Wang and J.P. Ge. 2016. Contrasting genetic patterns between two coexisting Eleutherococcus species in northern China. Ecol. Evol. 6:3311-3324. https://doi.org/10.1002/ece3.2118
  27. Zalapa, J.E., T.C. Bougie, T.A. Bougie, B.J. Schlautman, E. Wiesman, A. Guzman, S. Steffan and T. Smith. 2015. Clonal diversity and genetic differentiation revealed by SSR markers in wild Vaccinium macrocarpon and Vaccinium oxycoccos. Ann. Appl. Biol. 166:196-207. https://doi.org/10.1111/aab.12173
  28. Zhang, C.Z., B. Vornam, K. Volmer, K. Prinz, F. Kleemann, L. Kohler, A. Polle and R. Finkeldey. 2015. Genetic diversity in aspen and its relation to arthropod abundance. Front. Plant Sci. 5:806.
  29. Zhang, Q., B.Q. Ma, H. Li, Y.S. Chang, Y.Y. Han, J. Li, G.C. Wei, S. Zhao, M.A. Khan, Y. Zhou, C. Gu, X.Z. Zhang, Z.H. Han, S.S. Korban, S.H. Li and Y.P. Han. 2012. Identification, characterization, and utilization of genome-wide simple sequence repeats to identify a QTL for acidity in apple. BMC Genomics 13:537. https://doi.org/10.1186/1471-2164-13-537

피인용 문헌

  1. 변이밀집영역 유래 27개 InDel 마커를 이용한 콩(Glycine max (L.) Merrill) 신품종 판별 및 국내 149 품종과 유연관계 분석 vol.32, pp.5, 2017, https://doi.org/10.7732/kjpr.2019.32.5.519