Development and Characterization of Chloroplast Simple Sequence Repeat markers in Pinus koraiensis |
Lee, Jei-Wan
(Division of Forest Genetic Resources, National Institute of Forest Science)
Baek, Seung-Hoon (Division of Forest Genetic Resources, National Institute of Forest Science) Hong, Kyung-Nak (Division of Forest Genetic Resources, National Institute of Forest Science) Hong, Yong-Pyo (Division of Forest Genetic Resources, National Institute of Forest Science) Lee, Seok-Woo (Division of Forest Genetic Resources, National Institute of Forest Science) Ahn, Ji-Young (Division of Forest Genetic Resources, National Institute of Forest Science) |
1 | Vendramin, G.G., Lelli, L., Rossi, P., and Morgante, M. 1996. A set of primers for the amplification of 20 chloroplast microsatellites in Pinaceae. Molecular Ecology 5(4): 595-598. DOI |
2 | Wolfe, K.H., Li, W.H., and Sharp, P.M. 1987. Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proceedings of the National Academy of Sciences 84(24): 9054-9058. DOI |
3 | Bang, K.H., Lee, J.W., Kim, Y.C., Kim, D.H., Lee, E.H., and Jeung, J.U. 2010. Construction of genomic DNA library of Korean ginseng (Panax ginseng C.A. Meyer) and development of sequence-tagged sites. Biological and Pharmaceutical Bulletin 33(9): 1579-1588. DOI |
4 | Deguilloux, M.F., Pemonge, M.H., and Petit, R. J. 2004. Use of chloroplast microsatellites to differentiate oak populations. Annals of Forest Science 61(8): 825-830. DOI |
5 | Filiz, E. and Koc, I. 2014. Assessment of chloroplast microsatellite from pine family (Pinaceae) by using bioinformatics tools. Indian Journal of Biotechnology 13: 34-40. |
6 | Demesure, B., Sodzi, N., and Petit, R.J. 1995. A set of universal primers for amplification of polymorphic non-coding regions of mitochondrial and chloroplast DNA in plants. Molecular Ecology 4(1): 129-134. DOI |
7 | Feng, F.J., Han, S.J., and Wang, H.M. 2006. Genetic diversity and genetic differentiation of natural Pinus koraiensis population. Journal of Forestry Research 17(1): 21-24. DOI |
8 | Feng, F.J., Zhao, D., Sui, X., and Sun, X.Y. 2011. Study on mating system of Pinus koraiensis in natural population based on cpSSR technology. In Advanced Materials Research 183: 700-704. |
9 | Grauda, L., Aravanopoulos, F., Bennadji, Z., Changtragoon, S., Fady, B., Kjaer, E.D., Loo, J., Ramamonjisoa, L., and Vendramin, G.G. 2014. Global to local genetic diversity indicators of evolutionary potential in tree species within and outside forests. Forest Ecology and Management 333: 35-51. DOI |
10 | Grivet, D., Heinze, B., Vendramin, G.G., and Petit, R.J. 2001. Genome walking with consensus primers: application to the large single copy region of chloroplast DNA. Molecular Ecology Notes 1(4): 345-349. DOI |
11 | Hong, K.N., Kwon, Y.J., Chung, J.M., Shin, C.H., Hong, Y.P., and Kang, B.Y. 2001. Spatial genetic structure at a Korean pine (Pinus koraiensis) stand on Mt. Jumbong in Korea based on isozyme studies. Journal of Korean Forest Society 90(1): 43-54. |
12 | Hong, Y.P., Kwon, H.Y., Han, S.U., Choi, W.Y., and Kim, Y.Y. 2005. Identification of true full sib progenies of Japanese red pine via cpSSR haplotyping. Journal of Korean Forest Society 94(3): 178-182. |
13 | Kong, W.S. 2004. Species Composition and Distribution of Native Korean Conifers. The Korean Geographical Society 39(4): 528-543. |
14 | Hong, Y.P., Kwon, H.Y., and Kim, Y.Y. 2006. Distribution pattern of cpSSR variants in Korean populations of Japanese red pine. Journal of Korean Forest Society 95(4): 435-442. |
15 | Hong, Y.P., Kim, Y.M., Ahn, J.Y., and Park, J.I. 2012. Mating system of seed orchard of Japanese red pines revealed by DNA markers. Journal of Korean Forest Society 99(3): 344-352. |
16 | Hong, Y.P., Ahn, J.Y. Kim, Y.M., Hong, K.N., and Yang, B.H. 2013. Mating System in Natural Population of Pinus koraiensis at Mt. Seorak Based on Allozyme and cpSSR Markers. Journal of Korean Forest Society 102(2): 264-271. |
17 | Lee, J.W. 2010. Development of DNA markers for identification of Korean ginseng cultivars. Dongguk University, Ph. D. thesis paper. pp. 113. |
18 | Lee, J.W., Kim, Y.C., Jo, I.H., Seo, A.Y., Lee, J.H., Kim, O.T., Hyun D.Y., Cha S.W., Bang K.H., and Cho, J.H. 2011. Development of an ISSR-derived SCAR marker in Korean ginseng cultivars (Panax ginseng C.A. Meyer). Journal of Ginseng Research 35(1): 52-59. DOI |
19 | Melotto-Passarin, D.M., Tambarussi, E.V., Dressano, K., De Martin, V.F., and Carrer, H. 2011. Characterization of chloroplast DNA microsatellites from Saccharum spp and related species. Genetics Molecular Research 10(3): 2024-2033. |
20 | Mudunuri, S.B. and Nagarajaram, H.A. 2007. IMEx: imperfect microsatellite extractor. Bioinformatics 23(10): 1181- 1187. DOI |
21 | Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89(3): 583-590. |
22 | Provan, J., Powell, W., and Hollingsworth, P.M. 2001. Chloroplast microsatellites: new tools for studies in plant ecology and evolution. Trends in Ecology & Evolution 16(3): 142-147. DOI |
23 | Peakall, R.O.D. and Smouse, P.E. 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Molecular Ecology Notes 6(1): 288-295. DOI |
24 | Potenko, V.V., and Velikov, A.V. 1998. Genetic diversity and differentiation of natural populations of Pinus koraiensis (Sieb. et Zucc.) in Russia. Silvae Genetica 47(4): 202-207. |
25 | Powell, W., Morgante, M., McDevitt, R., Vendramin, G.G., and Rafalski, J.A. 1995. Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines. Proceedings of the National Academy of Sciences 92(17): 7759-7763. DOI |
26 | Provan, J., Soranzo, N., Wilson, N.J., Goldstein, D.B., and Powell, W. 1999. A low mutation rate for chloroplast microsatellites. Genetics 153(2): 943-947. |
27 | Provan, J., Soranzo, N., Wilson, N.J., McNicol, J.W., Forrest, G.I., Cottrell, J., and Powell, W. 1998. Gene pool variation in Caledonian and European Scots pine (Pinus sylvestris L.) revealed by chloroplast simple sequence repeats. Proceedings of the Royal Society of London B: Biological Sciences 265(1407): 1697-1705. DOI |
28 | Raubeson, L.A. and Jansen, R.K. 1992. A rare chloroplast-DNA structural mutation is shared by all conifers. Biochemical Systematics and Ecology 20(1): 17-24. DOI |
29 | Richardson, B.A., Brunsfeld, S.J., and Klopfenstein, N.B. 2002. DNA from bird-dispersed seed and wind-disseminated pollen provides insights into postglacial colonization and population genetic structure of whitebark pine (Pinus albicaulis). Molecular Ecology 11(2): 215-227. DOI |
30 | Sablok, G., Mudunuri, S.B., Patnana, S., Popova, M., Fares, M.A., and La Porta, N. 2013. ChloroMitoSSRDB 2.0: Open source repository of perfect and imperfect repeats in organelle genomes for evolutionary genomics. DNA Research 20(2): 127-133. DOI |
31 | Schlotterer, C. and Tautz, D. 1992. Slippage synthesis of simple sequence DNA. Nucleic Acids Research 20(2): 211-215. DOI |
32 | Sia, E.A., Jinks-Robertson, S., and Petes, T.D. 1997. Genetic control of microsatellite stability. Mutation Research 383: 61-70. DOI |
33 | Strauss, S.H., Palmer, J.D., Howe, G.T., and Doerksen, A.H. 1988. Chloroplast genomes of two conifers lack a large inverted repeat and are extensively rearranged. Proceedings of the National Academy of Sciences 85(11): 3898- 3902. DOI |
34 | Sugiura, M. 1992. The chloroplast genome. Plant Molecular Biology 19: 149-168. DOI |
35 | Sun, X. and Feng, F. 2011. Development and Analysis on Microsatellite Sequence of Chloroplast DNA of Pinus koraiensis. In Bioinformatics and Biomedical Engineering,( iCBBE) 2011 5th International Conference. IEEE. pp. 1-4. |
36 | Taberlet, P., Gielly, L., Pautou, G., and Bouvet, J. 1991. Universal primers for amplification of three non-coding regions of chloroplast DNA. Plant Molecular Biology 17(5): 1105- 1109. DOI |
37 | Toth, G., Gaspari, Z., and Jurka, J. 2000. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Research 10(7): 967-981. DOI |
38 | Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B.C., Remm, M., and Rozen, S.G. 2012. Primer3-new capabilities and interfaces. Nucleic Acids Research 40(15): e115-e115. DOI |