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http://dx.doi.org/10.7732/kjpr.2015.28.2.279

Genetic Variation of Pinus densiflora Populations in South Korea Based on ESTP Markers  

Ahn, Ji Young (Korea Forest Research Institute)
Hong, Kyung Nak (Korea Forest Research Institute)
Lee, Jei Wan (Korea Forest Research Institute)
Hong, Yong Pyo (Korea Forest Research Institute)
Kang, Hoduck (Department of Biological and Environmental Sciences, Dongguk University)
Publication Information
Korean Journal of Plant Resources / v.28, no.2, 2015 , pp. 279-289 More about this Journal
Abstract
Genetic diversity and genetic differentiation of thirteen Pinus densiflora populations in South Korea were estimated using nine ESTP (Expressed Sequence Tag Polymorphism) markers. The numbers of allele and the effective allele were 2.2 and 1.8, respectively. The percentage of polymorphic loci (P) was 98.8%. The observed and the expected heterozygosity were 0.391 and 0.402, respectively, and the eleven populations except for Ahngang and Gangneung population were under Hardy-Weinberg equilibrium state. The level of genetic differentiation (Wright’s FST = 0.057) was higher than those of isozyme or nSSR markers. We could not find out any relationship between the genetic distance and geographic distribution among populations from cluster analysis. Also, the genetic differentiation between populations was not correlated with the geographic distance (r = 0.017 and P = 0.344 from Mantel test). From the result of FST-outlier analysis to identify a locus under selection, six loci were detected at confidence interval of 99% by the frequentist’s method. However, only three loci (sams2+AluⅠ, sams2+RsaⅠ, PtNCS_p14A9+HaeⅢ) were presumed as outliers by Bayesian method. The sams2+AluⅠ and sams2+RsaⅠlocus were originated from the sams2 gene and seemed to be the loci under balancing selection.
Keywords
Population genetic structure; Genetic diversity; Genetic differentiation; FST-outlier;
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1 González-Martínez, S.C., E. Ersoz, G.R. Brown, N.C. Wheeler and D.B. Neale. 2006b. DNA sequence variation and selection of tag single-nucleotide polymorphisms at candidate genes for drought-stress response in Pinus taeda L. Genetics 172:1915-1926.   DOI
2 Holderegger, R., U. Kamm and F. Gugerli. 2006. Adaptive vs. neutral genetic diversity: implications for landscape genetics. Landscape Ecol. 21:797-807.   DOI
3 Goudet, J. 2002. FSTAT version 2.9.3 program to estimate and test gene diversities and fixation indices. Available from: http://www2.unil.ch/popgen/softwares/fstat.html.
4 Gupta, P.K. and S. Rustgi. 2004. Molecular markers from the transcribed/expressed region of the genome in higher plants. Funct. Integr. Genomics 4:139-162.
5 Harry, D.E., B. Temesgen and D.B. Neale. 1998. Codominant PCR-based markers for Pinus taeda developed from mapped cDNA clones. Theor. Appl. Genet. 97:327-336.   DOI
6 Hong, Y.P., H.Y. Kwon and I.S. Kim. 2007. I-SSR markers revealed inconsistent phylogeographic patterns among populations of Japanese red pine in Korea. Silvae Genet. 56(1):22-26.
7 Hong, Y.P., J.Y. Ahn, Y.M. Kim, B.H. Yang and J.H. Song. 2011. Genetic variation of nSSR markers in natural populations of Abies koreana and Abies nephrolepis in South Korea. J. Korean For. Soc. 100(4):577-584 (in Korean).
8 Jaramillo-Correa, J.P., J. Beaulieu and J. Bousquet. 2001. Contrasting evolutionary forces driving population structure at expressed sequence tag polymorphism, allozymes and quantitative traits in white spruce. Mol. Ecol. 10:2729-2740.   DOI
9 Karhu, A., P. Hurme, M. Karjalainen, P. Karvonen, K. Kärkkäinen, D.B. Neale and O. Savolainen. 1996. Do molecular markers reflect patterns of differentiation in adaptive traits of conifers? Theor. Appl. Genet. 93:215-221.   DOI
10 Kim, Z.S., C.H. Yi and S.W. Lee. 1994. Genetic variation and sampling strategy for conservation in Pinus species: In Kim, Z.S. and H.H. Hattemer (eds.), Conservation and Manipulation of Genetic Resources in Forestry, Kwang Moon Kag Publishibg Co., Seoul, Korea. pp. 294-321.
11 Krutovskii, K.V. and D.B. Neale. 2005. Forest genomics and new molecular genetic approaches to measuring and conserving adaptive genetic diversity in forest trees: In Geburek, T. and J. Turok (eds.), Conservation and Management of Forest Genetic Resources in Europe, Arbora Publishers, Zvolen, Slovakia. pp. 369-388.
12 Kim, Y.Y., J.O. Hyun, K.N. Hong, T.B. Choi and K.S. Kim. 1995. Genetic variation of natural populations of Pinus densiflora in Korea based on RAPD marker analysis. Korean J. Breeding 27(1):23-48 (in Korean).
13 Komulainen, P., G.R. Brown, M. Mikkonen, A. Karhu, M.R. Garcia-Gil, D. O'Malley, B. Lee, D.B. Neale and O. Savolainen. 2003. Comparing EST-based genetic maps between Pinus sylvestris and Pinus taeda. Theor. Appl. Genet. 107:667-678.   DOI
14 Kong, W.S., S.G. Lee, H.N. Park, Y.M. Lee and S.H. Oh. 2014. Time-spatial distribution of Pinus in the Korean Peninsular. Quatern. Int. 1-10.
15 Kwon, H.Y. and Z.S. Kim. 2002. I-SSR variation within and among Korean Populations in Taxus cuspidata. J. Korean For. Soc. 91(5):654-660.
16 Lee, S.W., Y.Y. Kim, J.O. Hyun and Z.S. Kim. 1997. Comparison of genetic variation in Pinus densiflora natural populations by allozyme and RAPD analysis. Korean. J. Breeding 29(1):72-83 (in Korean).
17 Luikart, G., P.R. England, D. Tallman, S. Jordan and P. Taberlet. 2003. The power and promise of population genomics: from genotyping to genome typing. Nat. Rev. Genet. 4:981-994.
18 Liang, C., G. Wang, L. Liu, G. Ji, L. Fang, Y. Liu, K. Carter, J.S. Webb and J.F.D. Dean. 2007. Conifer EST: an integrated bioinformatics system for data reprocessing and mining of conifer expressed sequence tags (ESTs). BMC Genomics 8:1-10.   DOI
19 Lorenz, W.W., F. Sun, C. Liang, D. Kolychev, H. Wang, X. Zhao, M.M. Cordonnier-Pratt, L.H. Pratt and J.F.D. Dean. 2006. Water stress-responsive genes in loblolly pine (Pinus taeda) roots identified by analyses of expressed sequence tag libraries. Tree Physiol. 26:1-16.   DOI
20 Olson, M., L. Hood, C. Cantor and D. Botstein. 1989. A common language for Physical Mapping of the Human Genome. Science 245:1434-1435.   DOI
21 Narum, S. and J.E. Hess. 2011. Comparison of FST outlier tests for SNP loci under selection. Mol. Ecol. Resour. 11:184-194.   DOI
22 Namroud, M.C., J. Beaulieu, N. Juge, J. Laroche and J. Bousquet. 2008. Scanning the genome for gene single nucleotide polymorphisms involved in adaptive population differentiation in white spruce. Mol. Ecol. 17:3599-3613.   DOI
23 Peakall, R. and P.E. Smouse. 2006. GENEALEX 6: genetic analysis in Excel. population genetic software for teaching and research. Mol. Ecol. Notes 6:288-295.   DOI
24 Perry, D.J. and J. Bousquet. 1998. Sequence-tagged-site (STS) markers of arbitrary genes: development, characterization and analysis of linkage in black spruce. Genetics 149:1089-1098.
25 Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
26 Seo, D.H., K.M. Jung, S.J. Kim and K.M. Kim. 2013. Development of EST-SSR markers and analysis of genetic diversity using persimmon (Diospyros kaki Thunb) cultivars collecting from domestic. Korean J. Plant Res. 26(4):491-502 (in Korean).   DOI
27 Ralph, S.G., H.J.E. Chun, N. Kolosova, D. Cooper, C. Oddy, C.E. Ritland, R. Kirkpatrick, R. Moore, S. Barber, R.A. Holt, S.J.M. Jones, M.A. Marra, C.J. Douglas, K. Ritland and J. Bohlmann. 2008. A conifer genomics resource of 200,000 spruce (Picea spp.) ESTs and 6,464 high-quality, sequence-finished full-length cDNAs for Sitka spruce (Picea sitchensis). BMC Genomics 9:484.   DOI
28 Rousset, F. 2008. Genepop'007: a complete re-implementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8:103-106.   DOI
29 Schubert, R., G. Mueller-Starck and R. Riegel. 2001. Development of EST-PCR markers and monitoring their intrapopulational genetic variation in Picea abies (L.) Karst. Theor. Appl. Genet. 103:1223-1231.   DOI
30 Takahashi, T., N. Tani, H. Taira and Y. Tsumura. 2005. Microsatellite markers reveal high allelic variation in natural populations of Cryptomeria japonica near refugial areas of the last glacial period. J. Plant Res. 118:83-90.   DOI
31 Temesgen, B., G.R. Brown, D.E. Harry, C.S. Kinlaw, M.M. Sewell and D.B. Neale. 2001. Genetic mapping of expressed sequence tag polymorphism (ESTP) markers in loblolly pine (Pinus taeda L.). Theor. Appl. Genet. 102:664-675.   DOI
32 Tomaru, N., Y. Tsumura and K. Ohba. 1994. Genetic variation and population differentiation in natural populations of Cryptomeria japonica. Plant Spec. Biol. 9(3): 191-199.   DOI
33 Tsumura, Y., T. Kado, T. Takahashi, N. Tani, T. Ujino-Ihara and H. Iwata. 2007. Genome scan to detect genetic structure and adaptive genes of natural populations of Cryptomeria japonica. Genetics 107:2393-2403.
34 Antao, T., A. Lopes, R.J. Lopes, A. Beja-Pereira and G. Luikart. 2008. LOSITAN: a workbench to detect molecular adaptation based on a Fst-outlier method. BMC Bioinformatics 9:323.   DOI
35 Vitalis, R., K. Dawson and P. Boursot. 2001. Interpretation of variation across marker loci as evidence of selection. Genetics 158:1811-1823.
36 Watersson, G.A. 1977. Heterosis or neutrality? Genetics 85:789-814.
37 Achere, V., J.M. Favre, G. Besnard and S. Jeandroz. 2005. Genomic organization of molecular differentiation in Norway spruce (Picea abies). Mol. Ecol. 14:3191-3201.   DOI
38 Bierne, N., D. Roze and J.J. Welch. 2013. Pervasive selection of is it? why are FST outliers sometimes so frequent? Mol. Ecol. 22:2061-2064.   DOI
39 Allona, I., M. Quinn, E. Shoop, S.S. Cyr, J. Carlis, J. Riedl, E. Retzel, M.M. Campbell, R. Sederoff and R.W. Whetten. 1998. Analysis of xylem formation in pine by cDNA sequencing. Proc. Natl. Acad. Sci. USA 95(16):9693-9698.   DOI
40 Beaumont, M.A. and R.A. Nichols. 1996. Evaluating loci for use in the genetic analysis of population structure. P. Roy. Soc. Lond. B. Bio. 263:1619-1623.   DOI
41 Beaumont, M.A. 2005. Adaptation and speciation: What can FST tell us? Trends Ecol. Evol. 20(8):435-440.   DOI
42 Brown, G.R., G.P. Gill, R.J. Kuntz, C.H. Langley and D.B. Neale. 2004. Nucleotide diversity and linkage disequilibrium in loblolly pine. Proc. Natl. Acad. Sci. USA. 101(42):15255-15260.   DOI
43 Cairney, J., L. Zheng, A. Cowels, J. Hsiao, V. Zismann, J. Liu, S. Ouyang, F. Thibaud-Nissen, J. Hamilton, K. Childs, G.S. Pullman, Y. Zhang, T. Oh and C.R. Buell. 2006. Expressed sequence tags from loblolly pine embryos reveal similarities with angiosperm embryogenesis. Plant Mol. Biol. 62:485-501.   DOI
44 Evanno, G., S. Reanaut and J. Goudet. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620.   DOI
45 Chagné, D., P. Chaumeil, A. Ramboer, C. Collada, A. Guevara, M.T. Cervera, G.G. Vendramin, V. Garcia, J.M. Frigerio, C. Echt, T. Richardson and C. Plomion. 2004. Cross-species transferability and mapping of genomic and cDNA SSRs in pines. Theor. Appl. Genet. 109:1204-1214.   DOI
46 Excoffier, L., T. Hofer and M. Foll. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103:285-298.   DOI
47 Eckert, A.J., J.L. Wegrzyn, B. Pande, K.D. Jermstad, J.M. Lee, J.D. Liechty, B.R. Tearse, K.V. Krutovsky and D.B. Neale. 2009. Multilocus patterns of nucleotide diversity and divergence reveal positive selection at candidate genes related to cold-hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Genetics 189(1):289-298.   DOI
48 Excoffier, L. and G. Heckel. 2006. Computer programs for population genetics data analysis: a survival guide. Nat. Rev. Genet. 7:745-758.   DOI
49 Felsenstein, J. 2002. Inferring Phylogenies. Sinauer Associates, Sunderland, MA (USA).
50 Foll, M. and O. Gaggiotti. 2008. A genome-scan method to identify selected loci appropriate for both dominant and codominant markers: a Bayesian perspective. Genetics 180:977-995.   DOI
51 Garcia-Gil, M.R., M. Mikkonen and O. Savolainen. 2003. Nucleotide diversity at two phytochrome loci along a latitudinal cline in Pinus sylvestris. Mol. Ecol. 12:1195-1206.   DOI
52 González-Martínez, S.C., K.V. Krutovsky and D.B. Neale. 2006a. Forest-tree population genomics and adaptive evolution. New Phytol. 170:227-238.   DOI
53 Chagné C., G. Brown, C. Lalanne, D. Madur, D. Pot, D.B. Neale and C. Plomion. 2003. Comparative genome and QTL mapping between maritime and loblolly pines. Mol. Breeding 12:185-195.   DOI