DOI QR코드

DOI QR Code

ESTP 표지를 이용한 국내 소나무 집단의 유전변이

안지영;홍경낙;이제완;홍용표;강호덕
Ahn, Ji Young;Hong, Kyung Nak;Lee, Jei Wan;Hong, Yong Pyo;Kang, Hoduck

  • 투고 : 2014.09.13
  • 심사 : 2014.11.17
  • 발행 : 2015.04.30

초록

소나무의 유전다양성과 유전구조를 추정하기 위해 9개의 ESTP 표지를 13개 소나무 집단에 적용하였다. 소나무 집단의 유전다양성은 관찰된 대립유전자 수(A)가 2.2개, 유효 대립유전자 수(Ae)가 1.8개, 다형적 유전자좌 비율(P)이 98.8%, 이형접합도 관찰치(Ho)가 0.391, 이형접합도 기대치(He)가 0.402로 나타났다. 안강과 강릉 집단을 제외한 11개 집단이 하디-바인베르그 평형을 만족하였다. 집단간 유전분화도(FST)는 0.057으로, 동위효소나 nSSR 표지분석 결과보다 강하게 나타났다. 군집분석에서 집단의 유전적 거리와 지리적 분포간에 뚜렷한 연관성은 확인할 수 없었으며, 집단의 유전분화와 지리적 인접성도 상관이 없는 것으로 나타났다(Mantel 검증, r = 0.017, P = 0.344). 유전자좌에 대한 FST-outlier 분석을 실시한 결과, 빈도주의 방법에서는 FST 값이 신뢰하한 이하인 3개 유전자좌와 신뢰상한 이상인 3개 유전자좌가 특이값으로 추정되었고, 베이즈 방법에서는 3개 유전자좌들만 특이값으로 확인되었다. 두 방법에서 공히 특이값으로 판정된 3개 유전자좌(sams2+AluⅠ, sams2+RsaⅠ, PtNCS_p14A9+HaeⅢ)중 sams2 표지에서 유래된 2개 유전자좌는 balancing selection의 영향을 받는 것으로 추정되었다.

키워드

Population genetic structure;Genetic diversity;Genetic differentiation;FST-outlier

참고문헌

  1. 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. https://doi.org/10.1111/j.1365-294X.2005.02646.x
  2. 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. https://doi.org/10.1111/mec.12241
  3. 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. https://doi.org/10.1073/pnas.95.16.9693
  4. 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. https://doi.org/10.1186/1471-2105-9-323
  5. 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. https://doi.org/10.1098/rspb.1996.0237
  6. Beaumont, M.A. 2005. Adaptation and speciation: What can FST tell us? Trends Ecol. Evol. 20(8):435-440. https://doi.org/10.1016/j.tree.2005.05.017
  7. 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. https://doi.org/10.1073/pnas.0404231101
  8. 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. https://doi.org/10.1007/s11103-006-9035-9
  9. 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. https://doi.org/10.1023/A:1026318327911
  10. 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. https://doi.org/10.1007/s00122-004-1683-z
  11. Excoffier, L., T. Hofer and M. Foll. 2009. Detecting loci under selection in a hierarchically structured population. Heredity 103:285-298. https://doi.org/10.1038/hdy.2009.74
  12. 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.
  13. 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. https://doi.org/10.1111/j.1365-294X.2005.02553.x
  14. Excoffier, L. and G. Heckel. 2006. Computer programs for population genetics data analysis: a survival guide. Nat. Rev. Genet. 7:745-758. https://doi.org/10.1038/nrg1904
  15. Felsenstein, J. 2002. Inferring Phylogenies. Sinauer Associates, Sunderland, MA (USA).
  16. 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. https://doi.org/10.1534/genetics.108.092221
  17. 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. https://doi.org/10.1046/j.1365-294X.2003.01826.x
  18. González-Martínez, S.C., K.V. Krutovsky and D.B. Neale. 2006a. Forest-tree population genomics and adaptive evolution. New Phytol. 170:227-238. https://doi.org/10.1111/j.1469-8137.2006.01686.x
  19. 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. https://doi.org/10.1534/genetics.105.047126
  20. Holderegger, R., U. Kamm and F. Gugerli. 2006. Adaptive vs. neutral genetic diversity: implications for landscape genetics. Landscape Ecol. 21:797-807. https://doi.org/10.1007/s10980-005-5245-9
  21. 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.
  22. 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.
  23. 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. https://doi.org/10.1007/s001220050903
  24. 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.
  25. 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).
  26. 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. https://doi.org/10.1046/j.0962-1083.2001.01386.x
  27. 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. https://doi.org/10.1007/BF00225748
  28. 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.
  29. 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.
  30. 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).
  31. 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. https://doi.org/10.1007/s00122-003-1312-2
  32. 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.
  33. 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.
  34. 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).
  35. 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. https://doi.org/10.1186/1471-2164-8-1
  36. 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. https://doi.org/10.1093/treephys/26.1.1
  37. Olson, M., L. Hood, C. Cantor and D. Botstein. 1989. A common language for Physical Mapping of the Human Genome. Science 245:1434-1435. https://doi.org/10.1126/science.2781285
  38. 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.
  39. Narum, S. and J.E. Hess. 2011. Comparison of FST outlier tests for SNP loci under selection. Mol. Ecol. Resour. 11:184-194. https://doi.org/10.1111/j.1755-0998.2011.02987.x
  40. 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. https://doi.org/10.1111/j.1365-294X.2008.03840.x
  41. 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. https://doi.org/10.1111/j.1471-8286.2005.01155.x
  42. 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.
  43. Pritchard, J.K., M. Stephens and P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959.
  44. 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. https://doi.org/10.1186/1471-2164-9-484
  45. Rousset, F. 2008. Genepop'007: a complete re-implementation of the Genepop software for Windows and Linux. Mol. Ecol. Resour. 8:103-106. https://doi.org/10.1111/j.1471-8286.2007.01931.x
  46. 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. https://doi.org/10.1007/s001220000501
  47. 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). https://doi.org/10.7732/kjpr.2013.26.4.491
  48. 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. https://doi.org/10.1007/s10265-005-0198-2
  49. 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. https://doi.org/10.1007/s001220051695
  50. 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. https://doi.org/10.1111/j.1442-1984.1994.tb00101.x
  51. 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.
  52. Vitalis, R., K. Dawson and P. Boursot. 2001. Interpretation of variation across marker loci as evidence of selection. Genetics 158:1811-1823.
  53. Watersson, G.A. 1977. Heterosis or neutrality? Genetics 85:789-814.

과제정보

연구 과제번호 : RRS를 이용한 주요 산림유전자원의 공우성 분자표지자 개발 및 유전특성 연구