생명과학회지 (Journal of Life Science)

  • 제25권11호
  • /
  • Pages.1204-1213
  • /
  • 2015
  • /
  • 1225-9918(pISSN)
  • /
  • 2287-3406(eISSN)
한국생명과학회 (Korean Society of Life Science)
권호 표지
DOI QR코드

DOI QR Code

Mitochondrial DNA와 microsatellite marker 분석을 통한 한국과 일본에 서식하는 5 지역의 도루묵(Arctoscopus japonicas)에 대한 유전학적 유연관계 분석

Genetic Relationships of Sandfish (Arctoscopus japonicas) from Five Different Areas of Korea and Japan Based on Mitochondrial DNA and Microsatellite Analyses

  • 김은미 (국립수산과학원 생명공학과) ;
  • 강현숙 (국립수산과학원 생명공학과) ;
  • 강정하 (국립수산과학원 생명공학과) ;
  • 김동균 (국립수산과학원 생명공학과) ;
  • 안철민 (국립수산과학원 생명공학과) ;
  • 이해원 (국립수산과학원 대외협력과) ;
  • 박중연 (국립수산과학원 생명공학과)
  • 투고 : 2015.09.02
  • 심사 : 2015.10.12
  • 발행 : 2015.11.30
PDF 다운로드
⟨ 이전 논문 다음 논문 ⟩

초록

도루묵은 우리나라 동해에서 어획되는 상업적으로 중요한 수산자원으로 동해안의 자원회복관리 대상어종이며, 자원량의 회복 및 보전과 관리가 필요한 어종이다. 하지만 우리나라 도루묵 자원의 관리를 위한 유전학적 분석에 따른 연구는 매우 미비한 실정이다. 따라서 본 연구는 mitochondrial DNA의 Cytochrome b (Cyt b) 유전자 서열과 5개의 microsatellite marker의 유전자형을 토대로 우리나라 동해안 도루묵과 일본 도루묵의 유전적 다양성과 집단 구조를 분석하여 유전학적 유연관계를 파악하고, 도루묵 자원의 보전과 관리를 위한 과학적 자료를 제공하기 위해 실시하였다. 한국 3개 지역(독도, 동해, 감포)과 일본의 2개 지역(북해도와 에리모)에서 채집된 총 83개 개체의 mtDNA Cyt b 영역을 분석하여 27개의 haplotype을 확인하였다. 유전적 다양성은 에리모에서 가장 높고 감포에서 가장 낮았다. Pairwise FST값과 유전적 거리, UPGMA와 주성분분석, AMOVA test 및 structure 분석 결과, 한국의 동해안 도루묵 집단 간 유전적 차이는 거의 없었으나 일본 도루묵 집단과는 유의적인 차이가 나타났으며(p<0.05), 한국의 동해안 집단과 일본의 집단으로 그룹을 형성하며 구분되는 유연관계를 확인하였다. 본 연구에서 확인된 도루묵의 유전적 특성 및 집단 간 유연관계는 중요한 수산유전자원으로서의 도루묵에 대한 중요한 과학적인 근거자료가 될 것이며, 앞으로 도루묵의 보존, 평가 및 이용에 활용 가능한 정보를 제공할 것이라 사료된다.

A comprehensive analysis of the population structure of the sandfish (Arctoscopus japonicas), the most abundant fishery resource in the East Sea of Korea, has not been carried out, despite its importance in Korea. The present study examined the genetic diversity and differences between five populations (two Japanese and three Korean populations) of A. japonicas captured in the East Sea using both the 401 bp sequence of mitochondrial DNA (mtDNA, cytochrome b) and five microsatellite DNA (msDNA) markers. The results of the analysis using the Cyt b sequence revealed 27 haplotypes. Based on msDNA variations, the estimated expected heterozygosity (HE) in each population ranged from 0.68 (Gampo, Korea) to 0.7765 (Erimo, Japan). Pairwise FST and AMOVA tests using both the Cyt b sequence and msDNA data pointed to significant differences between the Korean and Japanese populations (mtDNA; FST=0.2648, p<0.05, msDNA; FST=0.0814, p<0.05). These results were similar to the results of UPGMA, PCA, and structure analysis. In these analyses, the five populations were assigned to two groups (Korean populations and Japanese populations). These results shed light on the genetic diversity and relationships of A. japonicas and contribute to research on the evaluation, conservation, and utilization of Korean A. japonicas as genetic resources.

키워드

참고문헌

  1. An, H. C., Lee, K. H., Lee, S. I., Park, H. H., Bae, B. S., Yang, J. H. and Kim, J. B. 2011. Behaviour habitats of sailfin sandfish, Arctoscopus japonicas approaching toward the eastern coastal waters of Korea in the spawning season. Jour. Fish. Mar. Sci. Edu. 23, 35-42.
  2. Avise, J. C. 1994. Molecular markers, Natural History and Evolution. Chapman and Hall, New York.
  3. Beacham, T. D., Lapointe, M., Candy, J. R., Miller, K. M. and Withler, R. E. 2004. DNA in action: rapid application of DNA variation to sockeye salmon fisheries management. Conserv. Gen. 5, 411-416. https://doi.org/10.1023/B:COGE.0000031140.41379.73
  4. Brown, W. M., George, M. Jr. and Wilson, A. C. 1979. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA. 76, 1967-1971. https://doi.org/10.1073/pnas.76.4.1967
  5. Carr, S. M. and Marshall, H. D. 1991. Detection of intraspecific DNA sequence variation in the mitochondrial cytochrome b gene of Atlantic cod (Gadus morhua) by the polymerase chain reaction. Can. J. Fish. Aquat. Sci. 48, 48-52. https://doi.org/10.1139/f91-007
  6. DeWoody, J. A. and Avise, J. C. 2000. Microsatellite variation in marine, freshwater and anadromous fishes compared with other animals. J. Fish. Biol. 56, 461-473. https://doi.org/10.1111/j.1095-8649.2000.tb00748.x
  7. Evanno, G., Reguaut, S. and Goudet, J. 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
  8. Excoffier, L., Laval, G. and Schneider, S. 2005. Arlequin ver. 3.0: an integrated software package for population genetics data analysis. Evol. Bioinform. 1, 47-50.
  9. Excoffier, L., Smouse, P. E. and Quattro, J. M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131, 479-491.
  10. Goudet, J. 1995. FSTAT (version 1.2): a computer program to calculate F-statistics. J. Hered. 86, 485-486.
  11. Hillis, D. M., Mabel, B. K. and Moritz, C. 1996. Application of molecular systematic: the state of the field and a look to the future, pp. 515-543. In: Molecular Systematics, 2nd edn. (eds. Hillis, D., Moritz, C., Mable, B. K.), Sinauer Associates, Massachusetts.
  12. Jarne, P. and Lagoda, P. J. G. 1996. Microsatellites, from molecules to populations and back. Trends. Ecol. Evol. 11, 424-429. https://doi.org/10.1016/0169-5347(96)10049-5
  13. Kim, I. S., Choi, Y., Lee, C. Y., Lee, Y. J., Kim, B. J. and Kim, J. H. 2005. Illustrated book of Korean fishes. pp. 1-615. Kyohak Press, Seoul.
  14. Kim, J. Y., Yoon, M. G., Moon, C. H., Kang, C. K., Choi, K. H. and Lee, C. I. 2013. Morphological and genetic stock identification of Todarodes pacificus in Korean waters. J. Kor. Soc. Oceanogr. 18, 131-141.
  15. Kimura, M. 1980. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111-120. https://doi.org/10.1007/BF01731581
  16. Kobayashi, T. and Kaga, Y. 1981. Population of sandfish, Arctoscopus japonicas (Steindachner), in the seas around Hokkaido estimated from the variations of meristic characters (in Japanese). Bull. Hokkaido. Reg. Fish. Res. Lab. 46, 69-83.
  17. Langella, O. 2002. POPULATIONS 1.2.29. Population genetic software (individuals or populations distances, phylogenetic trees), http://bioinformatics.org/-tryphon/populations.
  18. Lansman, R. A., Shade, R. O., Shapira, J. F. and Avise, J. C. 1981. The use of restriction endonucleases to measure mitochondrial DNA sequence relatedness in natural populations. ΙΙΙ. Techniques and potential applications. J. Mol. Evol. 17, 214-226. https://doi.org/10.1007/BF01732759
  19. Lee, S. I., Yang, J. H., Yoon, S. C., Chun, Y. Y., Kim, J. B., Cha, H. K. and Choi, Y. M. 2009. Biomass estimation of sailfin sandfish, Arctoscopus japonicas, in Korean waters. Kor. J. Fish. Aquat. Sci. 42, 487-493.
  20. Liu, Z. 2011. Genomic variations and marker technologies for genome-based selection. In: Liu, Z. (ed.), Next Generation Sequencing and Whole Genome Selection in Aquaculture. WileyBlackwell, Oxford, U.K.
  21. Liu, Z. J. and Cordes, J. F. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture 238, 1-37. https://doi.org/10.1016/j.aquaculture.2004.05.027
  22. Nei, M. 1972. Genetic distance between populations. Am. Nat. 106, 283-292. https://doi.org/10.1086/282771
  23. NFRDI (National Fisheries Research and Development Institute). 2004. Commercial fishes of the coastal and offshore waters in Korea. pp. 1-333. 2nd ed Hangul Press, Busan.
  24. Ochiai, A. and Tanaka, M. 1986. Ichthyology, vol 2, new edn (in Japanese). Koseisha-Koseikaku, Tokyo.
  25. Okiyama, M. 1970. Studies on the population biology of the sandfish, Arctoscopus japonicas (Steindachner). ΙΙ. Population analysis (preliminary report) (in Japanese). Bull. Jpn. Sea. Reg. Fish. Res. Lab. 22, 59-69.
  26. Okiyama, M. 1990. Contrast in reproductive style between two species of sandfishes (family Trichodontidae). Fish. Bull. 88, 543-549.
  27. Park, C. J., Nam, W. S., Lee, J. H., Noh, J. K., Kim, H. C., Park, J. W., Hwang, I. J. and Kim, S. Y. 2013. Analysis of genetic divergence according to each mitochondrial DNA region of Haliotis discus hannai. Kor. J. Malacol. 29, 335-341. https://doi.org/10.9710/kjm.2013.29.4.335
  28. Park, J. Y., Lee, H. J., Kim, W. J., Lee, J. H. and Min, K. S. 2000. Mitochondrial cytochrome b sequence variation in Korean salmonids. J. Fish. Biol. 56, 1145-1154. https://doi.org/10.1111/j.1095-8649.2000.tb02130.x
  29. Park, J. Y., Lee, S. J., Lee, H. W., Lee, Y. G., Jung, S. J. and Kang, Y. J. 2006. Polymerase chain reaction primers for polymorphic microsatellite loci from the Korean sandfish, Arctoscopus japonicas. Mol. Ecol. Notes 6, 674-676. https://doi.org/10.1111/j.1471-8286.2006.01298.x
  30. Peakall, R. and Smouse, P. E. 2006. GENALEX 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
  31. Perez-Enriquez, R., Takagi, M. and Taniguchi, N. 1999. Genetic variability and pedigree tracting of a hatchery-reared stock of red sea bream (Pagrus major) used for stock enhancement, based on microsatellite DNA markers. Aquaculture 173, 413-423. https://doi.org/10.1016/S0044-8486(98)00469-4
  32. Pritchard, J. K., Stephens, M. and Donnelly, P. 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945-959.
  33. 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
  34. Sekino, M., Saitoh, K., Yamada, T., Kumagai, A., Hara, M. and Yamashita, Y. 2003. Microsatellite-based pedigree tracing in a Japanese flounder Paralichthys oliaceus hatchery strain: implications for hatchery management related to stock enhancement program. Aquaculture 221, 255-263. https://doi.org/10.1016/S0044-8486(02)00667-1
  35. Shirai, S. M., Kuranaga, R., Sugiyama, H. and Higuchi, M. 2006. Population structure of the sailfin sandfish, Arctoscopus japonicas (Trichodontidae), in the Sea of Japan. Ichthyol. Res. 53, 357-368. https://doi.org/10.1007/s10228-006-0356-0
  36. Sneath, P. H. A. and Sokal, R. R. 1973. Numerical taxonomy: The principles and practice of numerical classification. W. H. Freeman, San Francisco.
  37. Tamura, K. and Nei, M. 1993. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol. Biol. Evol. 10, 512-526.
  38. Tamura, K., Peterson, D., Peterson, N., Stecher, G., Nei, M. and Kumar, S. 2011. MEGA5: Molecular evolurionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28, 2731-2739. https://doi.org/10.1093/molbev/msr121
  39. Tautz, D. 1989. Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucl. Acids. Res. 17, 6463-6471. https://doi.org/10.1093/nar/17.16.6463
  40. Ward, R. D., Zemlak, T. S., Innes, B. H., Last, R. R. and Hebert, P. D. H. 2005. DNA barcoding Australia′s fish species. Philos. Trans. R. Soc. Biol. Sci. 360, 1847-1857. https://doi.org/10.1098/rstb.2005.1716
  41. Weir, B. S. and Cockerham, C. C. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38, 1358-1370. https://doi.org/10.2307/2408641
  42. Yang, J. H., Lee, S. I., Park, K. Y., Yoon, S. C., Kim, J. B., Chun, Y. Y., Kim, S. W. and Lee, J. B. 2012. Migration and distribution changes of the Sandfish, Arctoscopus japonicas in the East Sea. J. Kor. Soc. Fish. Tech. 48, 401-141. https://doi.org/10.3796/KSFT.2012.48.4.401
  43. Zardoya, R. and Doadri, I. 1999. Molecular evidence on the evolutionary and biogeographical patterns of European cyprinids. J. Mol. Evol. 49, 227-237. https://doi.org/10.1007/PL00006545