Korean Journal of Ichthyology (한국어류학회지)

The Ichthyological Society of Korea (한국어류학회)
권호 표지

Genetic Differences and Variation in Two Largehead Hairtail (Trichiurus lepturus) Populations Determined by RAPD-PCR Analysis

RAPD-PCR 분석에 의해 결정된 갈치 (Trichiurus lepturus) 2 집단의 유전적 차이와 변이

  • Park, Chang-Yi (Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University) ;
  • Yoon, Jong-Man (Department of Aquatic Life Medicine, College of Ocean Science and Technology, Kunsan National University)
  • 박창이 (군산대학교 해양과학대학 수산생명의학과) ;
  • 윤종만 (군산대학교 해양과학대학 수산생명의학과)
  • Received : 2005.07.18
  • Accepted : 2005.09.02
  • Published : 2005.09.30
Download PDF
⟨ Previous Next ⟩

Abstract

Genomic DNA was isolated from two geographic populations of largehead hairtail (Trichiurus lepturus) in Korea and the Atlantic Ocean. The eight arbitrarily selected primers were found to generate common, polymorphic, and specific fragments. The complexity of the banding patterns varied dramatically between primers from the two locations. The size of the DNA fragments also varied widely, from 150 bp (base pairs) to 3,000 bp. Here, 947 fragments were identified in the largehead hairtail population from Korea, and 642 in the largehead hairtail population from the Atlantic Ocean: 148 specific fragments (15.6%) in the Korean population, and 61 (9.5%) in the Atlantic population. In the Korean population, 638 common fragments with an average of 79.8 per primer were observed.; 429 common fragments, with an average of 53.6 per primer, were identified in the Atlantic population. The number of polymorphic fragments in the largehead hairtail population from Korea and the Atlantic Ocean was 76 and 27, respectively. Based on the average bandsharing values of all samples, the similarity matrix ranged from 0.784 to 0.922 in the Korean population, and from 0.833 to 0.990 in the Atlantic population. The bandsharing value of individuals within the Atlantic population was much higher than in the Korean population. The dendrogram obtained by the eight primers indicated two genetic clusters: cluster 1 (KOREAN 01~KOREAN 11), and cluster 2 (ATLANTIC 12~ATLANTIC 22). Individual KOREAN no. 10 from Korea was genetically most closely related to KOREAN no. 11 in the Korean population (genetic distance = 0.038). Ultimately, individual KOREAN no. 01 of the Korean population was most distantly related to ATLANTIC no. 16 of the Atlantic population (genetic distance = 0.708).

한국과 대서양산 갈치 (Trichiurus lepturus) 2지리적 집단으로부터 genomic DNA를 분리 추출하였다. 선택된 8개의 RAPD primer를 이용하여 common, polymorphic 그리고 specific fragment를 얻어냈다. 2지역으로부터 primer간 banding patterns 의 복잡성이 두드러지게 나타났다. DNA fragment 의 분자적 크기는 150 bp에서부터 3,000 bp까지 커다란 차이를 나타내었다. 본 연구에서 한국산 갈치 집단에서는 947개의 fragment가 나타났고, 대서양산 갈치 집단에서는 642개의 fragment 가 확인되었다. 또한 한국산 집단에서는 148개의 specific fragment (15.6%) 가 확인되었으며, 대서양산 갈치집단에서는 61개의 specific fragment (9.5%)가 발생되었다. 한국산 갈치집단에서는 638개의 common fragment가 나타났으며, 이는 primer 당 평균적으로 79.8개의 fragment 로 확인되었다. 또한 대서양산 갈치집단에서는 429개의 common fragment 가 확인되었고, 평균해서 primer 당 53.6개의 common fragment 가 나타났다. 한국산 갈치집단과 대서양산 갈치집단의 polymorphic fragment는 각각 76개와 27개로 확인되었다. 모든 갈치시료의 평균적인 bandsharing value를 기초로 해서 한국산 갈치집단의 similarity matrix를 조사해 본 결과 0.784 로부터 0.922까지 나타났고, 대서양산 갈치집단의 값은 0.833로부터 0.990까지 확인되었다. 결과적으로 대서양산 갈치집단내 개체의 bandsharing value 평균값은 한국산 갈치집단의 평균값보다 높게 나타났다. 8개의 primer를 사용하여 얻어진 dendrogram은 cluster 1 (KOREAN 01~KOREAN 11) 및cluster 2 (ATLANTIC 12~ATLANTIC 22)와 같이 2개의 유전적 클러스터로 나뉘어졌다. 한국산 갈치집단내의 10번째 개체(KOREAN no. 10)와 11번째 개체(KOREAN no. 11) 사이가 가장 가까운 유전적 관계(genetic distance = 0.038)를 나타내었다. 궁극적으로 볼 때 한국산 갈치집단의 1번째(KOREAN no. 01)와 대서양산 갈치집단의 16번째(ATLANTIC no. 16) 개체 사이가 가장 먼 유전적 거리(genetic distance = 0.708)를 나타내었다.

Keywords

References

  1. Badarcki, F. and D.O.F. Skibinski. 1994. Application of the RAPD technique in tilapia fish: species and subspecies identification. Heredity, 73 : 117-123 https://doi.org/10.1038/hdy.1994.110
  2. Bernardi, G. and D. Talley. 2000. Genetic evidence for limited dispersal in the coastal California killifish, Fundulus parvipinnis. J. Exp. Mar. Biol. Ecol., 255 : 187-199 https://doi.org/10.1016/S0022-0981(00)00298-7
  3. Cagigas, M.E., E. Vazquez, G. Blanco and J.A. Sanchez. 1999. Combined assessment of genetic variability in populations of brown trout (Salmo trutta L.) based on allozymes, microsatellites, and RAPD markers. Mar. Biotechnol., 1 : 286-296 https://doi.org/10.1007/PL00011778
  4. Callejas, C. and M.D. Ochando. 1998. Identification of Spanish barbel species using the RAPD technique. J. Fish Biol., 53 : 208-215 https://doi.org/10.1111/j.1095-8649.1998.tb00121.x
  5. Cha, H.K. and D.W. Lee. 2004. Reproduction of hairtail, Trichiurus lepturus Linnaeus, in Korean waters. - Maturation and spawning-. J. Korean Soc. Fish. Res., 6 : 54-62
  6. Chenyambuga, S.W., O. Hanotte, J. Hirbo, P.C. Watts, S. J. Kemp, G.C. Kifaro, P.S. Gwakisa, P.H. Petersen and J.E.O. Rege. 2004. Genetic characterization of indigenous goats of sub-Saharan Africa using microsatellite DNA markers. Asian-Aust. J. Anim. Sci., 17 : 445- 452 https://doi.org/10.5713/ajas.2004.445
  7. Diaz-Jaimes, P. and M. Uribe-Alcocer. 2003. Allozyme and RAPD variation in the eastern Pacific yellowfin tuna (Thunnus albacares). Fish. Bull., 101 : 769-777
  8. Huang, B.X., R. Peakall and P.J. Hanna. 2000. Analysis of genetic structure of blacklip abalone (Haliotis rubra) populations using RAPD, minisatellite and microsatellite markers. Mar. Biol., 136 : 207-216 https://doi.org/10.1007/s002270050678
  9. Huh, S.H. 1999. Feeding habits of hairtail, Trichiurus lepturus. Korean J. Ichthyol., 11 : 191-197
  10. Iyengar, A., S. Piyapattanakorn, D.M. Dtone, D.A. Heipel, B.R. Howell, S.M. Baynes and N. Maclean. 2000. Identification of microsatellite repeats in turbot (Scophthalmus maximus) and dover sole (Solea solea) using a RAPD-based technique: Characterization of microsatellite markers in dover sole. Mar. Biotechnol., 2 : 49-56
  11. Jeffreys, A.J. and D.B. Morton. 1987. DNA fingerprints of dogs and cats. Anim. Genet., 18 : 1-15 https://doi.org/10.1111/j.1365-2052.1987.tb00739.x
  12. Kim, J.Y., C.Y. Park and J.M. Yoon. 2004. Genetic differences and DNA polymorphism in oyster (Crassostrea spp.) analysed by RAPD-PCR. Korean J. Genet., 26 : 123-134
  13. Kim, S.K., Y.H. Jung, S.H. Han, Y.S. Oh, M.H. Ko and M. Y. Oh. 2000. Phylogenetic relationship among Haliotis spp. distributed in Korea by the RAPD analysis. Korean J. Genet., 22 : 43-49
  14. Kim, Y.U., J.G. Myoung, Y.S. Kim, K.H. Han, C.B. Kang and J.G. Kim. 2001. The Marine Fishes of Korea. Hanguel, Busan, Korea, pp. 278
  15. Klinbunga, S., P. Ampayup, A. Tassanakajon, P. Jarayabhand and W. Yoosukh. 2000a. Development of speciesspecific markers of the tropical oyster (Crassostrea belcheri) in Thailand. Mar. Biotechnol., 2 : 476-484
  16. Klinbunga, S., A. Boonyapakdee and B. Pratoomchat. 2000b. Genetic diversity and species-diagnostic markers of mud crabs (Genus Scylla) in Eastern Thailand determined by RAPD analysis. Mar. Biotechnol., 2 : 180-187
  17. Koh, M.C., C.H. Lim, S.B. Chua, S.T. Chew and S.T. Phang. 1998. Random amplified polymorphic DNA (RAPD) fingerprints for identification of red meat animal species. Meat Sci., 48 : 275-285 https://doi.org/10.1016/S0309-1740(97)00104-6
  18. Liu, Z., P. Li, B.J. Argue and R.A. Dunham. 1998. Inheritance of RAPD markers in channel catfish (Ictalurus punctatus), blue catfish (I. furcatus) and their $F_{1},\;F_{2}$ and backcross hybrids. Anim. Genet., 29 : 58-62 https://doi.org/10.1046/j.1365-2052.1998.00284.x
  19. Liu, Z.J. and J.F. Cordes. 2004. DNA marker technologies and their applications in aquaculture genetics. Aquaculture, 238 : 1-37 https://doi.org/10.1016/j.aquaculture.2004.05.027
  20. Mamuris, Z., C. Stamatis, M. Bani and C. Triantaphyllidis. 1999. Taxonomic relationships between four species of the Mullidae family revealed by three genetic methods: allozymes, random amplified polymorphic DNA and mitochondrial DNA. J. Fish Biol., 55 : 572-587 https://doi.org/10.1111/j.1095-8649.1999.tb00700.x
  21. McCormack, G.C., R. Powell and B. Keegan. 2000. Comparative analysis of two populations of the brittle star Amphiura filiformis (Echinodermata: Ophiuroidae) with different life history strategies using RAPD markers. Mar. Biotechnol., 2 : 100-106
  22. Nei, M. 1978. Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics, 89 : 583-590
  23. Park, C.S., D.W. Lee, Z.G. Kim and Y.J. Kang. 2000. Stock assessment and management of the hairtail, Trichiurus lepturus Linnaeus in Korean waters. J. Korean Soc. Fish. Res., 3 : 29-38
  24. Park, C.S., D.W. Lee and K.S. Hwang. 2002. Distribution and migration of hairtail, Trichiurus lepturus in Korean waters. J. Korean Soc. Fish. Res., 5 : 1-11
  25. Partis, L. and R.J. Wells. 1996. Identification of fish species using random amplified polymorphic DNA (RAPD). Mol. Cell. Probes, 10 : 435-441 https://doi.org/10.1006/mcpr.1996.0060
  26. Siti Azizah, M.N., A. Ruzainah and I. Patimah. 2005. Development of RAPD markers in the eel-loach (Pangio spp.) for genetic discrimination and monitoring of wild and cultured populations. World Aquacult., 36 : 37-43
  27. Smith, P.J., P.G. Benson and S.M. McVeagh. 1997. A comparison of three genetic methods used for stock discrimination of orange roughy, Hoplostethus atlanticus: allozymes, mitochondrial DNA, and random amplified polymorphic DNA. Fish. Bull., 95 : 800-811
  28. Tassanakajon, A., S. Pongsomboon, P. Jarayabhand, S. Klinbunga and V. Boonsaeng. 1998. Genetic structure in wild populations of black tiger shrimp (Penaeus monodon) using randomly amplified polymorphic DNA analysis. J. Mar. Biotechnol., 6 : 249-254
  29. Waldbieser, G.C. and W.R. Wolters. 1999. Application of polymorphic microsatellite loci in a channel catfish Ictalurus punctatus breeding program. J. World Aquacult. Soc., 30 : 256-262 https://doi.org/10.1111/j.1749-7345.1999.tb00873.x
  30. Welsh, J. and M. McClelland. 1990. Fingerprinting genomes using PCR with arbitrary primers. Nucleic Acids Res., 18 : 7213-7218 https://doi.org/10.1093/nar/18.24.7213
  31. Welsh, J., C. Petersen and M. McClelland. 1991. Polymorphisms generated by arbitrarily primed PCR in the mouse: application to strain identification and genetic mapping. Nucleic Acids Res., 19 : 303-306 https://doi.org/10.1093/nar/19.2.303
  32. Yoon, J.M. 2001. Genetic similarity and difference between common carp and Israeli carp (Cyprinus carpio) based on random amplified polymorphic DNAs analyses. Korean J. Biol. Sci., 5 : 333-339 https://doi.org/10.1080/12265071.2001.9647624
  33. Yoon, J.M. and G.W. Kim. 2001. Randomly amplified polymorphic DNA-polymerase chain reaction analysis of two different populations of cultured Korean catfish Silurus asotus. J. Biosci., 26 : 641-647 https://doi.org/10.1007/BF02704762
  34. Yoon, J.M. and H.Y. Park. 2002. Genetic similarity and variation in the cultured and wild crucian carp (Carassius carassius) estimated with random amplified polymorphic DNA. Asian-Aust. J. Anim. Sci., 15 : 470- 476 https://doi.org/10.5713/ajas.2002.470
  35. Yoon, J.M. and Y.H. Kim. 2003a. Wide marsh clam (Corbicula spp.) populations from three sites analysed by RAPD-PCR-AGE. Bull. Electrochem., 19 : 337-348
  36. Yoon, J.M. and G.W. Kim. 2003b. Genetic differences between cultured and wild penaeid shrimp (Penaeus chinensis) populations analysed by RAPD-PCR. Korean J. Genet., 25 : 21-32
  37. Yoon, J.M. and J.Y. Kim. 2004a. Genetic differences within and between populations of Korean catfish (S. asotus) and bullhead (P. fulvidraco) analysed by RAPD-PCR. Asian-Aust. J. Anim. Sci., 17 : 1053-1061 https://doi.org/10.5713/ajas.2004.1053
  38. Yoon, J.M. and Y.H. Kim. 2004b. Bandsharing values and genetic distances of two wild shortnecked clam, Reditapes philippinarum populations from the Yellow Sea assessed by random amplified polymorphic DNAspolymerase chain reaction. J. Aquacult., 17 : 12-23
  39. Zhang, C.I. and M.H. Sohn. 1997. A study on the stock assessment and management implications of the hairtail, Trichiurus lepturus Linne, in Korean waters. - 2. Variations in population biomass of the hairtail -. J. Korean Fish. Soc., 30 : 620-626