Genetic Differences within and between Populations of Korean Catfish (S. asotus) and Bullhead (P. fulvidraco) Analysed by RAPD-PCR

  • Yoon, Jong-Man ;
  • Kim, Jong-Yeon
  • Received : 2003.10.22
  • Accepted : 2004.03.03
  • Published : 2004.08.01


Of the 20 arbitrarily chosen primers, six oligonucleotides decamer primers were used on the basis of the number of the polymorphisms generated in catfish (Silurus asotus) from Yesan and bullhead (Pseudobagrus fulvidraco) from Dangjin in Korea. Six primers were used generating a total of 602 scorable bands in catfish and 195 in bullhead population, respectively, ranging in size of DNA fragments from less than approximately 100 to larger than 2,000 base pairs (bp). Six primers yielded 199 polymorphic fragments (33.1%) in catfish and 47 (24%) in bullhead, respectively. In the present study, a total of 328 common fragments (an average of 54.7 per primer) were observed in catfish population, whereas 84 (an average of 14.0 per primer) in bullhead. The total number of specific fragments in catfish and bullhead population were 76 and 64, respectively. In catfish population, random decamer, OPA-17 (GACCGCTTGT) generated the highest number of fragments (a total of 141) in comparison with other primers used, with an average of 11.8. The common bands in the molecular weight of 300 bp generated by random primer OPA-06 (GGTCCCTGAC) were present in every individuals in bullhead population. The major polymorphic bands in the molecular weight of 100 bp generated by OPA-17 were identified in lane 14, 15, 17, 18, 19 20 and 21, which were identifying species in bullhead population. The average bandsharing values (BS values) of all of the samples within catfish population ranged from 0.575 to 0.945, whereas 0.063-1.000 within bullhead population. The bandsharing value (index of similarity between individuals) between individual No. 5 and No. 9 showed the highest level within catfish population, whereas the bandsharing value between individual No. 1 and No. 2 showed the lowest level. The single linkage cluster analysis resulted from four primers, indicating four genetic groupings composed of group 1 (C1-C10, all of the catfish samples), group 2 (B11, B12, B13, B14, B16, B17, B18, B19), group 3 (B15) and group 4 (B20 and B21). The dendrogram reveals close relationships between individual identities within two species populations and individuals derived from the same ancestor, respectively. However, genetic distances between two species populations ranged from 0.124 to 0.333. The shortest genetic distance (0.042) displaying significant molecular differences was between individual No. 6 and No. 9 catfish population. The shortest genetic distance (0.033) displaying significant molecular differences also was between individual No. 18 and No. 19 in bullhead population. Reversely, the genetic distance of individual No. 20/21 among individuals in bullhead population was highest (0.333). This result showed that bullhead No. 20 and 21 were distinct from other individuals within bullhead population.


Bullhead;Catfish;Dendrogram;Genetic Distance;Pseudobagrus fulvidraco;Random Primer;Silurus asotus;Similarity Index


  1. Appannavar, M. M., M. G. Govindaiah and K. P. Ramesha. 2003. Genetic distance study among Deoni breed of cattle using random amplified DNA markers. Asian-Aust. J. Anim. Sci. 16 (3):315-319.
  2. Bommineni, V. R., P. P. Jauhar, T. S. Peterson, R. N. Chibbar and A. B. Almouslem. 1997. Analysis of hybrids of durum wheat with Thinopyrum juncelforme using RAPD markers. Theor. Appl. Genet. 95:757-763.
  3. Johnson, S. L., C. Midson, E. W. Ballinger and J. H. Postlethwait. 1994. Identification of RAPD primers that reveal extensive polymorphisms between laboratory strains of zebrafish. Genomics 19:152-156.
  4. Kim, I. S. 1997. Illustrated Encyclopedia of Fauna & Flora of Korea. Academy Publishing Company. Korea, Seoul. pp. 187-190.
  5. Mohd-Azmi, M., A. S. Ali and W. K. Kheng. 2000. DNA fingerprinting of red jungle fowl, village chicken and broilers. Asian-Aust. J. Anim. Sci. 13 (8):1040-1043.
  6. 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.
  7. Yoon, J. M. 2001. Genetic similarity and difference between common carp and Israeli carp (Cyprinus carpio) based on random amplified polymorphic DNAs analyses. Kor. J. Biol. Sci. 5:333-339.
  8. 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 (4):470-476.
  9. 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(2):303-306.
  10. Nei, M. and W. Li. 1979. Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76:5269-5273.
  11. Geng, S. M., W. Shen, G. Q. Qin, X. Wang, S. R. Hu, Q. Wang and J. Q. Zhang. 2002. DNA fingerprint polymorphism of 3-goat populations from China Chaidamu Basin. Asian-Aust. J. Anim. Sci. 15 (8):1076-1079.
  12. 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.
  13. Spooner, D. M., M. L. Ugarte and P. W. Skroch. 1997. Species boundaries and interrelationships of two closely related sympatric diploid wild potato species, Solanum astleyi and S. boliviense, based on RAPDs. Theor. Appl. Genet. 95:764-771.
  14. Dias Neto, E., M. Steindel, L. K. F. Passos, C. Pereira de Souza, D. Rollinson, N. Katz, A. J. Romanha, S. D. J. Pena and A. J. G. Simpson. 1993. The use of RAPDs for the study of the genetic diversity of Schistosoma mansoni and Trypanosoma cruzi. DNA Fingerprinting: 339-345.
  15. 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.
  16. Jeffreys, A. J. and D. B. Morton. 1987. DNA fingerprints of dogs and cats. Anim. Genet. 18:1-15.
  17. Ramesha, K. P., T. Saravanan, M. K. Rao, M. M. Appannavar and A. Obi Reddy. 2002. Genetic distance among south Indian breeds of zebu cattle uing random amplified DNA markers. Asian-Aust. J. Anim. Sci. 15(3):309-314.
  18. Nebauer, S. G., L. del Castillo-Agudo and J. Segura. 2000. An assessment of genetic relationships within the genus Digitalis based on PCR-generated RAPD markers. Theor. Appl. Genet. 100:1209-1216.
  19. Partis, L. and R. J. Wells. 1996. Identification of fish species using random amplified polymorphic DNA (RAPD). Mol. Cell. Probes. 10:435-441.
  20. Pejic, I., P. Ajmone-Marsan, M. Morgante, V. Kozumplick, P. Castiglioni, G. Taramino and M. Motto. 1994. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs and AFLPs. Theor. Appl. Genet. 97:1248-1255.
  21. Smith, P. J., P. G. Benson and S. M. McVeagh. 1997. A comparison of three genetic methods used for stock discriminaion of orange roughy, Hoplostethus atlanticus: allozymes, mitochondrial DNA, and random amplified polymorphic DNA. Fish. Bull. 95:800-811.
  22. Klinbunga, S., P. Ampayup, A. Tassanakajon, P. Jarayabhand and W. Yoosukh. 2000a. Development of species-specific markers of the tropical oyster (Crassostrea belcheri) in Thailand. Mar. Biotechnol. 2:476-484.
  23. Vierling, R. A., Z. Xiang, C. P. Joshi, M. L. Gilbert and H. T. Nguyen. 1994. Genetic diversity among elite Sorghum lines revealed by restriction fragment length polymorphisms and random amplified polymorphic DNAs. Theor. Appl. Genet. 87:816-820.
  24. Fischer, M., R. Husi, D. Prati, M. Peintinger, M. V. Kleunen and B. Schmid. 2000. RAPD variation among and within small and large populations of the rare clonal plant Ranunculus reptans (Ranunculaceae). Am. J. Botany 87 (8):1128-1137.
  25. 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.
  26. Callejas, C. and M. D. Ochando. 1998. Identification of Spanish barbel species using the RAPD technique. J. Fish Biol. 53:208-215.
  27. Hamm, D. E. and R. S. Burton. 2000. Population genetics of black abalone, Haliotis cracherodii, along the central California coast. J. Exp. Mar. Biol. Ecol. 254:235-247.
  28. Orozco-Castillo, C., K. J. Chalmers, R. Waugh and W. Powell. 1994. Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theor. Appl. Genet. 87:934-940.
  29. Debenham, P., M. Brzezinski, K. Foltz and S. Gaines. 2000. Genetic structure of populations of the red sea urchin, Strongylocentrotus franciscanus. J. Exp. Mar. Biol. Ecol. 253:49-62.
  30. Iyengar, A., S. Piyapattanakorn, D. M. Dtone, D. A. Heipel and 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.
  31. 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.
  32. Moeller, D. A. and B. A. Schaal. 1999. Genetic relationships among native American maize accessions of the Great Plains assessed by RAPDs. Theor. Appl. Genet. 99:1061-1067.

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Supported by : Kunsan National University