Journal of Aquaculture (한국양식학회지)

The Korean Society of Fisheries and Aquatic Science (한국양식학회)
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Genetic Variation and Polymorphism in Rainbow Trout, Oncorhynchus mykiss Analysed by Amplified Fragment Length Polymorphism

  • Yoon, Jong-Man (Department of Aquatic Life Medicine, College of Ocean Science and Technology, National University) ;
  • Yoo, Jae-Young (Department of Animal Science, College of Animal Husbandry, Konkuk University) ;
  • Park, Jae-Il (Department of Aquatic Life Medicine, College of Ocean Science and Technology, National University)
  • Published : 2004.02.01
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Abstract

The objective of the present study was to analyze genetic distances, variation and characteristics of individuals in rainbow trout, Oncorhynchus mykis using amplified fragment length polymorphism (AFLP) method as molecular genetic technique, to detect AFLP band patterns as genetic markers, and to compare the efficiency of agarosegel electrophoresis (AGE) and polyacrylamide gel electrophoresis (PAGE), respectively. Using 9 primer combinations, a total of 141 AFLP bands were produced, 108 bands (82.4%) of which were polymorphic in AGE. In PAGE, a total of 288 bands were detected, and 220 bands (76.4%) were polymorphic. The AFLP fingerprints of AGE were different from those of PAGE. Separation of the fragments with low molecular weight and genetic polymorphisms revealed a distinct pattern in the two gel systems. In the present study, the average bandsharing values of the individuals between two populations apart from the geographic sites in Kangwon-do ranged from 0.084 to 0.738 of AGE and PAGE. The bandsharing values between individuals No.9 and No. 10 showed the highest level within population, whereas the bandsharing values between individuals No.5 and No.7 showed the lowest level. As calculated by bandsharing analysis, an average of genetic difference (mean$\pm$SD) of individuals was approximately 0.590$\pm$0.125 in this population. In AGE, the single linkage dendrogram resulted from two primers (M11+H11 and M13+H11), indicating six genetic groupings composed of group 1 (No.9 and 10), group 2 (No. 1, 4, 5, 7, 10, 11, 16 and 17), group 3 (No. 2, 3, 6, 8, 12, 15 and 16), group 4 (No.9, 14 and 17), group 5 (No. 13, 19, 20 and 21) and group 6 (No. 23). In AGE, the genetic distances among individuals of between-population ranged from 0.108 to 0.392. In AGE, the shortest genetic distance (0.108) displaying significant molecular differences was between individuals No.9 and No. 10. Especially, the genetic distance between individuals No. 23 and the remnants among individuals within population was highest (0.392). Additionally, in the cluster analysis using the PAGE data, the single linkage dendrogram resulted from two primers (M12+H13 and M11+H13), indicating seven genetic groupings composed of group 1 (No. 15), group 2 (No. 14), group 3 (No. 11 and 12), group 4 (No.5, 6, 7, 8, 10 and 13), group 5 (No.1, 2, 3 and 4), group 6 (No.9) and group 7 (No. 16). By comparison with the individuals in PAGE, genetic distance between No. 10 and No. 7 showed the shortest value (0.071), also between No. 16 and No. 14 showed the highest value (0.242). As with the PAGE analysis, genetic differences were certainly apparent with 13 of 16 individuals showing greater than 80% AFLP-based similarity to their closest neighbor. The three individuals (No. 14, No. 15 and No. 16) of rainbow trout between two populations apart from the geographic sites in Kangwon-do formed distinct genetic distances as compared with other individuals. These results indicated that AFLP markers of this fish could be used as genetic information such as species identification, genetic relationship or analysis of genome structure, and selection aids for genetic improvement of economically important traits in fish species.

Keywords

References

  1. Anim. Genet. v.28 AFLP TMmarkers for DNA fingerprinting in cattle Ajmone-Marsan,P.;A.Valentini;M.Cassandro;G.Vecchiotti-Antaldi;G.Bertono;M.Kuiper https://doi.org/10.1111/j.1365-2052.1997.00204.x
  2. Crop Sci. v.39 Amplified fragment length polymorphism analysis of tefEragrostis tef (Zucc.) Trotter Bai,G.;M.Ayele;H.Tefera;H.T.Nguyen https://doi.org/10.2135/cropsci1999.0011183X003900030034x
  3. Mar. Biol. v.136 Polymorphism in soft coral larvae revealed by amplified fragment-length polymorphism (AFLP) markers Barki,Y.;J.Douek;D.Graur;D.Gateno;B.Rinkevich https://doi.org/10.1007/s002270050005
  4. Genome v.33 Intra-specific sequence variation in the mitochondrial genome of rainbow trout (Oncorhynchus mykiss) beckenbach,A.T.;W.K.Thomas;H.Sohrabi https://doi.org/10.1139/g90-003
  5. J. Industrial Microbiol. Biotechnol. v.21 Amplified fragment length polymorphism (AFLP): A review of the procedure and its applications Blears,M.J.;S.A.De Grandis;H.Lee;J.T.Trevors https://doi.org/10.1038/sj.jim.2900537
  6. J. Fish Biol. v.53 Identification of Spanish barbel species using the RAPD technique Callejas,C.;M.D.Ochando https://doi.org/10.1111/j.1095-8649.1998.tb00121.x
  7. Anim. Genet. v.31 Exclusion of the PDE6A gene for generalized progressive retinal atrophy in 11 breeds of dog Dekomien,G.;J.T.Epplen https://doi.org/10.1046/j.1365-2052.2000.00611.x
  8. DNA Fingerprinting v.69 The use of RAPDs for the study of the genetic diversity of Schistosoma mansoni and Trypanosoma cruzi Dias Neto,E.;M.Steindel;L.K.F.Passos;C.Pereira de Souza;D.Pollinson;N.Katz;A.J.Pomanha;S.D.J.Pena;A.J.G.Simpson
  9. Mar. Biotechnol. v.2 AFLP analysis confirms exclusive maternal genomic contribution of meiogynogentic sea bass (Dicentrachus labrax L.) Felip,A.;G.Martinez-Rodriguez;F.Piferrer;M.Carrilo;S.Zanuy https://doi.org/10.1007/s101260000000
  10. Aquaculture v.159 The application of microsatellite markers to breeding programmes in the sea bass, Dicentrarchus labrax Garcia de Leon,F.J.;M.Canonne;E.Quillet;F.Bonhomme;B.Chatain https://doi.org/10.1016/S0044-8486(97)00188-9
  11. Theor. Appl. Genet. v.101 Comparing AFLP, RAPD and RFLP markers for measuring genetic diversity in melon Garcia-Ma,s J.;M.Oliver;H.Gomez-Paniagua;M.C.Vicente https://doi.org/10.1007/s001220051553
  12. Asian-Aus. J. Anim. Sci. v.15 no.8 DNA fingerprint polymorphism of 3-goat populations from China Chaidamu Basin Geng,S.M.;W.Shen;G.Q.Qin;X.Wang;S.R.Hu;Q.Wang;J.Q.Zhang https://doi.org/10.5713/ajas.2002.1076
  13. Anim. Genet. v.25 Characterization of zebu cattle breeds in Tanzania using random amplified polymorphic DNA markers Gwakisa,P.S.;S.J.Kemp;A.J.Teale https://doi.org/10.1111/j.1365-2052.1994.tb00408.x
  14. Theor. Appl. Genet. v.98 Evaluation of AFLP in Beta Hansen,M.;T.Kraft;M.Christiansson;N.O.Nilsson https://doi.org/10.1007/s001220051143
  15. Theor. Appl. Genet. v.95 More on the effciency of marker-assisted selection Hospital,F.;L.Moreau;F.Lacoudre;A.Charcosset;A.Gallais https://doi.org/10.1007/s001220050679
  16. Korean J. Biol. Sci. v.5 no.2 AFLP Fingerprinting of Brassica campestis L. ssp. napus var. nippo-oleifera Makino from Korea Huh,M.K.;H.W.Huh https://doi.org/10.1080/12265071.2001.9647589
  17. Anim. Genet. v.18 DNA fingerprints of dogs and cats Jeffreys,A.J.;D.B.Morton https://doi.org/10.1111/j.1365-2052.1987.tb00739.x
  18. Mar. Biotechnol. v.2 Genetic diversity and species-diagnostic markers of mud crabs (Genus Scylla) in Eastern Thailand determined by RAPD analysis Klinbunga,S.;A.Boonyapakdee;B.Pratoomchat
  19. Anom. Genet. v.30 Application of AFLP markers to grnome mapping in poultry Knorr,C.;H.H.Cheng;J.B.Dodgson https://doi.org/10.1046/j.1365-2052.1999.00411.x
  20. Asian-Aus. J. Anim. Sci. v.13 no.9 The genetic diversity of seven pig breeds in China, estimated by means of microsatellites Li,X.;K.Li;B.Fan;Y.Gong;S.Zhao;Z.Peng;B.Liu https://doi.org/10.5713/ajas.2000.1193
  21. Nucleic Acids Res. v.24 no.18 A PCR-based DNA fingerprinting technique: AFLP for molecular typing of bacteria Lin,J.J.;J.Kuo;J.Ma https://doi.org/10.1093/nar/24.18.3649
  22. Anim. Genet. v.29 Inheritance of RAPD makers in channel catfish (Icralurus punctatus), blue catfish (I. Furcatus) and their &F_{1}, F_{2}$ and backcross hybrids Liu,Z.;P.Li;B.J.Argue;R.A.Dunham https://doi.org/10.1046/j.1365-2052.1998.00284.x
  23. Genome v.39 Level of polymorphism and genetic mapping of AFLP markers in rice Mackill,D.J.;Z.Zhang;E.D.Redona;P.M.Colowit https://doi.org/10.1139/g96-121
  24. Theor. Appl. Genet. v.93 Amplified fragment length polymorphism (AFLP) in soybean: psecies diversity, inheritance, and near-isogenic line analysis Maughan,P.J.;M.A.Saghai Maroof;G.R.Buss;G.M.Huestis https://doi.org/10.1007/BF00223181
  25. Asian-Aus. J. Anim. Sci. v.13 no.8 DNA fingerprinting of red jungle fowl, village chicken and broilers Mohd-Azmi,M.;A.S.Ali;W.K.Kheng https://doi.org/10.5713/ajas.2000.1040
  26. Theor. Appl. Genet. v.99 Genetic relationships among native American maize accessions of the Great Plains assessed by RAPDs Moeller,D.A.;B.A.Schaal https://doi.org/10.1007/s001220051415
  27. Theor. Appl. Genet. v.100 An assassment of genetic relationships within the genus Digitalis based on PCR-generated RAPD markers Nebauer,S.G.;L.del Castillo-Agudo;J.Segura https://doi.org/10.1007/s001220051426
  28. Proc. Natl. Acad. Sci. USA v.76 Mathematical model for studying genetic variation in terms of restriction endonucleases Nei,M.;W.Li https://doi.org/10.1073/pnas.76.10.5269
  29. Theor. Appl. Genet. v.87 Detection of genetic diversity and selective gene introgression in coffee using RAPD markers Orozco-Castillo,C.;K.J.Cha;mers;R.Waugh;W.Powell
  30. Mol. Cell. Probes v.10 Identification of fish species using random amplified polymorphic DNA (RAPD) Partis,L.;R.J.Wells https://doi.org/10.1006/mcpr.1996.0060
  31. Theor. Appl. Genet. v.94 Diversity and genetic differentiation among populations of Indian and Kenyan tea (Camellia sinensis (L.) O. Kuntze) revealed by AFLP markers Paul,S.;F.N.Wachira;W.Powell;R.Waugh https://doi.org/10.1007/s001220050408
  32. Theor. Appl. Genet. v.101 A new aspect of genetic diversity of Indonesian oil palm (Elaeis ruineensis Jacq) revealed by isoenzyme and AFLP markers and its consequences for breeding Purba,A.R.;J.L.Noyer;L.Baudouin;X.Perrier;S.Hamon;P.J.L.Lagoda https://doi.org/10.1007/s001220051567
  33. Proc. Natl. Acad. Sci. USA v.89 Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorpgic DNAs Peiter,R.;J.G.K.Williams;K.A.Feldann;J.A.Rafalski;S.V.Tingey;P.A.Scolnik https://doi.org/10.1073/pnas.89.4.1477
  34. Korean J. Biol. Sci. v.4 no.1 Systematic relationships among species of the Genus Dendronephthya(Alcyonacea; Octocorallia; Anthozoa) based on RAPD analysis Song,J.I.;Y.J.Lee https://doi.org/10.1080/12265071.2000.9647517
  35. BioTechniques v.26 Modification of the AFLP protocol applied to honey bee (Apis mellifera L.) DNA Suazo,A.;H.G.Hall
  36. Nucleic Acids Res. v.23 no.21 AFLP: a new technique for DNA fingerprinting Vos,P.;R.Hogers;M.Bleeker;M.Reijans;T.van de Lee;M.Hornes;A.Frijters;J.Peleman;M.Kuiper https://doi.org/10.1093/nar/23.21.4407
  37. J. World Aqua. Soc. v.30 no.2 Application of polymorpgic microsatellite loci in a channel catfish Ictalurus punctatus breeding program Waldbieser,G.C.;W.R.Wolters https://doi.org/10.1111/j.1749-7345.1999.tb00873.x
  38. Crop Sci. v.39 Diversity among selected Vigna angularis (Azuki) accessions on the basis of RAPD and AFLP markers Yww,E.;K.K.Kidwell;G.R.Sills;T.A.Lumpkin https://doi.org/10.2135/cropsci1999.0011183X003900010041x
  39. Korean J. Anim. Reprod. v.23 no.4 Genomic polymorphisms of genome DNA by polymerase chain reation-RAPD analysis using arbitrary primers in rainbow trout Yoon,J.M.
  40. Korean J. Biol. Sci. v.5 Genetic similarity and difference between common carp and Israrli carp (Cyprinus carpio) based on random amplified polymorphic DNAs analysis Yoon,J.M. https://doi.org/10.1080/12265071.2001.9647624
  41. J. Biosci. v.26 no.5 Randomly amplified polymorphic DNA-polymerase chain reaction analysis of two different populations of cultured Korea catfish Silurus asotus Yoon,J.M.;G.W.Kim https://doi.org/10.1007/BF02704762
  42. Asian-Aust. J. Anim. Sci. v.15 no.4 Genetic similarity and variation in the cultured and wild crucian carp (Carassius carassius) estimated with random amplified polymorphic DNA Yoon,J.M.;H.Y.Park
  43. Korean J. Genet. v.25 no.1 Genetic differences between cultured and wild penaeid shrimp (Penaeus chinensis) populations analysed by RAPD-PCR Yoon,J.M.;G.W.Kim
  44. Genetics v.148 A detailed linkage map of rainbow trout produced using doubled haploids Young,W.P.;P.A.Wheeler;V.H.Coryell;P.Kim;G.H.Thorgaard
  45. European Patent Application Number:9240269. 7, Publication Number: 0534 858 A1 Selective restriction fragment amplification: a general method for DNA figerprinting Zabeau,M.;P.Vos