A genetic linkage map for coho salmon (Oncorhynchus kisutch)

Animal Genetics

Volumn 39, Issue 2, 2008, Pages 169-179

  McClelland, E K ^a   Naish, K A ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Chromosome homology; Genome map; Salmonids

Indexed keywords

MICROSATELLITE DNA;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM; ANIMAL; ARTICLE; BREEDING; CHROMOSOME; CHROMOSOME MAP; FEMALE; GENETICS; GENOME; MALE; NUCLEOTIDE SEQUENCE; ONCORHYNCHUS KISUTCH; SALMONID; TROUT;

AMPLIFIED FRAGMENT LENGTH POLYMORPHISM ANALYSIS; ANIMALS; BASE SEQUENCE; BREEDING; CHROMOSOME MAPPING; CHROMOSOMES; FEMALE; GENOME; MALE; MICROSATELLITE REPEATS; ONCORHYNCHUS KISUTCH; SALMONIDAE; TROUT;

ONCORHYNCHUS KISUTCH; ONCORHYNCHUS MYKISS; SALMONIDAE;

EID: 41149162725     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2008.01699.x     Document Type: Article

References (54)

1. Allendorf F.W. Thorgaard G.H. (1984) Tetraploidy and the evolution of salmonid fishes. In : Evolutionary Genetics of Fishes (Ed. by B.J. Turner pp. 1 53. Plenum Press, New York.
2. Banks M.A., Blouin M.S., Baldwin B.A., Rashbrook V.K., Fitzgerald H.A., Blankenship S.M. Hedgecock D. (1999) Isolation and inheritance of novel microsatellites in chinook salmon (Oncorhynchus tschawytscha). Journal of Heredity 90, 281 8.
3. Danzmann R.G. Gharbi K. (2001) Gene mapping in fishes: a means to an end. Genetica 111, 3 23.
4. Danzmann R.G., Cairney M., Davidson W.S. et al. (2005) A comparative analysis of the rainbow trout genome with two other species of fish (Arctic charr and Atlantic salmon) within the tetraploid derivative Salmonidae family (subfamily: Salmoninae). Genome 48, 1037 51.
5. Eldridge W.H. Naish K.A. (2007) Long-term effects of translocation and release numbers on fine-scale population structure among coho salmon (Oncorhynchus kisutch). Molecular Ecology 16, 2407 21.
6. Erickson D.L., Fenster C.B., Stenoien H.K. Price D. (2004) Quantitative trail locus analyses and the study of evolutionary process. Molecular Ecology 13, 2505 22.
7. Food and Agriculture Organization of the United Nations (FAO) (2007) Fisheries and Aquaculture Department, Species Fact Sheets. http://www.fao.org/ fishery/species/2118.
8. Gharbi K., Gautier A., Danzmann R.G. et al. (2006) A linkage map for brown trout (Salmo trutta): chromosome homeologies and comparative genome organization with other salmonid fish. Genetics 172, 2405 19.
9. Gilbey J., Verspoor E., McLay A. Houlihan D. (2004) A microsatellite linkage map for Atlantic salmon (Salmo salar). Animal Genetics 35, 98 105.
10. Greig C., Jacobson D.P. Banks M.A. (2003) New tetranucleotide microsatellites for fine-scale discrimination among endangered chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Notes 3, 376 9.
11. Guyomard R., Mauger S., Tabet-Canale K., Martineau S., Genet C., Krieg F. Quillet E. (2006) A Type I and Type II microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) with presumptive coverage of all chromosome arms. BMC Genomics 7, 302.
12. Halbert N.D., Ward T.J., Schnabel R.D., Taylor J.F. Derr J.N. (2005) Conservation genomics: disequilibrium mapping of domestic cattle chromosomal segments in North American bison populations. Molecular Ecology 14, 2343 62.
13. Khoo S.K., Ozaki A., Sakamoto T. Okamoto N. (2000) Four highly polymorphic dinucleotide microsatellites in rainbow trout (Oncorhynchus mykiss). Animal Genetics 31, 73 4.
14. Lindner K.R., Seeb J.E., Habicht C., Knudsen K.L., Kretschmer E., Reedy D.J., Spruell P. Allendorf F.W. (2000) Gene-centromere mapping of 312 loci in pink salmon by half-tetrad analysis. Genome 43, 538 49.
15. Liu B.H. (1998) Statistical Genomics: Linkage, Mapping and QTL Analysis. CRC Press, New York.
16. McConnell S.K., O'Reilly P.T., Hamilton L.C., Wright J.M. Bentzen P. (1995) Polymorphic microsatellite loci from Atlantic salmon (Salmo salar): genetic differentiation of North American and European populations. Canadian Journal of Fisheries and Aquatic Science 52, 1863 72.
17. Mitchell-Olds T. (1995) The molecular basis of quantitative genetic variation in natural populations. Trends in Ecology and Evolution 10, 324 8.
18. Moen T., Hoyheim B., Munck H. Gomez-Raya L. (2004) A linkage map of Atlantic salmon (Salmo salar) reveals an uncommonly large difference in recombination rate between the sexes. Animal Genetics 35, 81 92.
19. Naish K.A. Park L.K. (2002) Linkage relationships for 35 new microsatellite loci in chinook salmon Oncorhynchus tshawytscha. Animal Genetics 33, 312 27.
20. Nelson R.J. Beacham T.D. (1999) Isolation and cross-species amplification of microsatellite loci useful for study of Pacific salmon. Animal Genetics 30, 228 9.
21. Nichols K.M., Young W.P., Danzmann R.G. et al. (2003) A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34, 102 15.
22. O'Connell M., Danzmann R.G., Cornuet J.-M., Wright J.M. Ferguson M.M. (1997) Differentiation of rainbow trout (Oncorhynchus mykiss) populations in Lake Ontario and the evaluation of the stepwise mutation and infinite allele mutation models using microsatellite variability. Canadian Journal of Fisheries and Aquatic Sciences 54, 1391 9.
23. Olsen J.B., Wilson S.L., Kretschmer E.J., Jones K.C. Seeb J.E. (2000) Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon. Molecular Ecology 9, 2185 7.
24. Ozaki A., Khoo S.K., Sakamoto T. Okamoto N. (1999) Two highly polymorphic dinucleotide microsatellites in rainbow trout (Oncorhynchus mykiss): OmyRGT7TUF and OmyRGT8TUF. Animal Genetics 30, 393 4.
25. Ozaki A., Sakamoto T., Khoo S., Nakamura K., Coimbra M.R.M., Akutsu T. Okamoto N. (2001) Quantitative trait loci (QTLs) associated with resistance/susceptibility to infectious pancreatic necrosis virus (IPNV) in rainbow trout (Oncorhynchus mykiss). Molecular Genetics and Genomics 265, 23 31.
26. Palti Y., Fincham M.R. Rexroad C.E.I. (2002) Characterization of 38 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Molecular Ecology Notes 2, 449 52.
27. Palti Y., Danzmann R.G. Rexroad C.E. (2003) Characterization and mapping of 19 polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34, 153 6.
28. Phillips R. Rab P. (2001) Chromosome evolution in the Salmonidae (Pisces): an update. Biological Review 76, 1 25.
29. Phillips R.B., Morasch M.R., Park L.K., Naish K.A. Devlin R.H. (2005) Identification of the sex chromosome pair in coho salmon (Oncorhynchus kisutch): lack of conservation of the sex linkage group with chinook salmon (Oncorhynchus tshawytscha). Cytogenetic and Genome Research 111, 166 70.
30. Phillips R.B., Nichols K., DeKoning J., Morasch M.R., Keatley K.A., Rexroad C., Gahr S.A., Danzmann R.G., Drew R.E. Thorgaard G.H. (2006) Assignment of rainbow trout linkage groups to specific chromosomes. Genetics 174, 1661 70.
31. Reid D.P., Szanto A., Glebe B., Danzmann R.G. Ferguson M.M. (2005) QTL for body weight and condition factor in Atlantic salmon (Salmo salar): comparative analysis with rainbow trout (Oncorhynchus mykiss) and Arctic charr (Salvelinus alpinus). Heredity 94, 166 72.
32. Rexroad C.E.I. Palti Y. (2003) Development of ninety-seven polymorphic microsatellite markers for rainbow trout. Transactions of the American Fisheries Society 132, 1214 21.
33. Rexroad C.E.I., Coleman R.L., Martin A.M., Hershberger W.K. Killefer J. (2001) Thirty-five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Animal Genetics 32, 316 31.
34. Rexroad C.E.I., Coleman R.L., Gustafson A.L., Hershberger W.K. Killefer J. (2002a) Development of rainbow trout microsatellite markers from repeat enriched libraries. Marine Biotechnology 3, 12 6.
35. Rexroad C.E.I., Coleman R.L., Hershberger W.K. Killefer J. (2002b) Eighteen polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss). Animal Genetics 33, 72 84.
36. Rexroad C.E.I., Coleman R.L., Hershberger W.K. Killefer J. (2002c) Rapid communication: thirty-eight polymorphic microsatellite markers for mapping in rainbow trout. Journal of Animal Science 80, 541 2.
37. Rexroad C., Rodriguez M.F., Coulibaly I., Gharbi K., Danzmann R.G., DeKoning J., Phillips R.B. Palti Y. (2005) Comparative mapping of expressed sequence tags containing microsatellites in rainbow trout (Oncorhynchus mykiss). BMC Genomics 6, 54.
38. Rodriguez F., Rexroad C.E.I. Palti Y. (2003) Characterization of twenty-four microsatellite markers for rainbow trout (Oncorhynchus mykiss). Molecular Ecology Notes 3, 619 22.
39. Rodriguez M.F., LaPatra S., Williams S., Famula T. May B. (2004) Genetic markers associated with resistance to infectious hematopoietic necrosis in rainbow and steelhead trout (Oncorhynchus mykiss) backcrosses. Aquaculture 241, 93 115.
40. Rogers S.M. Bernatchez L. (2005) Integrating QTL mapping and genome scans towards the characterization of candidate loci under parallel selection in the lake whitefish (Coregonus clupeaformis). Molecular Ecology 14, 351 61.
41. Sakamoto T., Danzmann R.G., Gharbi K. et al. (2000) A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics 155, 1331 45.
42. Schuelke M. (2000) An economic method for the fluorescent labeling of PCR fragments. Nature Biotechnology 18, 233 4.
43. Scribner K.T., Gust J.R. Fields R.L. (1996) Isolation and characterization of novel salmon microsatellite loci: cross-species amplification and population genetic applications. Canadian Journal of Fisheries and Aquatic Sciences 53, 833 41.
44. Slate J. (2005) Quantitative trait locus mapping in natural populations: progress, caveats and future directions. Molecular Ecology 14, 363 79.
45. Slate J., Visscher P.M., MacGregor S., Stevens D., Tate M.L. Pemberton J.M. (2002) A genome scan for quantitative trait loci in a wild population of red deer (Cervus elaphus). Genetics 162, 1863 73.
46. Smith C.T., Koop B.F. Nelson R.J. (1998) Isolation and characterization of coho salmon (Oncorhynchus kisutch) microsatellites and their use in other salmonids. Molecular Ecology 7, 1614 6.
47. Spies I.B., Brasier D.J., O'Reilly T.L., Seamons T.R. Bentzen P. (2005) Development and characterization of novel tetra-, tri-, and dinucleotide microsatellite markers in rainbow trout (Oncorhynchus mykiss). Molecular Ecology Notes 5, 278 81.
48. Thorgaard G.H., Allendorf F.W. Knudsen K.L. (1983) Gene-centromere mapping in rainbow trout: high interference over long map distances. Genetics 103, 771 83.
49. Vasemagi A., Nilsson J. Primmer C.R. (2005) Seventy-five EST-linked Atlantic salmon (Salmo salar L.) microsatellite markers and their cross-amplification in five salmonid species. Molecular Ecology Notes 5, 282 8.
50. Voorrips R.E. (2002) mapchart: software for the graphical presentation of linkage maps and QTLs. Journal of Heredity 93, 77 8.
51. Weitkamp L.A., Wainwright T.C., Bryant G.J., Milner G.B., Teel D.J., Kope R.G. Waples R.S. (1995) Status review of coho salmon from Washington, Oregon and California. NOAA Technical Memorandum NMFS-NWFSC-24.
52. Williamson K.S., Cordes J.F. May B. (2002) Characterization of microsatellite loci in chinook salmon (Oncorhynchus tshawytscha) and cross-species amplification in other salmonids. Molecular Ecology Notes 2, 17 9.
53. Woram R.A., Gharbi K., Sakamoto T. et al. (2003) Comparative genome analysis of the primary sex-determining locus in salmonid fishes. Genome Research 13, 272 80.
54. Woram R.A., McGowan C., Stout J.A., Gharbi K., Ferguson M.M., Hoyheim B., Davidson E.A., Davidson W.S., Rexroad C. Danzmann R.G. (2004) A genetic linkage map for Arctic char (Salvelinus alpinus): evidence for higher recombination rates and segregation distortion in hybrid versus pure strain mapping parents. Genome 47, 304 15.