Use of the 5′-nuclease reaction for single nucleotide polymorphism genotyping in Chinook salmon

Transactions of the American Fisheries Society

Volumn 134, Issue 1, 2005, Pages 207-217

  Smith, Christian T ^a   Seeb, James E ^a   Schwenke, Piper ^b   Seeb, Lisa W ^a  

^a ALASKA DEPARTMENT OF FISH AND GAME   (United States)

^b ALASKA FISHERIES SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENETIC MARKER; SALMONID;

ONCORHYNCHUS TSHAWYTSCHA; SALMONIDAE;

EID: 13844316976     PISSN: 00028487     EISSN: None     Source Type: Journal    
DOI: 10.1577/T04-019.1     Document Type: Article

References (44)

1. Banks, M. A., M. S. Blouin, B. A. Baldwin, V. K. Rashbrook, H. A. Fitzgerald, S. M. Blankenship, and D. Hedgecock. 1999. Isolation and inheritance of novel microsatellites in Chinook salmon (Oncorhynchus tshawytscha). Journal of Heredity 90:281-288.
2. Beacham, T. D., J. R. Candy, K. J. Supernault, T. Ming, B. Deagle, A. Schulze, D. Tuck, K. H. Kaukinen, J. R. Irvine, K. M. Miller, and R. E. Withler. 2001. Evaluation and application of microsatellite and major histocompatibility complex variation for stock identification of coho salmon in British Columbia. Transactions of the American Fisheries Society 130:1116-1149.
3. Beacham, T. D., J. R. Candy, K. J. Supernault, M. Wetklo, B. Deagle, K. Labaree, J. R. Irvine, K. M. Miller, R. J. Nelson, and R. E. Withler. 2003. Evaluation and application of microsatellites for population identification of Fraser River Chinook salmon (Oncorhynchus tshawytscha). Fishery Bulletin 101:243-259.
4. Blankenship, S. M., B. May, and D. Hedgecock. 2002. Evolution of a perfect simple-sequence-repeat locus in the context of its flanking sequence. Molecular Biology and Evolution 19:1943-1951.
5. Brumfield, R. T., P. Beerli, D. A. Nickerson, and S. V. Edwards. 2003. The utility of single-nucleotide polymorphisms in inferences of population history. Trends in Ecology and Evolution 18:249-256.
6. Buetow, K. H., M. N. Edmonson, and A. B. Cassidy. 1999. Reliable identification of large numbers of candidate SNPs from public EST data. Nature Genetics 21:323-325.
7. Campbell, D., P. Duchesne, and L. Bernatchez. 2003. AFLP utility for population assignment studies: analytical investigation and empirical comparison with microsatellites. Molecular Ecology 12:1979-1991.
8. Cavalli-Sforza, L. L., and A. W. Edwards. 1967. Phylogenetic analysis: models and estimation procedures. American Journal of Human Genetics 19:233-257.
9. Davison, A., and S. Chiba. 2003. Laboratory temperature variation is a previously unrecognized source of genotyping error during capillary electrophoresis. Molecular Ecology Notes 3:321-323.
10. Excoffier, L., P. E. Smouse, and J. M. Quattro. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131:479-491.
11. Felsenstein, J. 1995. PHYLIP, version 3.6. University of Washington, Seattle.
12. Ford, M. J. 1998. Testing models of migration and isolation among populations of Chinook salmon (Oncorhynchus tschawytscha). Evolution 52:539-557.
13. Ford, M. J., P. J. Thornton, and L. K. Park. 1999. Natural selection promotes divergence of transferrin among salmonid species. Molecular Ecology 8:1055-1061.
14. Gharrett, A. J., S. M. Shirley, and G. R. Tromble. 1987. Genetic relationships among populations of Alaskan Chinook salmon (Oncorhynchus tshawytscha). Canadian Journal of Fisheries and Aquatic Sciences 44:765-774.
15. Glaubitz, J. C., O. E. Rhodes, and J. A. DeWoody. 2003. Prospects for inferring pairwise relationships with single-nucleotide polymorphisms. Molecular Ecology 12:1039-1047.
16. Goudet, J. 2001. FSTAT, version 2.9.3: a program to estimate and test gene diversities and fixation indices. Available: http://www.unil.ch/izea/ softwares/fstat.html.
17. Guthrie, C. M., and R. L. Wilmot. 2004. Genetic structure of wild Chinook salmon populations of southeast Alaska and northern British Columbia. Environmental Biology of Fishes 69:81-93.
18. Healy, M. C. 1991. Life history of Chinook salmon. Pages 311-394 in C. Groot and L. Margolis, editors. Pacific salmon life histories. UBC Press, Vancouver.
19. Holland, P. M., R. D. Abramson, R. Watson, and D. H. Gelfand. 1991. Detection of specific polymerase chain reaction product by utilizing the 5′-3′ exonuclease activity of Thermus aquaticus DNA polymerase. Proceedings of the National Academy of Science of the USA 88:7276-7280.
20. Kim, T. J., K. M. Parker, and P. W. Hedrick. 1999. Major histocompatibility complex differentiation in Sacramento River Chinook salmon. Genetics 151:1115-1122.
21. Kimura, M. 1968. Evolutionary rate at the molecular level. Nature (London) 217:624-626.
22. Kwok, P.-Y., editor. 2003. Single-nucleotide Polymorphisms: methods and protocols. Humana Press, Totowa, New Jersey.
23. Lee, L. G., C. R. Connell, and B. Bloch. 1993. Allelic discrimination by nick-translation PCR with fluorogenic probes. Nucleic Acids Research 21:3761-3766.
24. McKay, S. J., R. H. Devlin, and M. J. Smith. 1996. Phylogeny of Pacific salmon and trout based on growth hormone type-2 and mitochondrial NADH dehydrogenase subunit 3 DNA sequences. Canadian Journal of Fisheries and Aquatic Sciences 53:1165-1176.
25. Miller, K. M., and R. E. Withler. 1998. The salmonid class I MHC: limited diversity in a primitive teleost. Immunological Reviews 166:279-293.
26. Morin, P. A., G. Luikart, R. K. Wayne, and the SNP workshop group. 2004. SNPs in ecology, evolution, and conservation. Trends in Ecology and Evolution 19:208-216.
27. Myers, K. W., C. K. Harris, C. M. Knudsen, R. V. Walker, N. D. Davis, and D. W. Rogers. 1987. Stock origins of Chinook salmon in the area of the Japanese mothership salmon fishery. North American Journal of Fishery Management 7:450-474.
28. Nei, M. 1987. Molecular evolutionary genetics. Columbia University Press, New York.
29. Nelson, R. J., M. P. Small, T. D. Beacham, and K. J. Supernault. 2001. Population structure of Fraser River Chinook salmon (Oncorhynchus tshawytscha): an analysis using microsatellite DNA markers. Fishery Bulletin 99:94-107.
30. Osman, A., B. Jordan, P. A. Lessard, N. Muhammad, M. R. Haron, N. M. Riffin, A. J. Sinskey, C. Rha, and D. E. Housman. 2003. Genetic diversity of Eurycoma longifolia inferred from single-nucleotide polymorphisms. Plant Physiology 131:1294-1301.
31. Park, L. K., P. Moran, and D. A. Dightman. 1995. A polymorphism in intron D of the Chinook salmon growth hormone 2 gene. Animal Genetics 26:285.
32. Park, L. K., P. Moran, and D. A. Dightman. 1996. A Chinook salmon PCR-RFLP marker in the p53 locus. Animal Genetics 27:121-128.
33. Ranade, K., M.-S. Chang, C.-T. Ting, D. Pei, C.-F. Hsiao, M. Olivier, R. Pesich, J. Hebert, Y.-D. I. Chen, V. Dzau, D. Curb, R. Olshen, N. Risch, D. R. Cox, and D. Botstein. 2001. High-throughput genotyping with single-nucleotide polymorphisms. Genome Research 11:1262-1268.
34. Raymond, M., and F. Rousset. 1997. GENEPOP, version 3.1b: an updated version of GENEPOP (version 1.2) - population genetics software for exact tests and ecumenicism. Journal of Heredity 86:248-249.
35. Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223-225.
36. Schlotterer, C. 2004. The evolution of molecular markers: just a matter of fashion? Nature Reviews Genetics 5:63-69.
37. Schneider, S., D. Roessli, and L. Excoffier. 1999. Arlequin, version 2. 0: a software for population genetic data analysis. Genetics and Biometry Laboratory, University of Geneva, Switzerland.
38. Seeb, L. W., P. A. Crane, C. M. Kondzela, R. L. Wilmot, S. Urawa, N. V. Varnavskaya, and J. E. Seeb. 2004. Migration of Pacific Rim chum salmon on the high seas: insights from genetic data. Environmental Biology of Fishes 69:21-36.
39. Teel, D. J., G. B. Milner, G. A. Winans, and W. S. Grant. 2000. Genetic population structure and origin of life history types in Chinook salmon in British Columbia, Canada. Transactions of the American Fisheries Society 129:194-209.
40. Wattier, R., C. R. Engel, P. Saumitou-Laprade, and M. Valero. 1998. Short-allele dominance as a source of heterozygote deficiency at microsatellite loci: experimental evidence at the dinucleotide locus Gv1ct in Gracilaria gracilis (Rhodophyta). Molecular Ecology 7:1569-1573.
41. Weir, B. S., and C. C. Cockerham. 1984. Estimating F-statistics for the analysis of population structure. Evolution 38:1358-1370.
42. Werner, F. A. O., G. Durstewitz, F. A. Habermann, G. Thaller, W. Kramer, S. Kollers, J. Buitkamp, M. Georges, G. Brem, J. Mosner, and R. Fries. 2004. Detection and characterization of SNPs useful for identity control and parentage testing in major European dairy breeds. Animal Genetics 35:44-49.
43. Wright, S. 1951. The genetical structure of populations. Annals of Eugenics 15:323-354.
44. Xiong, F., R. A. Chin, and C. L. Hew. 1992. A gene encoding Chinook salmon (Oncorhynchus tshawytscha) prolactin: gene structure and potential cis-acting regulatory elements. Molecular Marine Biology Biotechnology 1:155-164.