Fishing for SNPs: A targeted locus approach for single nucleotide polymorphism discovery in rainbow trout

Transactions of the American Fisheries Society

Volumn 135, Issue 6, 2006, Pages 1698-1721

  Sprowles, A E ^a   Stephens, M R ^a   Clipperton, N W ^a   May, B P ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALLELE; DNA; GENETIC ANALYSIS; GENETIC MARKER; GENETIC VARIATION; GENOME; GENOTYPE; MOLECULAR ANALYSIS; POLYMORPHISM; SALMONID; SUBSPECIES;

ONCORHYNCHUS MYKISS; ONCORHYNCHUS MYKISS AGUABONITA; ONCORHYNCHUS MYKISS IRIDEUS; ONCORHYNCHUS MYKISS WHITEI; SALMONIDAE;

EID: 34247593983     PISSN: 00028487     EISSN: 15488659     Source Type: Journal    
DOI: 10.1577/T05-291.1     Document Type: Article

References (72)

1. Aitken, N., S. Smith, C. Schwarz, and P. A. Morin. 2004. Single nucleotide polymorphism (SNP) discovery in mammals: a targeted-gene approach. Molecular Ecology 13(6):1423-1431.
2. Altschul, S., T. L. Madden, A. A. Schaffer, J. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25(17):3389-3402.
3. Bagley, M. J., and G. A. E. Gall. 1998. Mitochondrial and nuclear DNA sequence variability among populations of rainbow trout (Oncorhynchus mykiss). Molecular Ecology 7(8):945-961.
4. Behnke, R. J. 1992. Native trout of western North America. American Fisheries Society, Monograph 6, Bethesda, Maryland.
5. Benson, D. A., I. Karsch-Mizrachi, D. J. Lipman, J. Ostell, and D. L. Wheeler. 2005. GenBank. Nucleic Acids Research 33:D34-D38.
6. Bierne, N., S. A. Lehnert, E. Bedier, F. Bonhomme, and S. S. Moore. 2000. Screening for intron-length polymorphisms in penaeid shrimps using exon-primed intron-crossing (EPIC)-PCR. Molecular Ecology 9(2):233-235.
7. 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.
8. Busack, C. A., and G. A. E. Gall. 1980. Ancestry of artificially propagated California rainbow trout strains. California Fish and Game 66(1):17-24.
9. Chakraborty, R., D. N. Stivers, B. Su, Y. Zhong, and B. Budowle. 1999. The utility of short tandem repeat loci beyond human identification: applications for development of new DNA typing systems. Electrophoresis 20:1682-1696.
10. Chen, X., and P. F. Sullivan. 2003. Single nucleotide polymorphism genotyoping: biochemistry, protocol, cost, and throughput. Pharmacogenomics Journal 3:77-99.
11. Collins, F. S., L. D. Brooks, and A. Chakravarti. 1998. A DNA polymorphism discovery resource for research on human genetic variation. Genome Research 8:1229-1231.
12. Cordes, J. F., M. R. Stephens, M. A. Blumberg, and B. P. May. 2006. Identifying introgressive hybridization in native populations of California golden trout based on molecular markers. Transactions of the American Fisheries Society 134:110-128.
13. Docker, M. F., and D. D. Heath. 2002. PCR-based markers detect genetic variation at growth- and immune function-related loci in Chinook salmon (Oncorhynchus tshawytscha). Molecular Ecology Notes 2(4):606-609.
14. Ford, M. J. 2000. Effects of natural selection on patterns of DNA sequence variation at the transferrin, somatolactin, and p53 genes within and among Chinook salmon (Oncorhynchus tshawytscha) populations. Molecular Ecology 9(7):843-855.
15. Fries, R., D. Ewald, G. Thaller, and J. Buitkamp. 2001. Assessment of the nucleotide sequence variability in the bovine T-cell receptor alpha delta joining gene region. Animal Biotechnology 12(1):29-49.
16. Friesen, V. L., B. C. Congdon, M. G. Kidd, and T. P. Birt. 1999. Polymerase chain reaction (PCR) primers for the amplification of five nuclear introns in vertebrates. Molecular Ecology 8(12):2147-2149.
17. Gahr, S. A., Y. Palti, and C. E. Rexroad. 2004. Genomic characterization of a novel pair of ID genes in the rainbow trout (Oncorhynchus mykiss). Animal Genetics 35(4):317-321.
18. Ginzinger, D. G. 2002. Gene quantification using real-time quantitative PCR: an emerging technology hits the mainstream. Experimental Hematology 30:503-512.
19. Grewe, P. M., C. C. Krueger, C. F. Aquadro, E. Bermingham, H. Kincaid, and B. May. 1993. Mitochondrial DNA variation among lake trout strains (Salvelinus namaycush) stocked into Lake Ontario. Canadian Journal of Fisheries and Aquatic Sciences 50:2397-2403.
20. Guan, G., M. Tanaka, T. Todo, G. Young, M. Yoshikuni, and Y. Nagahama. 1999. Cloning and expression of two carbonyl reductase-like 20[beta]- hydroxysteroid dehydrogenase cDNAs in ovarian follicles of rainbow trout (Oncorhynchus mykiss). Biochemical and Biophysical Research Communications 255(1):123-128.
21. Hansen, J. D. 1997. Characterization of rainbow trout terminal deoxynucleotidyl transferase structure and expression: TdT and RAG1 co-expression define the trout primary lymphoid tissues. Immunogenetics 46(5):367-375.
22. Hassan, M., C. Lemaire, C. Fauvelot, and F. Bonhomme. 2002. Seventeen new exon-primed intron-crossing polymerase chain reaction amplifiable introns in fish. Molecular Ecology Notes 2(3):334-340.
23. Iturra, P., J. F. Medrano, M. Bagley, M. Lam, N. Vergara, and J. C. Marin. 1998. Identification of sex chromosome molecular markers using RAPDs and fluorescent in situ hybridization in rainbow trout. Genetica 101:209-213.
24. Kanz, C., P. Aldebert, N. Althorpe, W. Baker, A. Baldwin, K. Bates, P. Browne, A. van den Broek, M. Castro, G. Cochrane, K. Duggan, R. Eberhardt, N. Faruque, J. Gamble, F. G. Diez, N. Harte, T. Kulikova, Q. Lin, V. Lombard, R. Lopez, R. Mancuso, M. McHale, N. Nardone, V. Silventoinen, S. Sobhany, P. Stoehr, M. A. Tuli, K. Tzouvara, R. Vaughan, D. Wu, Z. Zhu, and R. Apweiler. 2005. The EMBL nucleotide sequence database. Nucleic Acids Research 33:D29-D33.
25. Kothary, R. K., D. Jones, and E. P. Candido. 1984. 70-Kilodalton heat shock polypeptides from rainbow trout: characterization of cDNA sequences. Molecular and Cellular Biology 4(9):1785-1791.
26. Kruglyak, S., R. T. Durrett, M. D. Schug, and C. F. Aquadro. 1998. Equilibrium distributions of microsatellite repeat length resulting from a balance between slippage events and point mutations. Proceedings of the National Academy of Sciences of the USA 95:10774-10778.
27. Lee, M. A., E. Bengten, A. Daggfeldt, A. S. Rytting, and L. Pilstrom. 1993. Characterization of rainbow trout cDNAs encoding a secreted and membrane-bound Ig heavy chain and the genomic intron upstream of the first constant exon. Molecular Immunology 30(7):641-648.
28. Lee, Y., J. Tsai, S. Sunkara, S. Karamycheva, G. Pertea, R. Sultana, V. Antonescu, A. Chan, F. Cheung, and J. Quackenbush. 2005. The TIGR gene indices: clustering and assembling EST and known genes and integration with eukaryotic genomes. Nucleic Acids Research 33:D71-D74.
29. Li, W. H., T. Gojobori, and M. Nei. 1981. Pseudogenes as a paradigm of neutral evolution. Nature (London) 292:237-239.
30. Lim, S. T., R. M. Kay, and G. S. Baily. 1975. Lactate dehydrogenase isozymes of salmonid fish: evidence for unique and rapid functional divergence of duplicated H-4 lactate dehydrogenases. Journal of Biological Chemistry 250(5):1790-1800.
31. Lyons, L. A., T. F. Laughlin, N. G. Copeland, N. A. Jenkins, J. E. Womack, and S. J. O'Brien. 1997. Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nature Genetics 15(1):47-56.
32. Manaster, C., W. Zheng, M. Teuber, S. Wachter, F. Doring, S. Schreiber, and J. Hampe. 2005. InSNP: a tool for automated detection and visualization of SNPs and InDels. Human Mutation 26(1):11-19.
33. Marth, G. T., I. Kort, M. D. Yandell, R. T. Yeh, Z. Gu, H. Zakeri, N. O. Stitziel, L. Hillier, P. Kwok, and W. R. Gish. 1999. A general approach to single nucleotide polymorphism discovery. Nature Genetics 23(4):452-456.
34. Martinez-Arias, R., F. Calafell, E. Mateau, D. Comas, A. Andres, and J. Bertranpetit. 2001. Sequence variability of a human pseudogene. Genome Research 11:1071-1085.
35. Mitra, A., J. Foster-Frey, C. E. Rexroad III, K. D. Wells, and R. J. Wall. 2003. Molecular characterization of lysozyme type II gene in rainbow trout (Oncorhynchus mykiss): evidence of gene duplication. Animal Biotechnology 14(1):7-12.
36. Moran, P. 2002. Current conservation genetics: building an ecological approach to the synthesis of molecular and quantitative genetic methods. Ecology of Freshwater Fish 11:30-55.
37. Moran, P., D. A. Dightman, R. S. Waples, and L. K. Park. 1997. PCR-RFLP analysis reveals substantial population-level variation in the introns of Pacific salmon (Oncorhynchus spp.) Molecular Marine Biology and Biotechnology 6(4):315-327.
38. Morin, P. A., G. Luikart, and R. K. Wayne. 2004. SNPs in ecology, evolution, and conservation. Trends in Ecology and Evolution 19(4):208-216.
39. Muller-Schmid, A., H. Rinder, F. Lottspeich, and E. M. Gertzen. 1992. Ependymins from the cerebrospinal fluid of salmonid fish: gene structure and molecular characterization. Gene 118(2):189-192.
40. Nichols, K. M., W. P. Young, R. G. Danzmann, B. D. Robinson, C. Rexroad, M. Noakes, R. B. Phillips, P. Bentzen, I. Spies, K. Knudsen, F. W. Allendorf, B. M. Cunningham, J. Brunelli, H. Zhang, S. Ristow, R. Drew, K. H. Brown, P. A. Wheeler, and G. H. Thorgaard. 2003. A consolidated linkage map for rainbow trout (Oncorhynchus mykiss). Animal Genetics 34(2):102-115.
41. Nickerson, D. A., V. O. Tobe, and S. L. Talyor. 1997. PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Research 25(14):2745-2751.
42. Nielsen, J. J., K. D. Crow, and M. C. Fountain. 1999. Microsatellite diversity and conservation of a relic trout population: McCloud River redband trout. Molecular Ecology 8:S129-S142.
43. Nielsen, R., M. J. Hubisz, and A. G. Clark. 2004. Reconstituting the frequency spectrum of ascertained single nucleotide polymorphism data. Genetics 168(4):2373-2382.
44. Nielsen, R., and J. Signorovitch. 2003. Correcting for ascertainment bias when analyzing SNP data: applications to the estimation of linkage disequilibrium. Theoretical Population Biology 63:245-255.
45. Ohno, S. M., J. Muramato, J. Klein, and N. B. Atkin. 1969. Diploid-tetraploid relationship in clupeoid and salmonid fish. Chromosomes Today 2:139-147.
46. Ojima, N., M. Yamashita, and S. Watabe. 2005. Comparative expression analysis of two paralogous Hsp70s in rainbow trout cells exposed to heat stress. Biochimica et Biophysica Acta 1681(2-3):99-106.
47. Pakdel, F., R. Metivier, G. Flouriot, and Y. Valotaire. 2000. Two estrogen receptor (ER) isoforms with different estrogen dependencies are generated from the trout ER gene. Endocrinology 141(2):571-580.
48. Palumbi, S. R., and C. S. Baker. 1994. Contrasting population structure from nuclear intron sequences and mtDNA of humpback whales. Molecular Biology and Evolution 11:426-435.
49. Panno, J. P., and B. A. McKeown. 1995. Cloning and expression of a myc family member from the pituitary gland of the rainbow trout, Oncorhynchus mykiss. Biochimica et Biophysica Acta 1264(1):7-11.
50. Pearson, T., J. D. Busch, J. Ravel, T. D. Read, S. D. Rhoton, J. M. U'Ren, T. J. Simonson, S. M. Kachur, R. R. Leadmen, M. L. Cardon, M. N. Van Ert, L. Y. Huynh, C. M. Fraser, and P. Keim. 2004. Phylogenetic discovery bias in Bacillus anthracis using single nucleotide polymorphisms from whole-genome sequencing. Proceedings of the National Academy of Sciences of the USA 101:13536-13541.
51. Primmer, C. R., T. Borge, J. Haavie, and G.-P. Sætre. 2002. Single nucleotide polymorphism (SNP) characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Molecular Ecology 11:603-612.
52. Radice, A. D., B. Bugaj, D. H. Fitch, and S. W. Emmons. 1994. Widespread occurrence of the Tcl transposon family: Tcl-like transposons from teleost fish. Molecular and General Genetics 244(6):606-612.
53. Rodzen, J. A., J. J. Agresti, G. Tranah, and B. May. 1998. Agarose overlays allow simplified staining of polyacrylamide gels. Biotechniques 25(4):584.
54. Rozen, S., and H. Skaletsky. 2000. Primer3 on the WWW for general users and for biologist programmers. Methods in Molecular Biology 132:365-386.
55. Sakamoto, T., R. G. Danzmann, K. Gharbi, P. Howard, A. Ozaki, S. K. Khoo, R. A. Woram, N. Okamoto, M. M. Ferguson, L. E. Holm, R. Guyomard, and B. Howheim. 2000. A microsatellite linkage map of rainbow trout (Oncorhynchus mykiss) characterized by large sex-specific differences in recombination rates. Genetics 155(3):1331-1345.
56. Seddon, J. M., H. G. Parker, E. A. Ostrander, and H. Ellegren. 2005. SNPs in ecological and conservation studies: a test in the Scandinavian wolf population. Molecular Ecology 14:503-511.
57. Shriver, M. D., M. W. Smith, L. Jin, A. Marcini, J. M. Akey, R. Deka, and R. E. Ferrell. 1997. Ethnic-affiliation estimation by use of population-specific DNA markers. American Journal of Human Genetics 60:957-964.
58. Shum, B. P., R. Rajalingam, K. E. Magor, K. Azumi, W. H. Carr, B. Dixon, R. J. M. Stet, M. A. Adkison, R. P. Hedrick, and P. Parham. 1999. A divergent, nonclassical class I gene conserved in salmonids. Immunogenetics 49(6):479-490.
59. Smith, C. T., J. Baker, L. Park, L. W. Seeb, C. Elfstrom, S. Abe, and J. E. Seeb. 2005a. Characterization of 13 single nucleotide polymorphism markers for chum salmon. Molecular Ecology Notes 5:259-262.
60. Smith, C. T., C. M. Elfstrom, L. W. Seeb, and J. E. Seeb. 2005b. Use of sequence data from rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology 14:4193-4203.
61. Smith, C. T., W. D. Templin, J. E. Seeb, and L. W. Seeb. 2005c. Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of U.S. and Canadian Chinook salmon caught in Yukon River fisheries. North American Journal of Fisheries Management 25:944-953.
62. Tateno, Y., N. Saitou, K. Okubo, H. Sugawara, and T. Gojobori. 2005. DDBJ in collaboration with mass-sequencing teams on annotation. Nucleic Acids Research 33:D25-D28.
63. Tsuchihashi, Z., and N. C. Dracopoli. 2002. Progress in high-throughput SNP genotyping methods. Pharmacogenomics Journal 2:103-110.
64. USFWS (U.S. Fish and Wildlife Service). 1978. Listing of the Little Kern golden trout as a threatened species with critical habitat. Federal Register 43 (13 April 1978):15427-15429.
65. Vignal, A., D. Milan, M. M. SanCristoball, and A. Eggen. 2002. A review of SNP and other types of molecular markers and their use in animal genetics. Genetics, Selection, Evolution 34:275-305.
66. Villablanca, F. X., G. K. Roderick, and S. R. Palumbi. 1998. Invasion genetics of the Mediterranean fruit fly: variation in multiple nuclear introns. Molecular Ecology 7(5):547-560.
67. Vogel, F., and A. G. Motulsky. Human genetics: problems and approaches. Springer, New York.
68. Wakeley, J., R. Nielsen, S. N. Liu-Cordero, and K. Ardlie. 2001. The discovery of single nucleotide polymorphisms and inferences about human demographic history. American Journal of Human Genetics 69:1332-1347.
69. Yoder, J. A., M. G. Mueller, K. M. Nichols, S. S. Ristow, G. H. Thorgaard, T. Ota, and G. W. Litman. 2002. Cloning novel immune-type inhibitory receptors from the rainbow trout, Oncorhynchus mykiss. Immunogenetics 54(9):662-670.
70. Young, W. P., P. A. Wheeler, V. H. Coryell, P. Keim, and G. H. Thorgaard. 1998. A detailed linkage map of rainbow trout produced using double haploids. Genetics 148(2):839-850.
71. Zardoya, A., A. Garrido-Pertierra, and J. M. Bautista. 1995. The complete sequence of the mitochondrial DNA genome of the rainbow trout, Oncorhynchus mykiss. Journal of Molecular Evolution 41(6):942-951.
72. Zhang, D. X., and G. M. Hewitt. 2003. Nuclear DNA analyses in genetic studies of populations: practice, problems, and prospects. Molecular Ecology 12:563-584.