Multiplex preamplification PCR and microsatellite validation enables accurate single nucleotide polymorphism genotyping of historical fish scales

Molecular Ecology Resources

Volumn 11, Issue SUPPL. 1, 2011, Pages 268-277

  Smith, Matt J ^a   Pascal, Carita E ^a   Grauvogel, Zac ^b   Habicht, Christopher ^b   Seeb, James E ^a   Seeb, Lisa W ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

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

Author keywords

Contamination; Genotype error; Preamplification; Salmon; SNP; Sockeye

Indexed keywords

MICROSATELLITE DNA;

ANIMAL; ARTICLE; DNA CONTAMINATION; GENETICS; GENOTYPE; METHODOLOGY; POLYMERASE CHAIN REACTION; SALMON; SINGLE NUCLEOTIDE POLYMORPHISM; VALIDATION STUDY;

ANIMALS; DNA CONTAMINATION; GENOTYPE; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SALMON;

ONCORHYNCHUS NERKA;

EID: 79951760007     PISSN: 1755098X     EISSN: 17550998     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2010.02965.x     Document Type: Article

References (30)

1. Brumfield RT, Beerli P, Nickerson DA, Edwards SV (2003) The utility of single nucleotide polymorphisms in inferences of population history. Trends in Ecology & Evolution, 18, 249-256.
2. n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout). Heredity, 71, 488-496.
3. Gill P, Buckleton J (2010) A universal strategy to interpret DNA profiles that does not require a definition of low-copy-number. Forensic Science International: Genetics, 4, 221-227.
4. Habicht C, Seeb LW, Seeb JE (2007) Genetic and ecological divergence defines population structure of sockeye salmon populations returning to Bristol Bay, Alaska, and provides a tool for admixture analysis. Transactions of the American Fisheries Society, 136, 82-94.
5. Habicht C, Seeb LW, Myers KW, Farley E, Seeb JE (2010) Summer-fall distribution of stocks of immature sockeye salmon in the Bering Sea as revealed by single-nucleotide polymorphisms (SNPs). Transactions of the American Fisheries Society, 139, 1171-1191.
6. Hansen MM (2002) Estimating the long-term effects of stocking domesticated trout into wild brown trout (Salmo trutta) populations: an approach using microsatellite DNA analysis of historical and contemporary samples. Molecular Ecology, 11, 1003-1015.
7. Hauser L, Seeb JE (2008) Advances in molecular technology and their impact on fisheries genetics. Fish and Fisheries, 9, 473-486.
8. Hauser L, Baird R, Hilborn R, Seeb LW, Seeb JE (2011) An empirical comparison of SNPs and microsatellites for parentage and kinship assignment in a wild sockeye salmon (Oncorhynchus nerka) population. Molecular Ecology Resources, 11 (Suppl. 1), 150-161.
9. Heid CA, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Research, 6, 986-994.
10. Hess JE, Matala AP, Narum SR (2011) Comparison of SNPs and microsatellites for fine-scale application of genetic stock identification of Chinook salmon in the Columbia River Basin. Molecular Ecology Resources, 11 (Suppl. 1), 137-149.
11. Karlsson S, Moen T, Hindar K (2010) Contrasting patterns of gene diversity between microsatellites and mitochondrial SNPs in farm and wild Atlantic salmon. Conservation Genetics, 11, 571-582.
12. Krause J, Dear PH, Pollack JL et al. (2006) Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature, 439, 724-727.
13. Kwoc P-Y (2003) Single Nucleotide Polymorphisms: Methods and Protocols. Humana Press, Totowa, NJ.
14. Morin PA, McCarthy M (2007) Highly accurate SNP genotyping from historical and low-quality samples. Molecular Ecology Notes, 7, 937-946.
15. Morin PA, Luikart G, Wayne RK, SNP Workshop Group (2004) SNPs in ecology, evolution and conservation. Trends in Ecology & Evolution, 19, 208-216.
16. Nielsen EE, Hansen MM (2008) Waking the dead: the value of population genetic analyses of historical samples. Fish and Fisheries, 9, 450-461.
17. Nielsen EE, Hansen MM, Loeschcke V (1997) Analysis of microsatellite DNA from old scale samples of Atlantic salmon Salmo salar: a comparison of genetic composition over 60years. Molecular Ecology, 6, 487-492.
18. Nielsen EE, Hansen MM, Loeschcke V (1999) Analysis of DNA from old scale samples: technical aspects, applications and perspectives for conservation. Hereditas, 130, 265-276.
19. Olsen JB, Wilson SL, Kretschmer EJ, Jones KC, Seeb JE (2000) Characterization of 14 tetranucleotide microsatellite loci derived from sockeye salmon. Molecular Ecology, 9, 2185-2187.
20. Paabo S, Poinar H, Serre D et al. (2004) Genetic analyses from ancient DNA. Annual Review of Genetics, 38, 645-679.
21. Ranade K, Chang MS, Ting CT et al. (2001) High-throughput genotyping with single nucleotide polymorphisms. Genome Research, 11, 1262-1268.
22. Rompler H, Dear PH, Krause J et al. (2006a) Multiplex amplification of ancient DNA. Nature Protocols, 1, 720-728.
23. Rompler H, Rohland N, Lalueza-Fox C et al. (2006b) Nuclear gene indicates coat-color polymorphism in mammoths. Science, 313, 62.
24. Schlotterer C (2004) The evolution of molecular markers-just a matter of fashion? Nature Reviews Genetics, 5, 63-69.
25. Seeb JE, Pascal CE, Ramakrishnan R, Seeb LW (2009) SNP genotyping by the 5'-nuclease reaction: advances in high-throughput genotyping with non-model organisms. In: Single Nucleotide Polymorphisms, Methods in Molecular Biology (ed. Komar AA), pp. 277-929. Humana Press, Totowa, NJ.
26. Seeb LW, Templin WD, Sato S et al. (2011) Single nucleotide polymorphisms across a species' range: implications for conservation studies of Pacific salmon. Molecular Ecology Resources, 11 (Suppl. 1), 117-122.
27. Smith CT, Templin WD, Seeb JE, Seeb UW (2005) Single nucleotide polymorphisms provide rapid and accurate estimates of the proportions of US and Canadian Chinook salmon caught in Yukon River fisheries. North American Journal of Fisheries Management, 25, 944-953.
28. Smith CT, Antonovich A, Templin WD et al. (2007) Impacts of marker class bias relative to locus-specific variability on population inferences in Chinook salmon: a comparison of single-nucleotide polymorphisms with short tandem repeats and allozymes. Transactions of the American Fisheries Society, 136, 1674-1687.
29. Taberlet P, Griffin S, Goossens B et al. (1996) Reliable genotyping of samples with very low DNA quantities using PCR. Nucleic Acids Research, 24, 3189-3194.
30. Templin WD, Seeb JE, Jasper JJ, Barclay AW, Seeb LW (2011) Genetic differentiation of Alaska Chinook salmon: the missing link for migratory studies. Molecular Ecology Resources, 11 (Suppl. 1), 215-235.