SNP Discovery References
Application and Discovery Reviews
Helyar S.J., Hemmer-Hansen J., Bekkevold D. et al. (2011) Application of SNPs for population genetics of
nonmodel organisms: new opportunities and challenges. Molecular Ecology Resources 11, 123-136.
Morin P.A., Luikart G., Wayne R.K. (2004) SNPs in ecology, evolution and conservation. Trends in Ecology
& Evolution 19, 208-216.
Morin P.A., Martien K.K., Archer F.I. et al. (2010) Applied conservation genetics and the need for quality
control and reporting of genetic data used in fisheries and wildlife management. Journal of Heredity 101,
1-10.
Ogden R.O.B. (2011) Unlocking the potential of genomic technologies for wildlife forensics. Molecular
Ecology Resources 11, 109-116.
Seeb J.E., Carvalho G., Hauser L., Naish K., Roberts S., Seeb L.W. (2011a) Single-nucleotide polymorphism
(SNP) discovery and applications of SNP genotyping in nonmodel organisms. Molecular Ecology
Resources 11, 1-8.
Shendure J., Ji H.L. (2008) Next-generation DNA sequencing. Nature Biotechnology 26, 1135-1145.
Slate J., Gratten J., Beraldi D., Stapley J., Hale M., Pemberton J.M. (2009) Gene mapping in the wild with
SNPs: guidelines and future directions. Genetica 136, 97-107.
EST mining and Sanger sequencing of targeted genes
Aitken N., Smith S., Schwarz C., Morin P.A. (2004) Single nucleotide polymorphism (SNP) discovery in
mammals: a targeted-gene approach. Molecular Ecology 13, 1423-1431.
Campbell N.R., Narum S.R. (2011) Development of 54 novel single-nucleotide polymorphism (SNP)
assays for sockeye and coho salmon and assessment of available SNPs to differentiate stocks within the
Columbia River. Molecular Ecology Resources 11, 20-30.
Elfstrom C.M., Gaffney P.M., Smith C.T., Seeb J.E. (2005a) Characterization of 12 single nucleotide
polymorphisms in weathervane scallop. Molecular Ecology Notes 5, 406-409.
Elfstrom C.M., Smith C.T., Seeb J.E. (2006) Thirty-two single nucleotide polymorphism markers for highthroughput genotyping of sockeye salmon. Molecular Ecology Notes 6, 1255-1259.
Elfstrom C.M., Smith C.T., Seeb L.W. (2007) Thirty-eight single nucleotide polymorphism markers for
high-throughput genotyping of chum salmon. Molecular Ecology Notes 7, 1211-1215.
Hansen M.H.H., Young S., Jorgensen H.B.H., Pascal C., Henryon M., Seeb J. (2011) Assembling a dual
purpose TaqMan-based panel of single-nucleotide polymorphism markers in rainbow trout and
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steelhead (Oncorhynchus mykiss) for association mapping and population genetics analysis. Molecular
Ecology Resources 11, 67-70.
He C., Chen L., Simmons M., Li P., Kim S., Liu Z.J. (2003) Putative Snp Discovery in Interspecific Hybrids of
Catfish by Comparative Est Analysis. Animal Genetics 34, 445-448.
Labate J.A., Baldo A.M. (2005) Tomato Snp Discovery by Est Mining and Resequencing. Molecular
Breeding 16, 343-349.
Morin P.A., Aitken N.C., Rubio-Cisneros N., Dizon A.E., Mesnick S. (2007) Characterization of 18 SNP
markers for sperm whale (Physeter macrocephalus). Molecular Ecology Notes 7, 626-630.
Ollitrault P., Terol J., Garcia-Lor A. et al. (2012) SNP mining in C. clementina BAC end sequences;
transferability in the Citrus genus (Rutaceae), phylogenetic inferences and perspectives for genetic
mapping. Bmc Genomics 13.
Smith C.T., Baker J., Park L. et al. (2005a) Characterization of 13 single nucleotide polymorphism markers
for chum salmon. Molecular Ecology Notes 5, 259-262.
Smith C.T., Elfstrom C.M., Seeb L.W., Seeb J.E. (2005b) Use of sequence data from rainbow trout and
Atlantic salmon for SNP detection in Pacific salmon. Molecular Ecology 14, 4193-4203.
Smith C.T., Grant W.S., Seeb L.W. (2005c) A rapid, high-throughput technique for detecting Tanner crabs
Chionoecetes bairdi illegally taken in Alaska's snow crab fishery. Transactions of the American Fisheries
Society 134, 620-623.
Smith C.T., Park L., Vandoornik D., Seeb L.W., Seeb J.E. (2006) Characterization of 19 single nucleotide
polymorphism markers for coho salmon. Molecular Ecology Notes 6, 715-720.
Sprowles A.E., Stephens M.R., Clipperton N.W., May B.P. (2006) Fishing for SNPs: A targeted locus
approach for single nucleotide polymorphism discovery in rainbow trout. Transactions of the American
Fisheries Society 135, 1698-1721.
Transcriptome sequencing
Barbazuk W.B., Emrich S.J., Chen H.D., Li L., Schnable P.S. (2007) SNP discovery via 454 transcriptome
sequencing. Plant Journal 51, 910-918.
Everett M.V., Grau E.D., Seeb J.E. (2011) Short reads and nonmodel species: exploring the complexities
of next-generation sequence assembly and SNP discovery in the absence of a reference genome.
Molecular Ecology Resources 11, 93-108.
Geraldes A., Pang J., Thiessen N. et al. (2011) SNP discovery in black cottonwood (Populus trichocarpa)
by population transcriptome resequencing. Molecular Ecology Resources 11, 81-92.
Milano I., Babbucci M., Panitz F. et al. (2011) Novel Tools for Conservation Genomics: Comparing Two
High-Throughput Approaches for SNP Discovery in the Transcriptome of the European Hake. Plos One 6.
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Roberts S.B., Hauser L., Seeb L.W., Seeb J.E. (2012) Development of Genomic Resources for Pacific
Herring through Targeted Transcriptome Pyrosequencing. PLoS ONE 7, e30908.
Seeb J.E., Pascal C.E., Grau E.D. et al. (2011b) Transcriptome sequencing and high-resolution melt
analysis advance single nucleotide polymorphism discovery in duplicated salmonids. Molecular Ecology
Resources 11, 335-348.
Next generation sequencing of reduced representation libraries
Baird N.A., Etter P.D., Atwood T.S. et al. (2008) Rapid SNP Discovery and Genetic Mapping Using
Sequenced RAD Markers. PLoS ONE 3.
Chutimanitsakun Y., Nipper R.W., Cuesta-Marcos A. et al. (2011) Construction and application for QTL
analysis of a Restriction Site Associated DNA (RAD) linkage map in barley. Bmc Genomics 12.
Cosart T., Beja-Pereira A., Chen S.Y., Ng S.B., Shendure J., Luikart G. (2011) Exome-wide DNA capture and
next generation sequencing in domestic and wild species. Bmc Genomics 12.
Crouch J., Oudemans P., Polashock J. (2010) Sequenced restriction-associated DNA (RAD) markers for
SNP discovery in the genus Colletotrichum. Phytopathology 100, S27-S27.
Fridjonsson O., Olafsson K., Tompsett S. et al. (2011) Detection and mapping of mtDNA SNPs in Atlantic
salmon using high throughput DNA sequencing. Bmc Genomics 12.
Sanchez C.C., Smith T.P.L., Wiedmann R.T. et al. (2009) Single nucleotide polymorphism discovery in
rainbow trout by deep sequencing of a reduced representation library. Bmc Genomics 10.
Wiedmann R.T., Smith T.P.L., Nonneman D.J. (2008) SNP discovery in swine by reduced representation
and high throughput pyrosequencing. Bmc Genetics 9.
Van Tassell C.P., Smith T.P.L., Matukumalli L.K. et al. (2008) SNP discovery and allele frequency
estimation by deep sequencing of reduced representation libraries. Nature Methods 5, 247-252.
High-resolution melt analysis
Bignell P.A., Keeling D.M., Giangrande P. (2008) Detection of F8 Mutations by High Resolution Melting
(HRM) Analysis. Blood 112, 446-446.
Cho M.H., Ciulla D., Klanderman B.J., Raby B.A., Silverman E.K. (2008) High-Resolution Melting Curve
Analysis of Genomic and Whole-Genome Amplified DNA. Clinical Chemistry 54, 2055-2058.
McGlauflin M.T., Smith M.J., Wang J.T. et al. (2010) High-resolution melting analysis for the discovery of
novel single-nucleotide polymorphisms in rainbow and cutthroat trout for species identification.
Transactions of the American Fisheries Society 139, 676-684.
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Wu S.B., Wirthensohn M., Hunt P., Gibson J., Sedgley M. (2008) High resolution melting analysis of
almond SNPs derived from ESTs. Theoretical and Applied Genetics 118, 1-14.
Yuan J.Z., Haroon M., Lightfoot D., Pelletier Y., Liu Q., Li X.Q. (2009) A High-Resolution Melting Approach
for Analyzing Allelic Expression Dynamics. Current Issues in Molecular Biology 11, I1-i9.
Smith B.L., Lu C.P., Bremer J.R.A. (2010) High-resolution melting analysis (HRMA): a highly sensitive
inexpensive genotyping alternative for population studies. Molecular Ecology Resources 10, 193-196.
Tajiri-Utagawa E., Hara M., Takahashi K., Watanabe M., Wakita T. (2009) Development of a Rapid HighThroughput Method for High-Resolution Melting Analysis for Routine Detection and Genotyping of
Noroviruses. Journal of Clinical Microbiology 47, 435-440.
Other
Hyten D.L., Smith J.R., Frederick R.D., Tucker M.L., Song Q.J., Cregan P.B. (2009) Bulked Segregant
Analysis Using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Soybean Rust
in Soybean. Crop Science 49, 265-271.
Gilchrist E.J., Haughn G.W., Ying C.C. et al. (2006) Use of Ecotilling as an Efficient Snp Discovery Tool to
Survey Genetic Variation in Wild Populations of Populus Trichocarpa. Molecular Ecology 15, 1367-1378.
Olsen M.T., Volny V.H., BÉRubÉ M. et al. (2011) A simple route to single-nucleotide polymorphisms in a
nonmodel species: identification and characterization of SNPs in the Artic ringed seal (Pusa hispida
hispida). Molecular Ecology Resources 11, 9-19.
Roden S.E., Dutton P.H., Morin P.A. (2009) AFLP Fragment Isolation Technique as a Method to Produce
Random Sequences for Single Nucleotide Polymorphism Discovery in the Green Turtle, Chelonia mydas.
Journal of Heredity 100, 390-393.
Seddon J.M., Parker H.G., Ostrander E.A., Ellegren H. (2005) SNPs in ecological and conservation Studies:
a test in the Scandinavian wolf population. Molecular Ecology 14, 503-511.
Ascertainment bias and SNP discovery
Akey J.M., Zhang K., Xiong M.M., Jin L. (2003) The effect of single nucleotide polymorphism
identification strategies on estimates of linkage disequilibrium. Molecular Biology and Evolution 20, 232242.
Albrechtsen A., Nielsen F.C., Nielsen R. (2010) Ascertainment Biases in SNP Chips Affect Measures of
Population Divergence. Molecular Biology and Evolution 27, 2534-2547.
Clark A.G., Hubisz M.J., Bustamante C.D., Williamson S.H., Nielsen R. (2005) Ascertainment bias in
studies of human genome-wide polymorphism. Genome Research 15, 1496-1502.
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Didion J.P., Yang H.N., Sheppard K. et al. (2012) Discovery of novel variants in genotyping arrays
improves genotype retention and reduces ascertainment bias. Bmc Genomics 13.
Nielsen R. (2004) Population genetic analysis of ascertained SNP data. Human Genomics 1, 218-224.
Ramirez-Soriano A., Nielsen R. (2009) Correcting Estimators of theta and Tajima's D for Ascertainment
Biases Caused by the Single-Nucleotide Polymorphism Discovery Process. Genetics 181, 701-710.
Rosenblum E.B., Novembre J. (2007) Ascertainment bias in spatially structured populations: A case study
in the eastern fence lizard. Journal of Heredity 98, 331-336.
Wang Y., Nielsen R. (2012) Estimating population divergence time and phylogeny from single-nucleotide
polymorphisms data with outgroup ascertainment bias. Molecular Ecology 21, 974-986.
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