publication . Article . Other literature type . 2012

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

Jesse N. Weber; Emily H. Kay; Brant K. Peterson; Hopi E. Hoekstra; Heidi S. Fisher;
Open Access
  • Published: 31 May 2012 Journal: PLoS ONE, volume 7, page e37135 (eissn: 1932-6203, Copyright policy)
  • Publisher: Public Library of Science (PLoS)
  • Country: United States
Abstract
The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via ‘‘SNP chip’’ microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a m...
Subjects
free text keywords: Research Article, Genomics, Genome Sequencing, Population Genetics, Genetic Polymorphism, Sequence Analysis, Evolutionary Biology, Heredity, Genotypes, Genome Analysis Tools, Genome Scans, Genome-Wide Association Studies, Linkage Maps, Sequence Assembly Tools, Trait Locus Analysis, Population Biology, Medicine, R, Science, Q, Massively parallel, SNP, Genotyping, Biology, Genome, SNP genotyping, Population, education.field_of_study, education, Genetics, Computational biology, DNA sequencing, Whole genome sequencing
Funded by
NSF| Evolution, Genetics and Development: The Origin of Adaptive Pigment Alleles in Beach Mice
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0919190
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| DISSERTATION RESEARCH: The genetic basis of adaptive burrowing behavior
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0910164
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
,
NSF| DISSERTATION RESEARCH: Behavioral and genomic evidence for reproductive isolation between two sister species of Peromyscus
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1110450
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
39 references, page 1 of 3

Mackay, TFC, Richards, S, Stone, EA, Barbadilla, A, Ayroles, JF. The Drosophila melanogaster Genetic Reference Panel.. Nature. 2012; 482: 173-178 [OpenAIRE] [PubMed]

Consortium 1000, GP. A map of human genome variation from population-scale sequencing.. Nature. 2010; 467: 1061-1073 [PubMed]

Altshuler, D, Pollara, VJ, Cowles, CR, van Etten, WJ, Baldwin, J. An SNP map of the human genome generated by reduced representation shotgun sequencing.. Nature. 2000; 407: 513-516 [OpenAIRE] [PubMed]

van Tassell, CP, Smith, TPL, Matukumalli, LK, Taylor, JF, Schnabel, RD. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.. Nature Methods. 2008; 5: 247-252 [PubMed]

Gompert, Z, Forister, ML, Fordyce, JA, Nice, CC, Williamson, RJ. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies.. Molecular Ecology. 2010; 19: 2455-2473 [PubMed]

Baird, NA, Etter, PD, Atwood, TS, Currey, MC, Shiver, AL. Rapid SNP discovery and genetic mapping using sequenced RAD markers.. PLoS One. 2008; 3: e3376 [OpenAIRE] [PubMed]

Hohenlohe, PA, Bassham, S, Etter, PD, Stiffler, N, Johnson, EA. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.. PLoS Genetics. 2010; 6: e1000862 [OpenAIRE] [PubMed]

Hohenlohe, PA, Bassham, S, Currey, M, Cresko, WA. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes.. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2012; 367: 395-408 [OpenAIRE] [PubMed]

Andolfatto, P, Davison, D, Erezyilmaz, D, Hu, TT, Mast, J. Multiplexed shotgun genotyping for rapid and efficient genetic mapping.. 2011: 610-617 [OpenAIRE]

Emerson, KJ, Merz, CR, Catchen, JM, Hohenlohe, PA, Cresko, WA. Resolving postglacial phylogeography using high-throughput sequencing.. Proceedings of the National Academy of Sciences. 2010; 107: 16196 [OpenAIRE]

Pfender, WF, Saha, MC, Johnson, EA, Slabaugh, MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.. Theoretical and Applied Genetics. 2011; 122: 1467-1480 [OpenAIRE] [PubMed]

Hohenlohe, PA, Amish, SJ, Catchen, JM, Allendorf, FW, Luikart, G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout.. Molecular Ecology Resources. 2011; 11: 117-122 [OpenAIRE] [PubMed]

Pollard, DA, Iyer, VN, Moses, AM, Eisen, MB. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.. PLoS Genetics. 2006; 2: e173 [OpenAIRE] [PubMed]

White, MA, Ané, C, Dewey, CN, Larget, BR, Payseur, BA. Fine-scale phylogenetic discordance across the house mouse genome.. PLoS Genetics. 2009; 5: e1000729 [OpenAIRE] [PubMed]

Felsenstein, J. Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?. Molecular Biology and Evolution. 2006; 23: 691-700 [PubMed]

39 references, page 1 of 3
Abstract
The ability to efficiently and accurately determine genotypes is a keystone technology in modern genetics, crucial to studies ranging from clinical diagnostics, to genotype-phenotype association, to reconstruction of ancestry and the detection of selection. To date, high capacity, low cost genotyping has been largely achieved via ‘‘SNP chip’’ microarray-based platforms which require substantial prior knowledge of both genome sequence and variability, and once designed are suitable only for those targeted variable nucleotide sites. This method introduces substantial ascertainment bias and inherently precludes detection of rare or population-specific variants, a m...
Subjects
free text keywords: Research Article, Genomics, Genome Sequencing, Population Genetics, Genetic Polymorphism, Sequence Analysis, Evolutionary Biology, Heredity, Genotypes, Genome Analysis Tools, Genome Scans, Genome-Wide Association Studies, Linkage Maps, Sequence Assembly Tools, Trait Locus Analysis, Population Biology, Medicine, R, Science, Q, Massively parallel, SNP, Genotyping, Biology, Genome, SNP genotyping, Population, education.field_of_study, education, Genetics, Computational biology, DNA sequencing, Whole genome sequencing
Funded by
NSF| Evolution, Genetics and Development: The Origin of Adaptive Pigment Alleles in Beach Mice
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0919190
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NSF| DISSERTATION RESEARCH: The genetic basis of adaptive burrowing behavior
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0910164
  • Funding stream: Directorate for Biological Sciences | Division of Integrative Organismal Systems
,
NSF| DISSERTATION RESEARCH: Behavioral and genomic evidence for reproductive isolation between two sister species of Peromyscus
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1110450
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
39 references, page 1 of 3

Mackay, TFC, Richards, S, Stone, EA, Barbadilla, A, Ayroles, JF. The Drosophila melanogaster Genetic Reference Panel.. Nature. 2012; 482: 173-178 [OpenAIRE] [PubMed]

Consortium 1000, GP. A map of human genome variation from population-scale sequencing.. Nature. 2010; 467: 1061-1073 [PubMed]

Altshuler, D, Pollara, VJ, Cowles, CR, van Etten, WJ, Baldwin, J. An SNP map of the human genome generated by reduced representation shotgun sequencing.. Nature. 2000; 407: 513-516 [OpenAIRE] [PubMed]

van Tassell, CP, Smith, TPL, Matukumalli, LK, Taylor, JF, Schnabel, RD. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries.. Nature Methods. 2008; 5: 247-252 [PubMed]

Gompert, Z, Forister, ML, Fordyce, JA, Nice, CC, Williamson, RJ. Bayesian analysis of molecular variance in pyrosequences quantifies population genetic structure across the genome of Lycaeides butterflies.. Molecular Ecology. 2010; 19: 2455-2473 [PubMed]

Baird, NA, Etter, PD, Atwood, TS, Currey, MC, Shiver, AL. Rapid SNP discovery and genetic mapping using sequenced RAD markers.. PLoS One. 2008; 3: e3376 [OpenAIRE] [PubMed]

Hohenlohe, PA, Bassham, S, Etter, PD, Stiffler, N, Johnson, EA. Population genomics of parallel adaptation in threespine stickleback using sequenced RAD tags.. PLoS Genetics. 2010; 6: e1000862 [OpenAIRE] [PubMed]

Hohenlohe, PA, Bassham, S, Currey, M, Cresko, WA. Extensive linkage disequilibrium and parallel adaptive divergence across threespine stickleback genomes.. Philosophical Transactions of the Royal Society of London Series B, Biological Sciences. 2012; 367: 395-408 [OpenAIRE] [PubMed]

Andolfatto, P, Davison, D, Erezyilmaz, D, Hu, TT, Mast, J. Multiplexed shotgun genotyping for rapid and efficient genetic mapping.. 2011: 610-617 [OpenAIRE]

Emerson, KJ, Merz, CR, Catchen, JM, Hohenlohe, PA, Cresko, WA. Resolving postglacial phylogeography using high-throughput sequencing.. Proceedings of the National Academy of Sciences. 2010; 107: 16196 [OpenAIRE]

Pfender, WF, Saha, MC, Johnson, EA, Slabaugh, MB. Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne.. Theoretical and Applied Genetics. 2011; 122: 1467-1480 [OpenAIRE] [PubMed]

Hohenlohe, PA, Amish, SJ, Catchen, JM, Allendorf, FW, Luikart, G. Next-generation RAD sequencing identifies thousands of SNPs for assessing hybridization between rainbow and westslope cutthroat trout.. Molecular Ecology Resources. 2011; 11: 117-122 [OpenAIRE] [PubMed]

Pollard, DA, Iyer, VN, Moses, AM, Eisen, MB. Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting.. PLoS Genetics. 2006; 2: e173 [OpenAIRE] [PubMed]

White, MA, Ané, C, Dewey, CN, Larget, BR, Payseur, BA. Fine-scale phylogenetic discordance across the house mouse genome.. PLoS Genetics. 2009; 5: e1000729 [OpenAIRE] [PubMed]

Felsenstein, J. Accuracy of coalescent likelihood estimates: do we need more sites, more sequences, or more loci?. Molecular Biology and Evolution. 2006; 23: 691-700 [PubMed]

39 references, page 1 of 3
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