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Volumn 193, Issue 4, 2013, Pages 1073-1081

Marker density and read depth for genotyping populations using genotyping-by-sequencing

Author keywords

[No Author keywords available]

Indexed keywords

GENOMIC DNA; GENETIC MARKER;

EID: 84876367781     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.147710     Document Type: Article
Times cited : (160)

References (31)
  • 1
    • 80051478843 scopus 로고    scopus 로고
    • Genome evolution and meiotic maps by massively parallel DNA sequencing: Spotted gar, an outgroup for the teleost genome duplication
    • Amores, A., J. Catchen, A. Ferrara, Q. Fontenot, and J. H. Postlethwait, 2011 Genome evolution and meiotic maps by massively parallel DNA sequencing: spotted gar, an outgroup for the teleost genome duplication. Genetics 188: 799-808.
    • (2011) Genetics , vol.188 , pp. 799-808
    • Amores, A.1    Catchen, J.2    Ferrara, A.3    Fontenot, Q.4    Postlethwait, J.H.5
  • 2
    • 54449098752 scopus 로고    scopus 로고
    • Rapid SNP discovery and genetic mapping using sequenced RAD markers
    • Baird, N. A., P. D. Etter, T. S. Atwood, M. C. Currey, A. L. Shiver et al., 2008 Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3(10): e3376.
    • (2008) PLoS ONE , vol.3 , Issue.10
    • Baird, N.A.1    Etter, P.D.2    Atwood, T.S.3    Currey, M.C.4    Shiver, A.L.5
  • 3
    • 79955609628 scopus 로고    scopus 로고
    • Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism
    • Baxter, S. W., J. W. Davey, J. S. Johnston, A. M. Shelton, and D. G. Heckel, 2011 Linkage mapping and comparative genomics using next-generation RAD sequencing of a non-model organism. PLoS ONE 6(4): e19315.
    • (2011) PLoS ONE , vol.6 , Issue.4
    • Baxter, S.W.1    Davey, J.W.2    Johnston, J.S.3    Shelton, A.M.4    Heckel, D.G.5
  • 5
    • 65549107163 scopus 로고    scopus 로고
    • Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
    • Brunner, A. L., D. S. Johnson, S. W. Kim, A. Valouev, T. E. Reddy et al., 2009 Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 19: 1044-1056.
    • (2009) Genome Res , vol.19 , pp. 1044-1056
    • Brunner, A.L.1    Johnson, D.S.2    Kim, S.W.3    Valouev, A.4    Reddy, T.E.5
  • 6
    • 78650792488 scopus 로고    scopus 로고
    • Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley
    • Chutimanitsakun, Y., R. W. Nipper, A. Cuesta-Marcos, L. Cistue, A. Corey et al., 2011 Construction and application for QTL analysis of a restriction site associated DNA (RAD) linkage map in barley. BMC Genomics 12: 4.
    • (2011) BMC Genomics , vol.12 , pp. 4
    • Chutimanitsakun, Y.1    Nipper, R.W.2    Cuesta-Marcos, A.3    Cistue, L.4    Corey, A.5
  • 7
    • 79959435199 scopus 로고    scopus 로고
    • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    • Davey, J. W., P. A. Hohenlohe, P. D. Etter, J. Q. Boone, J. M. Catchen et al., 2011 Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat. Rev. Genet. 12: 499-510.
    • (2011) Nat. Rev. Genet , vol.12 , pp. 499-510
    • Davey, J.W.1    Hohenlohe, P.A.2    Etter, P.D.3    Boone, J.Q.4    Catchen, J.M.5
  • 8
    • 79961184281 scopus 로고    scopus 로고
    • B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize
    • Eichten, S. R., J. M. Foerster, N. de Leon, Y. Kai, C. Yeh et al., 2011 B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize. Plant Physiol. 156(4): 1679-1690.
    • (2011) Plant Physiol , vol.156 , Issue.4 , pp. 1679-1690
    • Eichten, S.R.1    Foerster, J.M.2    de Leon, N.3    Kai, Y.4    Yeh, C.5
  • 9
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • Elshire, R. J., J. C. Glaubitz, Q. Sun, J. A. Poland, K. Kawamoto et al., 2011 A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6(5): e19379.
    • (2011) PLoS ONE , vol.6 , Issue.5
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3    Poland, J.A.4    Kawamoto, K.5
  • 11
    • 33751319169 scopus 로고    scopus 로고
    • Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize
    • Fu, Y., T. Wen, Y. I. Ronin, H. D. Chen, L. Guo et al., 2006 Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics 174: 1671-1683.
    • (2006) Genetics , vol.174 , pp. 1671-1683
    • Fu, Y.1    Wen, T.2    Ronin, Y.I.3    Chen, H.D.4    Guo, L.5
  • 13
    • 38749149152 scopus 로고    scopus 로고
    • Whole-genome sequencing and variant discovery in C. elegans
    • Hillier, L. W., G. T. Marth, A. R. Quinlan, D. Dooling, G. Gewell et al., 2008 Whole-genome sequencing and variant discovery in C. elegans. Nat. Methods 5(2): 183-188.
    • (2008) Nat. Methods , vol.5 , Issue.2 , pp. 183-188
    • Hillier, L.W.1    Marth, G.T.2    Quinlan, A.R.3    Dooling, D.4    Gewell, G.5
  • 14
    • 0023988195 scopus 로고
    • Genomic mapping by fingerprinting random clones: A mathematical analysis
    • Lander, E. S., and M. S. Waterman, 1988 Genomic mapping by fingerprinting random clones: a mathematical analysis. Genomics 2: 231-239.
    • (1988) Genomics , vol.2 , pp. 231-239
    • Lander, E.S.1    Waterman, M.S.2
  • 15
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., C. Trapnell, M. Pop, and S. L. Salzberg, 2009 Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10(3): R25.
    • (2009) Genome Biol , vol.10 , Issue.3
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 16
    • 0036010768 scopus 로고    scopus 로고
    • Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population
    • Lee, M., N. Sharapova, W. D. Beavis, D. Grant, M. Katt et al., 2002 Expanding the genetic map of maize with the intermated B73 × Mo17 (IBM) population. Plant Mol. Biol. 48: 453-461.
    • (2002) Plant Mol. Biol , vol.48 , pp. 453-461
    • Lee, M.1    Sharapova, N.2    Beavis, W.D.3    Grant, D.4    Katt, M.5
  • 17
    • 40849134474 scopus 로고    scopus 로고
    • Mitochondrial DNA transfer to the nucleus generates extensive insertion site variation in maize
    • Lough, A. N., L. M. Roark, K. Akio, T. S. Ream, J. C. Lamb et al., 2008 Mitochondrial DNA transfer to the nucleus generates extensive insertion site variation in maize. Genetics 178: 47-55.
    • (2008) Genetics , vol.178 , pp. 47-55
    • Lough, A.N.1    Roark, L.M.2    Akio, K.3    Ream, T.S.4    Lamb, J.C.5
  • 18
    • 84856770811 scopus 로고    scopus 로고
    • Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample
    • Luo, C., D. Tsementzi, N. Kyrpides, T. Read, and K. T. Konstantinidis, 2012 Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample. PLoS ONE 7(2): e30087.
    • (2012) PLoS ONE , vol.7 , Issue.2
    • Luo, C.1    Tsementzi, D.2    Kyrpides, N.3    Read, T.4    Konstantinidis, K.T.5
  • 19
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
    • Minoche, A. E., J. C. Dohm, and H. Himmelbauer, 2011 Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems. Genome Biol. 12: R112.
    • (2011) Genome Biol , vol.12
    • Minoche, A.E.1    Dohm, J.C.2    Himmelbauer, H.3
  • 20
    • 70249111091 scopus 로고    scopus 로고
    • Targeted capture and massively parallel sequencing of 12 human exomes
    • Ng, S. B., E. H. Turner, P. D. Robertson, S. D. Flygare, A. W. Bigham et al., 2009 Targeted capture and massively parallel sequencing of 12 human exomes. Nature 461: 272-276.
    • (2009) Nature , vol.461 , pp. 272-276
    • Ng, S.B.1    Turner, E.H.2    Robertson, P.D.3    Flygare, S.D.4    Bigham, A.W.5
  • 21
    • 79959297013 scopus 로고    scopus 로고
    • Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne
    • Pfender, W. F., M. C. Saha, E. A. Johnson, and M. B. Slabaugh, 2011 Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne. Theor. Appl. Genet. 122: 1467-1480.
    • (2011) Theor. Appl. Genet , vol.122 , pp. 1467-1480
    • Pfender, W.F.1    Saha, M.C.2    Johnson, E.A.3    Slabaugh, M.B.4
  • 22
    • 0034048442 scopus 로고    scopus 로고
    • Optimal marker density for interval mapping in a backcross population
    • Piepho, H. P., 2000 Optimal marker density for interval mapping in a backcross population. Heredity 84: 437-440.
    • (2000) Heredity , vol.84 , pp. 437-440
    • Piepho, H.P.1
  • 23
    • 84857520461 scopus 로고    scopus 로고
    • Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach
    • Poland, J. A., P. J. Brown, M. E. Sorrells, and J. Jannink, 2012 Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7(2): e32253.
    • (2012) PLoS ONE , vol.7 , Issue.2
    • Poland, J.A.1    Brown, P.J.2    Sorrells, M.E.3    Jannink, J.4
  • 24
    • 79961135005 scopus 로고    scopus 로고
    • R Foundation for Statistical Computing, Vienna. Available at, R Development Core Team
    • R Development Core Team, 2011 R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna. Available at http://www.r-project.org/.
    • (2011) R: A Language and Environment For Statistical Computing
  • 25
    • 0021695885 scopus 로고
    • Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics
    • Saghai-Maroof, M. A., K. M. Soliman, R. A. Jorgensen, and R. W. Allard, 1984 Ribosomal DNA spacer-length polymorphisms in barley: Mendelian inheritance, chromosomal location, and population dynamics. Proc. Natl. Acad. Sci. USA 81: 8014-8018.
    • (1984) Proc. Natl. Acad. Sci. USA , vol.81 , pp. 8014-8018
    • Saghai-Maroof, M.A.1    Soliman, K.M.2    Jorgensen, R.A.3    Allard, R.W.4
  • 26
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Schnable, P. S., D. Ware, R. S. Fulton, J. C. Stein, F. Wei et al., 2009 The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956): 1112-1115.
    • (2009) Science , vol.326 , Issue.5956 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3    Stein, J.C.4    Wei, F.5
  • 27
    • 0035979181 scopus 로고    scopus 로고
    • Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L)
    • Tenaillon, M. I., M. C. Sawkins, A. D. Long, R. L. Gaut, J. F. Doebley et al., 2001 Patterns of DNA sequence polymorphism along chromosome 1 of maize (Zea mays ssp. mays L.). Proc. Natl. Acad. Sci. USA 98: 9161-9166.
    • (2001) Proc. Natl. Acad. Sci. USA , vol.98 , pp. 9161-9166
    • Tenaillon, M.I.1    Sawkins, M.C.2    Long, A.D.3    Gaut, R.L.4    Doebley, J.F.5
  • 28
    • 22144476219 scopus 로고    scopus 로고
    • The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs
    • Teuscher, F., V. Guiard, P. E. Rudolph, and G. A. Brockmann, 2005 The map expansion obtained with recombinant inbred strains and intermated recombinant inbred populations for finite generation designs. Genetics 170: 875-879.
    • (2005) Genetics , vol.170 , pp. 875-879
    • Teuscher, F.1    Guiard, V.2    Rudolph, P.E.3    Brockmann, G.A.4
  • 29
    • 83855165105 scopus 로고    scopus 로고
    • Repetitive DNA and next-generation sequencing: Computational challenges and solutions
    • Treangen, T. J., and S. L. Salzberg, 2011 Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet. 13: 36-46.
    • (2011) Nat. Rev. Genet , vol.13 , pp. 36-46
    • Treangen, T.J.1    Salzberg, S.L.2
  • 30
    • 43149110423 scopus 로고    scopus 로고
    • Complexity reduction of polymorphic sequences (CRoPS): A novel approach for large-scale polymorphism discovery in complex genomes
    • Van Orsouw, N. J., R. C. J. Hogers, A. Janssen, F. Yalcin, S. Snoeijers et al., 2007 Complexity reduction of polymorphic sequences (CRoPS): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS ONE 2(11): e1172.
    • (2007) PLoS ONE , vol.2 , Issue.11
    • Van Orsouw, N.J.1    Hogers, R.C.J.2    Janssen, A.3    Yalcin, F.4    Snoeijers, S.5
  • 31
    • 33746590339 scopus 로고    scopus 로고
    • Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing
    • Wendl, M. C., 2006 Occupancy modeling of coverage distribution for whole genome shotgun DNA sequencing. Bull. Math. Biol. 68: 179-196.
    • (2006) Bull. Math. Biol , vol.68 , pp. 179-196
    • Wendl, M.C.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.