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Volumn 14, Issue 1, 2013, Pages

Digital genotyping of sorghum - a diverse plant species with a large repeat-rich genome

Author keywords

Genotyping; Grass; Polymorphism; Sorghum bicolor

Indexed keywords

PLANT DNA; RESTRICTION ENDONUCLEASE;

EID: 84879828066     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-448     Document Type: Article
Times cited : (58)

References (38)
  • 1
    • 0019302053 scopus 로고
    • Construction of a genetic-linkage map in man using restriction fragment length polymorphisms
    • 1686077, 6247908
    • Botstein D, White RL, Skolnick M, Davis RW. Construction of a genetic-linkage map in man using restriction fragment length polymorphisms. Am J Hum Genet 1980, 32(3):314-331. 1686077, 6247908.
    • (1980) Am J Hum Genet , vol.32 , Issue.3 , pp. 314-331
    • Botstein, D.1    White, R.L.2    Skolnick, M.3    Davis, R.W.4
  • 3
    • 18144425478 scopus 로고    scopus 로고
    • A genome-wide scalable SNP genotyping assay using microarray technology
    • 10.1038/ng1547, 15838508
    • Gunderson KL, Steemers FJ, Lee G, Mendoza LG, Chee MS. A genome-wide scalable SNP genotyping assay using microarray technology. Nat Genet 2005, 37(5):549-554. 10.1038/ng1547, 15838508.
    • (2005) Nat Genet , vol.37 , Issue.5 , pp. 549-554
    • Gunderson, K.L.1    Steemers, F.J.2    Lee, G.3    Mendoza, L.G.4    Chee, M.S.5
  • 4
    • 0034547263 scopus 로고    scopus 로고
    • Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay
    • 10.1093/nar/28.23.e100, 115184, 11095696
    • Sauer S, Lechner D, Berlin K, Plançon C, Heuermann A, Lehrach H, Gut IG. Full flexibility genotyping of single nucleotide polymorphisms by the GOOD assay. Nucleic Acids Res 2000, 28(23):e100. 10.1093/nar/28.23.e100, 115184, 11095696.
    • (2000) Nucleic Acids Res , vol.28 , Issue.23
    • Sauer, S.1    Lechner, D.2    Berlin, K.3    Plançon, C.4    Heuermann, A.5    Lehrach, H.6    Gut, I.G.7
  • 5
    • 33645384241 scopus 로고    scopus 로고
    • Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, amplifluor and TaqMan, in diploid and polyploid plants
    • 10.1007/s00122-006-0213-6, 16453133
    • Giancola S, McKhann H, Bérard A, Camilleri C, Durand S, Libeau P, Roux F, Reboud X, Gut I, Brunel D. Utilization of the three high-throughput SNP genotyping methods, the GOOD assay, amplifluor and TaqMan, in diploid and polyploid plants. Theor Appl Genet 2006, 112(6):1115-1124. 10.1007/s00122-006-0213-6, 16453133.
    • (2006) Theor Appl Genet , vol.112 , Issue.6 , pp. 1115-1124
    • Giancola, S.1    McKhann, H.2    Bérard, A.3    Camilleri, C.4    Durand, S.5    Libeau, P.6    Roux, F.7    Reboud, X.8    Gut, I.9    Brunel, D.10
  • 7
    • 31344476038 scopus 로고    scopus 로고
    • Whole-genome genotyping with the single-base extension assay
    • 10.1038/nmeth842, 16369550
    • Steemers FJ, Chang W, Lee G, Barker DL, Shen R, Gunderson KL. Whole-genome genotyping with the single-base extension assay. Nat Methods 2006, 3(1):31-33. 10.1038/nmeth842, 16369550.
    • (2006) Nat Methods , vol.3 , Issue.1 , pp. 31-33
    • Steemers, F.J.1    Chang, W.2    Lee, G.3    Barker, D.L.4    Shen, R.5    Gunderson, K.L.6
  • 9
    • 79959435199 scopus 로고    scopus 로고
    • Genome-wide genetic marker discovery and genotyping using next-generation sequencing
    • 10.1038/nrg3012, 21681211
    • Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML. Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 2011, 12(7):499-510. 10.1038/nrg3012, 21681211.
    • (2011) Nat Rev Genet , vol.12 , Issue.7 , pp. 499-510
    • Davey, J.W.1    Hohenlohe, P.A.2    Etter, P.D.3    Boone, J.Q.4    Catchen, J.M.5    Blaxter, M.L.6
  • 10
    • 79955783956 scopus 로고    scopus 로고
    • A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species
    • 10.1371/journal.pone.0019379, 3087801, 21573248
    • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 2011, 6(5):e19379. 10.1371/journal.pone.0019379, 3087801, 21573248.
    • (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    Buckler, E.S.6    Mitchell, S.E.7
  • 12
    • 77953796079 scopus 로고    scopus 로고
    • Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing
    • 10.1073/pnas.1005931107, 2890813, 20498060
    • Xie W, Feng Q, Yu H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing. Proc Natl Acad Sci USA 2010, 107(23):10578-10583. 10.1073/pnas.1005931107, 2890813, 20498060.
    • (2010) Proc Natl Acad Sci USA , vol.107 , Issue.23 , pp. 10578-10583
    • Xie, W.1    Feng, Q.2    Yu, H.3    Huang, X.4    Zhao, Q.5    Xing, Y.6    Yu, S.7    Han, B.8    Zhang, Q.9
  • 13
    • 43149110423 scopus 로고    scopus 로고
    • Complexity reduction of polymorphic sequences (CRoPS™): a novel approach for large-scale polymorphism discovery in complex genomes
    • 10.1371/journal.pone.0001172, 2048665, 18000544
    • van Orsouw NJ, Hogers RCJ, Janssen A, Yalcin F, Snoeijers S, Verstege E, Schneiders H, van der Poel H, van Oeveren J, Verstegen H, et al. Complexity reduction of polymorphic sequences (CRoPS™): a novel approach for large-scale polymorphism discovery in complex genomes. PLoS One 2007, 2(11):e1172. 10.1371/journal.pone.0001172, 2048665, 18000544.
    • (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    Verstege, E.6    Schneiders, H.7    van der Poel, H.8    van Oeveren, J.9    Verstegen, H.10
  • 15
    • 78649508578 scopus 로고    scopus 로고
    • MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes
    • 10.1002/gepi.20533, 3175618, 21058334
    • Li Y, Willer CJ, Ding J, Scheet P, Abecasis GR. MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes. Genet Epidemiol 2010, 34(8):816-834. 10.1002/gepi.20533, 3175618, 21058334.
    • (2010) Genet Epidemiol , vol.34 , Issue.8 , pp. 816-834
    • Li, Y.1    Willer, C.J.2    Ding, J.3    Scheet, P.4    Abecasis, G.R.5
  • 16
    • 15544375867 scopus 로고    scopus 로고
    • Genome evolution in the genus Sorghum (Poaceae)
    • 10.1093/aob/mci015, 15596469
    • Price HJ, Dillon SL, Hodnett G, Rooney WL, Ross L, Johnston JS. Genome evolution in the genus Sorghum (Poaceae). Ann Bot 2005, 95(1):219-227. 10.1093/aob/mci015, 15596469.
    • (2005) Ann Bot , vol.95 , Issue.1 , pp. 219-227
    • Price, H.J.1    Dillon, S.L.2    Hodnett, G.3    Rooney, W.L.4    Ross, L.5    Johnston, J.S.6
  • 19
    • 33645121316 scopus 로고    scopus 로고
    • Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice
    • 10.1534/genetics.105.048215, 1456119, 16143604
    • Kim JS, Islam-Faridi MN, Klein PE, Stelly DM, Price HJ, Klein RR, Mullet JE. Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice. Genetics 2005, 171(4):1963-1976. 10.1534/genetics.105.048215, 1456119, 16143604.
    • (2005) Genetics , vol.171 , Issue.4 , pp. 1963-1976
    • Kim, J.S.1    Islam-Faridi, M.N.2    Klein, P.E.3    Stelly, D.M.4    Price, H.J.5    Klein, R.R.6    Mullet, J.E.7
  • 20
    • 35349031183 scopus 로고    scopus 로고
    • Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae)
    • 10.1093/aob/mcm192, 2759214, 17766842
    • Dillon SL, Shapter FM, Henry RJ, Cordeiro G, Izquierdo L, Lee LS. Domestication to crop improvement: genetic resources for Sorghum and Saccharum (Andropogoneae). Ann Bot 2007, 100(5):975-989. 10.1093/aob/mcm192, 2759214, 17766842.
    • (2007) Ann Bot , vol.100 , Issue.5 , pp. 975-989
    • Dillon, S.L.1    Shapter, F.M.2    Henry, R.J.3    Cordeiro, G.4    Izquierdo, L.5    Lee, L.S.6
  • 23
    • 0023359272 scopus 로고
    • Why do chloroplasts and mitochondria contain so many copies of their genome?
    • 10.1002/bies.950060608, 3619888
    • Bendich AJ. Why do chloroplasts and mitochondria contain so many copies of their genome?. BioEssays 1987, 6(6):279-282. 10.1002/bies.950060608, 3619888.
    • (1987) BioEssays , vol.6 , Issue.6 , pp. 279-282
    • Bendich, A.J.1
  • 24
    • 0001355547 scopus 로고
    • Plastid transcription activity and DNA copy number increase early in barley chloroplast development
    • 10.1104/pp.89.3.1011, 1055959, 16666609
    • Baumgartner BJ, Rapp JC, Mullet JE. Plastid transcription activity and DNA copy number increase early in barley chloroplast development. Plant Physiol 1989, 89(3):1011-1018. 10.1104/pp.89.3.1011, 1055959, 16666609.
    • (1989) Plant Physiol , vol.89 , Issue.3 , pp. 1011-1018
    • Baumgartner, B.J.1    Rapp, J.C.2    Mullet, J.E.3
  • 25
    • 0032812030 scopus 로고    scopus 로고
    • Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines
    • Peng Y, Schertz KF, Cartinhour S, Hart GE. Comparative genome mapping of Sorghum bicolor (L.) Moench using an RFLP map constructed in a population of recombinant inbred lines. Plant Breeding 1999, 118(3):225-235.
    • (1999) Plant Breeding , vol.118 , Issue.3 , pp. 225-235
    • Peng, Y.1    Schertz, K.F.2    Cartinhour, S.3    Hart, G.E.4
  • 26
    • 0036010769 scopus 로고    scopus 로고
    • A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLPR, RFLP and SSR markers
    • Menz MA, Klein RR, Mullet JE, Obert JA, Unruh NC, Klein PE. A high-density genetic map of Sorghum bicolor (L.) Moench based on 2926 AFLPR, RFLP and SSR markers. Plant Mol Biol 2002, 48(5):483-499.
    • (2002) Plant Mol Biol , vol.48 , Issue.5 , pp. 483-499
    • Menz, M.A.1    Klein, R.R.2    Mullet, J.E.3    Obert, J.A.4    Unruh, N.C.5    Klein, P.E.6
  • 27
    • 79953328142 scopus 로고    scopus 로고
    • Registration of the BTx623/IS3620C recombinant inbred mapping population of Sorghum
    • Burow GB, Klein RR, Franks CD, Klein PE, Schertz KF. Registration of the BTx623/IS3620C recombinant inbred mapping population of Sorghum. J Plant Registrations 2011, 5(1):141-145.
    • (2011) J Plant Registrations , vol.5 , Issue.1 , pp. 141-145
    • Burow, G.B.1    Klein, R.R.2    Franks, C.D.3    Klein, P.E.4    Schertz, K.F.5
  • 28
    • 0023426747 scopus 로고
    • MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations
    • 10.1016/0888-7543(87)90010-3, 3692487
    • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L. MAPMAKER: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1987, 1(2):174-181. 10.1016/0888-7543(87)90010-3, 3692487.
    • (1987) Genomics , vol.1 , Issue.2 , pp. 174-181
    • Lander, E.S.1    Green, P.2    Abrahamson, J.3    Barlow, A.4    Daly, M.J.5    Lincoln, S.E.6    Newburg, L.7
  • 29
    • 0035670922 scopus 로고    scopus 로고
    • Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters
    • Hart GE, Schertz KF, Peng Y, Syed NH. Genetic mapping of Sorghum bicolor (L.) Moench QTLs that control variation in tillering and other morphological characters. Theor Appl Genet 2001, 103(8):1232-1242.
    • (2001) Theor Appl Genet , vol.103 , Issue.8 , pp. 1232-1242
    • Hart, G.E.1    Schertz, K.F.2    Peng, Y.3    Syed, N.H.4
  • 30
    • 0141865718 scopus 로고    scopus 로고
    • Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants
    • 10.1126/science.1086072, 14526073
    • Multani DS, Briggs SP, Chamberlin MA, Blakeslee JJ, Murphy AS, Johal GS. Loss of an MDR transporter in compact stalks of maize br2 and sorghum dw3 mutants. Science 2003, 302(5642):81-84. 10.1126/science.1086072, 14526073.
    • (2003) Science , vol.302 , Issue.5642 , pp. 81-84
    • Multani, D.S.1    Briggs, S.P.2    Chamberlin, M.A.3    Blakeslee, J.J.4    Murphy, A.S.5    Johal, G.S.6
  • 31
    • 80053632751 scopus 로고    scopus 로고
    • Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum
    • 10.1073/pnas.1106212108, 3182727, 21930910
    • Murphy RL, Klein RR, Morishige DT, Brady JA, Rooney WL, Miller FR, Dugas DV, Klein PE, Mullet JE. Coincident light and clock regulation of pseudoresponse regulator protein 37 (PRR37) controls photoperiodic flowering in sorghum. Proc Natl Acad Sci USA 2011, 108(39):16469-16474. 10.1073/pnas.1106212108, 3182727, 21930910.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.39 , pp. 16469-16474
    • Murphy, R.L.1    Klein, R.R.2    Morishige, D.T.3    Brady, J.A.4    Rooney, W.L.5    Miller, F.R.6    Dugas, D.V.7    Klein, P.E.8    Mullet, J.E.9
  • 32
    • 42449103452 scopus 로고    scopus 로고
    • The effect of tropical sorghum conversion and inbred development on genome diversity as revealed by high-resolution genotyping
    • Klein RR, Mullet JE, Jordan DR, Miller FR, Rooney WL, Menz MA, Franks CD, Klein PE. The effect of tropical sorghum conversion and inbred development on genome diversity as revealed by high-resolution genotyping. Crop Sci 2008, 48(Supplement_1):S12-S26.
    • (2008) Crop Sci , vol.48 , Issue.SUPPL. 1
    • Klein, R.R.1    Mullet, J.E.2    Jordan, D.R.3    Miller, F.R.4    Rooney, W.L.5    Menz, M.A.6    Franks, C.D.7    Klein, P.E.8
  • 34
    • 79951694175 scopus 로고    scopus 로고
    • Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries
    • 10.1186/gb-2011-12-2-r18, 3188800, 21338519
    • Aird D, Ross MG, Chen WS, Danielsson M, Fennell T, Russ C, Jaffe DB, Nusbaum C, Gnirke A. Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries. Genome Biol 2011, 12(2):R18. 10.1186/gb-2011-12-2-r18, 3188800, 21338519.
    • (2011) Genome Biol , vol.12 , Issue.2
    • Aird, D.1    Ross, M.G.2    Chen, W.S.3    Danielsson, M.4    Fennell, T.5    Russ, C.6    Jaffe, D.B.7    Nusbaum, C.8    Gnirke, A.9
  • 35
    • 57049122389 scopus 로고    scopus 로고
    • A large genome center's improvements to the Illumina sequencing system
    • 10.1038/nmeth.1270, 2610436, 19034268
    • Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ. A large genome center's improvements to the Illumina sequencing system. Nat Methods 2008, 5(12):1005-1010. 10.1038/nmeth.1270, 2610436, 19034268.
    • (2008) Nat Methods , vol.5 , Issue.12 , pp. 1005-1010
    • Quail, M.A.1    Kozarewa, I.2    Smith, F.3    Scally, A.4    Stephens, P.J.5    Durbin, R.6    Swerdlow, H.7    Turner, D.J.8
  • 36
    • 0029839535 scopus 로고    scopus 로고
    • Protection of DNA during preparative agarose gel electrophoresis against damage induced by ultraviolet light
    • Gründemann D, Schömig E. Protection of DNA during preparative agarose gel electrophoresis against damage induced by ultraviolet light. Biotechniques 1996, 21(5):898-903.
    • (1996) Biotechniques , vol.21 , Issue.5 , pp. 898-903
    • Gründemann, D.1    Schömig, E.2


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