메뉴 건너뛰기




Volumn 6, Issue 12, 2011, Pages

A large maize (zea mays L.) SNP genotyping array: Development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHROMOSOME 2; CHROMOSOME 3; CHROMOSOME 6; CHROMOSOME 7; CHROMOSOME 9; ERROR; EUROPE; GENE MAPPING; GENE REARRANGEMENT; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC LINKAGE; GENETIC VARIABILITY; GENOTYPE; GERMPLASM; MAIZE; MARKER GENE; NONHUMAN; NORTH AMERICA; PLANT GENOME; RECOMBINANT INBRED STRAIN; SINGLE NUCLEOTIDE POLYMORPHISM; CHROMOSOME MAP; CLUSTER ANALYSIS; COMPARATIVE STUDY; COMPUTER PROGRAM; GENETIC MARKER; GENETIC POLYMORPHISM; GENETIC RECOMBINATION; GENETICS; GENOTYPING TECHNIQUE; METHODOLOGY; NUCLEOTIDE SEQUENCE; PLANT CHROMOSOME; QUALITY CONTROL; REPRODUCIBILITY;

EID: 82955201636     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0028334     Document Type: Article
Times cited : (488)

References (41)
  • 1
    • 33845618112 scopus 로고    scopus 로고
    • The Molecular Genetics of Crop Domestication
    • Doebley JF, Gaut BS, Smith BD, (2006) The Molecular Genetics of Crop Domestication. Cell 127: 1309-1321.
    • (2006) Cell , vol.127 , pp. 1309-1321
    • Doebley, J.F.1    Gaut, B.S.2    Smith, B.D.3
  • 2
    • 70450202132 scopus 로고    scopus 로고
    • The B73 Maize Genome: Complexity, Diversity, and Dynamics
    • Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, et al. (2009) The B73 Maize Genome: Complexity, Diversity, and Dynamics. Science 326: 1112-1115.
    • (2009) Science , vol.326 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3    Stein, J.C.4    Wei, F.5
  • 4
    • 73649144195 scopus 로고    scopus 로고
    • Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome
    • Wei F, Stein JC, Liang C, Zhang J, Fulton RS, et al. (2009) Detailed Analysis of a Contiguous 22-Mb Region of the Maize Genome. PLoS Genet 5: e1000728.
    • (2009) PLoS Genet , vol.5
    • Wei, F.1    Stein, J.C.2    Liang, C.3    Zhang, J.4    Fulton, R.S.5
  • 5
    • 73649087948 scopus 로고    scopus 로고
    • The Physical and Genetic Framework of the Maize B73 Genome
    • Wei F, Zhang J, Zhou S, He R, Schaeffer M, et al. (2009) The Physical and Genetic Framework of the Maize B73 Genome. PLoS Genet 5: e1000715.
    • (2009) PLoS Genet , vol.5
    • Wei, F.1    Zhang, J.2    Zhou, S.3    He, R.4    Schaeffer, M.5
  • 8
    • 78049338441 scopus 로고    scopus 로고
    • Genome-wide patterns of genetic variation among elite maize inbred lines
    • Lai J, Li R, Xu X, Jin W, Xu M, et al. (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42: 1027-1030.
    • (2010) Nat Genet , vol.42 , pp. 1027-1030
    • Lai, J.1    Li, R.2    Xu, X.3    Jin, W.4    Xu, M.5
  • 10
    • 73649121258 scopus 로고    scopus 로고
    • Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content
    • Springer NM, Ying K, Fu Y, Ji T, Yeh C-T, et al. (2009) Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content. PLoS Genet 5: e1000734.
    • (2009) PLoS Genet , vol.5
    • Springer, N.M.1    Ying, K.2    Fu, Y.3    Ji, T.4    Yeh, C.-T.5
  • 11
    • 0001293453 scopus 로고
    • A linkage map based on information from four F2 populations of maize (Zea mays L.)
    • Beavis WD, Grant D, (1991) A linkage map based on information from four F2 populations of maize (Zea mays L.). Theoret. Appl. Genetics 82: 636-644.
    • (1991) Theoret. Appl. Genetics , vol.82 , pp. 636-644
    • Beavis, W.D.1    Grant, D.2
  • 13
    • 0002784965 scopus 로고
    • The influence of random mating on recombination among RFLP loci
    • Beavis W, Lee M, Grant D, Hallauer A, Owens T, et al. (1992) The influence of random mating on recombination among RFLP loci. Maize Newsl pp. 52-53.
    • (1992) Maize Newsl , pp. 52-53
    • Beavis, W.1    Lee, M.2    Grant, D.3    Hallauer, A.4    Owens, T.5
  • 15
    • 0038124403 scopus 로고    scopus 로고
    • On the Determination of Recombination Rates in Intermated Recombinant Inbred Populations
    • Winkler CR, Jensen NM, Cooper M, Podlich DW, Smith OS, (2003) On the Determination of Recombination Rates in Intermated Recombinant Inbred Populations. Genetics 164: 741-745.
    • (2003) Genetics , vol.164 , pp. 741-745
    • Winkler, C.R.1    Jensen, N.M.2    Cooper, M.3    Podlich, D.W.4    Smith, O.S.5
  • 16
  • 17
    • 40849089396 scopus 로고    scopus 로고
    • Genetic Design and Statistical Power of Nested Association Mapping in Maize
    • Yu J, Holland JB, McMullen MD, Buckler ES, (2008) Genetic Design and Statistical Power of Nested Association Mapping in Maize. Genetics 178: 539-551.
    • (2008) Genetics , vol.178 , pp. 539-551
    • Yu, J.1    Holland, J.B.2    McMullen, M.D.3    Buckler, E.S.4
  • 18
    • 31344476038 scopus 로고    scopus 로고
    • Whole-genome genotyping with the single-base extension assay
    • Steemers FJ, Chang W, Lee G, Barker DL, Shen R, et al. (2006) Whole-genome genotyping with the single-base extension assay. Nat Meth 3: 31-33.
    • (2006) Nat Meth , vol.3 , pp. 31-33
    • Steemers, F.J.1    Chang, W.2    Lee, G.3    Barker, D.L.4    Shen, R.5
  • 20
    • 79955783956 scopus 로고    scopus 로고
    • A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species
    • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, et al. (2011) A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species. PLoS ONE 6: e19379.
    • (2011) PLoS ONE , vol.6
    • Elshire, R.J.1    Glaubitz, J.C.2    Sun, Q.3    Poland, J.A.4    Kawamoto, K.5
  • 21
    • 42349112088 scopus 로고    scopus 로고
    • Genome-wide association studies for complex traits: consensus, uncertainty and challenges
    • McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, et al. (2008) Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nat Rev Genet 9: 356-369.
    • (2008) Nat Rev Genet , vol.9 , pp. 356-369
    • McCarthy, M.I.1    Abecasis, G.R.2    Cardon, L.R.3    Goldstein, D.B.4    Little, J.5
  • 23
    • 68349137618 scopus 로고    scopus 로고
    • Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology
    • Ramos AM, Crooijmans RPMA, Affara NA, Amaral AJ, Archibald AL, et al. (2009) Design of a High Density SNP Genotyping Assay in the Pig Using SNPs Identified and Characterized by Next Generation Sequencing Technology. PLoS ONE 4: e6524.
    • (2009) PLoS ONE , vol.4
    • Ramos, A.M.1    Crooijmans, R.P.M.A.2    Affara, N.A.3    Amaral, A.J.4    Archibald, A.L.5
  • 24
    • 0035045051 scopus 로고    scopus 로고
    • Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps
    • Meuwissen THE, Hayes BJ, Goddard ME, (2001) Prediction of Total Genetic Value Using Genome-Wide Dense Marker Maps. Genetics 157: 1819-1829.
    • (2001) Genetics , vol.157 , pp. 1819-1829
    • Meuwissen, T.H.E.1    Hayes, B.J.2    Goddard, M.E.3
  • 27
    • 78649244510 scopus 로고    scopus 로고
    • SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus
    • Durstewitz G, Polley A, Plieske J, Luerssen H, Graner EM, et al. (2010) SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napus. Genome 53: 948-956.
    • (2010) Genome , vol.53 , pp. 948-956
    • Durstewitz, G.1    Polley, A.2    Plieske, J.3    Luerssen, H.4    Graner, E.M.5
  • 28
    • 54949106977 scopus 로고    scopus 로고
    • Molecular Characterization of Maize Inbreds with Expired U.S. Plant Variety Protection
    • Nelson PT, Coles ND, Holland JB, Bubeck DM, Smith S, et al. (2008) Molecular Characterization of Maize Inbreds with Expired U.S. Plant Variety Protection. Crop Science 48: 1673-1685.
    • (2008) Crop Science , vol.48 , pp. 1673-1685
    • Nelson, P.T.1    Coles, N.D.2    Holland, J.B.3    Bubeck, D.M.4    Smith, S.5
  • 30
    • 0026053092 scopus 로고
    • Low Nucleotide Diversity in Man
    • Li WH, Sadler LA, (1991) Low Nucleotide Diversity in Man. Genetics 129: 513-523.
    • (1991) Genetics , vol.129 , pp. 513-523
    • Li, W.H.1    Sadler, L.A.2
  • 31
    • 33748915808 scopus 로고    scopus 로고
    • Nucleotide Variation and Haplotype Diversity in a 10-kb Noncoding Region in Three Continental Human Populations
    • Zhao Z, Yu N, Fu Y-X, Li W-H, (2006) Nucleotide Variation and Haplotype Diversity in a 10-kb Noncoding Region in Three Continental Human Populations. Genetics 174: 399-409.
    • (2006) Genetics , vol.174 , pp. 399-409
    • Zhao, Z.1    Yu, N.2    Fu, Y.-X.3    Li, W.-H.4
  • 32
    • 68449094455 scopus 로고    scopus 로고
    • Genetic Properties of the Maize Nested Association Mapping Population
    • McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, et al. (2009) Genetic Properties of the Maize Nested Association Mapping Population. Science 325: 737-740.
    • (2009) Science , vol.325 , pp. 737-740
    • McMullen, M.D.1    Kresovich, S.2    Villeda, H.S.3    Bradbury, P.4    Li, H.5
  • 33
    • 0242349686 scopus 로고    scopus 로고
    • High-Resolution Crossover Maps for Each Bivalent of Zea mays Using Recombination Nodules
    • Anderson LK, Doyle GG, Brigham B, Carter J, Hooker KD, et al. (2003) High-Resolution Crossover Maps for Each Bivalent of Zea mays Using Recombination Nodules. Genetics 165: 849-865.
    • (2003) Genetics , vol.165 , pp. 849-865
    • Anderson, L.K.1    Doyle, G.G.2    Brigham, B.3    Carter, J.4    Hooker, K.D.5
  • 34
    • 77949517584 scopus 로고    scopus 로고
    • Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers
    • Yan J, Shah T, Warburton ML, Buckler ES, McMullen MD, et al. (2009) Genetic Characterization and Linkage Disequilibrium Estimation of a Global Maize Collection Using SNP Markers. PLoS ONE 4: e8451.
    • (2009) PLoS ONE , vol.4
    • Yan, J.1    Shah, T.2    Warburton, M.L.3    Buckler, E.S.4    McMullen, M.D.5
  • 35
    • 0038744804 scopus 로고    scopus 로고
    • SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines
    • Ching A, Caldwell K, Jung M, Dolan M, Smith O, et al. (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genetics 3: 19.
    • (2002) BMC Genetics , vol.3 , pp. 19
    • Ching, A.1    Caldwell, K.2    Jung, M.3    Dolan, M.4    Smith, O.5
  • 36
    • 4544388331 scopus 로고    scopus 로고
    • Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm
    • Jung M, Ching A, Bhattramakki D, Dolan M, Tingey S, et al. (2004) Linkage disequilibrium and sequence diversity in a 500-kbp region around the adh1 locus in elite maize germplasm. Theor Appl Genet 109: 681-689.
    • (2004) Theor Appl Genet , vol.109 , pp. 681-689
    • Jung, M.1    Ching, A.2    Bhattramakki, D.3    Dolan, M.4    Tingey, S.5
  • 37
    • 36949038456 scopus 로고    scopus 로고
    • Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize
    • Beló A, Zheng P, Luck S, Shen B, Meyer DJ, et al. (2007) Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics 279: 1-10.
    • (2007) Mol Genet Genomics , vol.279 , pp. 1-10
    • Beló, A.1    Zheng, P.2    Luck, S.3    Shen, B.4    Meyer, D.J.5
  • 38
    • 79958163084 scopus 로고    scopus 로고
    • Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm
    • Inghelandt D, Reif JC, Dhillon BS, Flament P, Melchinger AE, (2011) Extent and genome-wide distribution of linkage disequilibrium in commercial maize germplasm. Theor Appl Genet 123: 11-20.
    • (2011) Theor Appl Genet , vol.123 , pp. 11-20
    • Inghelandt, D.1    Reif, J.C.2    Dhillon, B.S.3    Flament, P.4    Melchinger, A.E.5
  • 39
    • 70349978570 scopus 로고    scopus 로고
    • Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm
    • Jones E, Chu W-C, Ayele M, Ho J, Bruggeman E, et al. (2009) Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm. Mol Breeding 24: 165-176.
    • (2009) Mol Breeding , vol.24 , pp. 165-176
    • Jones, E.1    Chu, W.-C.2    Ayele, M.3    Ho, J.4    Bruggeman, E.5
  • 40
    • 17444404610 scopus 로고    scopus 로고
    • CarthaGene: multipopulation integrated genetic and radiation hybrid mapping
    • de Givry S, Bouchez M, Chabrier P, Milan D, Schiex T, (2004) CarthaGene: multipopulation integrated genetic and radiation hybrid mapping. Bioinformatics 21: 1703-1704.
    • (2004) Bioinformatics , vol.21 , pp. 1703-1704
    • de Givry, S.1    Bouchez, M.2    Chabrier, P.3    Milan, D.4    Schiex, T.5
  • 41
    • 24044437181 scopus 로고    scopus 로고
    • IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains
    • Falque M, (2005) IRILmap: linkage map distance correction for intermated recombinant inbred lines/advanced recombinant inbred strains. Bioinformatics 21: 3441-3442.
    • (2005) Bioinformatics , vol.21 , pp. 3441-3442
    • Falque, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.