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Volumn 10, Issue 9, 2014, Pages

Genome Wide Association Studies Using a New Nonparametric Model Reveal the Genetic Architecture of 17 Agronomic Traits in an Enlarged Maize Association Panel

Author keywords

[No Author keywords available]

Indexed keywords

AGRONOMIC TRAIT; ARTICLE; CONTROLLED STUDY; GENE LOCUS; GENE MAPPING; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC ASSOCIATION; GENETIC VARIABILITY; GENOTYPE; INBRED STRAIN; LINKAGE ANALYSIS; MAIZE; NONHUMAN; NONPARAMETRIC TEST; PHENOTYPIC VARIATION; PLANT BREEDING; PLANT GENETICS; PLANT HEIGHT; QUANTITATIVE TRAIT; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; BREEDING; GENE LINKAGE DISEQUILIBRIUM; GENETICS; PHENOTYPE; PLANT GENOME; PROCEDURES; QUANTITATIVE TRAIT LOCUS;

EID: 84907578015     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1004573     Document Type: Article
Times cited : (288)

References (45)
  • 1
    • 79952509464 scopus 로고    scopus 로고
    • Association mapping for enhancing maize (Zea mays L.) genetic improvement
    • Yan J, Warburton M, Crouch J, (2011) Association mapping for enhancing maize (Zea mays L.) genetic improvement. Crop Sci 51: 433–449.
    • (2011) Crop Sci , vol.51 , pp. 433-449
    • Yan, J.1    Warburton, M.2    Crouch, J.3
  • 2
    • 85164502327 scopus 로고    scopus 로고
    • Status and prospects of association Mapping in plants
    • Zhu C, Gore MA, Buckler ES, Yu J, (2008) Status and prospects of association Mapping in plants. Plant Genome 1: 5–20.
    • (2008) Plant Genome , vol.1 , pp. 5-20
    • Zhu, C.1    Gore, M.A.2    Buckler, E.S.3    Yu, J.4
  • 3
    • 77953233453 scopus 로고    scopus 로고
    • Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines
    • Atwell S, Huang YS, Vilhjálmsson BJ, Willems G, Horton M, et al. (2010) Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature 465: 627–631.
    • (2010) Nature , vol.465 , pp. 627-631
    • Atwell, S.1    Huang, Y.S.2    Vilhjálmsson, B.J.3    Willems, G.4    Horton, M.5
  • 4
    • 78049332150 scopus 로고    scopus 로고
    • Genome-wide association studies of 14 agronomic traits in rice landraces
    • Huang X, Wei X, Sang T, Zhao Q, Feng Q, et al. (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42: 961–967.
    • (2010) Nat Genet , vol.42 , pp. 961-967
    • Huang, X.1    Wei, X.2    Sang, T.3    Zhao, Q.4    Feng, Q.5
  • 5
    • 84871996129 scopus 로고    scopus 로고
    • Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels
    • Li H, Peng Z, Yang X, Wang W, Fu J, et al. (2013) Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels. Nat Genet 45: 43–50.
    • (2013) Nat Genet , vol.45 , pp. 43-50
    • Li, H.1    Peng, Z.2    Yang, X.3    Wang, W.4    Fu, J.5
  • 6
    • 77950299137 scopus 로고    scopus 로고
    • Mixed linear model approach adapted for genome-wide association studies
    • Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, et al. (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42: 355–360.
    • (2010) Nat Genet , vol.42 , pp. 355-360
    • Zhang, Z.1    Ersoz, E.2    Lai, C.Q.3    Todhunter, R.J.4    Tiwari, H.K.5
  • 7
    • 31744440502 scopus 로고    scopus 로고
    • A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    • Yu J, Pressoir G, Briggs WH, Vroh Bi I, Yamasaki M, et al. (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38: 203–208.
    • (2006) Nat Genet , vol.38 , pp. 203-208
    • Yu, J.1    Pressoir, G.2    Briggs, W.H.3    Vroh Bi, I.4    Yamasaki, M.5
  • 8
    • 80053388300 scopus 로고    scopus 로고
    • Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa
    • Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, et al. (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2: 467.
    • (2011) Nat Commun , vol.2 , pp. 467
    • Zhao, K.1    Tung, C.W.2    Eizenga, G.C.3    Wright, M.H.4    Ali, M.L.5
  • 10
    • 84885770388 scopus 로고    scopus 로고
    • Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies
    • Cheng R, Parker CC, Abney M, Palmer AA, (2013) Practical considerations regarding the use of genotype and pedigree data to model relatedness in the context of genome-wide association studies. G3 (Bethesda) 3: 1861–1867.
    • (2013) G3 (Bethesda) , vol.3 , pp. 1861-1867
    • Cheng, R.1    Parker, C.C.2    Abney, M.3    Palmer, A.A.4
  • 11
    • 84871345504 scopus 로고    scopus 로고
    • The nature of confounding in genome-wide association studies
    • Vilhjálmsson BJ, Nordborg M, (2013) The nature of confounding in genome-wide association studies. Nat Rev Genet 14: 1–2.
    • (2013) Nat Rev Genet , vol.14 , pp. 1-2
    • Vilhjálmsson, B.J.1    Nordborg, M.2
  • 12
    • 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. (2008) Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics 279: 1–10.
    • (2008) Mol Genet Genomics , vol.279 , pp. 1-10
    • Beló, A.1    Zheng, P.2    Luck, S.3    Shen, B.4    Meyer, D.J.5
  • 13
    • 81255144862 scopus 로고    scopus 로고
    • Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize
    • Yang X, Gao S, Xu S, Zhang Z, Prasanna B, et al. (2011) Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breed 28: 511–526.
    • (2011) Mol Breed , vol.28 , pp. 511-526
    • Yang, X.1    Gao, S.2    Xu, S.3    Zhang, Z.4    Prasanna, B.5
  • 14
    • 82955201636 scopus 로고    scopus 로고
    • A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome
    • Ganal MW, Durstewitz G, Polley A, Bérard A, Buckler ES, et al. (2011) A large maize (Zea mays L.) SNP genotyping array: development and germplasm genotyping, and genetic mapping to compare with the B73 reference genome. PloS One 6: e28334.
    • (2011) PloS One , vol.6 , pp. e28334
    • Ganal, M.W.1    Durstewitz, G.2    Polley, A.3    Bérard, A.4    Buckler, E.S.5
  • 15
    • 84866147379 scopus 로고    scopus 로고
    • Genome-wide association studies identified three independent polymorphisms associated with α-tocopherol content in maize kernels
    • Li Q, Yang X, Xu S, Cai Y, Zhang D, et al. (2012) Genome-wide association studies identified three independent polymorphisms associated with α-tocopherol content in maize kernels. PloS One 7: e36807.
    • (2012) PloS One , vol.7 , pp. e36807
    • Li, Q.1    Yang, X.2    Xu, S.3    Cai, Y.4    Zhang, D.5
  • 16
    • 84890685736 scopus 로고    scopus 로고
    • RNA sequencing reveals the complex regulatory network in maize kernel
    • Fu J, Cheng Y, Linghu J, Yang X, Kang L, et al. (2013) RNA sequencing reveals the complex regulatory network in maize kernel. Nat Commun 4: 2832.
    • (2013) Nat Commun , vol.4 , pp. 2832
    • Fu, J.1    Cheng, Y.2    Linghu, J.3    Yang, X.4    Kang, L.5
  • 17
    • 79959893242 scopus 로고    scopus 로고
    • A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics
    • Moltke I, Albrechtsen A, Hansen T, Nielsen FC, Nielsen R, (2011) A method for detecting IBD regions simultaneously in multiple individuals—with applications to disease genetics. Genome Res 21: 1168–1180.
    • (2011) Genome Res , vol.21 , pp. 1168-1180
    • Moltke, I.1    Albrechtsen, A.2    Hansen, T.3    Nielsen, F.C.4    Nielsen, R.5
  • 19
    • 84950433002 scopus 로고
    • K-sample Anderson–Darling tests
    • Scholz F, Stephens M, (1987) K-sample Anderson–Darling tests. J Am Stat Assoc 82: 918–924.
    • (1987) J Am Stat Assoc , vol.82 , pp. 918-924
    • Scholz, F.1    Stephens, M.2
  • 20
    • 84884644235 scopus 로고
    • Numerical recipes in C: the art of scientific computing (second edition). Cambridge University Press. Pp
    • Press WH, Flannery BP, Teudolsky SA, Vetterling WT (1992) Numerical recipes in C: the art of scientific computing (second edition). Cambridge University Press. Pp. 626–627.
    • (1992)
    • Press, W.H.1    Flannery, B.P.2    Teudolsky, S.A.3    Vetterling, W.T.4
  • 22
    • 84863955846 scopus 로고    scopus 로고
    • ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize
    • Hung HY, Shannon LM, Tian F, Bradbury PJ, Chen C, et al. (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci U S A 109: 1913–1921.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 1913-1921
    • Hung, H.Y.1    Shannon, L.M.2    Tian, F.3    Bradbury, P.J.4    Chen, C.5
  • 23
    • 84885829511 scopus 로고    scopus 로고
    • A CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the post-domestication spread of maize
    • Yang Q, Li Z, Li W, Ku L, Wang C, et al. (2013) A CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the post-domestication spread of maize. Proc Natl Acad Sci U S A 110: 16969–16974.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 16969-16974
    • Yang, Q.1    Li, Z.2    Li, W.3    Ku, L.4    Wang, C.5
  • 24
    • 57349088665 scopus 로고    scopus 로고
    • Photoexcited CRY2 Interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis
    • Liu H, Yu X, Li K, Klejnot J, Yang H, et al. (2008) Photoexcited CRY2 Interacts with CIB1 to regulate transcription and floral initiation in Arabidopsis. Science 322: 1535–1539.
    • (2008) Science , vol.322 , pp. 1535-1539
    • Liu, H.1    Yu, X.2    Li, K.3    Klejnot, J.4    Yang, H.5
  • 25
    • 84866702110 scopus 로고    scopus 로고
    • Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae
    • Cockram J, Thiel T, Steuernagel B, Stein N, Taudien S, et al. (2012) Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae. PloS One 7: e45307.
    • (2012) PloS One , vol.7 , pp. e45307
    • Cockram, J.1    Thiel, T.2    Steuernagel, B.3    Stein, N.4    Taudien, S.5
  • 26
    • 33749544787 scopus 로고    scopus 로고
    • The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family inhigher plants
    • Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, et al. (2006) The maize INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family inhigher plants. BMC Genomics 7: 158.
    • (2006) BMC Genomics , vol.7 , pp. 158
    • Colasanti, J.1    Tremblay, R.2    Wong, A.Y.3    Coneva, V.4    Kozaki, A.5
  • 27
    • 0032714352 scopus 로고    scopus 로고
    • Genomic control for association studies
    • Devlin B, Roeder K, (1999) Genomic control for association studies. Biometrics 55: 997–1004.
    • (1999) Biometrics , vol.55 , pp. 997-1004
    • Devlin, B.1    Roeder, K.2
  • 28
    • 73149106388 scopus 로고    scopus 로고
    • Correcting for cryptic relatedness by a regression-based genomic control method
    • Yan Ting, Hou Bo, Yang Yaning, (2009) Correcting for cryptic relatedness by a regression-based genomic control method. BMC Genet 10: 78.
    • (2009) BMC Genet , vol.10 , pp. 78
    • Yan, T.1    Hou, B.2    Yang, Y.3
  • 29
    • 15044352388 scopus 로고    scopus 로고
    • Genomic control for association studies under various genetic models
    • Zheng G, Freidlin B, Li Z, Gastwirth JL, (2005) Genomic control for association studies under various genetic models. Biometrics 61: 186–192.
    • (2005) Biometrics , vol.61 , pp. 186-192
    • Zheng, G.1    Freidlin, B.2    Li, Z.3    Gastwirth, J.L.4
  • 30
    • 84892997367 scopus 로고    scopus 로고
    • Development and application of genomic control methods for genome-wide association studies using non-additive models
    • Tsepilov YA, Ried JS, Strauch K, Grallert H, van Duijn CM, et al. (2013) Development and application of genomic control methods for genome-wide association studies using non-additive models. PloS One 8: e81431.
    • (2013) PloS One , vol.8 , pp. e81431
    • Tsepilov, Y.A.1    Ried, J.S.2    Strauch, K.3    Grallert, H.4    Van Duijn, C.M.5
  • 31
    • 84887555661 scopus 로고    scopus 로고
    • Luck SD
    • Beló A, Luck SD (2010) Association mapping for the exploration of genetic diversity and identification of useful loci for plant breeding. In: Khalid M, Günter K,editors. The handbook of plant mutation screening: mining of natural and induced alleles. New York: John Wiley & Sons. Pp. 231–246.
    • (2010) , pp. 231-246
    • Beló, A.1
  • 32
    • 77956218413 scopus 로고    scopus 로고
    • The control of axillary meristem fate in the maize ramosa pathway
    • Gallavotti A, Long JA, Stanfield S, Yang X, Jackson D, et al. (2010) The control of axillary meristem fate in the maize ramosa pathway. Development 137: 2849–2856.
    • (2010) Development , vol.137 , pp. 2849-2856
    • Gallavotti, A.1    Long, J.A.2    Stanfield, S.3    Yang, X.4    Jackson, D.5
  • 33
    • 84874247299 scopus 로고    scopus 로고
    • Rice zinc finger protein DST enhances grain production through controlling Gn1a/OsCKX2 expression
    • Li S, Zhao B, Yuan D, Duan M, Qian Q, et al. (2013) Rice zinc finger protein DST enhances grain production through controlling Gn1a/OsCKX2 expression. Proc Natl Acad Sci U S A 110: 3167–3172.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 3167-3172
    • Li, S.1    Zhao, B.2    Yuan, D.3    Duan, M.4    Qian, Q.5
  • 34
    • 80052679688 scopus 로고    scopus 로고
    • Imputation of missing genotypes from sparse to high density using long-range phasing
    • Daetwyler HD, Wiggans GR, Hayes BJ, Woolliams JA, Goddard ME, (2011) Imputation of missing genotypes from sparse to high density using long-range phasing. Genetics 189: 317–327.
    • (2011) Genetics , vol.189 , pp. 317-327
    • Daetwyler, H.D.1    Wiggans, G.R.2    Hayes, B.J.3    Woolliams, J.A.4    Goddard, M.E.5
  • 35
    • 67651049769 scopus 로고    scopus 로고
    • Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies
    • Hao K, Chudin E, McElwee J, Schadt E, (2009) Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies. BMC Genet 10: 27.
    • (2009) BMC Genet , vol.10 , pp. 27
    • Hao, K.1    Chudin, E.2    McElwee, J.3    Schadt, E.4
  • 36
    • 79251575784 scopus 로고    scopus 로고
    • Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population
    • Kump KL, Bradbury PJ, Wisser RJ, Buckler ES, et al. (2011) Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population. Nat Genet 43: 163–168.
    • (2011) Nat Genet , vol.43 , pp. 163-168
    • Kump, K.L.1    Bradbury, P.J.2    Wisser, R.J.3    Buckler, E.S.4
  • 37
    • 79955565301 scopus 로고    scopus 로고
    • Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize
    • Poland JA, Bradbury PJ, Buckler ES, Nelson RJ, (2011) Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize. Proc Natl Acad Sci U S A 108: 6893–6898.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 6893-6898
    • Poland, J.A.1    Bradbury, P.J.2    Buckler, E.S.3    Nelson, R.J.4
  • 38
    • 33846466407 scopus 로고    scopus 로고
    • An Arabidopsis example of association mapping in structured samples
    • Zhao K, Aranzana MJ, Kim S, Lister C, Shindo C, et al. (2007) An Arabidopsis example of association mapping in structured samples. PloS Genet 3: e4.
    • (2007) PloS Genet , vol.3 , pp. e4
    • Zhao, K.1    Aranzana, M.J.2    Kim, S.3    Lister, C.4    Shindo, C.5
  • 40
    • 62549153338 scopus 로고    scopus 로고
    • Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis
    • Stich B, Melchinger AE, (2009) Comparison of mixed-model approaches for association mapping in rapeseed, potato, sugar beet, maize, and Arabidopsis. BMC Genomics 10: 94.
    • (2009) BMC Genomics , vol.10 , pp. 94
    • Stich, B.1    Melchinger, A.E.2
  • 41
    • 79251561130 scopus 로고    scopus 로고
    • Genome-wide association study of leaf architecture in the maize nested association mapping population
    • Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q, et al. (2011) Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat Genet 43: 159–162.
    • (2011) Nat Genet , vol.43 , pp. 159-162
    • Tian, F.1    Bradbury, P.J.2    Brown, P.J.3    Hung, H.4    Sun, Q.5
  • 43
    • 0028224156 scopus 로고
    • Precision mapping of quantitative trait loci
    • Zeng ZB, (1994) Precision mapping of quantitative trait loci. Genetics 136: 1457–1468.
    • (1994) Genetics , vol.136 , pp. 1457-1468
    • Zeng, Z.B.1
  • 44
    • 84857629413 scopus 로고    scopus 로고
    • Windows QTL Cartographer 2.5. Department of Statistics
    • Wang S, Basten CJ and Zeng ZB (2012). Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC.
    • (2012)
    • Wang, S.1    Basten, C.J.2    Zeng, Z.B.3
  • 45
    • 35748946021 scopus 로고    scopus 로고
    • TASSEL: software for association mapping of complex traits in diverse samples
    • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, et al. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633–2635.
    • (2007) Bioinformatics , vol.23 , pp. 2633-2635
    • Bradbury, P.J.1    Zhang, Z.2    Kroon, D.E.3    Casstevens, T.M.4    Ramdoss, Y.5


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