메뉴 건너뛰기




Volumn 202, Issue 2, 2016, Pages 471-486

A random-model approach to QTL mapping in multiparent advanced generation intercross (MAGIC) populations

Author keywords

Best linear unbiased prediction; Empirical Bayes; Mixed model; MPP; Multiparent advanced generation inter cross (MAGIC); Multiparental populations; Polygene; Restricted maximum likelihood

Indexed keywords

ADVANCED INTERCROSS LINE; ALLELE; ARABIDOPSIS THALIANA; ARTICLE; FOUNDER EFFECT; GENE FREQUENCY; GENE LOCUS; GENETIC BACKGROUND; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HERITABILITY; MULTIPARENT ADVANCED GENERATION INTERCROSS; NONHUMAN; NORMAL DISTRIBUTION; PHENOTYPE; PRIORITY JOURNAL; QUANTITATIVE TRAIT LOCUS MAPPING; ALGORITHM; ANIMAL; ARABIDOPSIS; BIOLOGICAL MODEL; CHROMOSOMAL MAPPING; COMPUTER SIMULATION; CROSS BREEDING; GENETICS; MOUSE; MULTIFACTORIAL INHERITANCE; POPULATION GENETICS; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL;

EID: 84979879802     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.115.179945     Document Type: Article
Times cited : (55)

References (42)
  • 1
    • 84878774677 scopus 로고    scopus 로고
    • Multi-parent advanced generation inter-cross (MAGIC) populations in rice: Progress and potential for genetics research and breeding
    • Bandillo, N., C. Raghavan, P. A. Muyco, M. A. L. Sevilla, I. T. Lobina et al., 2013 Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6: 1–15.
    • (2013) Rice , vol.6 , pp. 1-15
    • Bandillo, N.1    Raghavan, C.2    Muyco, P.A.3    Sevilla, M.A.L.4    Lobina, I.T.5
  • 3
    • 84876433851 scopus 로고    scopus 로고
    • A simulation study of permutation, bootstrap, and gene dropping for assessing statistical significance in the case of unequal relatedness
    • Cheng, R., and A. A. Palmer, 2013 A simulation study of permutation, bootstrap, and gene dropping for assessing statistical significance in the case of unequal relatedness. Genetics 193: 1015–1018.
    • (2013) Genetics , vol.193 , pp. 1015-1018
    • Cheng, R.1    Palmer, A.A.2
  • 4
    • 0000926206 scopus 로고
    • On the distribution of the likelihood ratio
    • Chernoff, H., 1954 On the distribution of the likelihood ratio. Ann. Math. Statist. 25: 573–578.
    • (1954) Ann. Math. Statist , vol.25 , pp. 573-578
    • Chernoff, H.1
  • 5
    • 14644441018 scopus 로고    scopus 로고
    • The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat
    • Churchill, G. A., D. C. Airey, H. Allayee, J. M. Angel, A. D. Attie et al., 2004 The Collaborative Cross, a community resource for the genetic analysis of complex traits. Nat. Genet. 36: 1133– 1137.
    • (2004) Genet. , vol.36
    • Churchill, G.A.1    Airey, D.C.2    Allayee, H.3    Angel, J.M.4    Attie, A.D.5
  • 6
    • 84863115856 scopus 로고    scopus 로고
    • The genome architecture of the Collaborative Cross mouse genetic reference population
    • Collaborative Cross Consortium, 2012 The genome architecture of the Collaborative Cross mouse genetic reference population. Genetics 190: 389–401.
    • (2012) Genetics , vol.190 , pp. 389-401
  • 8
    • 85111736789 scopus 로고    scopus 로고
    • Impact of genomic technologies on chickpea breeding strategies
    • Gaur, P. M., A. K. Jukanti, and R. K. Varshney, 2012 Impact of genomic technologies on chickpea breeding strategies. Agronomy 2: 199–221.
    • (2012) Agronomy , vol.2 , pp. 199-221
    • Gaur, P.M.1    Jukanti, A.K.2    Varshney, R.K.3
  • 10
    • 79951983365 scopus 로고    scopus 로고
    • R/mpMap: A computational platform for the genetic analysis of multiparent recombinant inbred lines
    • Huang, B. E., and A. W. George, 2011 R/mpMap: a computational platform for the genetic analysis of multiparent recombinant inbred lines. Bioinformatics 27: 727–729.
    • (2011) Bioinformatics , vol.27 , pp. 727-729
    • Huang, B.E.1    George, A.W.2
  • 11
    • 84864509188 scopus 로고    scopus 로고
    • A multiparent advanced generation inter-cross population for genetic analysis in wheat
    • Huang, B. E., A. W. George, K. L. Forrest, A. Kilian, M. J. Hayden et al., 2012 A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol. J. 10: 826–839.
    • (2012) Plant Biotechnol. J , vol.10 , pp. 826-839
    • Huang, B.E.1    George, A.W.2    Forrest, K.L.3    Kilian, A.4    Hayden, M.J.5
  • 14
    • 45149105926 scopus 로고    scopus 로고
    • Efficient control of population structure in model organism association mapping
    • Kang, H. M., N. A. Zaitlen, C. M. Wade, A. Kirby, D. Heckerman et al., 2008 Efficient control of population structure in model organism association mapping. Genetics 178: 1709–1723.
    • (2008) Genetics , vol.178 , pp. 1709-1723
    • Kang, H.M.1    Zaitlen, N.A.2    Wade, C.M.3    Kirby, A.4    Heckerman, D.5
  • 15
    • 84863880314 scopus 로고    scopus 로고
    • Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits
    • King, E. G., S. J. MacDonald, and A. D. Long, 2012a Properties and power of the Drosophila Synthetic Population Resource for the routine dissection of complex traits. Genetics 191: 935–949.
    • (2012) Genetics , vol.191 , pp. 935-949
    • King, E.G.1    Macdonald, S.J.2    Long, A.D.3
  • 16
    • 84863868317 scopus 로고    scopus 로고
    • Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    • King, E. G., C. M. Merkes, C. L. McNeil, S. R. Hoofer, S. Sen et al., 2012b Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource. Genome Res. 22: 1558–1566.
    • (2012) Genome Res , vol.22 , pp. 1558-1566
    • King, E.G.1    Merkes, C.M.2    McNeil, C.L.3    Hoofer, S.R.4    Sen, S.5
  • 17
    • 68249120152 scopus 로고    scopus 로고
    • A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana
    • Kover, P. X., W. Valdar, J. Trakalo, N. Scarcelli, I. M. Ehrenreich et al., 2009 A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet. 5: e1000551.
    • (2009) Plos Genet , pp. 5
    • Kover, P.X.1    Valdar, W.2    Trakalo, J.3    Scarcelli, N.4    Ehrenreich, I.M.5
  • 18
    • 0024508964 scopus 로고
    • Mapping mendelian factors underlying quantitative traits using RFLP linkage maps
    • Lander, E. S., and D. Botstein, 1989 Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199.
    • (1989) Genetics , vol.121 , pp. 185-199
    • Lander, E.S.1    Botstein, D.2
  • 20
    • 34250784724 scopus 로고    scopus 로고
    • Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster
    • MacDonald, S. J., and A. D. Long, 2007 Joint estimates of quantitative trait locus effect and frequency using synthetic recombinant populations of Drosophila melanogaster. Genetics 176: 1261–1281.
    • (2007) Genetics , vol.176 , pp. 1261-1281
    • Macdonald, S.J.1    Long, A.D.2
  • 22
  • 23
    • 84928183520 scopus 로고    scopus 로고
    • Potential of a tomato
    • Pascual, L., N. Desplat, B. E. Huang, A. Desgroux, L. Bruguier et al., 2015 Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol. J. 13: 565–577.
    • (2015) Plant Biotechnol. J , vol.13 , pp. 565-577
    • Pascual, L.1    Desplat, N.2    Huang, B.E.3    Desgroux, A.4    Bruguier, L.5
  • 24
    • 80855132592 scopus 로고    scopus 로고
    • Arabidopsis RUGOSA2 encodes an mTERF family member required for mitochondrion, chloro-plast and leaf development
    • Quesada, V., R. Sarmiento-Mañús, R. González-Bayón, A. Hricová, R. Pérez-Marcos et al., 2011 Arabidopsis RUGOSA2 encodes an mTERF family member required for mitochondrion, chloro-plast and leaf development. Plant J. 68: 738–753.
    • (2011) Plant J , vol.68 , pp. 738-753
    • Quesada, V.1    Sarmiento-Mañús, R.2    González-Bayón, R.3    Hricová, A.4    Pérez-Marcos, R.5
  • 25
    • 84862499256 scopus 로고    scopus 로고
    • Multiparent intercross populations in analysis of quantitative traits
    • Rakshit, S., A. Rakshit, and J. Patil, 2012 Multiparent intercross populations in analysis of quantitative traits. J. Genet. 91: 111–117.
    • (2012) J. Genet , vol.91 , pp. 111-117
    • Rakshit, S.1    Rakshit, A.2    Patil, J.3
  • 26
    • 84908024349 scopus 로고    scopus 로고
    • Genetic regulation of Zfp30, CXCL1, and neutrophilic inflammation in murine lung
    • Rutledge, H., D. L. Aylor, D. E. Carpenter, B. C. Peck, P. Chines et al., 2014 Genetic regulation of Zfp30, CXCL1, and neutrophilic inflammation in murine lung. Genetics 198: 735–745.
    • (2014) Genetics , vol.198 , pp. 735-745
    • Rutledge, H.1    Aylor, D.L.2    Carpenter, D.E.3    Peck, B.C.4    Chines, P.5
  • 27
    • 84923367894 scopus 로고    scopus 로고
    • Multi-parent advanced generation inter-cross in barley: High-resolution quantitative trait locus mapping for flowering time as a proof of concept
    • Sannemann, W., B. E. Huang, B. Mathew, and J. Léon, 2015 Multi-parent advanced generation inter-cross in barley: high-resolution quantitative trait locus mapping for flowering time as a proof of concept. Mol. Breed. 35: 1–16.
    • (2015) Mol. Breed , vol.35 , pp. 1-16
    • Sannemann, W.1    Huang, B.E.2    Mathew, B.3    Léon, J.4
  • 28
    • 0028520249 scopus 로고
    • The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin bio-synthesis
    • Sun, T. P., and Y. Kamiya, 1994 The Arabidopsis GA1 locus encodes the cyclase ent-kaurene synthetase A of gibberellin bio-synthesis. Plant Cell 6: 1509–1518.
    • (1994) Plant Cell , vol.6 , pp. 1509-1518
    • Sun, T.P.1    Kamiya, Y.2
  • 29
    • 0036215090 scopus 로고    scopus 로고
    • Genetic dissection of complex and quantitative traits: From fantasy to reality via a community effort
    • Threadgill, D. W., K. W. Hunter, and R. W. Williams, 2002 Genetic dissection of complex and quantitative traits: from fantasy to reality via a community effort. Mamm. Genome 13: 175–178.
    • (2002) Mamm. Genome , vol.13 , pp. 175-178
    • Threadgill, D.W.1    Hunter, K.W.2    Williams, R.W.3
  • 30
    • 33645217146 scopus 로고    scopus 로고
    • Simulating the collaborative cross: Power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice
    • Valdar, W., J. Flint, and R. Mott, 2006 Simulating the collaborative cross: power of quantitative trait loci detection and mapping resolution in large sets of recombinant inbred strains of mice. Genetics 172: 1783–1797.
    • (2006) Genetics , vol.172 , pp. 1783-1797
    • Valdar, W.1    Flint, J.2    Mott, R.3
  • 31
    • 55849133422 scopus 로고    scopus 로고
    • Efficient methods to compute genomic predictions
    • VanRaden, P. M., 2008 Efficient methods to compute genomic predictions. J. Dairy Sci. 91: 4414–4423.
    • (2008) J. Dairy Sci , vol.91 , pp. 4414-4423
    • Vanraden, P.M.1
  • 32
    • 70350423199 scopus 로고    scopus 로고
    • Novel genomic tools and modern genetic and breeding approaches for crop improvement
    • Varshney, R. K., and A. Dubey, 2009 Novel genomic tools and modern genetic and breeding approaches for crop improvement. J. Plant Biochem. Biotechnol. 18: 127–138.
    • (2009) J. Plant Biochem. Biotechnol , vol.18 , pp. 127-138
    • Varshney, R.K.1    Dubey, A.2
  • 34
    • 33750127274 scopus 로고    scopus 로고
    • A note on the asymptotic distribution of likelihood ratio tests to test variance components
    • Visscher, P. M., 2006 A note on the asymptotic distribution of likelihood ratio tests to test variance components. Twin Res. Hum. Genet. 9: 490–495.
    • (2006) Twin Res. Hum. Genet , vol.9 , pp. 490-495
    • Visscher, P.M.1
  • 35
    • 34249044971 scopus 로고    scopus 로고
    • An empirical Bayes method for estimating epistatic effects of quantitative trait loci
    • Xu, S., 2007 An empirical Bayes method for estimating epistatic effects of quantitative trait loci. Biometrics 63: 513–521.
    • (2007) Biometrics , vol.63 , pp. 513-521
    • Xu, S.1
  • 36
    • 84887110908 scopus 로고    scopus 로고
    • Genetic mapping and genomic selection using recombination breakpoint data
    • Xu, S., 2013a Genetic mapping and genomic selection using recombination breakpoint data. Genetics 195: 1103–1115.
    • (2013) Genetics , vol.195 , pp. 1103-1115
    • Xu, S.1
  • 37
    • 84888988128 scopus 로고    scopus 로고
    • Mapping quantitative trait loci by controlling polygenic background effects
    • Xu, S., 2013b Mapping quantitative trait loci by controlling polygenic background effects. Genetics 195: 1209–1222.
    • (2013) Genetics , vol.195 , pp. 1209-1222
    • Xu, S.1
  • 38
    • 31744440502 scopus 로고    scopus 로고
    • A unified mixed-model method for association mapping that accounts for multiple levels of relatedness
    • Yu, J., G. Pressoir, W. H. Briggs, I. Vroh Bi, M. Yamasaki 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
  • 39
    • 40849089396 scopus 로고    scopus 로고
    • Genetic design and statistical power of nested association mapping in maize
    • Yu, J., J. B. Holland, M. D. McMullen, and E. S. Buckler, 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
  • 40
    • 0028224156 scopus 로고
    • Precision mapping of quantitative trait loci
    • Zeng, Z.-B., 1994 Precision mapping of quantitative trait loci. Genetics 136: 1457–1468.
    • (1994) Genetics , vol.136 , pp. 1457-1468
    • Zeng, Z.-B.1
  • 41
    • 84907912911 scopus 로고    scopus 로고
    • Bayesian modeling of haplotype effects in multiparent populations
    • Zhang, Z., W. Wang, and W. Valdar, 2014 Bayesian modeling of haplotype effects in multiparent populations. Genetics 198: 139–156.
    • (2014) Genetics , vol.198 , pp. 139-156
    • Zhang, Z.1    Wang, W.2    Valdar, W.3
  • 42
    • 84863003734 scopus 로고    scopus 로고
    • Genome-wide efficient mixedmodel analysis for association studies
    • Zhou, X., and M. Stephens, 2012 Genome-wide efficient mixedmodel analysis for association studies. Nat. Genet. 44: 821–824.
    • (2012) Nat. Genet. , vol.44 , pp. 821-824
    • Zhou, X.1    Stephens, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.