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Volumn 201, Issue 4, 2014, Pages 1227-1239

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grass Miscanthus sinensis

Author keywords

Genome wide association studies (GWAS); Genomic selection; Miscanthus sinensis; Molecular markers; RAD Seq; Single nucleotide variants

Indexed keywords

PLANT DNA;

EID: 84895066185     PISSN: 0028646X     EISSN: 14698137     Source Type: Journal    
DOI: 10.1111/nph.12621     Document Type: Article
Times cited : (85)

References (66)
  • 1
    • 0036178196 scopus 로고    scopus 로고
    • Bias in estimates of quantitative-trait-locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias
    • Allison DB, Fernandez JR, Heo M, Zhu SK, Etzel C, Beasley TM, Amos CI. 2002. Bias in estimates of quantitative-trait-locus effect in genome scans: demonstration of the phenomenon and a method-of-moments procedure for reducing bias. American Journal of Human Genetics 70: 575-585.
    • (2002) American Journal of Human Genetics , vol.70 , pp. 575-585
    • Allison, D.B.1    Fernandez, J.R.2    Heo, M.3    Zhu, S.K.4    Etzel, C.5    Beasley, T.M.6    Amos, C.I.7
  • 6
    • 0000169687 scopus 로고    scopus 로고
    • QTL analyses: power, precision, and accuracy
    • Paterson AH, ed. Boca Raton, FL, USA: CRC Press
    • Beavis WD. 1998. QTL analyses: power, precision, and accuracy. Paterson AH, ed. Molecular dissection of complex traits. Boca Raton, FL, USA: CRC Press, 145-162.
    • (1998) Molecular dissection of complex traits , pp. 145-162
    • Beavis, W.D.1
  • 8
    • 0035257236 scopus 로고    scopus 로고
    • Association study designs for complex diseases
    • Cardon LR, Bell JI. 2001. Association study designs for complex diseases. Nature Reviews Genetics 2: 91-99.
    • (2001) Nature Reviews Genetics , vol.2 , pp. 91-99
    • Cardon, L.R.1    Bell, J.I.2
  • 11
    • 6444220542 scopus 로고    scopus 로고
    • Miscanthus biomass production for energy in Europe and its potential contribution to decreasing fossil fuel carbon emissions
    • Clifton-Brown JC, Stampfl PF, Jones MB. 2004. Miscanthus biomass production for energy in Europe and its potential contribution to decreasing fossil fuel carbon emissions. Global Change Biology 10: 509-518.
    • (2004) Global Change Biology , vol.10 , pp. 509-518
    • Clifton-Brown, J.C.1    Stampfl, P.F.2    Jones, M.B.3
  • 12
    • 84895066696 scopus 로고    scopus 로고
    • qvalue: Q-value estimation for false discovery rate control. R package version 1.34.0. URL
    • Dabney A, Storey JD. 2013. qvalue: Q-value estimation for false discovery rate control. R package version 1.34.0. URL: http://www.bioconductor.org/packages/release/bioc/html/qvalue.html.
    • (2013)
    • Dabney, A.1    Storey, J.D.2
  • 13
    • 84876361750 scopus 로고    scopus 로고
    • Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking
    • Daetwyler HD, Calus MPL, Pong-Wong R, de Los Campos G, Hickey JM. 2013. Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking. Genetics 193: 347-365.
    • (2013) Genetics , vol.193 , pp. 347-365
    • Daetwyler, H.D.1    Calus, M.P.L.2    Pong-Wong, R.3    de Los Campos, G.4    Hickey, J.M.5
  • 14
    • 77958581195 scopus 로고    scopus 로고
    • The impact of genetic architecture on genome-wide evaluation methods
    • Daetwyler HD, Pong-Wong R, Villanueva B, Woolliams JA. 2010. The impact of genetic architecture on genome-wide evaluation methods. Genetics 185: 1021-1031.
    • (2010) Genetics , vol.185 , pp. 1021-1031
    • Daetwyler, H.D.1    Pong-Wong, R.2    Villanueva, B.3    Woolliams, J.A.4
  • 15
    • 54449097329 scopus 로고    scopus 로고
    • Accuracy of predicting the genetic risk of disease using a genome-wide approach
    • Daetwyler HD, Villanueva B, Woolliams JA. 2008. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS One 3: e3395.
    • (2008) PLoS One , vol.3
    • Daetwyler, H.D.1    Villanueva, B.2    Woolliams, J.A.3
  • 18
    • 84882759440 scopus 로고    scopus 로고
    • STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method
    • Earl D, vonHoldt B. 2012. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources 4: 359-361.
    • (2012) Conservation Genetics Resources , vol.4 , pp. 359-361
    • Earl, D.1    vonHoldt, B.2
  • 20
    • 85136354327 scopus 로고    scopus 로고
    • Ridge regression and other kernels for genomic selection with R package rrBLUP
    • Endelman JB. 2011. Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4: 250-255.
    • (2011) Plant Genome , vol.4 , pp. 250-255
    • Endelman, J.B.1
  • 21
    • 21244479740 scopus 로고    scopus 로고
    • Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study
    • Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology 14: 2611-2620.
    • (2005) Molecular Ecology , vol.14 , pp. 2611-2620
    • Evanno, G.1    Regnaut, S.2    Goudet, J.3
  • 23
    • 0041817568 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies
    • Falush D, Stephens M, Pritchard JK. 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567-1587.
    • (2003) Genetics , vol.164 , pp. 1567-1587
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 24
    • 34447120219 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data: dominant markers and null alleles
    • Falush D, Stephens M, Pritchard JK. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes 7: 574-578.
    • (2007) Molecular Ecology Notes , vol.7 , pp. 574-578
    • Falush, D.1    Stephens, M.2    Pritchard, J.K.3
  • 25
    • 84868257321 scopus 로고    scopus 로고
    • Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits
    • Feltus FA, Vandenbrink JP. 2012. Bioenergy grass feedstock: current options and prospects for trait improvement using emerging genetic, genomic, and systems biology toolkits. Biotechnology for Biofuels 5: 80.
    • (2012) Biotechnology for Biofuels , vol.5 , pp. 80
    • Feltus, F.A.1    Vandenbrink, J.P.2
  • 27
    • 79952102682 scopus 로고    scopus 로고
    • Population genetics of genomics-based crop improvement methods
    • Hamblin MT, Buckler ES, Jannink JL. 2011. Population genetics of genomics-based crop improvement methods. Trends in Genetics 27: 98-106.
    • (2011) Trends in Genetics , vol.27 , pp. 98-106
    • Hamblin, M.T.1    Buckler, E.S.2    Jannink, J.L.3
  • 29
    • 0033801369 scopus 로고    scopus 로고
    • Quantitative genetics of bud phenology, frost damage, and winter survival in an F2 family of hybrid poplars
    • Howe GT, Saruul P, Davis J, Chen THH. 2000. Quantitative genetics of bud phenology, frost damage, and winter survival in an F2 family of hybrid poplars. Theoretical and Applied Genetics 101: 632-642.
    • (2000) Theoretical and Applied Genetics , vol.101 , pp. 632-642
    • Howe, G.T.1    Saruul, P.2    Davis, J.3    Chen, T.H.H.4
  • 30
    • 45849093336 scopus 로고    scopus 로고
    • Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae)
    • Ingvarsson PK, Garcia MV, Luquez V, Hall D, Jansson S. 2008. Nucleotide polymorphism and phenotypic associations within and around the phytochrome B2 locus in European aspen (Populus tremula, Salicaceae). Genetics 178: 2217-2226.
    • (2008) Genetics , vol.178 , pp. 2217-2226
    • Ingvarsson, P.K.1    Garcia, M.V.2    Luquez, V.3    Hall, D.4    Jansson, S.5
  • 31
    • 34547861256 scopus 로고    scopus 로고
    • CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure
    • Jakobsson M, Rosenberg NA. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23: 1801-1806.
    • (2007) Bioinformatics , vol.23 , pp. 1801-1806
    • Jakobsson, M.1    Rosenberg, N.A.2
  • 34
    • 84865696774 scopus 로고    scopus 로고
    • A mixed-model approach for genome-wide association studies of correlated traits in structured populations
    • Korte A, Vilhjálmsson BJ, Segura V, Platt A, Long Q, Nordborg M. 2012. A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nature Genetics 44: 1066-1071.
    • (2012) Nature Genetics , vol.44 , pp. 1066-1071
    • Korte, A.1    Vilhjálmsson, B.J.2    Segura, V.3    Platt, A.4    Long, Q.5    Nordborg, M.6
  • 35
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biology 10: R25.
    • (2009) Genome Biology , vol.10
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 38
    • 55549097836 scopus 로고    scopus 로고
    • Mapping short DNA sequencing reads and calling variants using mapping quality scores
    • Li H, Ruan J, Durbin R. 2008. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Research 18: 1851-1858.
    • (2008) Genome Research , vol.18 , pp. 1851-1858
    • Li, H.1    Ruan, J.2    Durbin, R.3
  • 40
  • 41
    • 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
  • 45
    • 33846006923 scopus 로고    scopus 로고
    • Population structure and eigenanalysis
    • Patterson N, Price AL, Reich D. 2006. Population structure and eigenanalysis. PLoS Genetics 2: 2074-2093.
    • (2006) PLoS Genetics , vol.2 , pp. 2074-2093
    • Patterson, N.1    Price, A.L.2    Reich, D.3
  • 46
    • 85168500140 scopus 로고    scopus 로고
    • Genomic-enabled prediction based on molecular markers and pedigree using the Bayesian linear regression package in R
    • Perez P, de los Campos G, Crossa J, Gianola D. 2010. Genomic-enabled prediction based on molecular markers and pedigree using the Bayesian linear regression package in R. Plant Genome 3: 106-116.
    • (2010) Plant Genome , vol.3 , pp. 106-116
    • Perez, P.1    de los Campos, G.2    Crossa, J.3    Gianola, D.4
  • 47
    • 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 JA, Brown PJ, Sorrells ME, Jannink JL. 2012. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One 7: e32253.
    • (2012) PLoS One , vol.7
    • Poland, J.A.1    Brown, P.J.2    Sorrells, M.E.3    Jannink, J.L.4
  • 48
    • 77953811255 scopus 로고    scopus 로고
    • New approaches to population stratification in genome-wide association studies
    • Price AL, Zaitlen NA, Reich D, Patterson N. 2010. New approaches to population stratification in genome-wide association studies. Nature Reviews Genetics 11: 459-463.
    • (2010) Nature Reviews Genetics , vol.11 , pp. 459-463
    • Price, A.L.1    Zaitlen, N.A.2    Reich, D.3    Patterson, N.4
  • 49
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.3
  • 52
    • 84857638695 scopus 로고    scopus 로고
    • Phenotypic variation in senescence in Miscanthus: towards optimising biomass quality and quantity
    • Robson P, Mos M, Clifton-Brown J, Donnison I. 2012. Phenotypic variation in senescence in Miscanthus: towards optimising biomass quality and quantity. Bioenergy Research 5: 95-105.
    • (2012) Bioenergy Research , vol.5 , pp. 95-105
    • Robson, P.1    Mos, M.2    Clifton-Brown, J.3    Donnison, I.4
  • 53
    • 1342331102 scopus 로고    scopus 로고
    • DISTRUCT: a program for the graphical display of population structure
    • Rosenberg NA. 2004. DISTRUCT: a program for the graphical display of population structure. Molecular Ecology Notes 4: 137-138.
    • (2004) Molecular Ecology Notes , vol.4 , pp. 137-138
    • Rosenberg, N.A.1
  • 54
    • 49649106060 scopus 로고    scopus 로고
    • Genomics of cellulosic biofuels
    • Rubin EM. 2008. Genomics of cellulosic biofuels. Nature 454: 841-845.
    • (2008) Nature , vol.454 , pp. 841-845
    • Rubin, E.M.1
  • 55
    • 84862991434 scopus 로고    scopus 로고
    • An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations
    • Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren U, Long Q, Nordborg M. 2012. An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nature Genetics 44: 825-830.
    • (2012) Nature Genetics , vol.44 , pp. 825-830
    • Segura, V.1    Vilhjálmsson, B.J.2    Platt, A.3    Korte, A.4    Seren, U.5    Long, Q.6    Nordborg, M.7
  • 56
    • 84875465731 scopus 로고    scopus 로고
    • Battle for the barrel
    • Service RF. 2013. Battle for the barrel. Science 339: 1374-1379.
    • (2013) Science , vol.339 , pp. 1374-1379
    • Service, R.F.1
  • 58
    • 84895066699 scopus 로고    scopus 로고
    • Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus
    • Slavov GT, Allison GG, Bosch M. 2013a. Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus. Frontiers in Plant Science 4: 217.
    • (2013) Frontiers in Plant Science , vol.4 , pp. 217
    • Slavov, G.T.1    Allison, G.G.2    Bosch, M.3
  • 60
    • 84872468391 scopus 로고    scopus 로고
    • Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species
    • Stölting KN, Nipper R, Lindtke D, Caseys C, Waeber S, Castiglione S, Lexer C. 2013. Genomic scan for single nucleotide polymorphisms reveals patterns of divergence and gene flow between ecologically divergent species. Molecular Ecology 22: 842-855.
    • (2013) Molecular Ecology , vol.22 , pp. 842-855
    • Stölting, K.N.1    Nipper, R.2    Lindtke, D.3    Caseys, C.4    Waeber, S.5    Castiglione, S.6    Lexer, C.7
  • 61
    • 84865402320 scopus 로고    scopus 로고
    • Food vs. fuel: the use of land for lignocellulosic next generation energy crops that minimize competition with primary food production
    • Valentine J, Clifton-Brown J, Hastings A, Robson P, Allison G, Smith P. 2012. Food vs. fuel: the use of land for lignocellulosic next generation energy crops that minimize competition with primary food production. Global Change Biology Bioenergy 4: 1-19.
    • (2012) Global Change Biology Bioenergy , vol.4 , pp. 1-19
    • Valentine, J.1    Clifton-Brown, J.2    Hastings, A.3    Robson, P.4    Allison, G.5    Smith, P.6
  • 62
    • 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. Nature Reviews Genetics 14: 1-2.
    • (2013) Nature Reviews Genetics , vol.14 , pp. 1-2
    • Vilhjálmsson, B.J.1    Nordborg, M.2


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